debian-med-1.13.2ubuntu3/0000775000000000000000000000000012323032575012003 5ustar debian-med-1.13.2ubuntu3/debian-med-tasks.desc0000664000000000000000000002454712323032575015767 0ustar Task: med-bio Section: debian-med Description: Debian Med micro-biology packages This metapackage will install Debian packages related to molecular biology, structural biology and bioinformatics for use in life sciences. Relevance: 10 Enhances: t-coffee Key: med-bio Packages: list altree fastdnaml njplot tree-puzzle probalign treeviewx figtree fastlink loki plink r-cran-qtl r-cran-genabel amap-align boxshade fastx-toolkit gff2aplot muscle sim4 sibsim4 tabix wise maqview bwa mummer blast2 ncbi-blast+ mafft sra-toolkit t-coffee kalign hmmer exonerate dialign dialign-tx poa probcons proda sigma-align emboss embassy-domalign embassy-domainatrix embassy-domsearch clustalx clustalo clustalw mothur bowtie bowtie2 dotur transtermhp last-align maq ssake velvet qiime infernal rnahybrid adun.app garlic gamgi gdpc ghemical jmol pymol r-other-bio3d massxpert gromacs rasmol plasmidomics gff2ps ncbi-epcr ncbi-tools-bin ncbi-tools-x11 perlprimer readseq tigr-glimmer melting mipe primer3 gbrowse biomaj glam2 raster3d phyml autodock autogrid autodock-vina mustang theseus staden-io-lib-utils samtools bedtools filo r-bioc-hilbertvis r-other-mott-happy mira-assembler alien-hunter ncoils gentle picard-tools acedb-other-dotter acedb-other-belvu acedb-other python-cogent mrbayes squizz clonalframe dssp jellyfish ballview pynast raxml mlv-smile cd-hit r-bioc-cummerbund grinder jalview reprof tm-align proftmb hhsuite ffindex neobio fasttree abacas profnet-bval profnet-chop profnet-con profnet-isis profnet-md profnet-norsnet profnet-prof profnet-snapfun profphd-net profphd-utils profphd ampliconnoise disulfinder populations librg-utils-perl vcftools Task: med-bio-dev Section: debian-med Description: Debian Med packages for development of micro-biology applications This metapackage will install Debian packages which might be helpful for development of applications for micro-biological research. Relevance: 10 Key: med-bio-dev Packages: list bioperl bioperl-run libncbi6-dev mcl biosquid libvibrant6-dev python-biopython python-cogent ruby-bio libbiojava-java libbiojava3-java libgenome-1.3-dev libai-fann-perl libbio-mage-perl libtfbs-perl libgo-perl r-cran-genetics r-cran-haplo.stats libbio-graphics-perl libbio-primerdesigner-perl libace-perl libbiococoa-dev libstaden-read-dev libsrf-dev libzerg0-dev libzerg-perl librg-reprof-bundle-perl seqan-dev libbio-mage-utils-perl libchado-perl libpal-java libjebl2-java r-bioc-biobase libffindex0-dev librostlab3-dev librostlab-doc librostlab-blast0-dev librostlab-blast-doc librg-blast-parser-perl libsort-key-top-perl libhmsbeagle-dev Task: med-bio-ngs Section: debian-med Description: Debian Med bioinformatics applications usable in Next Generation Sequencing It aims at gettting packages which specializes in alignment of sequences produced by next generation sequencing. Relevance: 10 Packages: list mothur qiime mira-assembler Task: med-bio-phylogeny Section: debian-med Description: Debian Med phylogeny packages This lists Debian packages related to phylogeny for use in life sciences. The purpose of this compilation of packages is to have a handy subset of from the med-bio metapackage which contains a lot more than only phylogeny related software. Relevance: 10 Packages: list altree fastdnaml njplot tree-puzzle probalign treeviewx muscle t-coffee kalign hmmer exonerate dialign dialign-tx poa probcons proda sigma-align clustalx clustalw mustang phyml tm-align mrbayes figtree populations Task: med-cloud Section: debian-med Description: Debian Med bioinformatics applications usable in cloud computing This metapackage will install Debian packages related to molecular biology, structural biology and bioinformatics for use in life sciences, that do not depend on graphical toolkits and therefore can fit on system images for use in cloud computing clusters, where space can be limited. Relevance: 10 Key: med-cloud Packages: list clustalw autodock raster3d python-cogent Task: med-cms Section: debian-med Description: Debian Med content management systems Here you can find software that is useful to build a content management system for medical care. Relevance: 10 Packages: list Task: med-data Section: debian-med Description: Debian Med drug databases This metapackage will install free drug databases and related applications. The database can be accessed by any EMR using the application. Relevance: 10 Key: med-data Packages: list freediams freemedforms-freedata python-hl7 Task: med-dental Section: debian-med Description: Debian Med packages related to dental practice This metapackage contains dependencies for a collection of software which might be helpful for dentists to manage their practice. Relevance: 10 Key: med-dental Packages: list imagetooth Task: med-epi Section: debian-med Description: Debian Med epidemiology related packages This metapackage will install tools that are useful in epidemiological research. Several packages making use of the GNU R data language for statistical investigation. It might be a good idea to read the paper "A short introduction to R for Epidemiology" at http://staff.pubhealth.ku.dk/%7Ebxc/Epi/R-intro.pdf Relevance: 10 Key: med-epi Packages: list epigrass r-cran-epibasix r-cran-epitools r-cran-epi r-cran-diagnosismed r-cran-epicalc r-cran-epir Task: med-imaging Section: debian-med Description: Debian Med imaging packages This metapackage will install Debian packages which might be useful in medical image processing. . It installs several packages supporting DICOM (Digital Imaging and Communications in Medicine) which is the de-facto standard for medical image management. The standard defines data structures and services for the exchange of medical images and related information. The latest release has been published in 2008 and consists of 18 parts. . For more information, you can visit the NEMA homepage http://medical.nema.org/ . . The status of the official DICOM base standard plus all the supplements and correction items are summarized at David Clunie's webpage: http://www.dclunie.com/dicom-status/status.html where you'll find direct links to the most recent yearly edition ftp://medical.nema.org/medical/dicom/2008/ . Relevance: 10 Key: med-imaging Packages: list amide ctsim ctn dicomnifti imagej minc-tools medcon python-nifti xmedcon dcmtk nifti-bin aeskulap via-bin gwyddion sofa-apps python-mvpa python-nipy python-nipype caret libgdcm-tools dicom3tools imagevis3d odin dicomscope pixelmed-java gofigure2 ginkgocadx openslide-tools volview mricron voxbo mrtrix ants itksnap mriconvert sigviewer tifffile openmeeg-tools plastimatch biosig-tools king python-nitime python-dipy Task: med-imaging-dev Section: debian-med Description: Debian Med packages for medical image development This metapackage will install Debian packages which might be useful for developing applications for medical image processing. Relevance: 10 Key: med-imaging-dev Packages: list ctn-dev cimg-dev libminc-dev libmdc2-dev libvtk5-dev libnifti-dev libigstk4-dev libinsighttoolkit3-dev libvolpack1-dev libgdcm2-dev python-gdcm python-mvpa python-nipy python-nipype python-nitime libvia-dev odin libcv-dev libvxl1-dev gmic libgiftiio-dev libactiviz.net-cil libopenigtlink1-dev python-dicom libopenmeeg-dev python-nibabel libgdf-dev python-pyxnat python-dipy libbiosig-dev python-cfflib libopenslide-dev Task: med-oncology Section: debian-med Description: Debian Med packages for oncology This metapackage will install tools that are useful for radiation oncology. Relevance: 10 Key: med-oncology Packages: list dicompyler Task: med-pharmacy Section: debian-med Description: Debian Med packages for pharmaceutical research This metapackage contains dependencies for a collection of software and documentation which is useful for pharmaceutical research. Relevance: 10 Key: med-pharmacy Packages: list chemtool Task: med-physics Section: debian-med Description: Debian Med packages for medical physicists This metapackage contains dependencies for a collection of software and documentation which is useful for medical physicists in radiation oncology, diagnostics imaging and related fields. Relevance: 10 Key: med-physics Packages: list paw++ paw octave r-base Task: med-practice Section: debian-med Description: Debian Med packages for practice management This metapackage contains dependencies for a collection of software which might be helpful for practitioners to manage their practice. Relevance: 10 Key: med-practice Packages: list gnumed-client gnumed-server libchipcard-tools ginkgocadx freediams freemedforms-emr r-cran-medadherence clinica Task: med-psychology Section: debian-med Description: Debian Med packages for psychology This metapackage contains dependencies for a collection of software which might be helpful for psychological research. Relevance: 10 Key: med-psychology Packages: list python-pyepl praat r-cran-foreign psignifit r-cran-psy psychopy Task: med-rehabilitation Section: debian-med Description: Debian Med packages for rehabilitation technologies This metapackage will install tools that are useful for rehabilitation and therapy. Relevance: 10 Key: med-rehabilitation Packages: list sitplus Task: med-statistics Section: debian-med Description: Debian Med statistics This metapackage will install packages which are helpful to do statistics with a special focus on tasks in medical care. Relevance: 10 Key: med-statistics Packages: list r-bioc-edger r-bioc-limma r-bioc-qvalue r-cran-randomforest r-cran-pvclust Task: med-tools Section: debian-med Description: Debian Med several tools This metapackage will install tools for several purposes in health care. Currently it contains some simple programs for Personal Health. Relevance: 10 Key: med-tools Packages: list pcalendar pondus wgerman-medical hunspell-de-med quitcount workrave edfbrowser Task: med-typesetting Section: debian-med Description: Debian Med support for typesetting and publishing This metapackage will install Debian packages that might be helpful for typesetting and publishing in medical care and structural biology. Relevance: 10 Key: med-typesetting Packages: list texlive-science texlive-latex-extra king debian-med-1.13.2ubuntu3/COPYING0000664000000000000000000004311012124332225013027 0ustar GNU GENERAL PUBLIC LICENSE Version 2, June 1991 Copyright (C) 1989, 1991 Free Software Foundation, Inc. 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. Preamble The licenses for most software are designed to take away your freedom to share and change it. By contrast, the GNU General Public License is intended to guarantee your freedom to share and change free software--to make sure the software is free for all its users. This General Public License applies to most of the Free Software Foundation's software and to any other program whose authors commit to using it. (Some other Free Software Foundation software is covered by the GNU Library General Public License instead.) You can apply it to your programs, too. When we speak of free software, we are referring to freedom, not price. Our General Public Licenses are designed to make sure that you have the freedom to distribute copies of free software (and charge for this service if you wish), that you receive source code or can get it if you want it, that you can change the software or use pieces of it in new free programs; and that you know you can do these things. To protect your rights, we need to make restrictions that forbid anyone to deny you these rights or to ask you to surrender the rights. These restrictions translate to certain responsibilities for you if you distribute copies of the software, or if you modify it. For example, if you distribute copies of such a program, whether gratis or for a fee, you must give the recipients all the rights that you have. You must make sure that they, too, receive or can get the source code. And you must show them these terms so they know their rights. We protect your rights with two steps: (1) copyright the software, and (2) offer you this license which gives you legal permission to copy, distribute and/or modify the software. Also, for each author's protection and ours, we want to make certain that everyone understands that there is no warranty for this free software. If the software is modified by someone else and passed on, we want its recipients to know that what they have is not the original, so that any problems introduced by others will not reflect on the original authors' reputations. Finally, any free program is threatened constantly by software patents. We wish to avoid the danger that redistributors of a free program will individually obtain patent licenses, in effect making the program proprietary. To prevent this, we have made it clear that any patent must be licensed for everyone's free use or not licensed at all. The precise terms and conditions for copying, distribution and modification follow. GNU GENERAL PUBLIC LICENSE TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION 0. This License applies to any program or other work which contains a notice placed by the copyright holder saying it may be distributed under the terms of this General Public License. The "Program", below, refers to any such program or work, and a "work based on the Program" means either the Program or any derivative work under copyright law: that is to say, a work containing the Program or a portion of it, either verbatim or with modifications and/or translated into another language. (Hereinafter, translation is included without limitation in the term "modification".) Each licensee is addressed as "you". Activities other than copying, distribution and modification are not covered by this License; they are outside its scope. The act of running the Program is not restricted, and the output from the Program is covered only if its contents constitute a work based on the Program (independent of having been made by running the Program). Whether that is true depends on what the Program does. 1. You may copy and distribute verbatim copies of the Program's source code as you receive it, in any medium, provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice and disclaimer of warranty; keep intact all the notices that refer to this License and to the absence of any warranty; and give any other recipients of the Program a copy of this License along with the Program. You may charge a fee for the physical act of transferring a copy, and you may at your option offer warranty protection in exchange for a fee. 2. You may modify your copy or copies of the Program or any portion of it, thus forming a work based on the Program, and copy and distribute such modifications or work under the terms of Section 1 above, provided that you also meet all of these conditions: a) You must cause the modified files to carry prominent notices stating that you changed the files and the date of any change. b) You must cause any work that you distribute or publish, that in whole or in part contains or is derived from the Program or any part thereof, to be licensed as a whole at no charge to all third parties under the terms of this License. c) If the modified program normally reads commands interactively when run, you must cause it, when started running for such interactive use in the most ordinary way, to print or display an announcement including an appropriate copyright notice and a notice that there is no warranty (or else, saying that you provide a warranty) and that users may redistribute the program under these conditions, and telling the user how to view a copy of this License. (Exception: if the Program itself is interactive but does not normally print such an announcement, your work based on the Program is not required to print an announcement.) These requirements apply to the modified work as a whole. If identifiable sections of that work are not derived from the Program, and can be reasonably considered independent and separate works in themselves, then this License, and its terms, do not apply to those sections when you distribute them as separate works. But when you distribute the same sections as part of a whole which is a work based on the Program, the distribution of the whole must be on the terms of this License, whose permissions for other licensees extend to the entire whole, and thus to each and every part regardless of who wrote it. Thus, it is not the intent of this section to claim rights or contest your rights to work written entirely by you; rather, the intent is to exercise the right to control the distribution of derivative or collective works based on the Program. In addition, mere aggregation of another work not based on the Program with the Program (or with a work based on the Program) on a volume of a storage or distribution medium does not bring the other work under the scope of this License. 3. You may copy and distribute the Program (or a work based on it, under Section 2) in object code or executable form under the terms of Sections 1 and 2 above provided that you also do one of the following: a) Accompany it with the complete corresponding machine-readable source code, which must be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or, b) Accompany it with a written offer, valid for at least three years, to give any third party, for a charge no more than your cost of physically performing source distribution, a complete machine-readable copy of the corresponding source code, to be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or, c) Accompany it with the information you received as to the offer to distribute corresponding source code. (This alternative is allowed only for noncommercial distribution and only if you received the program in object code or executable form with such an offer, in accord with Subsection b above.) The source code for a work means the preferred form of the work for making modifications to it. For an executable work, complete source code means all the source code for all modules it contains, plus any associated interface definition files, plus the scripts used to control compilation and installation of the executable. However, as a special exception, the source code distributed need not include anything that is normally distributed (in either source or binary form) with the major components (compiler, kernel, and so on) of the operating system on which the executable runs, unless that component itself accompanies the executable. If distribution of executable or object code is made by offering access to copy from a designated place, then offering equivalent access to copy the source code from the same place counts as distribution of the source code, even though third parties are not compelled to copy the source along with the object code. 4. You may not copy, modify, sublicense, or distribute the Program except as expressly provided under this License. Any attempt otherwise to copy, modify, sublicense or distribute the Program is void, and will automatically terminate your rights under this License. However, parties who have received copies, or rights, from you under this License will not have their licenses terminated so long as such parties remain in full compliance. 5. You are not required to accept this License, since you have not signed it. However, nothing else grants you permission to modify or distribute the Program or its derivative works. These actions are prohibited by law if you do not accept this License. Therefore, by modifying or distributing the Program (or any work based on the Program), you indicate your acceptance of this License to do so, and all its terms and conditions for copying, distributing or modifying the Program or works based on it. 6. Each time you redistribute the Program (or any work based on the Program), the recipient automatically receives a license from the original licensor to copy, distribute or modify the Program subject to these terms and conditions. You may not impose any further restrictions on the recipients' exercise of the rights granted herein. You are not responsible for enforcing compliance by third parties to this License. 7. If, as a consequence of a court judgment or allegation of patent infringement or for any other reason (not limited to patent issues), conditions are imposed on you (whether by court order, agreement or otherwise) that contradict the conditions of this License, they do not excuse you from the conditions of this License. If you cannot distribute so as to satisfy simultaneously your obligations under this License and any other pertinent obligations, then as a consequence you may not distribute the Program at all. For example, if a patent license would not permit royalty-free redistribution of the Program by all those who receive copies directly or indirectly through you, then the only way you could satisfy both it and this License would be to refrain entirely from distribution of the Program. If any portion of this section is held invalid or unenforceable under any particular circumstance, the balance of the section is intended to apply and the section as a whole is intended to apply in other circumstances. It is not the purpose of this section to induce you to infringe any patents or other property right claims or to contest validity of any such claims; this section has the sole purpose of protecting the integrity of the free software distribution system, which is implemented by public license practices. Many people have made generous contributions to the wide range of software distributed through that system in reliance on consistent application of that system; it is up to the author/donor to decide if he or she is willing to distribute software through any other system and a licensee cannot impose that choice. This section is intended to make thoroughly clear what is believed to be a consequence of the rest of this License. 8. If the distribution and/or use of the Program is restricted in certain countries either by patents or by copyrighted interfaces, the original copyright holder who places the Program under this License may add an explicit geographical distribution limitation excluding those countries, so that distribution is permitted only in or among countries not thus excluded. In such case, this License incorporates the limitation as if written in the body of this License. 9. The Free Software Foundation may publish revised and/or new versions of the General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns. Each version is given a distinguishing version number. If the Program specifies a version number of this License which applies to it and "any later version", you have the option of following the terms and conditions either of that version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of this License, you may choose any version ever published by the Free Software Foundation. 10. If you wish to incorporate parts of the Program into other free programs whose distribution conditions are different, write to the author to ask for permission. For software which is copyrighted by the Free Software Foundation, write to the Free Software Foundation; we sometimes make exceptions for this. Our decision will be guided by the two goals of preserving the free status of all derivatives of our free software and of promoting the sharing and reuse of software generally. NO WARRANTY 11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION. 12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. END OF TERMS AND CONDITIONS How to Apply These Terms to Your New Programs If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms. To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to most effectively convey the exclusion of warranty; and each file should have at least the "copyright" line and a pointer to where the full notice is found. Copyright (C) This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA Also add information on how to contact you by electronic and paper mail. If the program is interactive, make it output a short notice like this when it starts in an interactive mode: Gnomovision version 69, Copyright (C) year name of author Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'. This is free software, and you are welcome to redistribute it under certain conditions; type `show c' for details. The hypothetical commands `show w' and `show c' should show the appropriate parts of the General Public License. Of course, the commands you use may be called something other than `show w' and `show c'; they could even be mouse-clicks or menu items--whatever suits your program. You should also get your employer (if you work as a programmer) or your school, if any, to sign a "copyright disclaimer" for the program, if necessary. Here is a sample; alter the names: Yoyodyne, Inc., hereby disclaims all copyright interest in the program `Gnomovision' (which makes passes at compilers) written by James Hacker. , 1 April 1989 Ty Coon, President of Vice This General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Library General Public License instead of this License. debian-med-1.13.2ubuntu3/sources.list.raring0000664000000000000000000000010612124332225015633 0ustar deb http://archive.ubuntu.com/ubuntu/ raring main universe multiverse debian-med-1.13.2ubuntu3/config/0000775000000000000000000000000012124332546013250 5ustar debian-med-1.13.2ubuntu3/config/conf0000664000000000000000000000040412124332225014110 0ustar ## This is a configuration file for Debian Med Blend ## It is read after /etc/blends/blends.conf and can override or add variables ## Some Blends do not build their name generic like "Debian #BLEND#" so ## we need the correct name here BLENDNAME="Debian Med" debian-med-1.13.2ubuntu3/config/config0000775000000000000000000000027212124332225014436 0ustar #!/bin/sh ## Prints some info about that package and lets auto-apt work dpkg --status `basename $0` | \ grep -v ^Priority | \ grep -v ^Section | \ grep -v ^Installed-Size debian-med-1.13.2ubuntu3/config/config.10000664000000000000000000000110412124332225014565 0ustar .TH med-config 1 "Oct 18, 2007" "Debian-Med" .SH NAME med-config \- general Debian-Med package information and auto-apt helper med- \- Debian-Med package information and auto-apt helper .SH SYNOPSIS .B med-config .B med- .SH DESCRIPTION Print just a simple information page about every med-* package of the Debian-Med Custom Debian Distribution. Each metapackage has a .I /usr/bin/med- file which should print some useful information and could be serve as auto-apt helper. .SH AUTHOR Andreas Tille . debian-med-1.13.2ubuntu3/config/control0000664000000000000000000000257512124332225014656 0ustar Package: med-config Architecture: all Depends: adduser, ${misc:Depends}, menu, blends-common (>= 0.6.15) Conflicts: med-common Replaces: med-common Provides: med-common Description: Debian Med general config package This package provides the basic infrastructure of all metapackages assembled by the Debian Med team. . This metapackage provides common features shared between the different metapackages of the project. Moreover it introduces a method to handle a 'med' system users group using debconf. . The Debian Med Project include metapackages for different tasks, which are: * applications for microbiological research and support for development of biological applications * cloud computing in microbiological research * drug databases * dental surgery practice * epidemiology and medical statistics * image processing and support for imaging application development * pharmacological research * radiation oncology, diagnostic imaging and related fields * medical practice * psychological research and practice * rehabilitation * typesetting and publishing * miscellaneous tools . Each task is represented by a metapackage. Metapackages do not contain executable programs, but rather dependencies from other packages. This way you will conveniently get all free medical software which is available for Debian by simply installing the relevant metapackage debian-med-1.13.2ubuntu3/README0000664000000000000000000000067612124332225012666 0ustar This folder collects information on packages that have been built for the Debian Med Blend or that are currently prepared to be uploaded. If you want to add package descriptions, then edit the respective file in tasks/ and make sure to have read through http://blends.alioth.debian.org/blends/ch-sentinel.en.html. For more advanced issues please refer to the Blends paper in full and consider to talk back to Andreas Tille . debian-med-1.13.2ubuntu3/tasks.ctl0000664000000000000000000000075112124332225013631 0ustar priority-high:bio priority-high:bio-dev priotity-none:bio-ngs priotity-none:bio-phylogeny priotity-med:cloud priority-none:cms priotity-high:data priotity-none:dental priority-high:epi priotity-none:his priority-high:imaging priority-high:imaging-dev priotity-none:laboratory priority-high:oncology priority-high:pharmacy priority-high:physics priority-high:practice priority-high:psychology priority-med:rehabilitation priority-high:statistics priority-med:tools priority-med:typesetting debian-med-1.13.2ubuntu3/menu/0000775000000000000000000000000012124332546012747 5ustar debian-med-1.13.2ubuntu3/menu/cms/0000775000000000000000000000000012124332546013531 5ustar debian-med-1.13.2ubuntu3/menu/cms/zope-zms.txt0000664000000000000000000000230012124332225016043 0ustar zope-zms: Content management for science, technology and medicine Some information about Zope ZMS from the Debian Med project. ZMS (Zope based Content Management for Science, Technology and Medicine) is a ready to use solution for efficient electronic publishing. An easy to handle graphical user interface for editors and flexible modelling features (multiple languages, Metadata, content objects, XML import/export, workflow etc.) allow an optimum of productivity: A basic configuration to start with can be created with a few mouse clicks. ZMS is perfectly suitable for hospitals, research institutions, NGOs and small to medium-size international companies. The ZMS concept is based on a consulting approach for the rational publishing on the internet: the professional user is able to pursue a consequently efficiency oriented producing base with the ZMS software and can hereby also achieve important economic results in the so-called low budget area. The modulation possibilities of the ZMS components and the experienced producing steps makes out of ZMS an incomparable fast tool. Homepage: http://www.zms-publishing.com/ Read /usr/share/doc/zope-zms/README.Debian for the first steps. debian-med-1.13.2ubuntu3/menu/imaging-dev/0000775000000000000000000000000012124332546015136 5ustar debian-med-1.13.2ubuntu3/menu/imaging-dev/libmdc2-dev.txt0000664000000000000000000000074212124332225017764 0ustar MedCon Development: Medical Image Conversion development Some information about libmdc-dev from the Debian Med project. We are sorry that we can not present a more detailed description to this development package. We suggest further reading at the xmedcon homepage http://xmedcon.sourceforge.net because it belongs to the XMedCon package. The following manpages might help you in getting started: xmedcon-config medcon m-gif m-inw m-acr m-ecat m-anlz m-intf debian-med-1.13.2ubuntu3/menu/imaging-dev/libminc0-dev.txt0000664000000000000000000000053212124332225020142 0ustar MINC Development: MNI medical image format development Some information about libminc0-dev from the Debian Med project. The best way to get started with this development package is to read http://localhost/doc/libminc0-dev/ if you have a working webserver installed on your local machine or just browse /usr/share/doc/libminc0-dev debian-med-1.13.2ubuntu3/menu/imaging-dev/ctn-dev.txt0000664000000000000000000000075112124332225017234 0ustar CTN Development: CTN-Dicom support Some information about ctn from the Debian Med project. The ctn package provides runtime files for Central Test Node, a DICOM implementation. DICOM is the standard for image storage, annotation, and networking. It is used widely for medical imaging. This is the development package. For further information have a look into the extensive documentation which is in the Debian package ctn-doc. The homepage is http://www.erl.wustl.edu/DICOM/ctn.html. debian-med-1.13.2ubuntu3/menu/imaging-dev/libgtkimreg-dev.txt0000664000000000000000000000047412124332225020752 0ustar Imreg Development: Image Sequences Development Support Some information about libgtkimreg-dev from the Debian Med project. Please read man gtkimreg man gtkimmov for a detailed description for cutting and moving sets of images. A complex example of the usage of these libraries is the image viewer paul. debian-med-1.13.2ubuntu3/menu/practice/0000775000000000000000000000000012124332546014541 5ustar debian-med-1.13.2ubuntu3/menu/bio-dev/0000775000000000000000000000000012124332546014274 5ustar debian-med-1.13.2ubuntu3/menu/bio-dev/mcl.txt0000664000000000000000000000160212124332225015601 0ustar MCL: Markov Cluster algorithm Some information about mcl from the Debian Med project. The MCL package is an implementation of the MCL algorithm, and offers utilities for manipulating sparse matrices (the essential data structure in the MCL algorithm) and conducting cluster experiments. MCL is currently being used in sciences like biology (protein family detection, genomics), computer sciense (node clustering in Peer-to-Peer networks), and linguistics (text analysis). Homepage: http://micans.org/mcl/ An overview about the various tools are given by the following manpages: man mcx man clmimac man clmmate man clmmeet man clmformat man clmdist man clminfo man mcxconvert man mcxassemble man mcxmap man mcxsubs man mcxarray man mcxdeblast man mclblastline man mcl man clmresidue man mclpipeline debian-med-1.13.2ubuntu3/menu/bio-dev/libbio-ruby.txt0000664000000000000000000000107512124332225017251 0ustar BioRuby tools for computational molecular biology Some information about libbio-ruby from the Debian Med project. BioRuby project aims to implement an integrated environment for Bioinformatics with Ruby language. Design philosophy of the BioRuby library is KISS (keep it simple and stupid) to maximize the usability and the efficiency for biologists as a daily tool. The project was started in Japan and supported by University of Tokyo (Human Genome Center), Kyoto University (Bioinformatics Center) and the Open Bio Foundation. Homepage: http://www.bioruby.org/ debian-med-1.13.2ubuntu3/menu/bio-dev/libncbi6-dev.menu0000664000000000000000000000056312124332225017424 0ustar ?package(libncbi6-dev):command="/usr/bin/vibrate /usr/bin/asntool" needs="X11" \ section="Med/Biology development" title="asntool" hints="Biology" icon="/usr/share/pixmaps/asntool.xpm" ?package(libncbi6-dev):command="/usr/bin/vibrate /usr/bin/errhdr" needs="X11" \ section="Med/Biology development" title="errhdr" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm" debian-med-1.13.2ubuntu3/menu/bio-dev/biomode.txt0000664000000000000000000000074612124332225016454 0ustar BioMode: Emacs mode to edit genetic data Some information about Biomode from the Debian Med project. It provides you several interesting commands to take the antiparallel of a region, convert it using readseq, runs blast on it, etc. This package is not really installed by the med-bio package but it is suggested. That means if you are comfortable with the powerful editor Emacs you might wish to install also the biomode package and make use of it by typing "M-x biomode". debian-med-1.13.2ubuntu3/menu/bio-dev/libvibrant6-dev.txt0000664000000000000000000000064112124332225020026 0ustar libvibrant6-dev: NCBI libraries for graphic biology applications (development files) Some information about libvibrant6-dev from the Debian Med project. Vibrant allows you to develop portable (Motif, MS-Windows, Mac-OS) graphic biological applications. The Homepage is http://www.ncbi.nlm.nih.gov/ You can get a good overview by reading zless /usr/share/doc/libvibrant6-dev/README.gz debian-med-1.13.2ubuntu3/menu/bio-dev/python-biopython.txt0000664000000000000000000000130012124332225020353 0ustar Python library for bioinformatics Some information about python-biopython from the Debian Med project. The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology. It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics. The source code is made available under the Biopython License, which is extremely liberal and compatible with almost every license in the world. We work along with the Open Bioinformatics Foundation, who generously provide web and CVS space for the project. Homepage: http://biopython.org/ debian-med-1.13.2ubuntu3/menu/bio-dev/bioperl.txt0000664000000000000000000000065212124332225016466 0ustar Bioperl: Perl tools for computational molecular biology Some information about Bioperl from the Debian Med project. The Bioperl project is a coordinated effort to collect computational methods routinely used in bioinformatics into a set of standard CPAN-style, well-documented, and freely available Perl modules. The Homepage is http://bio.perl.org/ You can get a good overview by the main manpage: man bioperl debian-med-1.13.2ubuntu3/menu/bio/0000775000000000000000000000000012124332546013520 5ustar debian-med-1.13.2ubuntu3/menu/bio/phylip.txt0000664000000000000000000000216512124332225015564 0ustar Some information about Phylip from the Debian Med project. A package of programs for inferring phylogenies. The PHYLogeny Inference Package is a package of programs for inferring phylogenies (evolutionary trees) from sequences. Methods that are available in the package include parsimony, distance matrix, and likelihood methods, including bootstrapping and consensus trees. Data types that can be handled include molecular sequences, gene frequencies, restriction sites, distance matrices, and 0/1 discrete characters. If you call phylip in a text console you get some help: Usage: /usr/bin/phylip Existing programs are: clique dnacomp dnamlk dollop drawtree kitsch penny retree consense dnadist dnamove dolmove factor mix protdist seqboot contml dnainvar dnapars dolpenny fitch move protpars contrast dnaml dnapenny drawgram gendist neighbor restml which is quite the same information as the Debian manpage of phylip contains. There is extensive documentation at /usr/share/doc/phylip and some examples in the examples dir at this location. debian-med-1.13.2ubuntu3/menu/bio/glimmer.txt0000664000000000000000000000170412124332225015711 0ustar Tigr Glimmer: Gene detection in archea and bacteria Some information about tigr-glimmer from the Debian Med project. Developed by the TIGR institute this software detects coding sequences in bacteria and archea. Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria and archaea. Glimmer (Gene Locator and Interpolated Markov Modeler) uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA. Homepage: http://www.tigr.org/software/glimmer/ An overview about the various tools are given by the following manpages: man glimmer2 (start with this) man build-icm man extract man long-orfs More or less simple syntax help without detailed information is given by man adjust man anomaly man check man codon-usage man compare-lists man generate man get-len man run-glimmer2 man get-putative debian-med-1.13.2ubuntu3/menu/bio/poa.txt0000664000000000000000000000146112124332225015034 0ustar Partial Order Alignment for multiple sequence alignment Some information about t-coffee from the Debian Med project. POA is Partial Order Alignment, a fast program for multiple sequence alignment (MSA) in bioinformatics. Its advantages are speed, scalability, sensitivity, and the superior ability to handle branching / indels in the alignment. Partial order alignment is an approach to MSA, which can be combined with existing methods such as progressive alignment. POA optimally aligns a pair of MSAs and which therefore can be applied directly to progressive alignment methods such as CLUSTAL. For large alignments, Progressive POA is 10-30 times faster than CLUSTALW. POA is published in Bioinformatics. 2004 Jul 10;20(10):1546-56. See also: man poa Homepage: http://www.bioinformatics.ucla.edu/poa debian-med-1.13.2ubuntu3/menu/bio/t-coffee.txt0000664000000000000000000000130212124332225015737 0ustar Multiple Sequence Alignment Some information about t-coffee from the Debian Med project. T-Coffee is a multiple sequence alignment package. Given a set of sequences (Proteins or DNA), T-Coffee generates a multiple sequence alignment. Version 2.00 and higher can mix sequences and structures. T-Coffee allows the combination of a collection of multiple/pairwise, global or local alignments into a single model. It also allows to estimate the level of consistency of each position within the new alignment with the rest of the alignments. See the pre-print for more information See also: man t_coffee Homepage: http://igs-server.cnrs-mrs.fr/~cnotred/Projects_home_page/t_coffee_home_page.html debian-med-1.13.2ubuntu3/menu/bio/molphy.txt0000664000000000000000000000067412124332225015572 0ustar Some information about MolPhy from the Debian Med project. Molphy is an extensive set of tools for MOLecular PHYlogenetics. You can get a first overview by the two manpages man protml man mollist For further reading the files in /usr/share/doc/molphy are suggested. Moreover you can find several examples in /usr/share/doc/molphy/examples/tests/ which contains a makefile to give you an idea how to call the MolPhy tools. debian-med-1.13.2ubuntu3/menu/bio/boxshade.txt0000664000000000000000000000064612124332225016056 0ustar Pretty-printing of multiple sequence alignments Some information about boxshade from the Debian Med project. Boxshade reads a sequence alignment as input (e.g. from ClustalW) and outputs files that may be incorporated to text processing software (TeX via xfig, Word and OpenOffice via RTF). The post script format is also supported. See also: man boxshade Homepage: http://www.ch.embnet.org/software/BOX_form.html debian-med-1.13.2ubuntu3/menu/bio/gff2ps.txt0000664000000000000000000000127012124332225015442 0ustar Produce PostScript graphical output from GFF-files Some information about gff2ps from the Debian Med project. gff2ps is a script program developed with the aim of converting gff-formatted records into high quality one-dimensional plots in PostScript. Such plots maybe useful for comparing genomic structures and to visualizing outputs from genome annotation programs. It can be used in a very simple way, because it assumes that the GFF file itself carries enough formatting information, but it also allows through a number of options and/or a configuration file, for a great degree of customization. See also: man gff2ps Homepage: http://genome.imim.es/software/gfftools/GFF2PS.html debian-med-1.13.2ubuntu3/menu/bio/sim4.txt0000664000000000000000000000213512124332225015130 0ustar Tool for aligning cDNA and genomic DNA Some information about sim4 from the Debian Med project. sim4 is a similarity-based tool for aligning an expressed DNA sequence (EST, cDNA, mRNA) with a genomic sequence for the gene. It also detects end matches when the two input sequences overlap at one end (i.e., the start of one sequence overlaps the end of the other). sim4 employs a blast-based technique to first determine the basic matching blocks representing the "exon cores". In this first stage, it detects all possible exact matches of W-mers (i.e., DNA words of size W) between the two sequences and extends them to maximal scoring gap-free segments. In the second stage, the exon cores are extended into the adjacent as-yet-unmatched fragments using greedy alignment algorithms, and heuristics are used to favor configurations that conform to the splice-site recognition signals (GT-AG, CT-AC). If necessary, the process is repeated with less stringent parameters on the unmatched fragments. Homepage: http://www.bx.psu.edu/miller_lab/ Please read the man page of this project: man sim4 debian-med-1.13.2ubuntu3/menu/bio/loki.txt0000664000000000000000000000120112124332225015203 0ustar Loki: MCMC linkage analysis on general pedigrees Some information about Loki from the Debian Med project. Performs Markov chain Monte Carlo multipoint linkage analysis on large, complex pedigrees. The current package supports analyses on quantitative traits only, although this restriction will be lifted in later versions. Joint estimation of QTL number, position and effects uses Reversible Jump MCMC. It is also possible to perform affected only IBD sharing analyses. Homepage: http://loki.homeunix.net. You can get a good overview by the main manpage: man loki It is suggested to install the loki-doc package. debian-med-1.13.2ubuntu3/menu/bio/ncbi-tools-bin.menu0000664000000000000000000000770012124332225017223 0ustar # The lot of entries just blast the menu to much ?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/asn2asn" needs="X11" \ section="Med/Biology/ncbi-tools-bin" title="asn2asn" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm" ?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/asn2ff" needs="X11" \ section="Med/Biology/ncbi-tools-bin" title="asn2ff" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm" ?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/asn2gb" needs="X11" \ section="Med/Biology/ncbi-tools-bin" title="asn2gb" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm" ?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/asn2xml" needs="X11" \ section="Med/Biology/ncbi-tools-bin" title="asn2xml" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm" ?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/asndhuff" needs="X11" \ section="Med/Biology/ncbi-tools-bin" title="asndhuff" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm" ?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/checksub" needs="X11" \ section="Med/Biology/ncbi-tools-bin" title="checksub" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm" ?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/debruijn" needs="X11" \ section="Med/Biology/ncbi-tools-bin" title="debruijn" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm" ?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/entrcmd" needs="X11" \ section="Med/Biology/ncbi-tools-bin" title="entrcmd" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm" ?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/fa2htgs" needs="X11" \ section="Med/Biology/ncbi-tools-bin" title="fa2htgs" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm" ?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/fastamerge" needs="X11" \ section="Med/Biology/ncbi-tools-bin" title="fastamerge" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm" ?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/findspl" needs="X11" \ section="Med/Biology/ncbi-tools-bin" title="findspl" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm" ?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/gbseqget" needs="X11" \ section="Med/Biology/ncbi-tools-bin" title="gbseqget" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm" ?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/getfeat" needs="X11" \ section="Med/Biology/ncbi-tools-bin" title="getfeat" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm" ?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/getmesh" needs="X11" \ section="Med/Biology/ncbi-tools-bin" title="getmesh" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm" ?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/getpub" needs="X11" \ section="Med/Biology/ncbi-tools-bin" title="getpub" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm" ?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/gil2bin" needs="X11" \ section="Med/Biology/ncbi-tools-bin" title="gil2bin" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm" ?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/idfetch" needs="X11" \ section="Med/Biology/ncbi-tools-bin" title="idfetch" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm" ?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/indexpub" needs="X11" \ section="Med/Biology/ncbi-tools-bin" title="indexpub" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm" ?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/makeset" needs="X11" \ section="Med/Biology/ncbi-tools-bin" title="makeset" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm" ?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/tbl2asn" needs="X11" \ section="Med/Biology/ncbi-tools-bin" title="tbl2asn" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm" ?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/vecscreen" needs="X11" \ section="Med/Biology/ncbi-tools-bin" title="vecscreen" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm" debian-med-1.13.2ubuntu3/menu/bio/gff2aplot.txt0000664000000000000000000000061212124332225016136 0ustar Pair-wise alignment-plots for genomic sequences in PostScript Some information about gff2aplot from the Debian Med project. A program to visualize the alignment of two genomic sequences together with their annotations. From GFF-format input files it produces PostScript figures for that alignment. See also: man gff2aplot Homepage: http://genome.imim.es/software/gfftools/GFF2APLOT.html debian-med-1.13.2ubuntu3/menu/bio/blast2.menu0000664000000000000000000000504712124332225015575 0ustar # The lot of entries just blast the menu to much ?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/bl2seq" needs="X11" \ section="Med/Biology/Blast2" title="bl2seq" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm" ?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/blast2" needs="X11" \ section="Med/Biology/Blast2" title="blast2" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm" ?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/blastall" needs="X11" \ section="Med/Biology/Blast2" title="blastall" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm" ?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/blastcl3" needs="X11" \ section="Med/Biology/Blast2" title="blastcl3" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm" ?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/blastclust" needs="X11" \ section="Med/Biology/Blast2" title="blastclust" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm" ?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/blastpgp" needs="X11" \ section="Med/Biology/Blast2" title="blastpgp" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm" ?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/copymat" needs="X11" \ section="Med/Biology/Blast2" title="copymat" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm" ?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/fastacmd" needs="X11" \ section="Med/Biology/Blast2" title="fastacmd" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm" ?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/formatdb" needs="X11" \ section="Med/Biology/Blast2" title="formatdb" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm" ?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/impala" needs="X11" \ section="Med/Biology/Blast2" title="impala" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm" ?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/makemat" needs="X11" \ section="Med/Biology/Blast2" title="makemat" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm" ?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/megablast" needs="X11" \ section="Med/Biology/Blast2" title="megablast" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm" ?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/rpsblast" needs="X11" \ section="Med/Biology/Blast2" title="rpsblast" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm" ?package(libvibrant6):command="/usr/bin/vibrate /usr/bin/seedtop" needs="X11" \ section="Med/Biology/Blast2" title="seedtop" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm" debian-med-1.13.2ubuntu3/menu/bio/readseq.txt0000664000000000000000000000101012124332225015667 0ustar ReadSeq: Conversion between sequence formats Some information about readseq from the Debian Med project. Reads and writes nucleic/protein sequences in various formats. Data files may have multiple sequences. Readseq is particularly useful as it automatically detects many sequence formats, and converts between them. Please read the manual for this program by man readseq To test the program you could also test the examples under /usr/share/doc/readseq/tests using the provided Makefile. debian-med-1.13.2ubuntu3/menu/bio/r-cran-qtl.txt0000664000000000000000000000215112124332225016232 0ustar r-cran-qtl: GNU R package for genetic marker linkage analysis Some information about r-cran-qtl from the Debian Med project. R/qtl is an extensible, interactive environment for mapping quantitative trait loci (QTLs) in experimental crosses. It is implemented as an add-on-package for the freely available and widely used statistical language/software R (see http://www.r-project.org). The user will benefit from the seamless integration of the QTL mapping software into a general statistical analysis program. The current version of R/qtl includes facilities for estimating genetic maps, identifying genotyping errors, and performing single-QTL genome scans and two-QTL, two-dimensional genome scans, by interval mapping (with EM algorithm), Haley-Knott regression, and multiple imputation. All of this may be done in the presence of covariates (such as sex, age or treatment). The fit of higher-order QTL models, with sophisticated techniques for model comparisons and model search, will be incorporated soon. More information can be found at Homepage: http://www.biostat.jhsph.edu/~kbroman/qtl/index.html debian-med-1.13.2ubuntu3/menu/bio/fastlink.txt0000664000000000000000000000070412124332225016067 0ustar FastLink: Faster Pedigree Some information about fastlink from the Debian Med project. A faster version of pedigree programs of Linkage Fastlink is much faster than the original Linkage but does not implement all the programs. Unfortunately there is no manpage for the included tools which are ilink, linkmap, lodscore, mlink Extensive documentation inclusive PostScript formatted papers are provided under /usr/share/doc/fastlink debian-med-1.13.2ubuntu3/menu/bio/hmmer.txt0000664000000000000000000000077512124332225015374 0ustar Hmmer: Biological sequence analysis using profile hidden Markov models Some information about Hmmer from the Debian Med project. Hmmer is a suite of programs which use profile hidden Markov models (profile HMMs) to model the primary structure consensus of a family of protein or nucleic acid sequences. Homepage: http://hmmer.wustl.edu/ You can get a good overview by the main manpage: man hmmer The Hmmer users guide is available at http://localhost/doc/hmmer/hmmer-html/index.html debian-med-1.13.2ubuntu3/menu/bio/ncbi-epcr.txt0000664000000000000000000000121212124332225016111 0ustar NCBI-EPCR: Tool to test a DNA sequence for the presence of sequence tagged sites Some information about NCBI-Tools-Bin from the Debian Med project. Electronic PCR feature to test a DNA sequence for the presence of sequence tagged sites. e-PCR looks for STSs in DNA sequences by searching for subsequences that closely match the PCR primers and have the correct order, orientation, and spacing that they could plausibly prime the amplification of a PCR product of the correct molecular weight (Schuler, Genome Research 7:541-50, 1997). Homepage: http://www.ncbi.nlm.nih.gov/genome/sts/epcr.cgi For further information try: man e-PCR debian-med-1.13.2ubuntu3/menu/bio/fastdnaml.html0000664000000000000000000000224112124332225016350 0ustar Construction of Phylogenetic Trees

FastDNAml: Construction of Phylogenetic Trees

Some information about fastDNAml from the Debian Med project.

fastdnaml provides tools for construction of phylogenetic trees of DNA sequences

fastDNAml is a program derived from Joseph Felsenstein's version 3.3 DNAML (part of his PHYLIP package). Users should consult the documentation for DNAML before using this program. fastDNAml is an attempt to solve the same problem as DNAML, but to do so faster and using less memory, so that larger trees and/or more bootstrap replicates become tractable. Much of fastDNAml is merely a recoding of the PHYLIP 3.3 DNAML program from PASCAL to C.

For more detailed information see

man fastDNAml man fastDNAml-util view /usr/share/doc/fastdnaml/fastDNAml_doc_1.2.txt.gz or test the examples under /usr/share/doc/fastdnaml/examples using the Makefile provided under /usr/share/doc/fastdnaml/examples/tests debian-med-1.13.2ubuntu3/menu/bio/ncbi-tools-x11.menu0000664000000000000000000000230412124332225017057 0ustar ?package(ncbi-tools-x11):command="/usr/bin/Cn3D-3.0" needs="X11" \ section="Med/Biology/ncbi-tools-x11" title="Cn3D-3.0" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm" ?package(ncbi-tools-x11):command="/usr/bin/Nentrez" needs="X11" \ section="Med/Biology/ncbi-tools-x11" title="Entrez" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm" ?package(ncbi-tools-x11):command="/usr/bin/Psequin" needs="X11" \ section="Med/Biology/ncbi-tools-x11" title="Sequin" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm" ?package(ncbi-tools-x11):command="/usr/bin/ddv" needs="X11" \ section="Med/Biology/ncbi-tools-x11" title="ddv" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm" ?package(ncbi-tools-x11):command="/usr/bin/entrez2" needs="X11" \ section="Med/Biology/ncbi-tools-x11" title="entrez2" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm" ?package(ncbi-tools-x11):command="/usr/bin/netentcf" needs="X11" \ section="Med/Biology/ncbi-tools-x11" title="Entrez net config" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm" ?package(ncbi-tools-x11):command="/usr/bin/udv" needs="X11" \ section="Med/Biology/ncbi-tools-x11" title="udv" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm" debian-med-1.13.2ubuntu3/menu/bio/muscle.txt0000664000000000000000000000350012124332225015541 0ustar Multiple alignment program of protein sequences Some information about Muscle from the Debian Med project. MUSCLE is a multiple alignment program for protein sequences. MUSCLE stands for multiple sequence comparison by log-expectation. In the authors tests, MUSCLE achieved the highest scores of all tested programs on several alignment accuracy benchmarks, and is also one of the fastest programs out there. Homepage: http://www.drive5.com/muscle Basic usage muscle -in -out Common options (for a complete list please see the User Guide): -in Input file in FASTA format (default stdin) -out Output alignment in FASTA format (default stdout) -diags Find diagonals (faster for similar sequences) -maxiters Maximum number of iterations (integer, default 16) -maxhours Maximum time to iterate in hours (default no limit) -maxmb Maximum memory to allocate in Mb (default 80% of RAM) -html Write output in HTML format (default FASTA) -msf Write output in GCG MSF format (default FASTA) -clw Write output in CLUSTALW format (default FASTA) -clwstrict As -clw, with 'CLUSTAL W (1.81)' header -log[a] Log to file (append if -loga, overwrite if -log) -quiet Do not write progress messages to stderr -stable Output sequences in input order (default is -group) -group Group sequences by similarity (this is the default) -version Display version information and exit Without refinement (very fast, avg accuracy similar to T-Coffee): -maxiters 2 Fastest possible (amino acids): -maxiters 1 -diags -sv -distance1 kbit20_3 Fastest possible (nucleotides): -maxiters 1 -diags See also: man muscle debian-med-1.13.2ubuntu3/menu/bio/mipe.txt0000664000000000000000000000255712124332225015216 0ustar Tools to store PCR-derived data Some information about mipe from the Debian Med project. MIPE provides a standard format to exchange and/or storage of all information associated with PCR experiments using a flat text file. This will: * allow for exchange of PCR data between researchers/laboratories * enable traceability of the data * prevent problems when submitting data to dbSTS or dbSNP * enable the writing of standard scripts to extract data (e.g. a list of PCR primers, SNP positions or haplotypes for different animals) Although this tool can be used for data storage, it's primary focus should be data exchange. For larger reporisitories, relational databases are more appropriate for storage of these data. The MIPE format could then be used as a standard format to import into and/or export from these databases. Homepage: http://mipe.sourceforge.net You should also read the relevant man pages: man mipe06to07 man mipe08to09 man mipe0_9to1_0 man mipe2dbSTS man mipe2fas man mipe2html man mipe2pcroverview man mipe2pcrprimers man mipe2putativesbeprimers man mipe2sbeprimers man mipe2snps man mipeCheckSanity man removePcrFromMipe man removeSbeFromMipe man sbe2mipe man snp2mipe man snpPosOnDesign man snpPosOnSource man csv2mipe man genotype2mipe man mipe2genotypes man removeSnpFromMipe debian-med-1.13.2ubuntu3/menu/tools/0000775000000000000000000000000012124332546014107 5ustar debian-med-1.13.2ubuntu3/menu/tools/mencal.txt0000664000000000000000000000041212124332225016076 0ustar MenCal: Menstruation Calendar Some information about mencal from the Debian Med project. Please read man mencal for a detailed description of options and the configuration file of the menstruation calendar. It is intended to be called from a text console. debian-med-1.13.2ubuntu3/menu/imaging/0000775000000000000000000000000012124332546014362 5ustar debian-med-1.13.2ubuntu3/menu/imaging/nifti-bin.txt0000664000000000000000000000101112124332225016765 0ustar Tool for reading and writing NIfTI-1 MRI and fMRI brain images Some information about nifti-bin from the Debian Med project. Niftilib is a set of i/o libraries for reading and writing files in the NIfTI-1 data format. NIfTI-1 is a binary file format for storing medical image data, e.g. magnetic resonance image (MRI) and functional MRI (fMRI) brain images. Please read: man nifti_tool man nifti_stats man nifti1_test Further reading: http://niftilib.sourceforge.net/ http://nifti.nimh.nih.gov/ debian-med-1.13.2ubuntu3/menu/imaging/minc-tools.txt0000664000000000000000000000237012124332225017203 0ustar MINC Tools: MNI medical image format tools Some information about minc-tools from the Debian Med project. The Minc file format is a highly flexible medical image file format built on top of the NetCDF generalized data format. The format is simple, self-describing, extensible, portable and N-dimensional, with programming interfaces for both low-level data access and high-level volume manipulation. On top of the libraries is a suite of generic image-file manipulation tools. The format, libraries and tools are designed for use in a medical-imaging research environment : they are simple and powerful and make no attempt to provide a pretty interface to users. The best way to start using minc-tools is to read the document /usr/share/doc/minc-tools/GETTING_STARTED A reasonable resource of information is http://www.nmr.mgh.harvard.edu/~rhoge/minc/ The following manpages are available for the MINC tools suite: mincaverage minccalc mincconcat minccopy mincdiff mincedit mincexpand mincextract mincheader mincinfo mincmakescalar mincmakevector mincmath mincresample mincreshape mincstats invert_raw_image mincview mincwindow rawtominc xfmconcat xfminvert voxeltoworld minc_modify_header minclookup minctoraw transformtags worldtovoxel debian-med-1.13.2ubuntu3/menu/imaging/ctn.txt0000664000000000000000000000131212124332225015676 0ustar CTN: Runtime files for Central Test Node, a DICOM implementation Some information about ctn from the Debian Med project. The ctn package provides runtime files for Central Test Node, a DICOM implementation. DICOM is the standard for image storage, annotation, and networking. It is used widely for medical imaging. Information about the tools which are provided can be obtained by man dcm_ctnto10 man dcm_diff man dcm_dump_element man dcm_dump_file man dcm_make_object man dcm_map_to_8 man dcm_rm_element man dcm_verify man dcm_add_fragments man dcm_create_object The homepage is http://www.erl.wustl.edu/DICOM/ctn.html. Extensive documentation is provided in the Debian package ctn-doc. debian-med-1.13.2ubuntu3/menu/imaging/dcmtk.txt0000664000000000000000000000211612124332225016217 0ustar The OFFIS DICOM toolkit command line utilities Some information about dcmtk from the Debian Med project. DCMTK includes a collection of libraries and applications for examining, constructing and converting DICOM image files, handling offline media, sending and receiving images over a network connection, as well as demonstrative image storage and worklist servers. Homepage: http://dicom.offis.de/ The package contains a set of utilities. They are described in the relevant man pages which are: man dbregimg man dcm2pnm man dcm2xml man dcmcjpeg man dcmconv man dcmcrle man dcmdjpeg man dcmdrle man dcmdspfn man dcmdump man dcmftest man dcmgpdir man dcmj2pnm man dcmmkcrv man dcmmkdir man dcmmklut man dcmodify man dcmp2pgm man dcmprscp man dcmprscu man dcmpschk man dcmpsmk man dcmpsprt man dcmpsrcv man dcmpssnd man dcmquant man dcmscale man dcmsign man dcod2lum man dconvlum man dsr2html man dsr2xml man dsrdump man dump2dcm man echoscu man findscu man imagectn man movescu man storescp man storescu man ti man wlmscpfs man xml2dcm man xml2dsr debian-med-1.13.2ubuntu3/menu/imaging/medcon.txt0000664000000000000000000000055112124332225016363 0ustar MedCon: MEDical image (DICOM, ECAT, ...) CONversion tool Some information about medcon from the Debian Med project. The homepage is at http://xmedcon.sourceforge.net There exists a xmedcon tool which provides a nice graphical interface and might be a good start for beginners. Alternatively you can type man medcon to learn how to use medcon. debian-med-1.13.2ubuntu3/menu/physics/0000775000000000000000000000000012124332546014431 5ustar debian-med-1.13.2ubuntu3/menu/physics/octave.menu0000664000000000000000000000017012124332225016570 0ustar ?package(octave2.1):needs="text" \ section="Med/Physics" \ title="Octave (2.1)" \ command="/usr/bin/octave2.1" debian-med-1.13.2ubuntu3/menu/physics/r-base.menu0000664000000000000000000000015012124332225016456 0ustar ?package(r-base-core):needs="text" \ section="Med/Physics" \ title="GNU R" \ command="/usr/bin/R" debian-med-1.13.2ubuntu3/tasks/0000775000000000000000000000000012323032575013130 5ustar debian-med-1.13.2ubuntu3/tasks/cms0000664000000000000000000000666312124332225013642 0ustar Task: Content Management Metapackage: false Description: Debian Med content management systems Here you can find software that is useful to build a content management system for medical care. Suggests: zope-zms Homepage: http://www.zms-publishing.com/ Vcs-Svn: svn://svn.debian.org/svn/pkg-zope/zope-zms/trunk/ Pkg-Description: Content management for science, technology and medicine ZMS (Zope based Content Management for Science, Technology and Medicine) is a ready to use solution for efficient electronic publishing. An easy to handle graphical user interface for editors and flexible modelling features (multiple languages, Metadata, content objects, XML import/export, workflow etc.) allow an optimum of productivity: A basic configuration to start with can be created with a few mouse clicks. . ZMS is perfectly suitable for hospitals, research institutions, NGOs and small to medium-size international companies. . The ZMS concept is based on a consulting approach for the rational publishing on the internet: the professional user is able to pursue a consequently efficiency oriented producing base with the ZMS software and can hereby also achieve important economic results in the so-called low budget area. The modulation possibilities of the ZMS components and the experienced producing steps makes out of ZMS an incomparable fast tool. Remark: Zope ZMS needs Zope 2.x which is not any more packaged for Debian and thus we can here only give a hint that this software exists and might be useful for content management in medical care. ; Added by blends-inject 0.0.7. [Please note here if modified manually] Suggests: xnat Homepage: http://www.xnat.org Language: java WNPP: 629143 License: XNAT SLA Pkg-Description: platform for data management and productivity tasks in neuroimaging The primary functionality of XNAT is to provide a place to store and control access to neuroimaging data. This includes sophisticated user control, search and retrieval, and archiving capabilities. As open-source software, XNAT also supports a wide variety of research-based processing pipelines, and is able to link up with supercomputer processing power to dramatically shorten image processing time. Published-Authors: Marcus, D.S., Olsen T., Ramaratnam M., and Buckner, R.L. Published-In: Neuroinformatics 5(1): 11-34 Published-Title: The Extensible Neuroimaging Archive Toolkit (XNAT): An informatics platform for managing, exploring, and sharing neuroimaging data. Published-Year: 2007 Registration: http://www.xnat.org/download-xnat.html ; Added by blends-inject 0.0.7. [Please note here if modified manually] Suggests: hid Homepage: http://www.nitrc.org/projects/hid Language: java License: BSD, BIRN Pkg-Description: database management system for clinical imaging The Human Imaging Database (HID) is an extensible database management system developed to handle the increasingly large and diverse datasets collected as part of the MBIRN and FBIRN collaboratories and throughout clinical imaging communities at large. Published-Authors: Keator, D.B.; Grethe, J.S.; Marcus, D.; Ozyurt, B.; Gadde, S.; Murphy, S.; Pieper, S.; Greve, D.;Notestine, R.; Bockholt, H.J.; Papadopoulos, P. Published-In: IEEE Transactions on Information Technology in Biomedicine, 12 (2) Published-Title: A National Human Neuroimaging Collaboratory Enabled By The Biomedical Informatics Research Network (BIRN) Published-Year: 2008 Registration: http://www.nitrc.org/account/register.php debian-med-1.13.2ubuntu3/tasks/statistics0000664000000000000000000000105012124332225015233 0ustar Task: Statistics Description: Debian Med statistics This metapackage will install packages which are helpful to do statistics with a special focus on tasks in medical care. Depends: r-bioc-edger, r-bioc-limma Why: Statistical analysis of transcriptome expression assays. Depends: r-bioc-qvalue Depends: r-cran-randomforest Suggests: science-statistics Why: This more or less includes all statistics relevant packages which might be a bit to much for medical purposes - so it is only suggested. Depends: r-cran-beeswarm Depends: r-cran-pvclust debian-med-1.13.2ubuntu3/tasks/cloud0000664000000000000000000000413612124332225014157 0ustar Task: Cloud Description: Debian Med bioinformatics applications usable in cloud computing This metapackage will install Debian packages related to molecular biology, structural biology and bioinformatics for use in life sciences, that do not depend on graphical toolkits and therefore can fit on system images for use in cloud computing clusters, where space can be limited. X-Begin-Category: Phylogenetic analysis Depends: altree, fastdnaml, phyml, tree-puzzle | tree-ppuzzle X-End-Category: Phylogenetic analysis X-Begin-Category: Genetics Depends: alien-hunter, fastlink, loki, plink, r-cran-qtl, r-other-mott-happy Depends: bagphenotype Depends: r-other-valdar-bagphenotype.library X-End-Category: Genetics X-Begin-Category: Sequence alignments and related programs. Depends: amap-align, blast2, boxshade, dialign, dialign-tx, exonerate, fastx-toolkit, gff2aplot, glam2, gmap, hmmer, kalign, mafft, mummer, muscle, poa, probcons, proda, python-pynast, sibsim4, sigma-align, sim4, t-coffee, vcftools, wise Depends: clustalw | clustalw-mpi Comment: non-free X-End-Category: Sequence alignments and related programs. X-Begin-Category: EMBOSS Depends: emboss, embassy-domalign, embassy-domainatrix, embassy-domsearch, embassy-phylip X-End-Category: EMBOSS X-Begin-Category: High throughput sequencing Depends: bedtools, bwa, filo, last-align, maq, picard-tools, r-bioc-hilbertvis, samtools, ssake, tophat, velvet X-End-Category: High throughput sequencing X-Begin-Category: Analysis of RNA sequences. Depends: infernal, rnahybrid X-End-Category: Analysis of RNA sequences. X-Begin-Category: Molecular modelling and molecular dynamics Depends: gromacs, mustang, theseus Depends: autodock, raster3d Comment: non-free X-End-Category: Molecular modelling and molecular dynamics X-Begin-Category: Tools for the molecular biologist. Depends: acedb-other, melting, mipe, ncbi-epcr, ncbi-tools-bin, ncoils, primer3, readseq, tigr-glimmer, seqan-apps, staden-io-libs-utils Depends: python-cogent Comment: non-free X-End-Category: Tools for the molecular biologist. debian-med-1.13.2ubuntu3/tasks/imaging-dev0000664000000000000000000001232412124332225015236 0ustar Task: Imaging Development Description: Debian Med packages for medical image development This metapackage will install Debian packages which might be useful for developing applications for medical image processing. Depends: ctn-dev, cimg-dev, libminc-dev, libmdc2-dev, libvtk5-dev Depends: libnifti-dev Depends: libigstk4-dev Suggests: igstk-examples Depends: libinsighttoolkit3-dev Suggests: insighttoolkit3-examples Suggests: libnifti-doc Suggests: libvtk5.4 Depends: libvolpack1-dev Depends: libgdcm2-dev Depends: python-gdcm Suggests: python-libavg Homepage: http://www.libavg.de License: LGPL Vcs-Svn: svn://svn.debian.org/collab-maint/deb-maint/libavg/trunk/ Vcs-Browser: http://svn.debian.org/wsvn/collab-maint/deb-maint/libavg/trunk/ Pkg-URL: http://snapshot.debian.org/archive/debian/20100503T045439Z/pool/main/liba/libavg/python-libavg_1.0.1-1_amd64.deb Pkg-Description: Description: libavg Ain't Vector Graphics libavg is a high-level multimedia platform with a focus on interactive installations. It is meant to pick up where Macromedia Director leaves off and gives you high-quality hardware-accelerated visuals as well as easy and flexible authoring, testing and deployment. libavg integrates well with other open-source solutions for sound, networking and hardware device support, resulting in a complete and well-integrated package. It uses an xml-based layout language for screen design and Python as scripting language. Remark: Homepage shows some potential medical applications The package was once part of Debian but is orphaned now. Feel free to pick the latest snapshot from http://snapshot.debian.org/package/libavg/1.0.1-1/ or use the packaging in collab-maint for reintroducing. Depends: python-mvpa Why: Suggested by maintainer Michael Hanke Depends: python-nipy ; Added by blends-inject 0.0.4. [Please note here if modified manually] Depends: python-nipype Published-Authors: SS Ghosh, C Burns, D Clark, K Gorgolewski, YO Halchenko, C Madison, R Tungaraza, KJ Millman Published-In: 16th Annual Meeting of the Organization for Human Brain Mapping Published-Title: Nipype: Opensource platform for unified and replicable interaction with existing neuroimaging tools Published-URL: https://github.com/satra/ohbm2010/raw/master/NIPYPE/POSTER/poster_nipype.pdf Published-Year: 2010 Depends: python-nitime Depends: python-casmoothing Depends: libvia-dev Depends: odin Depends: libcv-dev Depends: libvxl1-dev Depends: libteem1-dev Depends: gmic Depends: libgiftiio-dev Depends: libactiviz.net-cil Depends: libvistaio-dev Depends: libmia-2.0-dev Depends: libopenigtlink1-dev Depends: libmni-perllib-perl Homepage: http://packages.bic.mni.mcgill.ca/tgz/ License: Artistic License Responsible: NeuroDebian Team Pkg-URL: http://apsy.gse.uni-magdeburg.de/svn/fsl/libmni-perllib-perl/trunk/debian/ Pkg-Description: The MNI Perl Library Collection of various Perl module used by other MNI software packages. Remark: There was some previous work on this software which is stalled currently Michael Hanke agreed to take over his stuff from mentors http://mentors.debian.net/cgi-bin/sponsor-pkglist?action=details;package=libmni-perllib-perl to Debian Med svn and start group maintenance. Depends: libgiftiio-dev License: Public domain Pkg-URL: http://neuro.debian.net/pkgs/libgifti-dev.html Depends: python-dicom License: MIT Pkg-URL: http://neuro.debian.net/pkgs/python-dicom.html Depends: libopenmeeg-dev Published-Authors: Alexandre Gramfort, Théodore Papadopoulo, Emmanuel Olivi, Maureen Clerc Published-In: BioMedical Engineering OnLine 45:9 Published-Title: OpenMEEG: opensource software for quasistatic bioelectromagnetics Published-URL: http://www.biomedical-engineering-online.com/content/9/1/45 Published-Year: 2010 Depends: python-nibabel ; Added by blends-inject 0.0.2. [now official package] Depends: libgdf-dev ; Added by blends-inject 0.0.6. [Please note here if modified manually] Suggests: emokit Homepage: https://github.com/daeken/Emokit Language: Python, C License: BSD-3 Vcs-Browser: https://github.com/daeken/Emokit Vcs-Git: git://github.com/daeken/Emokit.git Pkg-Description: Emotiv EPOC headset Python interface Emotive is an interface to a budget Emotiv EPOC EEG headset. ; Added by blends-inject 0.0.7. [s/pyxnat/python-pyxnat/] Depends: python-pyxnat Depends: python-dipy Published-Authors: Garyfallidis E, Brett M, Tsiaras V, Vogiatzis G, Nimmo-Smith I Published-In: Proc. Intl. Soc. Mag. Reson. Med. 18 Published-Title: Identification of corresponding tracks in diffusion MRI tractographies Published-Year: 2010 ; Added by blends-inject 0.0.7. [Removed unneeded publication dat] Depends: libbiosig-dev Depends: libctk-dev ; Added by blends-inject 0.0.7. [now official package] Depends: python-cfflib Depends: libopenslide-dev Depends: python-openslide Depends: libopenslide-java Depends: libbio-formats-java Language: Java Remark: This library would enhance the package imagej Suggests: libeegdev-dev Suggests: libxdffileio-dev Depends: octave-dicom Homepage: http://octave.sourceforge.net/dicom/ License: GPL-v3+ Pkg-Description: Dicom support in Octave Digital communications in medicine (DICOM) file io. Depends on Grassroots DICOM (GDCM) Depends: libcamitk3-dev debian-med-1.13.2ubuntu3/tasks/practice0000664000000000000000000003130012124332225014634 0ustar Task: Practice Description: Debian Med packages for practice management This metapackage contains dependencies for a collection of software which might be helpful for practitioners to manage their practice. Depends: gnumed-client Depends: gnumed-server Depends: libchipcard-tools Why: Reading German "Gesundheitskarte" Depends: ginkgocadx Suggests: libctapimkt0 Depends: freediams, freemedforms-emr Depends: r-cran-medadherence Depends: clinica Depends: entangle Depends: freeicd X-Homepage: http://www.freemedforms.com/ X-License: GPL3 X-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/freeicd/trunk/ X-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/freeicd/trunk/ X-Pkg-Description: ICD10 coding assistant FreeICD is the result of FreeMedForms ICD10 assistant plugins built into a standalone application. It is developed by medical doctors and is intended for use by these same professionals. It can be used alone. Depends: medintux Homepage: http://medintux.org/medintux/en/ License: CeCILL (free) Pkg-Description: Medical practice management system MedinTux is a powerful medical software, multiuser (using MySQL for data storage), easy-to-use, complete, working from the GP to the hospital. . Help wanted: Unfortunately, MedinTux is written in french, closing its use to many countries in the world. Help is wanted to translate . * The GUI (directly in the source code, which will be reverse translated later to french, using Qt Linguist) * The documentation and installation instructions . Any person with real french to english skill is wellcome. Please, contact Gérard Delafond : gerard-at-delafond.org Depends: mirth Homepage: http://www.mirthproject.org/ License: MPL 1.1 Pkg-Description: HL7 integration engine "Swiss army knife" HL7 integration engine. Specifically designed for HL7 message integration, Mirth provides the necessary tools for developing, deploying, and monitoring interfaces. . Filtering can be performed on incoming messages using the default message filters that are included with Mirth, or your own custom filtering scripts. Mirth's web interface makes it easy to write new scripts by proving a template and editing field that allows you to validate your script code. Mirth also supports filters written in Java if you require more complex filtering options. Depends: tinyheb Homepage: http://tinyheb.sourceforge.net/ License: GPL Pkg-URL: http://home.arcor.de/thomas.baum/tinyheb/source/ Pkg-Description: billing system for midwives This billing system enables midwives to exchange data with health insurances in Germany (compliant to §302 SGB V). Ignore: clearhealth Homepage: http://www.clear-health.com/ License: GPL Pkg-Description: medical practice management For larger practices or those with multiple locations ClearHealth Advantage is an enterprise scalable system to meet the most demanding needs. . The ClearHealth medical suite now offers a next generation set of capabilities to practices large and small. Combining best of breed scheduling, patient management, EMR, reporting, document storage, labs, prescriptions and billing it gives you the tools you need to effectively run your practice and keep your focus where it counts, on improving patient care. . With support for a huge variety of payers and clearing houses you have many options in who you can bill electroncally. Paper forms support for the HCFA (CMS 1500) format as well as UB92 support. Scheduling . Practice management begins with scheduling, while not specifically a medical problem as any doctor knows there are several unique aspects of medical scheduling that can make life miserable for the front end staff. ClearHealth scheduling was built from the ground up in close consultation with medical professionals to ensure that it meets those special needs. Being extremely flexible you can schedule based on providers, rooms, or equipment across facilities and regions. Comment: I do not really remember why this is set to "Ignore" - my only guess is that it once was GPL and now the homepage quoted above seems to provide some proprietary software. Some investigation might be needed (at). . The guessing above is manifested by the fact that the source code repository of clearhealth which was linked from http://www.op-en.org/ vanished. Depends: mirrormed Homepage: http://www.mirrormed.org/ License: GPL Pkg-Description: EHR and practice management system MirrorMed is a free and open source EHR and practice management system written in PHP. MirrorMed is a web-based application that is capable of running a healthcare practice. MirrorMed shares code with FreeMED, and OpenEMR. MirrorMed is primarily sponsored by SynSeer. Depends: elexis Homepage: http://sourceforge.net/projects/elexis License: Eclipse Public License WNPP: 570433 Responsible: Niklaus Giger Language: Java (Eclipse Rich Client Platform) Pkg-Description: medical practice managemant system for use in Switzerland An Eclipse RCP program for all aspects of a medical practice: electronic medical record (EMR), laboratory findings etc., as well as accounting, billing (swiss TARMED-System, other systems to be developped) and other daily work. Depends: freeb Homepage: http://freeb.org/ License: GPL Pkg-Description: Medical Bill formating module FreeB is Medical Bill formating module. It is designed to be used with any EHR system that tracks basic demographics, procedure codes and diagnosis codes. An EHR sends the basic billing data to FreeB using a simple XML-based interface (XML-RPC or SOAP as needed). FreeB then handles the bill formating and bill revision. FreeB has standard templates for X12 837, HFCA 1500 (now the NPI modified CMS-1500) and UB-92 series formats. FreeB is designed so that it can send bills to a printer, to a payers web interface, or to a clearinghouse. FreeB also performs bill revision, as you modify the claim data in order to meet the payor requirements, FreeB keeps track of those changes over time so that you can easily see the progression of the claim over time. The current version of FreeB is written in PHP and uses the Smarty template language for bill templates. FreeB has a web interface that allows users to modify any aspect of a claim, and send groups of claims in different directions. . FreeB 1.0 (Perl) is still used by the OpenEMR project. FreeB 1.0 was rewritten as REMITT which used by the FreeMED project. Depends: freemed Homepage: http://www.freemedsoftware.org/ License: GPL Pkg-URL: http://downloads.sourceforge.net/freemed/freemed_0.8.4-1_all.deb?use_mirror=mesh Pkg-Description: Electronic Medical Record and Practice Management system Electronic Medical Record and Practice Management system for medical providers that runs in any web browser in multiple languages. It provides an XML-RPC backend and multiple import and export formats, as well as reporting and other features. Depends: elementalclinic Homepage: http://www.elementalclinic.com/ License: GPL2+ Responsible: Hans Dieter Pearcey Pkg-URL: http://svn.opensourcery.com/public/ubuntu/pool/main/e/elementalclinic/ Pkg-Description: Electronical Medical Health record system for mental health Elemental Clinic is medical records management system for mental health professionals. . * Implement an affordable web-based alternative to paper records keeping * Train and support clinicians to get the most from your EMR * Customize software to fit unique practice needs Depends: openemr Pkg-URL: http://www.oemr.org/Download_OpenEMR/ Depends: clearhealth Homepage: http://www.op-en.org/site/clearhealth License: GPL Pkg-Description: Medical practice management system ClearHealth is a Ppractice Management System to address the big five features: Medical Billing, Medical Accounts Recievable, Scheduling, Access Control, and EMR. Suggests: openpms Homepage: http://sourceforge.net/projects/openpms License: GPL Pkg-Description: medical billing, scheduling, and account management system HIPAA compliant medical billing, scheduling, and account management system. Integrated with x12 standard electronic transactions, OpenBilling XML standards, and hcfa-1500 legacy support. Complete cross platform performance with java 2 standards. Remark: Status of this software This project has not issued any release since March 2004 and thus might be considered dead. There are some chances to cherry pick some code from SourceForge repository. Suggests: resmedicinae Homepage: http://resmedicinae.sourceforge.net/ License: GPL: Pkg-Description: comprising software solution for use in medicine Res Medicinae is to become a comprising software solution for use in Medicine which combines intuitive ease of use with great flexibility, reached through the usage of CYBOP technology. It wants to adhere to common standards for medical software, wherever useful, and will thus be open to other systems. Using the CYBOL language, users are enabled to, themselves, modify applications. . Res Medicinae is the attempt to overcome high pricing in the realm of Medical Information Systems and to provide users with a free, stable, secure, platform-independent, extensive system. . This project does not provide a complete solution for medical practice. It will take another couple of years before being so far. Suggests: sqlclinic Homepage: http://www.sqlclinic.net/ License: GPL Pkg-Description: intranet solution for Saint Vincents Catholic Medical Centers of New York This is a complete clinical and administrative application for providers of psychiatric housing, although the software is designed to accommodate an entire Community Mental Health Care Center (CMHC) or private practitioners (both clinical social workers and psychiatrists) working in behavioral health. Technical support is free via mailing lists. Support contracts are available from Saint Vincent Catholic Medical Centers of New York. . Features: * Administrative Tools * Built In DBA Utilities * Complete Clinical Chart * Email Alerts, Reports and Reminders * Intake and Placement Tracking * Integrated DSM IV * Quality Assurance Instruments * Purchase Orders * Unit (Shift) Logs * Work Orders X-Comment: torch seems to be dead (last release in 2004) Sourceforge page: http://sourceforge.net/projects/op-torch/ X-Comment: Circare project seems to be dead X-Comment: OIO project seems to be dead Homepage: http://www.txoutcome.org/ X-Comment: Open PM ToolWorks seems to be dead Suggests: openrep Homepage: http://www.homeopathyonline.org/about_OpenRep.html License: GPLv3 or later WNPP: 533044 Responsible: Y Giridhar Appaji Nag Pkg-Description: software for homeopathic repertorization and viewing materia medicae OpenRep is a Java desktop application designed to serve as a homeopathic software with capabilities to open and use multiple repertories, perform repertorizations and view its results, manage patients and view different materia medicae. It is also designed to save and load data in human readable xml format. Remark: scientific use? Please read the thread about homeopathic software on the Debian Med mailing list starting at http://lists.debian.org/debian-med/2009/06/msg00028.html . Depends: proteus Homepage: http://proteme.org/ License: EPL Pkg-Description: clinical decision support guidelines model Proteus is a software technology that allows creating clinical executable decision support guidelines with little effort. Once a guideline for a condition has been created, it can be executed to provide stepwise advice for any patient having that condition. Depends: thera-pi Homepage: http://www.thera-pi.org/ License: GPL Pkg-Description: organization and management of outpatient clinics and rehabilitation-medicine companies This project seems to target at the German health care system and it should be clarified in how far it can be extended for other countries. . The source code is available in CVS only and can be downloaded at http://thera-pi.cvs.sourceforge.net/viewvc/thera-pi/ . Depends: freeshim Pkg-URL: https://launchpad.net/~rufustfirefly/+archive/ppa/+buildjob/2489799/+files/shim_0.1.1-1ubuntu2~maverick_all.deb Remark: Needs Java prerequisites Missing Java prerequisites in Debian: * org.hsqldb:hsqldb:2.0.0 * org.reflections:reflections:0.9.5-RC2 Depends: remitt Homepage: http://remitt.org/ License: GPL Pkg-Description: preparing and submitting medical billing data Medical information translation and transmission system, which is primarily used for preparing and submitting medical billing data. . REMITT works independent of any specific electronic medical record (EMR) or practice management (PM) system, and can interface with any EMR or PM system which implements its application programming interface (API). The first system to do so has been FreeMED. Depends: qrisk2 debian-med-1.13.2ubuntu3/tasks/bio-dev0000664000000000000000000001627312323032575014411 0ustar Task: Biology Development Description: Debian Med packages for development of micro-biology applications This metapackage will install Debian packages which might be helpful for development of applications for micro-biological research. Depends: bioperl, bioperl-run, libncbi6-dev Depends: mcl X-Category: Analysis of network structure X-Importance: Clustering of graphs Depends: biosquid Depends: libvibrant6-dev Depends: python-biopython Depends: python-cogent Depends: ruby-bio Depends: libbiojava-java, libbiojava3-java Depends: libqsearch-dev Depends: libgenome-1.3-dev Depends: libai-fann-perl Depends: libbio-mage-perl Why: Useful for the submission of microarray data to public repositories. Depends: libnhgri-blastall-perl Depends: libtfbs-perl Depends: libgo-perl Depends: r-cran-genetics, r-cran-haplo.stats Depends: octave-bioinfo Depends: libbio-graphics-perl Depends: libbio-primerdesigner-perl Depends: libace-perl Depends: libbiococoa-dev Depends: libstaden-read-dev Depends: libsrf-dev Depends: libzerg0-dev, libzerg-perl Depends: librg-reprof-bundle-perl Depends: python-librcsb-core-wrapper, librcsb-core-wrapper0-dev Depends: libsbml5-dev Suggests: r-cran-rocr Why: Even if this package is not directly connected to biology it is maintained by Debian Med team and should be in our focus and it is not wrong to suggest this package for development of biological applications based on R Depends: seqan-dev Depends: libbio-mage-utils-perl Depends: libchado-perl Depends: libpal-java Depends: libjebl2-java Remark: Fork from jebl This is a branch of the original JEBL on http://sourceforge.net/projects/jebl/ to develop a new API and class library. Suggests: r-bioc-biocgenerics Depends: r-bioc-biobase Remark: This is a part of Bioconductor project A nice overview about all modules of BioDonductor is given at http://www.bioconductor.org/packages/release/bioc/ Depends: libffindex0-dev Depends: librostlab3-dev, librostlab-doc Depends: librostlab-blast0-dev, librostlab-blast-doc Depends: librg-blast-parser-perl Depends: libsort-key-top-perl Depends: libhmsbeagle-dev Depends: libbiojava3-java Depends: libforester-java X-Mark: Prospective packages are starting here. X-Mark: Packages in Vcs - Information about these is queried from UDD as well Depends: libbamtools-dev Depends: libbio-das-perl Depends: python-mmtk Language: C, Python Depends: libopenmm4-dev Depends: libgenometools0-dev Depends: python-biom-format Suggests: libswarm2-dev Depends: bioclipse Homepage: http://www.bioclipse.net/ License: Eclipse Public License (EPL) + exception Pkg-Description: platform for chemo- and bioinformatics based on Eclipse The Bioclipse project is aimed at creating a Java-based, open source, visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform (RCP). Bioclipse, as any RCP application, is based on a plugin architecture that inherits basic functionality and visual interfaces from Eclipse, such as help system, software updates, preferences, cross-platform deployment etc. . Bioclipse will provide functionality for chemo- and bioinformatics, and extension points that easily can be extended by plugins to provide added functionality. The first version of Bioclipse includes a CDK-plugin (bc_cdk) to provide a chemoinformatic backend, a Jmol-plugin (bc_jmol) for 3D-visualization and a general logging plugin. To stay updated on upcoming features, releases, new plugins etc, please register for the mailing list bioclipse-announce. The development is best followed on the Bioclipse Wiki where we document the progress and ideas of the development on a daily basis. Depends: biostrings Vcs-Git: git://git.debian.org/debian-med/r-bioc-biostrings.git Homepage: http://www.bioconductor.org/packages/release/bioc/html/Biostrings.html Pkg-Description: String objects representing biological sequences, and matching algorithms Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences. Depends: iranges Vcs-Git: git://git.debian.org/git/debian-med/iranges.git Homepage: http://www.bioconductor.org/packages/release/bioc/html/IRanges.html Pkg-Description: Infrastructure for manipulating intervals on sequences The package provides efficient low-level and highly reusable S4 classes for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more generally, data that can be organized sequentially (formally defined as Vector objects), as well as views on these Vector objects. Efficient list-like classes are also provided for storing big collections of instances of the basic classes. All classes in the package use consistent naming and share the same rich and consistent "Vector API" as much as possible. Depends: libgff-perl Homepage: http://www.sanger.ac.uk/Software/formats/GFF/ Responsible: David Paleino License: GPL-1+ WNPP: 468826 Pkg-Description: Perl bindings for GFF Annotation Protocol GFF (Gene Finding Feature) is a format for describing genes and other features associated with DNA, RNA and Protein sequences. . This package provides a Perl module to use GFF objects. Depends: libmems-1.5-1 Homepage: http://asap.ahabs.wisc.edu/software/software-development-libraries/libmems.html Responsible: Andreas Tille License: GPL Pkg-URL: http://people.debian.org/~tille/packages/libmems/ Pkg-Description: library to support DNA string matching and comparative genomics libMems is a freely available software development library to support DNA string matching and comparative genomics. Among other things, libMems implements an algorithm to perform approximate multi-MUM and multi-MEM identification. The algorithm uses spaced seed patterns in conjunction with a seed-and-extend style hashing method to identify matches. The method is efficient, requiring a maximum of only 16 bytes per base of the largest input sequence, and this data can be stored externally (i.e. on disk) to further reduce memory requirements. Depends: python-pysam Remark: Given the large amount of code duplication (samtools, tabix), this package may be difficult to accept for Debian. It is nevertheless listed here as it is a useable draft, hoping it may be useful to others. Depends: libgbfp-dev Homepage: http://code.google.com/p/gbfp/ License: GPL Language: C WNPP: 612814 Responsible: Scott Christley Pkg-Description: GBParsy is a GenBank flatfile parser library GBParsy is a library of functions that parses the GenBank flatfile, which is a representative and popular sequence format. The library is optimized for speed and efficient use of memory so it can rapidly parse large sequence such as Arabidopsis chromosome for genomic analysis. Depends: octace-bioinfo Homepage: http://octave.sourceforge.net/bioinfo/index.html License: GPL-2+ Pkg-Description: Bioinformatics manipulation for Octave aa2int: Convert amino acid characters into integers. aminolookup: Convert between amino acid representations. cleave: Cleave a peptide SEQUENCE using the PATTERN at the POSITION relative to the pattern. int2aa Convert amino acid integers into characters. seqreverse Reverse a nucleotide sequence. debian-med-1.13.2ubuntu3/tasks/bio0000664000000000000000000035075512124332225013635 0ustar Task: Biology Description: Debian Med micro-biology packages This metapackage will install Debian packages related to molecular biology, structural biology and bioinformatics for use in life sciences. X-Begin-Category: Phylogenetic analysis Depends: altree Depends: beast-mcmc Depends: fastdnaml, njplot, tree-puzzle | tree-ppuzzle Depends: probalign Depends: treeviewx Depends: figtree Depends: phy-spread | spread-phy X-End-Category: Phylogenetic analysis Depends: phylip Why: Phylogenetic analysis (Non-free, thus only suggested). X-Comment: treetool is removed from Debian because it is not maintained upstream since 1995 and cause the Xserver to freeze under Squeeze Depends: fastlink, loki, plink, r-cran-qtl, r-cran-genabel Why: Genetics X-Begin-Category: Sequence alignments and related programs. Depends: amap-align Remark: Dead upstream The homepage of this project vanished as well as the Download area. An old unmaintained version remained at code.google.com. Please drop the maintainer a note if you have any news of this project. Depends: boxshade, fastx-toolkit, gff2aplot, muscle, sim4, sibsim4, tabix, tophat, wise Depends: maqview Depends: bwa Depends: mummer Depends: blast2 Depends: ncbi-blast+ Depends: mafft Depends: sra-toolkit Depends: t-coffee Depends: kalign Depends: hmmer Depends: exonerate Depends: dialign Depends: dialign-tx Depends: poa Depends: probcons Depends: proda Depends: seaview Depends: sigma-align Depends: emboss Depends: embassy-domalign, embassy-domainatrix, embassy-domsearch, embassy-phylip Suggests: emboss-explorer Why: The EMBOSS sequence analysis suite and its galaxy. Depends: arb Why: Sequence alignments and related programs (Non-free, thus only suggested). Depends: clustalx, clustalo Depends: clustalw | clustalw-mpi Depends: mothur, bowtie, bowtie2, dotur Depends: transtermhp X-End-Category: Sequence alignments and related programs. X-Begin-Category: high-throughput sequencing Depends: last-align, maq, ssake, velvet Depends: qiime X-End-Category: high-throughput sequencing X-Begin-Category: Analysis of RNA sequences. Depends: infernal Depends: rnahybrid X-Category: Target duplex prediction X-End-Category: Analysis of RNA sequences. X-Begin-Category: Molecular modelling and molecular dynamics Depends: adun.app Depends: garlic, gamgi, gdpc, ghemical, jmol, pymol, r-other-bio3d, massxpert Comment: r-other-bio3d depends from r-cran-rocr which is also maintained by Debian Med team Depends: gromacs Depends: rasmol X-End-Category: Molecular modelling and molecular dynamics Depends: plasmidomics Why: Presentation X-Begin-Category: Tools for the molecular biologist. Depends: gff2ps, ncbi-epcr, ncbi-tools-bin, ncbi-tools-x11, perlprimer, readseq, tigr-glimmer Depends: melting Suggests: melting-gui Comment: I think it makes sense to point users to GUI applications as well as to the console applications - in this case melting (Andreas Tille) Depends: mipe Depends: primer3 X-End-Category: Tools for the molecular biologist. X-Begin-Category: Genome Browser Depends: gbrowse X-Importance: Academic ones are really expensive for commercial use X-End-Category: Genome Browser Depends: biomaj Suggests: mozilla-biofox Why: Tools for the molecular biologist. Because of the dependency from firefox we only suggest this package to not bloat the system of the user. Depends: glam2 Why: Motif search Depends: raster3d Depends: phyml Depends: autodock Registration: http://autodock.scripps.edu/downloads/autodock-registration Why: Molecular modelling and molecular dynamics. Depends: autogrid Depends: autodock-vina Depends: autodocktools Comment: The package autodocktools depends from the mgltools-* packages mentioned above, so they will be installed even if they would not be mentioned in the list of Depends in the metapackage med-bio. But leaving them out here would hide them from the tasks and bugs list as well from the sectioning in http://qa.debian.org/developer.php?login=debian-med-packaging@lists.alioth.debian.org&ordering=3 so they are mentioned here in addition to autodocktools. . This was changed by adding Enhances field to the packages in question. Depends: mustang Depends: theseus Depends: staden-io-lib-utils Depends: samtools, bedtools, filo Depends: gassst Depends: r-bioc-hilbertvis Remark: It would be interesting to package HilbertVisGUI (see below) as well. Depends: r-other-mott-happy Remark: Do not upgrade this package Steffen Möller is scientifically collaborating with upstream and nothing shall happen to that package until authors give their confirmation. Depends: seq-gen Depends: mira-assembler Depends: alien-hunter Suggests: seqan-apps Depends: ncoils Depends: gentle Depends: gmap Depends: igv Depends: picard-tools Depends: acedb-other-dotter, acedb-other-belvu, acedb-other Depends: python-cogent Depends: paml Depends: ensembl Pkg-URL: http://snapshot.debian.org/package/ensembl/63-1/ Remark: Ensembl was removed from Debian due #645487 Ensembl used to be in Debian experimental branch but was removed for formal reasons which are explained in http://bugs.debian.org/645487 Depends: mrbayes Suggests: pdb2pqr Depends: squizz Depends: clonalframe Depends: dssp Depends: jellyfish Depends: cytoscape Homepage: http://cytoscape.org/ Responsible: Mike Smoot License: LGPL WNPP: 465331 Pkg-Description: visualizing molecular interaction networks Cytoscape is a bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data. Additional features are available as plugins. Depends: ballview Depends: pynast Depends: raxml Depends: mlv-smile Suggests: cain Depends: cd-hit Depends: cufflinks Depends: r-bioc-cummerbund Suggests: eigensoft Depends: grinder Depends: jalview Depends: reprof Depends: tm-align Depends: norsnet Depends: norsp Depends: predictnls Depends: proftmb Depends: profbval Depends: profisis Depends: hhsuite Depends: ffindex Suggests: blimps-utils Depends: sift Depends: neobio Depends: ugene Depends: logol-bin Depends: soapdenovo X-Mark: Prospective packages are starting here. X-Mark: Packages in Vcs - Information about these is queried from UDD as well Depends: amos-assembler, hawkeye Language: Perl Depends: anfo Depends: apollo Depends: axparafit, axpcoords Depends: bamtools Depends: bagphenotype Depends: bigsdb Depends: cdbfasta Depends: cinema Language: Java Depends: clonalorigin Depends: cluster3 Depends: crossbow X-Category: Sequencing Depends: dazzle Depends: ecell Depends: edtsurf Depends: fasttree Depends: fastqc Depends: forester Depends: genometools Depends: grogui Depends: haploview Depends: hmmer2 Remark: This older version of HMMER is used in some applications While Debian has HMMER 3 since some time there are users of HMMER 2 interested in having this old version available and thus the package is reintroduced. Depends: jbrowse Depends: kempbasu Depends: lagan X-Category: Comparative genomics Depends: ltrsift Depends: logomat-m Depends: macs Depends: mage2tab Depends: martj Depends: mauvealigner Pkg-URL: http://people.debian.org/~tille/packages/mauvealigner/ Language: C++ and Java X-Category: Multiple genome alignment X-Importance: efficient Remark: There are instructions for compiling Mauve from source available at http://asap.ahabs.wisc.edu/mauve/mauve-developer-guide/compiling-mauvealigner-from-source.html Depends: meme License: non-free for commercial purpose (http://meme.nbcr.net/meme/COPYRIGHT.html) Depends: microbiomeutil Note: In Vcs there are four binary packages however, the descriptions are broken and can not be used here - this needs to be fixed first Depends: molekel Depends: mosaik-aligner Depends: mpsqed Depends: mugsy Depends: murasaki Depends: ncbi-seg Depends: ngila Depends: nw-align Depends: oases Depends: pal2nal Depends: patman Depends: patristic Language: Java Depends: pcma Remark: Precondition for T-Coffee see http://wiki.debian.org/DebianMed/TCoffee . Check with authors about licensing, they adopted code from clustalw which is now free. Thus a change might be possible Depends: phyloviz-core Remark: There are several plugins to package The download page http://www.phyloviz.net/wiki/plugins/ lists several plugins that should be packaged (single or as bundle) as well. Depends: plato Depends: prank Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/ Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html Precondition for T-Coffee (see http://wiki.debian.org/DebianMed/TCoffee) Depends: predictprotein Depends: proalign Depends: pscan-tfbs Depends: psipred Depends: python-reaper Depends: r-other-valdar-bagphenotype.library Depends: ray-denovoassembler Depends: rdp-classifier Depends: rosetta Depends: sap Remark: Precondition for T-Coffee see http://wiki.debian.org/DebianMed/TCoffee Depends: sga Depends: seqtk Depends: sequenceconverter.app Remark: Formerly part of Debian as biococoa.app but removed The package was part of Debian under the name biococoa.app which is confusing because biococoa is actually a library for working with sequences under GNUstep. There was an attempt to reupload under the name sequenceconverter.app but ftpmaster did not accepted the package. The reasons can be read here: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2009-May/003430.html . Version 1.6 is the last upstream version that works with GNUstep. If newer versions are needed to work under Linux try to convince upstream to support GNUstep. Depends: snpeff Depends: ssaha Remark: Successor for ssaha2 available: smalt The program smalt is from the same author is according to its author faster and more precise than ssaha2 (except for sequences > 2000bp) Depends: strap License: GNU + some external components with different licenses Language: Java Depends: tacg X-Category: Motif detection X-Importance: powerful Depends: treeview X-Category: Visualisation X-Depends: treevolve X-Comment: Homepage of software vanished, packaging in SVN is obviosely stalled Feel free to delete the 'X-' in front if you intend to do something on this package Depends: vienna-rna X-Category: Secondary structure of nucleic acids Depends: vmd Depends: wgs-assembler Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/) Depends: zalign Depends: zodiac-zeden Language: C, C++ X-Mark: The information below needs to be checked whether it can be obtained from Vcs or needs to stay here Depends: copycat Homepage: http://www-ab.informatik.uni-tuebingen.de/software/copycat/welcome.html License: Use of the program is free for academic purposes at an academic institute. For all other uses, please contact the authors. Pkg-Description: fast access to cophylogenetic analyses CopyCat provides an easy and fast access to cophylogenetic analyses. It incorporates a wrapper for the program ParaFit, which conducts a statistical test for the presence of congruence between host and parasite phylogenies. CopyCat offers various features, such as the creation of customized host-parasite association data and the computation of phylogenetic host/parasite trees based on the NCBI taxonomy. Depends: btk-core Homepage: http://sourceforge.net/projects/btk/ Responsible: Morten Kjeldgaard License: GPL WNPP: 459753 Pkg-Description: biomolecule Toolkit C++ library The Biomolecule Toolkit is a library for modeling biological macromolecules such as proteins, DNA and RNA. It provides a C++ interface for common tasks in structural biology to facilitate the development of molecular modeling, design and analysis tools. Depends: asap Homepage: http://asap.ahabs.wisc.edu/software/asap/ Responsible: Andreas Tille License: GPL Pkg-Description: organize the data associated with a genome Developments in genome-wide approaches to biological research have yielded greatly increased quantities of data, necessitating the cooperation of communities of scientists focusing on shared sets of data. ASAP leverages the internet and database technologies to meet these needs. ASAP is designed to organize the data associated with a genome from the early stages of sequence annotation through genetic and biochemical characterization, providing a vehicle for ongoing updates of the annotation and a repository for genome-scale experimental data. Development was motivated by the need to more directly involve a greater community of researchers, with their collective expertise, in keeping the genome annotation current and to provide a synergistic link between up-to-date annotation and functional genomic data. The system is continually under development at the Genome Evolution Lab with the stable, in-use, publicly available University of Wisconsin installation updated regularly. . Software development on ASAP began in early 2002, and ASAP has been continually improved up until the present day. A longstanding goal of the ASAP project was to make the source code of ASAP available so that other installations of ASAP could be implemented. As future ASAP installations come to pass, ASAP will be further extended to be inter-operable between sites. X-Category: Annotation Depends: cactus Homepage: http://www.cactuscode.org/Community/Biology.html License: GPL Pkg-Description: Cactus is an open source problem solving environment designed for scientists and engineers. Its modular structure easily enables parallel computation across different architectures and collaborative code development between different groups. . Cactus provides easy access to many cutting edge software technologies being developed in the academic research community, including the Globus Metacomputing Toolkit, HDF5 parallel file I/O, the PETSc scientific library, adaptive mesh refinement, web interfaces, and advanced visualization tools. Depends: contralign Homepage: http://contra.stanford.edu/contralign/ License: Public Domain Pkg-Description: parameter learning framework for protein pairwise sequence alignment CONTRAlign is an extensible and fully automatic parameter learning framework for protein pairwise sequence alignment based on pair conditional random fields. The CONTRAlign framework enables the development of feature-rich alignment models which generalize well to previously unseen sequences and avoid overfitting by controlling model complexity through regularization. Depends: concavity Homepage: http://compbio.cs.princeton.edu/concavity/ Depends: conservation-code Homepage: http://compbio.cs.princeton.edu/conservation/ WNPP: 690058 Depends: galaxy Homepage: http://g2.trac.bx.psu.edu/ License: MIT WNPP: 432472 Pkg-Description: manipulate sequences and annotation files Galaxy is a web-based tool allowing users to perform operations which are usually done with command-line interface. Using galaxy, one can manipulate sequences and annotation files in many formats. Galaxy has strong ties with the UCSC genome browser, and makes it easy to visualise modified annotation files as a custom track. Depends: genographer Homepage: http://hordeum.oscs.montana.edu/genographer/ License: GPL Pkg-Description: read data and reconstruct them into a gel image This program will read in data from an ABI 3700, 3100, 377 or 373, CEQ 2000 or SCF and reconstruct them into a gel image which is straightened and sized. Bins can be defined easily and viewed as thumbnails, which allows for a fairly quick and easy way of scoring a gel. . The program is written in Java and uses the Java 1.3 API. Therefore, it should run on any machine that can run java. Depends: pftools Homepage: ftp://us.expasy.org/databases/prosite/tools/ps_scan/sources License: GPL Pkg-Description: tools to handle profiles of protein domains from PROSITE The 'pftools' package is a collection of experimental programs supporting the generalized profile format and search method of PROSITE. . ps_scan is a perl program used to scan one or several patterns, rules and/or profiles from PROSITE against one or several protein sequences in Swiss-Prot or FASTA format. It requires two compiled external programs from the PFTOOLS, which are also distributed with the sources. . Also seen on http://www.isrec.isb-sib.ch/profile/profile.html Responsible: BioLinux - Stewart Houten Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/ Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html Depends: phylographer Homepage: http://www.atgc.org/PhyloGrapher/PhyloGrapher_Welcome.html License: GPL X-Category: Graphical representation of sequence conservation Language: Tcl/Tk Pkg-Description: Graph Visualization Tool PhyloGrapher is a program designed to visualize and study evolutionary relationships within families of homologous genes or proteins (elements). PhyloGrapher is a drawing tool that generates custom graphs for a given set of elements. In general, it is possible to use PhyloGrapher to visualize any type of relations between elements. Used in conjunction with tcl_blast_parser, PhyloGrapher can represent the results of a BLAST search as a graph. . PhyloGrapher and tcl_blast_parser are useful tools to analyse BLAST biological sequence alignment reports (BLAST is provided by Debian's blast2 package). Remark: Outdated upstream, better alternatives available The former packaging effort of this package was dropped. It seems that http://cytoscape.org/ is a reasonable replacement. Depends: phylowin Homepage: http://pbil.univ-lyon1.fr/software/phylowin.html WNPP: 395840 License: unknown Pkg-Description: Graphical interface for molecular phylogenetic inference Phylo_win is a graphical colour interface for molecular phylogenetic inference. It performs neighbor-joining, parsimony and maximum likelihood methods and bootstrap with any of them. Many distances can be used including Jukes & Cantor, Kimura, Tajima & Nei, HKY, Galtier & Gouy (1995), LogDet for nucleotidic sequences, Poisson correction for protein sequences, Ka and Ks for codon sequences. Species and sites to include in the analysis are selected by mouse. Reconstructed trees can be drawn, edited, printed, stored and evaluated according to numerous criteria. . This program uses sources files from the Phylip program, which forbids its use for profit. Therfore, Phylo_win will unfortunately have to be distributed in contrib or non-free. Remark: Issuer of previous ITP said: Because I could never figure out the license of Phylo_win, and because the upstream authors released SeaView 4, which provides similar functionalities, I will not package Phylo_win. . Probably it makes sense to remove this project from the prospective packages list. Depends: gbioseq Homepage: http://www.bioinformatics.org/project/?group_id=94 License: GPL Pkg-Description: DNA sequence editor for Linux gBioSeq is in an early stage of development, but it is already running. The goal is to provide an easy to use software to edit DNA sequences under Linux, Windows, MacOsX, using GTK C# (Mono). Depends: phpphylotree Homepage: http://www.bioinformatics.org/project/?group_id=372 License: GPL Pkg-Description: draw phylogenetic trees PhpPhylotree is a web application that is able to draw phylogenetic trees. It produces an SVG (Scalable Vector Graphic) file from phylip/newick tree files. Depends: tracetuner Homepage: http://www.jcvi.org/cms/research/software/tracetuner/overview License: GPL; but US Patent #6,681,186 Pkg-Description: DNA sequencing and trace processing TraceTuner is a DNA sequencing quality value, base calling and trace processing software application originally developed by Paracel, Inc. While providing a flexible interface and capability to adopt the "pure" base calls produced by Phred, KB or any other "original" caller, it offers competitive features not currently available in other tools, such as customized calibration of quality values, advanced heterozygote and mixed base calling and deconvolving the "mixed" electropherograms resulting from the presence of indels into a couple of "pure" electropherograms. Previous versions of TraceTuner were used by Celera Genomics to process over 27 million reads from both Drosophila and human genome projects and by Applied Biosystems, as a component of its SNP detection and genotyping software product SeqScape. TraceTuner implements an advanced peak processing technology for resolving overlapping peaks of the same dye color into individual, or "intrinsic" peaks. This technology was protected by US Patent #6,681,186. Currently, TraceTuner is an open source software, which has been used by J. Craig Venter Institute's DNA Sequencing and Resequencing pipelines. . The TraceTuner Software (Copyright 1999-2003, Paracel, Inc. All rights reserved.) (the "Software") is covered by US Patent #6,681,186 and is being made available free of charge by Applera Corporation subject to the terms and conditions of the GNU General Public License, version 2, as published by the Free Software Foundation (the "GNU General Public License"). Depends: twain Homepage: http://cbcb.umd.edu/software/pirate/twain/twain.shtml License: Open Source Pkg-Description: syntenic genefinder employing a Generalized Pair Hidden Markov Model TWAIN is a new syntenic genefinder which employs a Generalized Pair Hidden Markov Model (GPHMM) to predict genes in two closely related eukaryotic genomes simultaneously. It utilizes the MUMmer package to perform approximate alignment before applying a GPHMM based on an enhanced version of the TigrScan gene finder. TWAIN was written by Bill Majoros and Mihaela Pertea while at The Institute for Genomic Research (TIGR). . TWAIN consists of two components: (1) ROSE, the Region Of Synteny Extractor, which identifies contiguous regions likely to contain one or more syntenic genes, and (2) OASIS, a generalized pair hidden Markov model (GPHMM) for predicting genes in the regions identified by ROSE. The system utilizes approximate alignments constructed by the PROmer and NUCmer programs in the MUMmer package to assess approximate alignment scores efficiently. More detailed information on the architecture of this system will be made available soon. Slides from a talk at Computational Genomics 2004 are now available. Note: Computational Gene Finding (http://www.cbcb.umd.edu/software/) Depends: rose Homepage: http://www.cbcb.umd.edu/software/rose/Rose.html License: Open Source Pkg-Description: Region-Of-Synteny Extractor ROSE is a program which identifies regions between two genomes which are likely to contain orthologous genes. The two genomes are given as two multi fasta files of DNA sequences. The PROmer program from the MUMmer package needs to be run first between the two genomes, and the resulting delta file is then input to ROSE. If a previous annotation is available for one or both genomes, then the coordinates of the annotated genes from a genome can be optionally given as input in a gff file. The gene coordinates will be used to guide the length of the regions produced by ROSE. By default, when finding a region of consistent alignments, ROSE will add a user-defined margin (1000 bp by default) on either side of that region. When a predicted gene overlaps an alignment we use the gene prediction to extend the boundaries of the output region. Note: Computational Gene Finding (http://www.cbcb.umd.edu/software/) Depends: glimmerhmm Homepage: http://www.cbcb.umd.edu/software/glimmerhmm/ License: Artistic Pkg-Description: Eukaryotic Gene-Finding System GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM). Although the gene finder conforms to the overall mathematical framework of a GHMM, additionally it incorporates splice site models adapted from the GeneSplicer program and a decision tree adapted from GlimmerM. It also utilizes Interpolated Markov Models for the coding and noncoding models . Currently, GlimmerHMM's GHMM structure includes introns of each phase, intergenic regions, and four types of exons (initial, internal, final, and single). A basic user manual can be consulted here. Note: Computational Gene Finding (http://www.cbcb.umd.edu/software/) Depends: genezilla Homepage: http://www.genezilla.org/ License: Artistic Language: C++ X-Importance: state-of-art X-Category: Gene prediction (through GHMM) Pkg-Description: eukaryotic gene finder GeneZilla is a state-of-the-art program for computational prediction of protein-coding genes in eukaryotic DNA, and is based on the Generalized Hidden Markov Model (GHMM) framework, similar to GENSCAN and GENIE. It is highly reconfigurable and includes software for retraining by the end-user. It is written in highly optimized C++ and runs under most UNIX/Linux platforms. The run time and memory requirements are linear in the sequence length, and are in general much better than those of competing systems, due to GeneZilla's novel decoding algorithm. Graph-theoretic representations of the high scoring open reading frames are provided, allowing for exploration of sub-optimal gene models. It utilizes Interpolated Markov Models (IMMs), Maximal Dependence Decomposition (MDD), and includes states for signal peptides, branch points, TATA boxes, CAP sites, and will soon model CpG islands as well. . GeneZilla is an open-source project hosted at bioinformatics.org and currently consists of ~20,000 lines of code. GeneZilla evolved out of the ab initio eukaryotic gene finder TIGRscan, which was developed at The Institute for Genomic Research over a 3-year period under NIH grants R01-LM06845 and R01-LM007938, and which served as the basis for the comparative gene finder TWAIN. Note: Computational Gene Finding (http://www.cbcb.umd.edu/software/) Depends: exalt Homepage: http://www.cbcb.umd.edu/software/exalt/ License: Artistic Pkg-Description: phylogenetic generalized hidden Markov model for predicting alternatively spliced exons ExAlt is a software program designed to predict alternatively spliced overlapping exons in genomic sequence. The program works in several ways depending on the available input. ExAlt can use information of existing gene structure as well as sequence conservation to improve the precision of it's predictions. ExAlt can also make predictions when only a single genomic sequence is available. ExAlt has been extensively tested on Drosophila melanogaster, but can be adapted to run on other species. Note: Computational Gene Finding (http://www.cbcb.umd.edu/software/) Depends: jigsaw Homepage: http://www.cbcb.umd.edu/software/jigsaw/ License: Artistic Pkg-Description: gene prediction using multiple sources of evidence JIGSAW is a program designed to use the output from gene finders, splice site prediction programs and sequence alignments to predict gene models. The program provides an automated way to take advantage of the many succsessful methods for computational gene prediction and can provide substantial improvements in accuracy over an individual gene prediction program. . JIGSAW is available for all species. It is tested on Human, Rice (Oryza sativa), Arabidopsis thaliana , Brugia malayi, Cryptococcus neoformans, Entamoeba histolytica, Theileria parva, Aspergillus fumigatus, Plasmodium falciparum and Plasmodium yoelii. . The linear combiner option is now available in the current JIGSAW software distribution. This allows JIGSAW to be run without the use of training data. A weight is assigned to each evidence source, and gene predictions are based on a weighted voting scheme, yielding the best 'consensus' predictions. . Predictions are now available for the ENCODE regions in Human and viewable as custom tracks in the UCSC Human Genome Browser. Predictions available for the Human genome and viewable as custom tracks in the UCSC Human Genome Browser Note: Computational Gene Finding (http://www.cbcb.umd.edu/software/) Depends: genesplicer Homepage: http://www.cbcb.umd.edu/software/GeneSplicer/ License: Artistic Pkg-Description: computational method for splice site prediction A fast, flexible system for detecting splice sites in the genomic DNA of various eukaryotes. The system has been trained and tested successfully on Plasmodium falciparum (malaria), Arabidopsis thaliana, human, Drosophila, and rice . Training data sets for human and Arabidopsis thaliana are included. Use the GeneSplicer Web Interface to run GeneSplicer directly, or see below for instructions on downloading the complete system including source code. . There is no independent program to train GeneSplicer, but there is a way to obtain the necessary files by using the training procedure of GlimmerHMM. Note: Computational Gene Finding (http://www.cbcb.umd.edu/software/) Ignore: riso Homepage: http://kdbio.inesc-id.pt/~asmc/software/riso.html License: not specified Pkg-Description: motif discovery tool RISO discovers motifs composed of many binding sites separated by spacers. Each binding site is called a box . The author of SMILE claims at his homepage http://www-igm.univ-mlv.fr/~marsan/smile_english.html that RISO is faster and more powerfull than SMILE which is described itself as "SMILE is a tool that infers motifs in a set of sequences, according to some criterias. It was first made to infer exceptionnal sites as binding sites in DNA sequences. It allows to infer motifs written on any alphabet (even degenerate) in any kind of sequences. The specificity of SMILE is to allow to deal with what we call "structured motifs", which are motifs associated by some distance constraints. In particular, SMILE is able to group under a unique model different occurrences composed of several boxes separated by spacers of different lengths." . The reference to SMILE is made here especially because there is some work done in the Debian Med SVN at http://svn.debian.org/wsvn/debian-med/trunk/packages/smile/trunk/ . On the other hand the SMILE author told us in private mail that he thinks that RISO is dead and SMILE continues to have some importance. Depends: mummergpu Homepage: http://mummergpu.sourceforge.net/ License: Artistic Pkg-Description: High-throughput sequence alignment using Graphics Processing Units The recent availability of new, less expensive high-throughput DNA sequencing technologies has yielded a dramatic increase in the volume of sequence data that must be analyzed. These data are being generated for several purposes, including genotyping, genome resequencing, metagenomics, and de novo genome assembly projects. Sequence alignment programs such as MUMmer have proven essential for analysis of these data, but researchers will need ever faster, high-throughput alignment tools running on inexpensive hardware to keep up with new sequence technologies. . MUMmerGPU is a low cost, ultra-fast sequence alignment program designed to handle the increasing volume of data produced by new, high-throughput sequencing technologies. MUMmerGPU is a GPGPU drop-in replacement for MUMmer, using the GPUs in common workstations to simultaneously align multiple query sequences against a single reference sequence stored as a suffix tree. By processing the queries in parallel on the highly parallel graphics card, MUMmerGPU achieves more than a 10-fold speedup over a serial CPU version of the sequence alignment kernel, and outperforms MUMmer on a high end CPU by 3.5-fold in total application time when aligning reads from recent sequencing projects using Solexa/Illumina, 454, and Sanger sequencing technologies. Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/) Depends: amoscmp Homepage: http://amos.sourceforge.net/docs/pipeline/AMOScmp.html License: Artistic Pkg-Description: comparative genome assembly package A comparative assembler is a program that can assemble a set of shotgun reads from an organism by mapping them to the finished sequence of a related organism. Thus, a comparative assembler transforms the traditional overlap-layout-consensus approach to alignment-layout-consensus. The AMOScmp package uses the MUMmer program to perform a mapping of the reads to the reference genome, then processes the alignment results with a sophisticated layout program designed to take into account polymorphisms between the two genomes. For a detailed description of the algorithms involved please refer to the paper listed in the References section. . AMOScmp uses as AMOS messages as both the inputs and the outputs (see documentation). Two utilities are provided to process these files: tarchive2amos - a versatile converter from trace archive .seq, .qual, and .xml information into AMOS formatted data; amos2ace - a converter from AMOS formatted data to the .ACE assembly format. In addition, the AMOS::AmosLib Perl module is provided as a tool for users who prefer to write their own conversion utilities. Please see the documentation included with the distribution for more information. . AMOScmp is part of the AMOS package (see http://amos.sourceforge.net/)- a collaborative effort to develop a modular open-source framework for assembly development. Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/) Depends: minimus Homepage: http://amos.sourceforge.net/docs/pipeline/minimus.html License: Artistic Pkg-Description: AMOS lightweight assembler minimus is an assembly pipeline designed specifically for small data-sets, such as the set of reads covering a specific gene. Note that the code will work for larger assemblies (we have used it to assemble bacterial genomes), however, due to its stringency, the resulting assembly will be highly fragmented. For large and/or complex assemblies the execution of Minimus should be followed by additional processing steps, such as scaffolding. . minimus follows the Overlap-Layout-Consensus paradigm and consists of three main modules: * overlapper - computes the overlaps between the reads using a modified version of the Smith-Waterman local alignment algorithm * tigger - uses the read overlaps to generate the layouts of reads representing individual contigs * make-consensus - refines the layouts produced by the tigger to generate accurate multiple alignments within the reads . minimus uses as AMOS messages as both the inputs and the outputs (see documentation). Two utilities are provided to process these files: tarchive2amos - a versatile converter from trace archive .seq, .qual, and .xml information into AMOS formatted data; amos2ace - a converter from AMOS formatted data to the .ACE assembly format. In addition, the AMOS::AmosLib Perl module is provided as a tool for users who prefer to write their own conversion utilities. Please see the documentation included with the distribution for more information. . minimus is part of the AMOS package - a collaborative effort to develop a modular open-source framework for assembly development. Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/) Ignore: catissuecore Homepage: https://cabig.nci.nih.gov/tools/catissuecore License: to be clarified, NCICB Open Source Project Site Pkg-Description: biospecimen inventory, tracking, and basic annotation caTissue Core is caBIG's tissue bank repository tool for biospecimen inventory, tracking, and basic annotation. Version 1.2.1 of caTissue permits users to track the collection, storage, quality assurance, and distribution of specimens as well as the derivation and aliquotting of new specimens from an existing ones (e.g. for DNA analysis). It also allows users to find and request specimens that may then be used in molecular, correlative studies. . Intended Audiences: Translational Researchers, Pathologists, Biobank Managers Note: A lot of stuff can be found at National Cancer Institute's Center for Bioinformatics (NCICB) Open Source Project Site http://gforge.nci.nih.gov/ which has to be evaluated and put into the right category of our tasks files Ignore: trapss Homepage: https://putt.eng.uiowa.edu/ License: Creative Commons for Science license Pkg-Description: Transcript Annotation Prioritization and Screening System TrAPSS stands for Transcript Annotation Prioritization and Screening System. It is a system comprised of several tools written by researchers at the Coordinated Lab for Computational Genomics in the University of Iowa. The system aims to aid scientists who are searching for the genetic mutation or mutations that are linked to expression of a disease phentotype. The system offers support for almost all areas of a mutation discovery project from the creation and prioritization of a large candidate gene list, to the selection, ordering, and managing of primer pairs, and even support for SSCP assay results. TrAPSS is a currently deployed and often used tool for several laboratories here at the University of Iowa in the College of Medicine. The system is composed of several Java applications, many web-based PHP tools, and a local MySQL database. Even the Java applications are available through a web browser due to Sun's Java Web Start. Director of the CLCG, Professor Terry A. Braun, heads the project along with Dr. Todd Scheetz and Prof. Thomas L. Casavant. Eight developers create and maintain the software: Bartley Brown , Hakeem Almabrazi, Steven Davis and Jason Grundstad; along with three graduate students, Brian O'Leary, John Ritchison and Michael Smith; and one undergraduate student, Matthew Kemp. Importance of TrAPSS . The true importance of TrAPSS is that it is based upon a novel way to examine a large candidate list of genes. Rather than sequentially examining full genes, the scheme often followed in current target identification projects, TrAPSS provides tools that offer the user the opportunity to screen certain small parts of several genes from the candidate list at once. This "parallel" screening idea was envisioned by researchers here at the University of Iowa including Dr. Edwin Stone and Prof. Thomas L. Casavant. Research by graduate students Steven Davis and Brian O'Leary has demonstrated the advantage of the parallel screening method over the sequential sequencing of large candidate lists. Note: Found at http://gforge.nci.nih.gov/softwaremap/trove_list.php?form_cat=337 Depends: bambus Homepage: http://amos.sourceforge.net/docs/bambus/ License: Artistic Pkg-Description: hierarchical approach to building contig scaffolds BAMBUS is the first publicly available scaffolding program. It orders and orients contigs into scaffolds based on various types of linking information. Additionally, BAMBUS allows the users to build scaffolds in a hierarchical fashion by prioritizing the order in which links are used. For more information please check out the online documentation. . Note that currently Bambus is undergoing a transition in order to be integrated with the AMOS package (see http://amos.sourceforge.net/) Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/) Depends: gmv Homepage: http://murasaki.dna.bio.keio.ac.jp/wiki/index.php?GMV License: GPL Pkg-Description: comparative genome browser for Murasaki GMV is a comparative genome browser for Murasaki. GMV visualizes anchors from Murasaki, annotation data from GenBank files, and expression / prediction score from GFF files. Depends: pyrophosphate-tools Homepage: http://www-naweb.iaea.org/nafa/ipc/public/d4_pbl_6a.html License: not specified Pkg-Description: for assembling and searching pyrophosphate sequence data Simple tools for assembling and searching high-density picolitre pyrophosphate sequence data. Depends: figaro Homepage: http://amos.sourceforge.net/Figaro/Figaro.html License: Artistic Pkg-Description: novel vector trimming software Figaro is a software tool for identifying and removing the vector from raw DNA sequence data without prior knowledge of the vector sequence. By statistically modeling short oligonucleotide frequencies within a set of reads, Figaro is able to determine which DNA words are most likely associated with vector sequence. For a description of Figaro's algorithms please see our paper. Figaro is part of the AMOS suite. Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/) Depends: mirbase Homepage: http://microrna.sanger.ac.uk/ License: Public Domain WNPP: 420938 Responsible: Charles Plessy Pkg-Description: The microRNA sequence database The miRBase Sequence Database provides a searchable repository for published microRNA sequences and associated annotation, functionality previously provided by the microRNA Registry. miRBase also contains predicted miRNA target genes in miRBase Targets, and provides a gene naming and nomenclature function in the miRBase Registry. . Release 9.1 of the database contains 4449 entries representing hairpin precursor miRNAs, expressing 4274 mature miRNA products, in primates, rodents, birds, fish, worms, flies, plants and viruses. . This package will install the miRBase database for mySQL, EMBOSS, and/or ncbi-blast if you have the corresponding packages installed. . It is possible that mirbase will not be a package from the main archive, but will be autogenerated as part of a larger data packaging effort. Depends: elph Homepage: http://www.cbcb.umd.edu/software/ELPH/ License: Artistic Pkg-Description: motif finder that can find ribosome binding sites, exon splicing enhancers, or regulatory sites ELPH (Estimated Locations of Pattern Hits) is a general-purpose Gibbs sampler for finding motifs in a set of DNA or protein sequences. The program takes as input a set containing anywhere from a few dozen to thousands of sequences, and searches through them for the most common motif, assuming that each sequence contains one copy of the motif. We have used ELPH to find patterns such as ribosome binding sites (RBSs) and exon splicing enhancers (ESEs). See below for instructions on downloading the complete system, including source code. . An online tool that uses ELPH output for identifying exon splicing enhancers can be found at http://www.cbcb.umd.edu/software/SeeEse/index.html . Note: Other sequence analysis tools (http://www.cbcb.umd.edu/software/) X-Depends: repeatfinder X-Homepage: http://www.cbcb.umd.edu/software/RepeatFinder/ X-License: Artistic X-Pkg-Description: finding repetitive sequences complete and draft genomes Two programs for finding repeats in genomic DNA sequences. The first program, described in the paper by Volfovsky et al. (2001) Genome Biology is RepeatFinder. A second program, designed specifically to find repeats likely to confuse a genome assembly, is called ClosureRepeatFinder. The two programs are quite different and have different purposes; RepeatFinder is intended to be the more comprehensive approach. Note that RepeatFinder depends on Stefan Kurtz's REPuter. X-Note: Depends from non-distributable code reputer (see below) X-Depends: reputer X-Homepage: http://citeseer.ist.psu.edu/kurtz95reputer.html X-License: non-commercial X-Pkg-Description: fast computation of maximal repeats in complete genomes A software tool was implemented that computes exact repeats and palindromes in entire genomes very efficiently. X-Note: Code is not redistributable see mailing list discussion at http://lists.debian.org/debian-med/2012/07/msg00195.html Depends: uniprime Homepage: http://code.google.com/p/uniprime/ License: GPL-3+ Responsible: Charles Plessy Pkg-Description: workflow-based platform for universal primer design UniPrime automatically designs large sets of universal primers by simply inputting a GeneID reference. It automatically retrieves and aligns orthologous sequences from GenBank, identifies regions of conservation within the alignment and generates suitable primers that can amplify variable genomic regions. UniPrime differs from previous automatic primer design programs in that all steps of primer design are automated, saved and are phylogenetically limited. We have experimentally verified the efficiency and success of this program. UniPrime is an experimentally validated, fully automated program that generates successful cross-species primers that take into account the biological aspects of the PCR. Depends: genetrack Homepage: http://sysbio.bx.psu.edu/genetrack.html License: MIT Responsible: Charles Plessy Pkg-Description: genomic data storage and visualization framework GeneTrack is a high performance bioinformatics data storage and analysis system designed to store genome wide information. It is currently used to analyze data obtained via high-throughput rapid sequencing platforms such as the 454 and Solexa as well as tiling array data based on various platforms. Depends: operondb Homepage: http://www.cbcb.umd.edu/cgi-bin/operons/operons.cgi License: to be clarified Pkg-Description: detect and analyze conserved gene pairs Comparison of complete microbial genomes reveals a large number of conserved gene clusters - sets of genes that have the same order in two or more different genomes. Such gene clusters often, but not always represent a co-transcribed unit, or operon. A method was developed to detect and analyze conserved gene pairs - pairs of genes that are located close on the same DNA strand in two or more bacterial genomes. For each conserved gene pair, an estimate of probability is calculated that the genes belong to the same operon. The algorithm takes into account several alternative possibilities. One is that functionally unrelated genes may have the same order due simply because they were adjacent in a common ancestor. Other possibilities are that genes may be adjacent in two genomes by chance alone, or due to horizontal transfer of the gene pair. . The method is modified from the one described in: Maria D. Ermolaeva, Owen White and Steven L. Salzberg. Prediction of Operons in Microbial Genomes. Nucleic Acids Research, 29, 1216-1221, (2001) . OperonDB was supported by the NIH under grant R01-LM007938 and by the NSF under grant DBI-0234704. Note: Other sequence analysis tools (http://www.cbcb.umd.edu/software/); no info about license or downloadable code found, but tried to contact authors. Depends: trnascan-se Homepage: http://lowelab.ucsc.edu/tRNAscan-SE/ License: GPL Pkg-URL: http://bioweb.ucr.edu/debian-local/pool/main/t/trnascan-se/ X-Category: tRNA discovery Pkg-Description: program for improved detection of transfer RNA genes in genomic sequence tRNAscan-SE identifies 99-100% of transfer RNA genes in DNA sequence while giving less than one false positive per 15 gigabases. Two previously described tRNA detection programs are used as fast, first-pass prefilters to identify candidate tRNAs, which are then analyzed by a highly selective tRNA covariance model. This work represents a practical application of RNA covariance models, which are general, probabilistic secondary structure profiles based on stochastic context-free grammars. tRNAscan-SE searches at ~ 30 000 bp/s. Additional extensions to tRNAscan-SE detect unusual tRNA homologues such as selenocysteine tRNAs, tRNA-derived repetitive elements and tRNA pseudogenes. Depends: artemis Homepage: http://www.sanger.ac.uk/Software/Artemis/ License: GPL 2+ Responsible: BioLinux - Stewart Houten Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/ Pkg-Description: genome viewer and annotation tool Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation. Artemis is written in Java, and is available for UNIX, Macintosh and Windows systems. It can read EMBL and GENBANK database entries or sequence in FASTA or raw format. Extra sequence features can be in EMBL, GENBANK or GFF format. Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html Depends: act Homepage: http://www.sanger.ac.uk/Software/ACT/ License: GPL Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/ Responsible: BioLinux - Stewart Houten Pkg-Description: DNA Sequence Comparison Viewer ACT (Artemis Comparison Tool) is a DNA sequence comparison viewer based on Artemis. In common with Artemis, ACT is written in Java and runs on UNIX, GNU/Linux, Macintosh and MS Windows systems. It can read complete EMBL and GENBANK entries or sequence in FASTA or raw format. Extra sequence features can be in EMBL, GENBANK or GFF format. . The sequence comparison displayed by ACT is usually the result of running a blastn or tblastx search. See the user manual for more information. . To see ACT in action go to the examples page http://www.sanger.ac.uk/Software/ACT/Examples/ Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html Comment: If you stumble upon alfresco at http://www.sanger.ac.uk/Software/Alfresco/ - it seems outdated and tarball vanished from the downlowad page. So this is not for us even if it is linked from Sanger Institute web site. Comment: If you stumble upon angler at http://www.sanger.ac.uk/Software/Angler/ - it seems outdated because it is not updated since 1997. I found no license statement and so this is probably also not for us except somebody has real interest and volunteers to clarify the license. Depends: cdna-db Homepage: http://www.sanger.ac.uk/Software/analysis/cdna_db/ License: Artistic Pkg-Description: quality-control checking of finished cDNA clone sequences cdna_db is a software system designed for quality-control checking of finished cDNA clone sequences, and their computational analysis. The combination of a relational db (MySQL) schema, and an object-orientated perl API make it easy to implement high-level analyses of these transcript sequences. . The cdna_db can store cDNA clone sequences, and ESTs and consensus/contig sequences also derived from these clones. These are then used by the system to check cDNA clone sequence identity etc (see deneral_doc.txt). For each clone multiple DNA sequence versions can be stored, if for instance, the finished DNA sequence is revised as part of the sequencing process. . A blast pipeline is implemented together with a job control system (with LSF underlying) so that multiple CPUs can be used in parallel to carry out the blasts of large datasets. The searches can be made incremental, so as more cDNA sequences are added to the databank, just the new clones are blasted. . Utility scripts are provided to delete previous search results, and dump cDNA clones sequences (such as those that passed the QC checking) from the cdna_db. Depends: das-proserver Homepage: http://www.sanger.ac.uk/Software/analysis/proserver/ License: Same as Perl Pkg-Description: lightweight Distributed Annotation System (DAS) server The Distributed Annotation System (DAS) is a data exchange protocol for open sharing of biological information. . ProServer is a very lightweight DAS server written in Perl. It is simple to install and configure and has existing adaptors for a wide variety of data sources. It is also easily extensible allowing adaptors to be written for other data sources. More information about the DAS protocol and what it is useful for is available over at http://biodas.org. . New large scale techniques in biology are producing a rapidly growing amount of public available data. Centralized database resources are confronted with the task how to scale their storage facilities, how to manage frequent updates and how to exchange the data with the community. . The Distributed Annotation System (DAS) addresses these issues. It is frequently being used to openly exchange biological annotations between distributed sites. Data distribution, performed by DAS servers, is separated from visualization, which is done by DAS clients. . DAS is a client-server system in which a client like Ensembl integrates information from multiple servers. It allows a single machine to gather up genome annotation information from multiple distant web sites, collate the information, and display it to the user in a single view. Little coordination is needed among the various information providers. . DAS is heavily used in the genome bioinformatics community. Over the last years we have also seen growing acceptance in the protein sequence and structure communities. Depends: spice Homepage: http://www.efamily.org.uk/software/dasclients/spice/ License: GPL Pkg-Description: Distributed Annotation System (DAS) client The Distributed Annotation System (DAS) is a data exchange protocol for open sharing of biological information. . SPICE is a browser for protein sequences, structures and their annotations. It can display annotations for PDB, UniProt and Ensembl Peptides. All data is retrieved from different sites on the Internet, that make their annotations available using the DAS protocol. It is possible to add new annotations to SPICE, and to compare them with the already available information. Depends: decipher Homepage: http://www.sanger.ac.uk/Software/analysis/decipher/ License: To be clarified Pkg-Description: tracks duplications and deletions of DNA in patients DECIPHER tracks submicroscopic duplications and deletions of DNA in patients together with phenotypes exhibited by those patients. DECIPHER tallies these genetic abnormalities with genes and other features of interest in the affected areas. The aim of DECIPHER is to provide a research tool to aid clinical diagnosis and treatment of these conditions. DECIPHER makes use of DAS technology to integrate with Ensembl, the world's leading genome browser. Depends: est-db Homepage: http://www.sanger.ac.uk/Software/analysis/est_db/ License: Artistic Pkg-Description: Software suite for expressed sequence tag (EST) sequencing The est_db package is a software suite and database system designed to support expressed sequence tag (EST) sequencing projects, and to provide comprehensive bioinformatic analysis of sequenced EST libraries, for gene discovery and other purposes. The database can hold and efficiently process hundreds of thousands of EST sequences, track the cDNA libraries and clones to which they belong, and store the results of their analysis. Should they be available, large compute farms can be used for the analysis. . Extensive bioinformatic analysis can be carried out on the sequenced EST libraries, including similarity (BLAST) searches, protein sequence prediction, and the import of EST clustering and assembly data from external sources. Results are searchable via a web page, with graphic output of the various analyses, enabling one to retrieve information pertaining to a particular cDNA clone, or EST read, as well as view EST clustering results, or graphical representations of BLAST results on the searched EST sequences. . The est_db package is likely to appeal not only to sequencing groups directly employed in EST sequencing, but also to groups interested in performing bespoke analysis of ESTs that may already be publically available, in order to support their ongoing research aims. The package is easily-extensible, via an API designed specifically to handle ESTs and their analysis. It is open source and is made available free of charge, and, where possible, similarly open-licensed components have been used in its development. Depends: finex Homepage: http://www.sanger.ac.uk/Software/analysis/finex/ License: To be clarified Pkg-Description: sequence homology searching The FINEX program allows sequence homology searching techniques to be applied, where the sequence data is replaced with a fingerprint abstracted from the intron/exon boundary phase and the exon length. . Please note FINEX is no longer supported but is available for download. Depends: hexamer Homepage: http://www.sanger.ac.uk/Software/analysis/hexamer/ License: GPL Pkg-Description: scan DNA sequences to look for likely coding regions Hexamer is a program to scan DNA sequences to look for likely coding regions. The principle is to use 6mers, but to avoid deriving any information from base composition. Therefore, the frequencies of each 6mer are normalized by dividing by the total frequency of all 6mers with the same base composition. . There are two programs involved in this process: * hextable hextable makes files of statistics that hexamer uses to scan for likely coding regions. The input of hextable is a fasta file of coding sequences in frame. The -o file output is an ascii list of 4096 floating point numbers giving log likelihood ratio scores in bits. The output on stdout is a summary of the information content of the table, indicating how disriminative it is likely to be. * hexamer Uses the .hex file from hextable to scan a DNA sequence for likely coding regions. The input is a fasta DNA file (n.b. that these programs assume all 'a','c','g','t'. 'n's found in the sequence files will be converted to 'c'. The output of hexamer is in General Feature Format (GFF) format. Depends: coot Homepage: http://www.ysbl.york.ac.uk/~emsley/coot/ License: GPL Pkg-Description: protein structure model-building, -completion, -validation The Crystallographic Object-Oriented Toolkit (Coot) displays maps and models and allows model manipulations such as idealization, real space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers, Ramachandran plots... Depends: r-ape Homepage: http://ape.mpl.ird.fr/ License: GPL Responsible: BioLinux - Stewart Houten Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/ Pkg-Description: Analyses of Phylogenetics and Evolution APE (Analyses of Phylogenetics and Evolution) is a package written in R. APE aims to be both a computing tool to analyse phylogenetic and evolutionary data, and an environment to develop and implement new analytical methods. Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html Depends: caftools Homepage: http://www.sanger.ac.uk/Software/formats/CAF/userguide.shtml License: Free for non-commercial purposes Responsible: BioLinux - Bela Tiwari Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/ Pkg-Description: Tools to maintain DNA sequence assemblies This is V2 of the CAF (Common Assembly Format) C-tools. It comprises a set of libraries and programs for manipulating DNA sequence assemblies using CAF files. . The CAF specification can be found at: http://www.sanger.ac.uk/Software/formats/CAF/ Remark: The BioLinux distribution http://envgen.nox.ac.uk/biolinux.html maintains a package called bio-linux-assembly-conversion-tools which contains caftools and roche2gap in one package with the following description: . Conversion tools for handling 454 assemblies. . This package contains code from different authors that allow sequence assemblies to be converted into formats such as CAF (Common Assembly Format) or GAP4. This package includes tools to convert assemblies from Newbler's ace format for loading into a gap4 assembly. Depends: roche454ace2caf Homepage: http://genome.imb-jena.de/software/roche454ace2caf/ License: not specified Responsible: BioLinux - Bela Tiwari Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/ Pkg-Description: convert GS20 or FLX assemblies into CAF format Some tools to convert GS20 or FLX assemblies (454Contigs.ace) into CAF format so that these are correct viewable/editable/... whithin the staden package (gap4). You have then access to "hidden data", exact aligned trace and there positions, base values etc and whith staden-1-7-0 you have graphical access to the associated flowgramm traces (SFF format). . Description, Goals - please take a look at http://genome.imb-jena.de/software/roche454ace2caf/Poster_UserMeeting_GS20_Munich_070328.pdf Remark: The BioLinux distribution http://envgen.nox.ac.uk/biolinux.html maintains a package called bio-linux-assembly-conversion-tools which contains caftools and roche2gap in one package with the following description: . Conversion tools for handling 454 assemblies. . This package contains code from different authors that allow sequence assemblies to be converted into formats such as CAF (Common Assembly Format) or GAP4. This package includes tools to convert assemblies from Newbler's ace format for loading into a gap4 assembly. Depends: big-blast Homepage: ftp://ftp.sanger.ac.uk/pub/pathogens/software/artemis/extra/big_blast.pl License: not specified Responsible: BioLinux - Stewart Houten Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/ Pkg-Description: Helper tool to run blast on large sequences This script will chop up a large sequence, run blast on each bit and then write out an EMBL feature table and a MSPcrunch -d file containing the hits. Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html Depends: blixem Homepage: http://bioinformatics.abc.hu/tothg/biocomp/other/Blixem.html License: not specified Responsible: BioLinux - Dan Swan Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/ Pkg-Description: interactive browser of pairwise Blast matches Blixem (BLast matches In an X-windows Embedded Multiple alignment), is an interactive browser of pairwise Blast matches that have been stacked up in a ma ster-slave multiple alignment Remark: The link to the source archive on the web pages is not valid any more - it might be a problem to obtain the source. Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html Depends: cap3 Homepage: http://genome.cs.mtu.edu/cap/cap3.html License: free for governmental agency or a non-profit educational institution Responsible: BioLinux - Bela Tiwari X-Category: Sequence assembly X-Importance: not a lot of alternatives Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/ Pkg-Description: DNA Sequence Assembly Program CAP3 contains the following improvements to the CAP sequence assembly program. 1. Use of forward-reverse constraints to correct assembly errors and link contigs. 2. Use of base quality values in alignment of sequence reads. 3. Automatic clipping of 5' and 3' poor regions of reads. 4. Generation of assembly results in ace file format for Consed. 5. CAP3 can be used in GAP4 of the Staden package. These improvements allow CAP3 to take longer sequences of higher errors and produce more accurate consensus sequences. Remark: Obtaining the source requires to fill in a registration form Official distribution in Debian is probably impossible. The package included in the BioLinux distribution http://envgen.nox.ac.uk/biolinux.html containins only the binaries cap3 and formcon, dated Aug 29, 2002. This package exists purely for convenience to Bio-Linux users so that the files are placed in locations consistent with the Bio-Linux setup. Comment: BioLinux contains a clcworkbench package which is available at http://www.clcbio.com/index.php?id=28 but this seems to be only "free as in beer" binary download - so this is not for us ... Depends: coalesce Homepage: http://evolution.gs.washington.edu/lamarc/coalesce.html License: not specified Responsible: BioLinux - Nathan S Haigh Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/ Pkg-Description: outdated program to estimate population-genetic parameters COALESCE fits the model which has a single population of constant size, and estimates 4Nu, where N is the effective population size and u is the neutral mutation rate per site. You may also want the Postscript or the TeX file of the preprint version of the Kuhner, Yamato, and Felsenstein 1995 paper. Remark: This software is probably outdated The homepage contains the explicite link: "We are no longer supporting COALESCE as its functions can be done just as well by LAMARC and it's easier for us to support just one program. You may still want the paper, however." So this is actually no target for the Debian Med distribution but just a hint for users about the existence of this program and the even better alternative even if BioLinux distribution http://envgen.nox.ac.uk/biolinux.html contains a package. Comment: BioLinux contains a dendroscope package which is available at http://www.dendroscope.org but this project has only a "free as in beer" binary download - so this is not for us ... Depends: estferret Homepage: http://legr.liv.ac.uk/EST-ferret/index.htm License: to be clarified Responsible: BioLinux - Bela Tiwari Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/ Pkg-Description: processes, clusters and annotates EST data ESTFerret processes, clusters and annotates EST data. It is user-configurable. Results are currently stored in a series of text tables. Annotation consists of searches against use r-defined blast databases, prosite, GO and allocation of EC numbers where possible. . EST-ferret is a user-configurable, automated pipeline for the convenient analysis of EST sequence data that includes all of the necessary steps for cleanup and trimming, submission to external sequence repositories, clustering, identification by BLAST homology searches and by searches of protein domain databases, annotation with computer-addressable terms and production of outputs for direct entry into microarray analysis packages. It is composed of several widely used, open-source algorithms, including PHRED, CAP3, BLAST, and a range of sequence and annotation databases, including Gene Ontology and Conserved Domain Database to deliver a putative identity and a detailed annotation of each clone. It can be run either step-by-step to track the outputs, or as a single batch process. Users can easily edit the configuration file to define parameter settings. . This package has five major components: (1) ESTs coding system; (2) sequence processing; (3) sequence clustering; (4) sequence annotating and (5) storage and reporting of results. DNA trace files are renamed and converted into FASTA format, cleaned and submitted to dbEST(Boguski, et al, 1993). Sequence assembly uses two rounds of CAP3 to assemble the ESTs into groups corresponding to separate gene families and unique genes. Sequence identification and annotation is provided by a series of BLAST homology searches (Parallel_BLAST and Priority_BLAST) against user-defined sequence databases implemented with the NCBI BLASTALL algorithm. The BLAST results are parsed and annotation terms that reflect functional attributes are captured from Gene Ontology (The Gene Ontology Consortium, 2000), KEGG and Enzyme Commission (EC) databases and applied to each of the clones. CDD (and InterPro) searches are performed for seeking protein domains in the sequences. Other options are provided to run PatSearch, RepeatMasker and BLAT to find UTRs, repeats and EST candidates in genomes. Finally, the package generates analysis reports in a variety of flat file formats, sources of which can be serve as inputs for some gene annotation and gene expression profiling tools, and also as a MySQL database or web-browsable search tool. Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html Depends: estscan Homepage: http://estscan.sourceforge.net/ License: free Responsible: BioLinux - Bela Tiwari Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/ Pkg-Description: detect coding regions in DNA sequences, even if of low quality ESTScan is a program that can detect coding regions in DNA sequences, even if they are of low quality. It will also detect and correct sequencing errors that lead to fr ameshifts. . ESTScan is not a gene prediction program, nor is it an open reading frame detector. In fact, its strength lies in the fact that it does not require an open reading frame to detect a coding region. As a result, the program may miss a few translated amino acids at either the N or the C terminus, but will detect coding regions with high selectivity and sensitivity. . Similarly to GENSCAN, ESTScan uses a Markov model to represent the bias in hexanucleotide usage found in coding regions relative to non-coding regions. Additionally, ESTScan allows insertions and deletions when these improve the coding region statistics. Further details can be found at: http://www.ch.embnet.org/software/ESTScan2_help.html . References: * Lottaz C, Iseli C, Jongeneel CV, Bucher P. (2003) Modeling sequencing errors by combining Hidden Markov models Bioinformatics 19, ii103-ii112. * Iseli C, Jongeneel CV, Bucher P. (1999) ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proc Int Conf Intell Syst Mol Biol.138-48. Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html Depends: fasta Homepage: http://www.ebi.ac.uk/Tools/fasta/ License: no inclusion into commercial product Responsible: BioLinux - Stewart Houten Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/ Pkg-Description: searching DNA and protein databases FASTA (pronounced FAST-AYE) stands for FAST-ALL, reflecting the fact that it can be used for a fast protein comparison or a fast nucleotide comparison. This program achieves a high level of sensitivity for similarity searching at high speed. This is achieved by performing optimised searches for local alignments using a substitution matrix. The high speed of this program is achieved by using the observed pattern of word hits to identify potential matches before attempting the more time consuming optimised search. The trade-off between speed and sensitivity is controlled by the ktup parameter, which specifies the size of the word. Increasing the ktup decreases the number of background hits. Not every word hit is investigated but instead initially looks for segment's containing several nearby hits. Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html Depends: fluctuate Homepage: http://evolution.gs.washington.edu/lamarc/fluctuate.html License: not specified Responsible: BioLinux - Nathan S Haigh Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/ Pkg-Description: outdated program to model a single population FLUCTUATE fits the model which has a single population which has been growing (or shrinking) according to an exponential growth law. It estimates 4Nu and g, where N is the effective population size, u is the neutral mutation rate per site, and g is the growth rate of the population. Remark: This software is probably outdated The homepage contains the explicite link: "We are no longer supporting FLUCTUATE as its functions can be done just as well by LAMARC and it's easier for us to support just one program. You may still want the paper, however." So this is actually no target for the Debian Med distribution but just a hint for users about the existence of this program and the even better alternative even if BioLinux distribution http://envgen.nox.ac.uk/biolinux.html contains a package. Depends: forester Homepage: http://sourceforge.net/projects/forester-atv/ License: LGPL Responsible: BioLinux - Stewart Houten Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/ Pkg-Description: visualization of annotated phylogenetic trees FORESTER is a Java/Perl based software package for phylogenomic analyses. Currently, it includes the phylogenetic tree visualization and manipulation tool ATV and implementations of the SDI algorithm and the RIO method (http://www.phylosoft.org/). Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html Depends: lamarc Homepage: http://evolution.gs.washington.edu/lamarc/ License: Apache V2.0 Responsible: BioLinux - Nathan S Haigh Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/ Pkg-Description: estimate population-genetic parameters LAMARC is a program which estimates population-genetic parameters such as population size, population growth rate, recombination rate, and migration rates. It approximates a summation over all possible genealogies that could explain the observed sample, which may be sequence, SNP, microsatellite, or electrophoretic data. LAMARC and its sister program Migrate are successor programs to the older programs Coalesce, Fluctuate, and Recombine, which are no longer being supported. The programs are memory-intensive but can run effectively on workstations. Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html Depends: lucy Homepage: http://rcc.uga.edu/applications/bioinformatics/lucy.html License: GPL Responsible: BioLinux - Dan Swan Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/ Pkg-Description: DNA sequence quality and vector trimming tool Lucy is a utility that prepares raw DNA sequence fragments for sequence assembly, possibly using the TIGR Assembler. The cleanup process includes quality assessment, confidence reassurance, vector trimming and vector removal. The primary advantage of Lucy over other similar utilities is that it is a fully integrated, stand alone program. . Lucy was designed and written at The Institute for Genomic Research (TIGR, now the J. Craig Venter Institute), and it has been used here for several years to clean sequence data from automated DNA sequencers prior to sequence assembly and other downstream uses. The quality trimming portion of lucy makes use of phred quality scores, such as those produced by many automated sequencers based on the Sanger sequencing method. As such, lucy’s quality trimming may not be appropriate for sequence data produced by some of the new “next-generation” sequencers. . See also the SourceForge page at http://lucy.sourceforge.net/. Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html Depends: maxd Homepage: http://www.bioinf.man.ac.uk/microarray/maxd/ License: Artistic Responsible: BioLinux - Stewart Houten Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/ Pkg-Description: data warehouse and visualisation environment for genomic expression data Maxd is a data warehouse and visualisation environment for genomic expression data. It is being developed in the University of Manchester by the Microarray Bioinformatics Group. . Software components: maxdLoad2 - standards-compliant, highly customisable transcriptomics database maxdView - modular and easily extensible data visualisation and analysis environment maxdSetup - installation management utility Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html Depends: mesquite Homepage: http://mesquiteproject.org/mesquite/mesquite.html License: LGPL Responsible: BioLinux - Stewart Houten Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/ Pkg-Description: help biologists analyze comparative data about organisms Mesquite is software for evolutionary biology, designed to help biologists analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of its modules concern population genetics, while others do non-phylogenetic multivariate analysis. Because it is modular, the analyses available depend on the modules installed. Analyses include: * Reconstruction of ancestral states (parsimony, likelihood) * Tests of process of character evolution, including correlation * Analysis of speciation and extinction rates * Simulation of character evolution (categorical, DNA, continuous) * Parametric bootstrapping (integration with programs such as PAUP* and NONA) * Morphometrics (PCA, CVA, geometric morphometrics) * Coalescence (simulations, other calculations) * Tree comparisons and simulations (tree similarity, Markov speciation models) There is a brief outline of features, which includes screenshots. Mesquite is not primarily designed to infer phylogenetic trees, but rather for diverse analyses using already inferred trees. Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html Depends: migrate Homepage: http://popgen.scs.fsu.edu/Migrate-n.html License: to be clarified Responsible: BioLinux - Nathan S Haigh Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/ Pkg-Description: estimation of population sizes and gene flow using the coalescent Migrate estimates effective population sizes and past migration rates between n population assuming a migration matrix model with asymmetric migration rates and different subpopulation sizes. Migrate uses maximum likelihood or Bayesian inference to jointly estimate all parameters. It can use the followind data types: sequence data using Felsenstein's 84 model with or without site rate variation, single nucleotide polymorphism data, microsatellite data using a stepwise mutation model or a brownian motion mutation model, and electrophoretic data using an 'infinite' allele model. The output can contain: Estimates of all migration rates and all population sizes, assuming constant mutation rates among loci or a gamma distributed mutation rate among loci. Profile likelihood tables, Percentiles, Likelihood-ratio tests, and simple plots of the log-likelihood surfaces for all populations and all loci. Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html Depends: msatfinder Homepage: http://www.genomics.ceh.ac.uk/msatfinder/ License: GPL Responsible: BioLinux - Stewart Houten Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/ Pkg-Description: identification and characterization of microsatellites in a comparative genomic context Msatfinder is a Perl script designed to allow the identification and characterization of microsatellites in a comparative genomic context. There is also an online manual, a discussion forum and an online interface where users can do searches in any number of DNA or protein sequences (as long as the maximum size of all sequences does not exceed 10MB). Nucleotide and amino acid sequences in GenBank, FASTA, EMBL and Swissprot formats are supported. Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html Depends: mview Homepage: http://bio-mview.sourceforge.net/ License: GPL Responsible: BioLinux - Stewart Houten Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/ Pkg-Description: reformat results of a sequence database search or a multiple alignment MView is a tool for converting the results of a sequence database search (BLAST, FASTA, etc.) into the form of a coloured multiple alignment of hits stacked against the query. Alternatively, an existing multiple alignment (MSF, PIR, CLUSTAL, etc.) can be pr ocessed. It reformats the results of a sequence database search or a multiple alignment adding optional HTML markup to control colouring and web page layout. MView is not a multiple alignment program, nor is it a general purpose alignment editor. Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html Depends: oligoarrayaux Homepage: http://dinamelt.bioinfo.rpi.edu/OligoArrayAux.php License: non-free (fre academical use) Responsible: BioLinux - Bela Tiwari Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/ Pkg-Description: Prediction of Melting Profiles for Nucleic Acids OligoArrayAux is a subset of the UNAFold package for use with OligoArray (http://berry.engin.umich.edu/oligoarray2_1/). OligoArray is a free software that computes gene specific oligonucleotides for genome-scale oligonucleotide microarray construction. (It is not really specified what they mean with "free software". You can download the source code after registration: "registration is the only way for me to keep trace of OligoArray users and be able to send you a bug fix or a new release".) . The original UNAFold server is available at http://dinamelt.bioinfo.rpi.edu/download.php and you should probably read http://dinamelt.bioinfo.rpi.edu/ if you want to know more about "Prediction of Melting Profiles for Nucleic Acids". Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html Finally it is hard to find some documentation what OligoArrayAux is really doing because it is only specified into relation to OligoArray (as precondition) and UNAFold (as subset of this) but BioLinux distribution http://envgen.nox.ac.uk/biolinux.html decided to package this and so it might make soem sense to list it here - further investigation is needed. Depends: omegamap Homepage: http://www.danielwilson.me.uk/software.html License: to be clarified Responsible: BioLinux - Stewart Houten Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/ Pkg-Description: detecting natural selection and recombination in DNA or RNA sequences OmegaMap is a program for detecting natural selection and recombination in DNA or RNA sequences. It is based on a model of population genetics and molecular evolution. The signature of natural selection is detected using the dN/dS ratio (which measures the relative excess of non-synonymous to synonymous polymorphism) and the signature of recombination is detected from the patterns of linkage disequilibrium. The model and the method of estimation are described in Wilson, D. J. and G. McVean (2006) Estimating diversifying selection and functional constraint in the presence of recombination. Genetics doi:10.1534/genetics.105.044917. Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html Depends: partigene Homepage: http://www.nematodes.org/bioinformatics/PartiGene/ License: GPL Responsible: BioLinux - Bela Tiwari Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/ Pkg-Description: generating partial gemomes PartiGene is part of the Edinburgh-EGTDC developed EST-software pipeline at the moment consisting of trace2dbEST, PartiGene, wwwPartiGene, port4EST and annot8r. PartiGene is a menu-driven, multi-step software tool which takes sequences (usually ESTs) and creates a dataabase of a non-redundant set of sequence objects (putative genes) which we term a partial genome. Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html Depends: pfaat Homepage: http://pfaat.sourceforge.net/ License: GPL Responsible: BioLinux - Dan Swan Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/ Pkg-Description: Protein Family Alignment Annotation Tool Pfaat is a Java application that allows one to edit, analyze, and annotate multiple sequence alignments. The annotation features are a key component as they provide a framework to for further sequence, structure and statistical analysis. Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html Comment: priam BioLinux contains a priam package which is available at http://bioinfo.genotoul.fr/priam/REL_JUL06/index_jul06.html but this project has only a "free as in beer" binary download - so this is not for us ... Depends: prot4est Homepage: http://xyala.cap.ed.ac.uk/bioinformatics/prot4EST/index.shtml License: GPL Responsible: BioLinux - Bela Tiwari Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/ Pkg-Description: EST protein translation suite prot4EST is a perl script that takes expressed sequence tags (ESTs) and translates them optimally to produce putative peptides. prot4EST intergrates a number of programs to overcome problems inherent with translating ESTs. Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html Depends: qtlcart Homepage: http://statgen.ncsu.edu/qtlcart/ License: GPL Responsible: BioLinux - Dan Swan Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/ Pkg-Description: map quantitative traits using a map of molecular markers QTL Cartographer is a suite of programs to map quantitative traits using a map of molecular markers. It contains a set of programs that will aid in locating the genes that control quantitative traits using a molecular map of markers. It includes some programs to allow simulation studies of experiments. Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html Depends: rbs-finder Homepage: http://www.genomics.jhu.edu/RBSfinder/ License: not specified Responsible: BioLinux - Stewart Houten Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/ Pkg-Description: find ribosome binding sites(RBS) The program implements an algorithm to find ribosome binding sites(RBS) in the upstream regions of the genes annotated by Glimmer2, GeneMark, or other prokaryotic gene finders. If there is no RBS-like patterns in this region, program searches for a start codon having a RBS-like pattern ,in the same reading frame upstream or downstream and relocates start codon accordingly. . You can find more detailed information at http://nbc11.biologie.uni-kl.de/docbook/doc_userguide_bioinformatics_server/chunk/ch01s06.html Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html Depends: recombine Homepage: http://evolution.genetics.washington.edu/lamarc/recombine.html License: not specified Responsible: BioLinux - Nathan S Haigh Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/ Pkg-Description: effective population size of populations RECOMBINE fits a model which has a single population of constant size with a single recombination rate across all sites. It can accomodate either plain DNA or RNA data or SNP (Single Nucleotide Polymorphism) data. It estimates 4Nu and r, where N is the effective population size, u is the neutral mutation rate per site, and r is the ratio of the per-site recombination rate to the per-site mutation rate. Remark: This software might be outdated The homepage contains the explicite link: "We are no longer supporting RECOMBINE as its functions can be done just as well by LAMARC and it's easier for us to support just one program. You may still want the paper, however." So this is actually no target for the Debian Med distribution but just a hint for users about the existence of this program and the even better alternative even if BioLinux distribution http://envgen.nox.ac.uk/biolinux.html contains a package. Depends: splitstree Homepage: http://www-ab.informatik.uni-tuebingen.de/software/splitstree3/welcome.html License: to be clarified Responsible: BioLinux - Stewart Houten Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/ Pkg-Description: Analyzing and Visualizing Evolutionary Data Evolutionary data is most often presented as a phylogentic tree, the underlying assumption being that evolution is a branching process. However, real data is never ideal and thus doesn't always support a unique tree, but often supports more than one possible tree. Hence, it makes sense to consider tree reconstruction methods that produce a tree, if the given data heavily favors one tree over all others, but otherwise produces a more general graph that indicates different possible phylogenies. One such method is the Split Decomposition introduced by Hans-Juergen Bandelt and Andreas Dress (1992) and its variations. Another example is Spectral Analysis developed by Hendy, Penny and others. . These and other methods are implemented in the program SplitsTree, that I wrote with contributions from Dave Bryant, Mike Hendy, Holger Paschke, Dave Penny and Udo Toenges. It is based on the Nexus format. . Note: There is a new version 4.0 written from scratch at http://www.splitstree.org/ which requires a license key - so this is probably non-free. Version 3.2 which is linked above has some downloadable source code without any license or copyright statement - so it has to be clarified whether we are able to distribute this code or not. Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html Depends: taverna Homepage: http://taverna.sourceforge.net/ License: LGPL Responsible: BioLinux - Bela Tiwari Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/ Pkg-Description: designing and executing myGrid workflows for bioinformatics The Taverna workbench is a free software tool for designing and executing workflows, created by the myGrid project, and funded through OMII-UK. Taverna allows users to integrate many different software tools, including web services, such as those provided by the National Center for Biotechnology Information, The European Bioinformatics Institute, the DNA Databank of Japan (DDBJ), SoapLab, BioMOBY and EMBOSS. . The Taverna Workbench provides a desktop authoring environment and enactment engine for scientific workflows expressed in Scufl (Simple Conceptual Unified Flow language). The Taverna enactment engine is also available separately, and other Scufl enactors are available including Moteur. The myExperiment social web site supports finding and sharing of workflows and has special support for Scufl workflows. The Taverna workbench, myExperiment and associated components are developed and maintained by the myGrid team, in collaboration with the open source community. Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html Depends: taxinspector Homepage: http://nebc.nox.ac.uk/projects/taxinspector.html License: Artistic + other free licenses Responsible: BioLinux - Tim Booth Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/ Pkg-Description: browser for entries in the NCBI taxonomy TaxInspector is a browser for entries in the NCBI taxonomy. It is designed to run as a plugin to annotation software such as maxdLoad2 and Pedro, but also has a standalone mode. Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html Depends: tetra Homepage: http://www.megx.net/tetra/ License: free academic Responsible: BioLinux - Stewart Houten Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/ Pkg-Description: tetranucleotide frequency calculator The TETRA program can be used to calculate how well tetranucleotide usage patterns in DNA sequences correlate. Such correlations can provide valuable hints on the relatedne ss of DNA sequences, and are particularly useful for metagenomic sequences. Remark: for the Linux version Version 1.0.2 (Mac OSX has version 2.0b30) is deprecated and hence a feature-limited version of TETRA. At the time writing, no decisions have been made about adapting and cross-compiling the Mac OS X code for this platform. A Linux version might happen when REALbasic's Linux IDE is more mature. Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html Depends: trace2dbest Homepage: http://www.nematodes.org/bioinformatics/trace2dbEST/ License: GPL Responsible: BioLinux - Bela Tiwari Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/ Pkg-Description: process trace files into dbEST submissions Trace2dbest is part of the PartiGene pipeline. . Trace2dbest takes a series of sequence traces and converts them into basecalled files. It also creates files in the appropriate format for submission to dbEST and allows you to submit them directly if your machine is configured to allow mailing to external sites. The output from trace2dbest can be used as input to the PartiGene program. . Trace2dbEST process raw sequenceing chromatograph trace files from EST projects into quality-checked sequences, ready for submission to dbEST. trace2dbEST guides you through the creation of all the necessary files for submission of ESTs to dbEST. trace2dbest makes use of other software (available free under academic licence) that you will need to have installed, namely phred, cross_match and (optionaly) BLAST. Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html Depends: profit Homepage: http://www.bioinf.org.uk/software/profit/ License: non-free Responsible: Steffen Moeller WNPP: 525428 Pkg-Description: structural alignment of multiple proteins ProFit is designed to be the ultimate protein least squares fitting program. It has many features including flexible specification of fitting zones and atoms, calculation of RMS over different zones or atoms, RMS-by-residue calculation, on-line help facility, etc. Remark: The authors need to change the license, still. The debian folder should appear in Debian Med Svn in some near future. Depends: obo-edit Homepage: http://www.geneontology.org License: something free Pkg-Description: editor for biological ontologies (Open Biological Ontologies) Obo-Edit supports the formal representation of biological entities and the specification of is-a (specialisation) and part-of relations. Amongst the databases cureated by this tool is the GeneOntology. Depends: jstreeview Homepage: http://www.sanger.ac.uk/Users/lh3/treeview.shtml License: MIT/X11 Language: JavaScript Pkg-Description: Editor for Phylogenetic Trees A concise viewer/editor for phylogenetic trees in the Newick format. The core functions are written in JavaScript, using the canvas tag proposed by HTML 5. No server side support is needed for rendering the picture and therefore you can grab this page together with knhx.js and canvastext.js to locally view your trees in a supported web browser. . The source can be downloaded at http://www.sanger.ac.uk/Users/lh3/download/jstreeview.zip Depends: phagefinder Homepage: http://phage-finder.sourceforge.net/ License: GPL Language: Perl X-Category: Genomics; Prophage detection in prokaryotes Pkg-Description: heuristic computer program to identify prophage regions within bacterial genomes It uses tab-delimited results from NCBI BLASTALL or WU BLASTP 2.0 searches against a collection of bacteriophage protein sequences and results from HMMSEARCH analysis of 441 phage-specific HMMs to locate prophage regions. By using FASTA33, MUMMER or BLASTN, it can find potential attachment (att) sites of the phage region(s). Data from tRNAscan-SE and Aragorn are used to determine whether a tRNA or tmRNA served as the putative target for integration. Additionally, by looking for the presence or absence of specific proteins using specific HMM models, Phage_Finder can predict whether the region is most likely prophage and which type (Mu, P2, or retron R73), an integrated element, a plasmid, or a degenerate phage region. . The goal of this project is to provide an open-sourced, standardized and automated system to identify and classify prophages within prokaryotic genomes. It is hoped that this package will facilitate future studies on the biology and evolution of these prophages by providing a level of microbial genome annotation that was previously void. Depends: codonw Homepage: http://codonw.sourceforge.net/ License: GPL X-Category: Genomics; Codon usage analysis Pkg-Description: Correspondence Analysis of Codon Usage CodonW is a programme designed to simplify the Multivariate analysis (correspondence analysis) of codon and amino acid usage. It also calculates standard indices of codon usage. It has both menu and command-line interfaces. It was written by John Peden in the lab of Paul Sharp, Dept of Genetics, University of Nottingham. John is working in human genetics and is currently employed as ProCardis database manager at the WTCHG in Oxford University. Depends: compclust Homepage: http://woldlab.caltech.edu/compclust/ License: MLX (http://woldlab.caltech.edu/compclust/LICENSE.txt) Language: Python X-Category: Genomics; Clustering analysis (+GUI) Pkg-URL: http://woldlab.caltech.edu/compclust/debian_install.shtml Pkg-Description: explore and quantify relationships between clustering results CompClust is a python package written using the pyMLX and IPlot APIs. It provides software tools to explore and quantify relationships between clustering results. Its development has been largely built around needs of microarray data analysis but could be easily used in other domains. . Briefly pyMLX provides for efficient and convenient execution of many clustering algorithms using a extendable library of algorithms. It also provides many-to-many linkages between data features and annotations (such as cluster labels, gene names, gene ontology information, etc.) These linkages persist through varied data manipulations. IPlot provides an abstraction of the plotting process in which any arbitrary feature or derived feature of the data can be projected onto any feature of the plot, including the X,Y coordinates of points, marker symbol, marker size, maker/line color, etc. These plots are intrinsically linked to the dataset, the View and the Labeling classes found within pyMLX. Depends: treebuilder3d Homepage: http://www.bcgsc.ca/platform/bioinfo/software/treebuilder License: GPL Language: Java X-Category: Clustering; SAGE expression Pkg-Description: viewer of SAGE and other types of gene expression data TreeBuilder3D is an interactive viewer that allows organization of SAGE and other types of gene expression data such as microarrays into hierarchical dendrograms, or phenetic networks (the term 'phenetic' used as the analysis relies on principals, used in phylogenetic analysis by system biology). Might be used as a visual aid when analyzing differences in expression profiles of SAGE libraries, serves as an alternative to Venn diagrams. Depends: excavator Homepage: http://csbl.bmb.uga.edu/downloads/excavator/ License: GPL Language: Java X-Category: Clustering; Gene expression data Pkg-Description: gene expression data clustering Excavator is a program for gene expression data clustering. It uses a set of unique clustering algorithms developed by the Computational Systems Biology Lab (CSBL) at the University of Georgia. Excavator represents data internally as a minimum spanning tree and outputs results to the user through the use of a micro-array data window, graphs, and a dendrogram viewer. . Features * partitioning gene expressions profiles using multiple methods of clustering and definitions of distance between profiles. * automatic selection of the most plausible number of clusters in a data set * three different ways of viewing data: Micro-array, Gene Expression, and Dendrogram. As well as graphing individual genes from each cluster independently. * identification of genes with expression profiles similar to specified seed genes * cluster identification from a noisy background * numerical comparison between different clustering results of the same data set * runnable on command line as well as through a Java GUI Depends: tigr-assembler Homepage: http://www.jcvi.org/cms/research/software/ License: free (OSI-certified) X-Category: Assembling Pkg-Description: whole-genome assembly Enabled the first published whole-genome assembly of a free-living organism in 1995. Last revised in 2003. . See also http://www.jcvi.org/cms/publications/listing/abstract/article/tigr-assembler-a-new-tool-for-assembling-large-shotgun-sequencing-projects/ Remark: It seems that wgs-assembler is the more up to date program. Moreover there seems to be no download option for TIGR Assembler at the J. Craig Venter Institute (formerly TIGR) any more. Depends: treetime Homepage: http://treetime.linhi.com/ License: GPL Pkg-Description: Bayesian sampling of phylogenetic trees from molecular data TreeTime is controlled by input files in nexus format and does bayesian sampling of phylogenetic trees from these data. Depends: biomaj Depends: abacas Depends: profnet-bval, profnet-chop, profnet-con, profnet-isis, profnet-md, profnet-norsnet, profnet-prof, profnet-snapfun X-Remark: The profnet homepage contains an image of a complete Debian system. The Debian Med team tries to support the authors by providing binary packages inside Debian. Depends: profphd-net, profphd-utils Depends: profphd Depends: abyss Depends: ampliconnoise Depends: disulfinder Suggests: circos Depends: populations Depends: raccoon Depends: librg-utils-perl Depends: snap Depends: vcftools Suggests: mobyle Depends: hilbertvisgui Homepage: http://www.bioconductor.org/help/bioc-views/2.7/bioc/html/HilbertVisGUI.html License: GPL-3 Pkg-Description: interactive tool to visualize long vectors of integer data by means of Hilbert curves An interactive tool to visualize long vectors of integer data by means of Hilbert curves. It provides a GUI for the Debian packaged r-bioc-hilbertvis and is thus interesting for giving users some comfort. Until this software is not yet packaged you can follow the hint at the homepage how to use it with R. Depends: sra-sdk Homepage: http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software License: Public domain (U. S. A. governmental work) WNPP: 610603 Responsible: Charles Plessy Language: C Pkg-Description: utilities for the NCBI Sequence Read Archive Tools for reading the SRA archive, generally by converting individual runs into some commonly used format such as fastq. It also includes sources to loader tools that are still under test. The intention is to give pre-release access to the reader code. . The textual dumpers "sra-dump" and "vdb-dump" are provided in this release as an aid in visual inspection. It is likely that their actual output formatting will be changed in the near future to a stricter, more formalized representation[s]. PLEASE DO NOT RELY UPON THE OUTPUT FORMAT SEEN IN THIS RELEASE. . The "help" information will be improved in near future releases, and the tool options will become standardized across the set. We will also be providing documentation on our web site. . Tool options may change in the next release. Version 1 tool options will remain supported wherever possible in order to preserve operation of any existing scripts. Depends: fas Homepage: http://fsa.sourceforge.net/ License: GPL v3 Enhances: t-coffee Pkg-Description: Fast Statistical Alignment FSA is a probabilistic multiple sequence alignment algorithm which uses a "distance-based" approach to aligning homologous protein, RNA or DNA sequences. Much as distance-based phylogenetic reconstruction methods like Neighbor-Joining build a phylogeny using only pairwise divergence estimates, FSA builds a multiple alignment using only pairwise estimations of homology. This is made possible by the sequence annealing technique for constructing a multiple alignment from pairwise comparisons, developed by Ariel Schwartz in "Posterior Decoding Methods for Optimization and Control of Multiple Alignments." Remark: Precondition for T-Coffee see http://wiki.debian.org/DebianMed/TCoffee Depends: beads Homepage: http://pappso.inra.fr/bioinfo/beads License: CeCILL Pkg-URL: https://launchpad.net/~olivier-langella/+archive/ppa/+packages Pkg-Description: 2-DE electrophoresis gel image spot detection BEADS is a program for spot detection on 2-D gel images. It is based on an analogy with beads flowing uphill on the surface of the gel image and on the analysis of their paths Depends: x-tandem-pipeline Homepage: http://pappso.inra.fr/bioinfo/xtandempipeline/ License: GPL Language: Java Pkg-Description: peptide/protein identification from MS/MS mass spectra X!Tandem is an open-source software performing peptide/protein identification from MS/MS mass spectra. X!Tandem is fast and accurate, but the Global Proteome Machine (GPM) is relatively limited regarding the processing of identification results. X!Tandem pipeline is an alternative to the installation of the GPM on local servers. X!Tandem pipeline performs database searching and matching on a list of MS/MS runs in one shot, using a list of easily user selected paramaters and databases. X!Tandem pipeline also performs filtering of data according to statistical values at peptide and protein levels. The results are stored into TSV (Tab Separated Values) files. Moreover, redundancy of protein databases are fully filtered as follows : * proteins identified without specific peptides compared to others are eliminated; * proteins identified with the same pool of peptides are assembled; * proteins are grouped by function (identified with at least one common peptide), and the specific peptides for each sub-group of proteins are indicated. Suggests: maude Depends: forge Homepage: http://combiol.org/forge/ License: Apache 2.0 Pkg-Description: genome assembler for mixed read types Forge Genome Assembler is a parallel, MPI based genome assembler for mixed read types. . Forge is a classic "Overlap layout consensus" genome assembler written by Darren Platt and Dirk Evers. Implemented in C++ and using the parallel MPI library, it runs on one or more machines in a network and can scale to very large numbers of reads provided there is enough collective memory on the machines used. It generates a full consensus alignment of all reads, can handle mixtures of sanger, 454 and illumina reads. There is some support for solid color space and it includes built in tools for vector trimming and contamination screening. . Forge and was originally developed at Exelixis and they have kindly agreed to place the software which underwent much subsequent development outside Exelixis, into the public domain. Forge works with most of the common MPI implementations. Remark: Competitor to MIRA2 and wgs-assembler This package was requested by William Spooner as a competitor to MIRA2 and wgs-assembler. Depends: metarep License: MIT Homepage: http://www.jcvi.org/metarep/ Pkg-Description: JCVI Metagenomics Reports JCVI Metagenomics Reports (METAREP) is a new open source tool for high-performance comparative metagenomics. It provides a suite of web based tools to help scientists to view, query, browse and compare metagenomics annotation data derived from ORFs called on metagenomics reads. . METAREP supports browsing of functional and taxonomic assignments. Users can either specify fields, or logical combinations of fields to flexibly filter datasets on the fly. Users can compare multiple datasets at various functional and taxonomic levels applying statistical tests as well as hierarchical clustering, multidimensional scaling and heatmaps. Depends: smalt License: "shortly" under GPL Homepage: http://www.sanger.ac.uk/resources/software/smalt/ Pkg-Description: align DNA sequencing reads with genomic reference sequences SMALT reads from a range of sequencing platforms, for example Illumina-Solexa, Roche-454 or ABI-Sanger, can be processed including paired-end reads. . The software employs a perfect hash index of short words (< 20 nucleotides long), sampled at equidistant steps along the genomic reference sequences. . For each read, potentially matching segments in the reference are identified from seed matches in the index and subsequently aligned with the read using a banded Smith-Waterman algorithm. . The best gapped alignments of each read is reported including a score for the reliability of the best mapping. The user can adjust the trade-off between sensitivity and speed by tuning the length and spacing of the hashed words. . A mode for the detection of split (chimeric) reads is provided. Multi-threaded program execution is supported. Remark: This can be regarded as successor of ssaha2 This program is from the same author as ssaha2 and according to its author faster and more precise than ssaha2 (except for sequences > 2000bp). X-Comment: Not sure whether this can be distributed at all - asking might not harm because I've got a serious hint that this software is quite interesting X-Depends: megan X-License: Registriation required X-Homepage: http://www-ab.informatik.uni-tuebingen.de/software/megan X-Pkg-Description: MEtaGenome ANalyzer In metagenomics, the aim is to understand the composition and operation of complex microbial consortia in environmental samples through sequencing and analysis of their DNA. Similarly, metatranscriptomics and metaproteomics target the RNA and proteins obtained from such samples. Technological advances in next-generation sequencing methods are fueling a rapid increase in the number and scope of environmental sequencing projects. In consequence, there is a dramatic increase in the volume of sequence data to be analyzed. Depends: arachne Homepage: http://www.broadinstitute.org/crd/wiki/index.php/Arachne License: free Pkg-Description: toolkit for Whole Genome Shotgun Assembly Arachne is a toolkit developed for Whole Genome Shotgun Assembly. Arachne consists of a comprehensive set of modules, including a central pipeline (Assemblez) that can be run on almost any genome to produce a draft assembly. Arachne's mandate explicitly includes accommodating difficult genomes with complications such as extreme size, repeats, and high polymorphism rates. In order to construct a reasonably well-connected assembly from such tricky genomes, Arachne provides further tools that can be used after the main module pipeline. . The Arachne code package has been under continuous development since 2000. It began with the classic "overlap-layout-consensus" paradigm and has since developed into a vast collection of tools, implemented in numerous modules, to analyze, visualize and manipulate assemblies. New and improved algorithms are becoming available on a regular basis. Depends: maker2 Homepage: http://www.yandell-lab.org/software/maker.html License: GPL / Artistic Pkg-Description: annotate genomes and create genome databases MAKER is a portable and easily configurable genome annotation pipeline. It's purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. MAKER is also easily trainable: outputs of preliminary runs can be used to automatically retrain its gene prediction algorithm, producing higher quality gene-models on seusequent runs. MAKER's inputs are minimal and its ouputs can be directly loaded into a GMOD database. They can also be viewed in the Apollo genome browser; this feature of MAKER provides an easy means to annotate, view and edit individual contigs and BACs without the overhead of a database. MAKER should prove especially useful for emerging model organism projects with minimal bioinformatics expertise and computer resources Depends: repeatmasker Homepage: http://www.repeatmasker.org/ License: Open Software License v. 2.1 Pkg-Description: screens DNA sequences for interspersed repeats RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). On average, almost 50% of a human genomic DNA sequence currently will be masked by the program. Sequence comparisons in RepeatMasker are performed by one of several popular search engines including, cross_match, ABBlast/WUBlast, RMBlast and Decypher. Depends: rmblast Homepage: http://tandem.bu.edu/trf/trf.html License: Same as blast2 Pkg-Description: RepeatMasker compatible version of the standard NCBI BLAST RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST suite. The primary difference between this distribution and the NCBI distribution is the addition of a new program "rmblastn" for use with RepeatMasker and RepeatModeler. RMBlast supports RepeatMasker searches by adding a few necessary features to the stock NCBI blastn program. These include: Support for custom matrices ( without KA-Statistics ). Support for cross_match-like complexity adjusted scoring. Cross_match is Phil Green's seeded smith-waterman search algorithm. Support for cross_match-like masklevel filtering. Depends: augustus Homepage: http://augustus.gobics.de/ License: not explicitely specified Pkg-Description: predict genes in eukaryotic genomic sequences AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. It can be run on this web server or be downloaded and run locally. It is open source so you can compile it for your computing platform. You can now run AUGUSTUS on the German MediGRID. This enables you to submit larger sequence files and allows to use protein homology information in the prediction. The MediGRID requires an instant easy registration by email for first-time users. Depends: e-hive Homepage: http://www.ensembl.org/info/docs/eHive/index.html License: Not specified Pkg-Description: distributed processing system based on 'autonomous agents' This is a distributed processing system based on 'autonomous agents' and Hive behavioural structure of Honey Bees . It implements all functionality of both data-flow graphs and block-branch diagrams which should allow it to codify any program, algorithm, or parallel processing job control system. It is not bound to any processing 'farm' system and can be adapted to any GRID. Depends: cmap Homepage: http://gmod.org/wiki/CMap License: Not specified Pkg-Description: view comparisons of genetic and physical maps CMap is a web-based tool that allows users to view comparisons of genetic and physical maps. The package also includes tools for curating map data. Depends: gbrowse-syn Homepage: http://gmod.org/wiki/GBrowse_syn License: Not specified Pkg-Description: Generic Synteny Browser GBrowse_syn, or the Generic Synteny Browser, is a GBrowse-based synteny browser designed to display multiple genomes, with a central reference species compared to two or more additional species. It can be used to view multiple sequence alignment data, synteny or co-linearity data from other sources against genome annotations provided by GBrowse. GBrowse_syn is included with the standard GBrowse package (version 1.69 and later). Working examples can be seen at TAIR and WormBase. Depends: tripal Homepage: http://www.genome.clemson.edu/software/tripal License: GPL ( as Drupal a derivative ) Pkg-Description: collection of Drupal modules for genomic research Tripal is a collection of open-source freely available Drupal modules under development at CUGI and a member of the GMOD family of tools. Tripal serve as a web interface for the GMOD Chado database. Tripal intially started as a web front-end for the Marine Genomics Project (MG.org). Work on the interface is currently ongoing for the MG.org project as well as the Fagaceae Genomics Web, and other CUGI projects. Tripal is currently being implemented for the new Cacao Genome Database, and Citrus Genome Database and will be used for the Genome Database for Rosaceae. These latter three databases are projects of the Main Bioinformatics Laboratory at Washington State University Depends: genemark Homepage: http://exon.biology.gatech.edu/ License: Academic License Agreement Pkg-Description: family of gene prediction programs A family of gene prediction programs developed at Georgia Institute of Technology, Atlanta, Georgia, USA. Suggests: python-rdkit Depends: python-orange License: GPLv3 Homepage: http://orange.biolab.si/ Pkg-URL: http://orange.biolab.si/debian/ Responsible: Mitar Pkg-Description: Data mining framework Orange is a component-based data mining software. It includes a range of data visualization, exploration, preprocessing and modeling techniques. It can be used through a nice and intuitive user interface or, for more advanced users, as a module for Python programming language. Depends: vegan WNPP: 659863 Homepage: http://vegan.r-forge.r-project.org/ License: GPL-2 Language: R, C, FORTRAN Responsible: Charles Plessy Pkg-Description: Community Ecology Package for R R package for community ecologists. It contains most multivariate analysis needed in analysing ecological communities, and tools for diversity analysis. Most diversity methods assume that data are counts of individuals. . These tools are sometimes used outside the field of ecology, for instance to study populations of white blood cells or RNA molecules. Depends: tigr-glimmer-mg Comment: Several related R packages are listed at CRAN: http://cran.r-project.org/web/views/Genetics.html Comment: There is a Gentoo page featuring some projects we do not have mentioned here: http://gentoo-overlays.zugaina.org/dberkholz/sci-biology.html.en Comment: Phylogenie centric Ubuntu derivative with some additional derivatives http://www.eve.ucdavis.edu/rcthomson/phylis/ Comment: SEQanswers: The next generation sequencing community http://seqanswers.com/forums/showthread.php?t=43 Comment: Other sequence analysis tools (http://www.cbcb.umd.edu/software/) debian-med-1.13.2ubuntu3/tasks/epi0000664000000000000000000000775412124332225013637 0ustar Task: Epidemiology Description: Debian Med epidemiology related packages This metapackage will install tools that are useful in epidemiological research. Several packages making use of the GNU R data language for statistical investigation. It might be a good idea to read the paper "A short introduction to R for Epidemiology" at http://staff.pubhealth.ku.dk/%7Ebxc/Epi/R-intro.pdf Depends: epigrass Suggests: r-cran-msm Depends: r-cran-epibasix Depends: r-cran-epitools X-Comment: See also: http://sites.google.com/site/medepi/epitools Depends: r-cran-surveillance Depends: r-cran-epi Depends: r-cran-diagnosismed, r-cran-epicalc, r-cran-epir Depends: netepi-analysis Remark: See also: http://www.stockholmchallenge.se/data/2123 and http://www.publish.csiro.au/?act=view_file&file_id=NB07103.pdf Depends: netepi-collection Remark: See also: http://www.stockholmchallenge.se/data/2123 and http://www.publish.csiro.au/?act=view_file&file_id=NB07103.pdf Suggests: repast Homepage: http://repast.sourceforge.net/ License: BSD WNPP: 179183 Pkg-Description: framework for creating agent based simulations Repast Simphony is a free and open source agent-based modeling toolkit that simplifies model creation and use. Repast Simphony offers users a rich variety of features including the following: * Fluid model component development using any mixture of Java, Groovy, and flowcharts in each project; * A pure Java point-and-click model execution environment that includes built-in results logging and graphing tools as well as automated connections to a variety of optional external tools including the R statistics environment, *ORA and Pajek network analysis plugins, A live agent SQL query tool plugin, the VisAD scientific visualization package, the Weka data mining platform, many popular spreadsheets, the MATLAB computational mathematics environment, and the iReport visual report designer; * An extremely flexible hierarchically nested definition of space including the ability to do point-and-click and modeling and visualization of 2D environments; 3D environments; networks including full integration with the JUNG network modeling library as well as Microsoft Excel spreadsheets and UCINET DL file importing; and geographical spaces including 2D and 3D Geographical Information Systems (GIS) support; * A range of data storage "freeze dryers" for model check pointing and restoration including XML file storage, text file storage, and database storage; * A fully concurrent multithreaded discrete event scheduler; * Libraries for genetic algorithms, neural networks, regression, random number generation, and specialized mathematics; * An automated Monte Carlo simulation framework which supports multiple modes of model results optimization; * Built-in tools for integrating external models; * Distributed computing with Terracotta; * Full object-orientation; * Optional end-to-end XML simulation * A point-and-click model deployment system Remark: Please read also http://www.tbiomed.com/content/5/1/11 http://lists.debian.org/debian-med/2009/08/msg00013.html (and following mails) X-Suggests: swarm X-Homepage: http://www.swarm.org/ X-License: GPL X-WNPP: 179182 X-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/swarm/trunk/ X-Pkg-Description: multi-agent simulation of complex systems Swarm is a software package for multi-agent simulation of complex systems, originally developed at the Santa Fe Institute. Swarm is intended to be a useful tool for researchers in a variety of disciplines. The basic architecture of Swarm is the simulation of collections of concurrently interacting agents: with this architecture, we can implement a large variety of agent based models. X-Remark: Jakson Alves de Aquino has a guide to installing Swarm 2.2 on Ubuntu and Debian This guide vanished from the web but the WayBackMachine conserved a copy at http://web.archive.org/web/20071225020842/http://jalvesaq.googlepages.com/swarm.html debian-med-1.13.2ubuntu3/tasks/typesetting0000664000000000000000000000255412124332225015432 0ustar Task: Typesetting Description: Debian Med support for typesetting and publishing This metapackage will install Debian packages that might be helpful for typesetting and publishing in medical care and structural biology. Depends: texlive-science Remark: For biologists specifically biotex.sty and textopo.sty are interesting The texlive-science package contains a lot of interesting LaTeX styles for different sciences. As a biologist you are most probably interested in . TeXTopo: http://www.uni-kiel.de/Pharmazie/chem/Prof_Beitz/textopo.htm . You might like to install texlive-science-doc as well and read the documents in /usr/share/doc/texlive-science-doc/latex/textopo/ Depends: texlive-latex-extra Remark: For biologists specifically texshade.sty is interesting The texlive-latex-extra package contains a lot of interesting LaTeX styles for different purposes. As a biologist you are most probably interested in . TeXShade: http://www.uni-kiel.de/Pharmazie/chem/Prof_Beitz/texshade.htm . You might like to install texlive-latex-extra-doc as well and read the documents in /usr/share/doc/texlive-latex-extra-doc/latex/texshade/ Suggests: kbibtex, biber Suggests: bibus, referencer, jabref-plugin-oo Remark: Desktop tools that help inserting references in LibreOffice, or help managing PDF collections. This list is probably incomplete… Depends: king debian-med-1.13.2ubuntu3/tasks/laboratory0000664000000000000000000001034612124332225015227 0ustar Task: Laboratory Description: Debian Med suggestions for medical laboratories Currently Debian Med does not yet contain any software which is specifically intended to run a medical laboratory. We just provide a list of Free Software that might be used and which might be included into Debian at a later point in time provided somebody is willing to take over the packaging work. Depends: openelis Homepage: http://openelis.uhl.uiowa.edu/ License: UIRF Open-source Based Public Software License Pkg-Description: Enterprise Laboratory Information System OpenELIS is a robust Enterprise Laboratory Information System built around an extensible and scalable framework. OpenELIS is designed and developed through the collaborative efforts of Public Health Laboratories to accommodate business processes that are common to all public health laboratories; encompassing clinical, environmental, newborn screening, and animal testing. . The goal of the OpenELIS team is to develop a state of the art system that is economically sustainable by reducing both initial investment and ongoing maintenance costs. By using an open source approach, we ensure that the project will continue to evolve and meet the changing needs of the community. Depends: openfreezer Homepage: http://www.openfreezer.org/ License: GPLv4 Registration: http://www.openfreezer.org/download.html Pkg-Description: Laboratory analysis, research and investigation software application OpenFreezer Laboratory Reagent Tracking and Workflow Management System is an open-source information management system for biological laboratories. The system tracks information on all reagents within the laboratory, including specific properties of each reagent (i.e. sequences, external identifiers), and on all the physical preparations of these reagents (storage locations, physical characteristics). Complementing this repository are workflow tools, such as primer design and automated feature mapping, making OpenFreezer a valuable tool for the bench scientist. Published-Title: OpenFreezer: a reagent information management software system Published-Authors: Olhovsky et al. Published-In: Nature Methods Vol. 8 Published-Year: 2011 Published-URL: http://www.nature.com/nmeth/journal/v8/n8/full/nmeth.1658.html Published-DOI: 10.1038/nmeth.1658 Depends: catissuesuite License: to be clarified Homepage: https://cabig.nci.nih.gov/tools/catissuesuite Pkg-Description: tool for biospecimen inventory management CaTissue Suite is caBIG's biorepository tool for biospecimen inventory management, tracking, and annotation. This tool permits users to enter and retrieve data concerning the collection, storage, quality assurance, and distribution of biospecimens. caTissue Suite is sufficiently scalable and configurable for deployment across biospecimen resources of varying size and function, and that manage multiple types of biospecimens (tissue, biofluids, nucleic acid). The tool provides search functionality for both the biorepository staff and research scientist, who may be interested in searching for and requesting biospecimens for correlative science studies. . caTissue Suite features include: * Customizable user roles and privileges structure to support multiple, independent repositories within a single caTissue installation. * Collection Protocol template creation allows representation of pre-defined specimen processing schemes and multiple study arms and time points in order to expedite data entry. * Patient study registration with duplicate patient checking algorithm. * Facilitated specimen accessioning, recording of processing events, creation and recording of biospecimen derivatives and aliquots. * Recording of biospecimen shipping and tracking events across repositories in a single caTissue installation. * Improved data form display for custom annotations (Dynamic Extensions tool), including new CAP checklist based forms for pathology annotation of major organ systems. * caTIES-like pathology report text annotation. * Advanced Query “Wizard”, allowing for the creation and saving of complex queries which can be run as pre-defined or parameterized searches. * Searches based on temporal relationships. * Specimen requisition and request tracking. debian-med-1.13.2ubuntu3/tasks/pharmacy0000664000000000000000000000116112124332225014650 0ustar Task: Pharmacology Description: Debian Med packages for pharmaceutical research This metapackage contains dependencies for a collection of software and documentation which is useful for pharmaceutical research. Depends: chemtool Depends: raccoon Comment: Several related R packages are listed at CRAN: http://cran.r-project.org/web/views/Pharmacokinetics.html Specifically these might be of interest: http://cran.r-project.org/web/packages/PK/index.html http://cran.r-project.org/web/packages/PKfit/index.html http://cran.r-project.org/web/packages/PKtools/index.html debian-med-1.13.2ubuntu3/tasks/tools0000664000000000000000000000306312124332225014207 0ustar Task: Tools Description: Debian Med several tools This metapackage will install tools for several purposes in health care. Currently it contains some simple programs for Personal Health. Depends: pcalendar Suggests: cycle Remark: Use pcalendar instead Please consider using pcalendar instead of cycle because cycle is outdated, not maintained any more and pcalendar simply overpasses it. Suggests: mencal Remark: Use pcalendar instead Please consider using pcalendar instead of mencal because mencal is outdated, not maintained any more and pcalendar simply overpasses it. Depends: pondus Suggests: cl-pubmed Why: Strong dependency would cost installing a large amount of Common Lisp tools which in most cases is not worth the effort Depends: mssstest Depends: wgerman-medical, hunspell-de-med Depends: quitcount Depends: workrave Depends: edfbrowser Suggests: entangle Depends: hunspell-en-med Homepage: http://e-medtools.com/openmedspel.html License: GPL Pkg-Description: English medical spelling word list OpenMedSpel includes nearly 50,000 medical terms ranging from abdominis to zygomatic, which allows you to concentrate on your work instead of looking up words in a medical dictionary that are not in a standard USA English spelling dictionary. Depends: python-clips Homepage: http://pyclips.sourceforge.net License: LGPL WNPP: 544706 Pkg-Description: Python binding for the CLIPS expert system engine CLIPS is an expert system shell / inference engine written by NASA (see Debian package clips). . pyclips are the Python bindings to that engine. debian-med-1.13.2ubuntu3/tasks/rehabilitation0000664000000000000000000000043412124332225016044 0ustar Task: Rehabilitation Description: Debian Med packages for rehabilitation technologies This metapackage will install tools that are useful for rehabilitation and therapy. Depends: sitplus ; Added by blends-inject 0.0.7. [Please note here if modified manually] Suggests: aghermann debian-med-1.13.2ubuntu3/tasks/oncology0000664000000000000000000000235012124332225014676 0ustar Task: Oncology Description: Debian Med packages for oncology This metapackage will install tools that are useful for radiation oncology. Depends: uw-prism Depends: planunc Homepage: http://planunc.radonc.unc.edu/about/ License: nedds to be clarified, registration required Pkg-Description: tools for radiotherapy treatment planning PLanUNC (PLUNC) is a portable, adaptable, and extensible set of software tools for radiotherapy treatment planning (RTP) that has been under active development in the Department of Radiation Oncology at the University of North Carolina (UNC) for approximately 20 years. In 1992, development work branched into separate paths at UNC (PLanUNC) and Sherouse Systems, Inc. (GRATISTM). The current UNC tools encompass the full range of RTP functions including image importing and processing, virtual simulation, dose calculation, plan evaluation, and planning for intensity modulated radiotherapy. PLanUNC source code and related software are licensed without fee to qualified facilities to support research involving new methods for planning and delivering radiation therapy, and to support RTP training for dosimetrists, physicists, radiation therapists, and radiation oncology residents. Depends: dicompyler debian-med-1.13.2ubuntu3/tasks/data0000664000000000000000000000243212124332225013757 0ustar Task: Medical data Description: Debian Med drug databases This metapackage will install free drug databases and related applications. The database can be accessed by any EMR using the application. Depends: freediams, freemedforms-freedata Depends: python-hl7 Depends: drugref.org Homepage: http://savannah.nongnu.org/projects/php-drugref/ License: GPL2+ Pkg-Description: pharmaceutical reference database Important note: The project seems to be dead and the domain drugref.org does not exist any more. Thanks to the GNU Savannah project the code was kept for the past but there is no guarantee at all that the project is of any use. . The aim to to allow the collaborative construction of a free, peer-reviewed pharmaceutical reference. . The primary motivation is to support the gnumed project -- a free software medical information system, but it may have other uses. . It will support logging and versioning of all data, changes made by contributors can be audited and reverted if necessary. The data can be peer-reviewed by several authorities, end-users can opt to have only data which is peer-reviewed. . Drug names, indications, interactions, contra-indications, adverse reactions and side-effects are supported. Product information for multiple countries can be entered. debian-med-1.13.2ubuntu3/tasks/psychology0000664000000000000000000001231212124332225015244 0ustar Task: Psychology Description: Debian Med packages for psychology This metapackage contains dependencies for a collection of software which might be helpful for psychological research. Suggests: science-psychophysics Meta-Suggests: svn://svn.debian.org/blends/projects/science/trunk/debian-science/tasks/psychophysics Depends: python-pyepl Depends: praat Depends: r-cran-foreign, psignifit Why: analysis packages of particular relevance for psych. data Depends: r-cran-psy Remark: r-cran-psy is orphaned upstream. Hint to users of statistical psychological software. This package seems to be orphaned upstream. There are several related packages at CRAN for instance. See the list of prospective packages below and drop the Debian Med team a note if you are interested in one of them. ; Added by blends-inject 0.0.6. [Please note here if modified manually] Depends: psychopy Pkg-URL: http://neuro.debian.net/pkgs/psychopy.html Published-Authors: J. W. Peirce Published-DOI: 10.1016/j.jneumeth.2006.11.017 Published-In: Journal of Neuroscience Methods, 162:8-13 Published-Title: PsychoPy - Psychophysics software in Python Published-Year: 2007 ; Added by blends-inject 0.0.6. [Please note here if modified manually] Suggests: visionegg Homepage: http://www.visionegg.org WNPP: 365856 License: LGPL Pkg-Description: Python library for 2D/3D visual stimulus generation The Vision Egg is a programming library that uses standard, inexpensive computer graphics cards to produce visual stimuli for vision research experiments. Published-Authors: Andrew Straw Published-DOI: 10.3389/neuro.11.004.2008 Published-In: Frontiers in Neuroinformatics Published-Title: Vision Egg: An Open-Source Library for Realtime Visual Stimulus Generation Published-URL: http://frontiersin.org/neuroinformatics/paper/10.3389/neuro.11/004.2008/ Published-Year: 2008 Depends: miscpsycho Homepage: http://cran.r-project.org/web/packages/MiscPsycho License: GPL Language: R Pkg-URL: http://debian.cran.r-project.org/cran2deb/debian-amd64/testing/ Pkg-Description: Miscellaneous Psychometric Analyses Miscellaneous functions for psychometric problems Depends: psych Homepage: http://cran.r-project.org/web/packages/psych/ License: GPL2+ Language: R Pkg-URL: http://debian.cran.r-project.org/cran2deb/debian-amd64/testing/ Pkg-Description: Procedures for Psychological, Psychometric, and Personality Research A number of routines for personality, psychometrics and experimental psychology. Functions are primarily for scale construction using factor analysis, cluster analysis and reliability analysis, although others provide basic descriptive statistics. Functions for simulating particular item and test structures are included. Several functions serve as a useful front end for structural equation modeling. Graphical displays of path diagrams, factor analysis and structural equation models are created using basic graphics. Some of the functions are written to support a book on psychometrics as well as publications in personality research. For more information, see the personality-project.org/r webpage. Depends: psychometric Homepage: http://cran.r-project.org/web/packages/psychometric License: GPL2+ Language: R Pkg-URL: http://debian.cran.r-project.org/cran2deb/debian-amd64/testing/ Pkg-Description: Applied Psychometric Theory Contains functions useful for correlation theory, meta-analysis (validity-generalization), reliability, item analysis, inter-rater reliability, and classical utility Depends: psychotree Homepage: http://cran.r-project.org/web/packages/psychotree/ License: GPL2 Language: R Pkg-URL: http://debian.cran.r-project.org/cran2deb/debian-amd64/testing/ Pkg-Description: Recursive Partitioning Based on Psychometric Models Recursive partitioning based on psychometric models, employing the general MOB algorithm (from package party). Currently, only Bradley-Terry trees are implemented. Depends: psyphy Homepage: http://cran.r-project.org/web/packages/psyphy/ License: GPL Language: R Pkg-URL: http://debian.cran.r-project.org/cran2deb/debian-amd64/testing/ Pkg-Description: Functions for analyzing psychophysical data in R An assortment of functions that could be useful in analyzing data from pyschophysical experiments. It includes functions for calculating d' from several different experimental designs, links for m-alternative forced-choice (mafc) data to be used with the binomial family in glm (and possibly other contexts) and self-Start functions for estimating gamma values for CRT screen calibrations. Comment: Several related R packages are listed at CRAN: http://cran.r-project.org/web/views/Psychometrics.html Depends: psignifit3 Homepage: http://psignifit.sourceforge.net/ License: MIT Language: C++, Python Responsible: Michael Hanke WNPP: 580499 Pkg-Description: fitting and testing hypotheses about psychometric functions This package allows fitting of psychometric functions to datasets while maintaining full control over a large number of parameters. Psignifit performs the calculation of confidence intervals as well as goodness-of-fit tests. . This is the successor of 'psignifit' a commandline-based toolbox. The new version is primarily a python module, but other bindings will be added eventually. debian-med-1.13.2ubuntu3/tasks/research0000664000000000000000000000136212124332225014643 0ustar Task: Research Description: Debian Med packages for medical research This metapackage will install tools that are useful for medical research. Depends: openclinica License: GPL Homepage: https://openclinica.com/ WNPP: 438868 Pkg-Description: electronic data capture and clinical data management With OpenClinica trials for medical studies can be created and evaluated. . OpenClinica is the world's first professionally supported open source clinical trial software for Electronic Data Capture (EDC) Clinical Data Management (CDM). In just over 4 years since its first release, OpenClinica has already become one of the world's most widely adopted clinical trial software technologies powering research in over 100 countries around the world. debian-med-1.13.2ubuntu3/tasks/his0000664000000000000000000001440012124332225013627 0ustar Task: Hospital Information Systems Description: Debian Med suggestions for Hospital Information Systems Currently Debian Med does not yet contain any software which can be regarded as Hospital Information System. There is some Free Software out there which might be interesting targets for inclusion into Debian and so we provide a list of these projects which might be included at a later point in time provided somebody is willing to take over the packaging work. Depends: care2x Pkg-URL: http://sourceforge.net/projects/care2002/files/CARE2X/Care2X%202.6%20alpha/ Depends: fis-gtm Depends: vista Depends: ewd-920 Depends: gnuhealth Depends: world-vista Homepage: http://worldvista.org/World_VistA_EHR License: GPL v2 Responsible: K.S. Bhaskar WNPP: 541245 Pkg-Description: repackage and extended version of VistA produced by WorldVistA Developed by WorldVistA (http://worldvista.org) and released under GPL v2, WorldVistA EHR is a repackaged and extended version of the VistA health care information system (HIS) developed by the US Department of Veterans Affairs, and in the public domain through the US Freedom of Information Act. . WorldVistA successfully submitted WorldVistA EHR for certification by CCHIT (http://cchit.org) in 2007. WorldVistA EHR VOE/ 1.0 was tested and passed inspection of 100 percent of a set of criteria for functionality (ability to create and manage electronic records for all patients, as well as automating workflow in a physician's office), interoperability (a first step in the ability to receive and send electronic data to other entities such as laboratories), and security (ability to keep patients' information safe). Depends: ipath Homepage: http://ipath.sourceforge.net/ License: GPL Pkg-Description: telemedicine platform iPath is an open source platform for telemedicine applications such as consulations, case disucssions, virtual staff meetings, etc. It was originally developed at University of Basel where a public iPath server for projects with developing countries is hosted. Depends: patientos Homepage: http://www.patientos.org/ License: GPL v3 Language: Java Pkg-Description: Healthcare Information System (HIS) for small hospitals and clinics The software can be used as an Electronic Medical Record, Electronic Health Record or as a Personal Medical System. It provides a wide range of functionality including scheduling, orders, medications, pharmacy, clinical doc, HL7, billing and more. The software architecture, design patterns and framework has been built for the complexities and challenges of an enterprise wide information system. . Features include: * WYIWYG view of the registration forms through the ordering and extensive properties of a control list * Makes extensive use of organizing reference data into tree structure * WebReach Inc. advanced Open Source interface engine * Clinical Documentation - Nursing assessments, therapy, progress notes * Standards - LOINC lab results, ICD9/10, CPT, OpenEHR, CCR, CDA * Orders - medications, lab tests, nursing care * Registration and Scheduling - multi-facility, EMPI * Interfaces - HL7 2.2, 2.3 ADT, Billing, Orders, Results * Billing - Charges, Invoices, Claims * Medication Management - Med orders, administration, eMAR * Physician - H&P, Progress Notes * Add-ons are available to add new features or functionality including plugins, custom forms, themes, and translations * Supports multiple languages Depends: openmrs Pkg-URL: http://mentors.debian.net/debian/pool/main/o/openmrs/ Depends: hkma-cms Homepage: http://www.hkma.org/taoyuan/ License: free Pkg-Description: clinic management system HKMA CMS is an open-source clinical management system project jointly implemented by the Hong Kong Medical Association (HKMA) and the Information and Software Industry Association (ISIA), with funding support from the Office of the Government Chief Information Officer (OGCIO) under the Sector-specific Programme (SSP) for the Medical and Health Sector, and was developed by Mobigator Technology Group. Depends: oscar-mcmaster License: to be clarified Homepage: http://oscarmanual.org Pkg-URL: http://sourceforge.net/projects/oscarmcmaster/files/ Pkg-Description: Oscar (Web) A medical web application for electronic medical records OSCAR supports all the necessary functions to run a clinic large and small: * Patient registration for capitation or fee for service practices and roster management * Scheduling with highly customizable view of provider groups and individualized booking preference * Billing also features super-code for smart and simplified billing and third party billing * Complete electronic charting of all encounters with an up to date Cumulative Patient Profile * Prescriptions with drug-drug interaction and renal dosage adjustment * Chronic disease management * A sophisticated antenatal care record with antenatal care planner * Disease Registry is provided to support population health analyses * All laboratory results from private laboratories will be imported directly into the EMR * Diagnostic imaging results and consultation notes can be scanned into the EMR where required Depends: openeyes Homepage: http://www.openeyes.org.uk License: GPLv3 Pkg-Description: ophthalmology electronic patient record system OpenEyes is a collaborative project led by Moorfields Eye Hospital. The goal is to produce a framework which will allow the rapid, and continuous development of electronic patient records (EPR) with contributions from Hospitals, Institutions, Academic departments, Companies, and Individuals. . The initial focus is on Ophthalmology, but the design is sufficiently flexible to be used for any clinical specialty. . Ophthalmic units of any size, from a single practitioner to a large eye hospital, should be able to make use of the structure, design, and code to produce a functional, easy to use EPR at minimal cost. By sharing experience, pooling ideas, and distributing development effort, it is expected that the range and capability of OpenEyes will evolve rapidly. . OpenEyes is supported by a rapidly increasing number of Ophthalmic Units including Moorfields Eye Hospital, St Thomas' Hospital, Manchester Royal Eye Hospital, Maidstone, Royal Victoria Eye and Ear Hospital. debian-med-1.13.2ubuntu3/tasks/bio-phylogeny0000664000000000000000000001313212124332225015632 0ustar Task: Phylogeny Metapackage: false Description: Debian Med phylogeny packages This lists Debian packages related to phylogeny for use in life sciences. The purpose of this compilation of packages is to have a handy subset of from the med-bio metapackage which contains a lot more than only phylogeny related software. Comment: Do not build a metapackage because it is not clear in how far this set of packages is complete regarding phylogeny. X-Begin-Category: Phylogenetic analysis Depends: altree Remark: altree 1.1.0 should be not be packaged According to Vincent Danjean version 1.1.0 should not be packaged for two reasons: . 1. New dependencies (libtamuanova-perl, nanova and libnanova-perl) which need to be packaged. 2. There are still bugs in the new method added in altree 1.1.0 and the doc is not updated. . See http://lists.debian.org/debian-med/2009/08/msg00104.html for further details. Depends: fastdnaml, njplot, tree-puzzle | tree-ppuzzle Depends: probalign Depends: treeviewx X-End-Category: Phylogenetic analysis Depends: phylip Why: Phylogenetic analysis (Non-free, thus only suggested). X-Comment: treetool is removed from Debian because it is not maintained upstream since 1995 and cause the Xserver to freeze under Squeeze X-Begin-Category: Sequence alignments and related programs. Depends: muscle Depends: t-coffee Depends: kalign Depends: hmmer Depends: exonerate Depends: dialign Depends: dialign-tx Depends: poa Depends: probcons Depends: proda Depends: seaview Depends: sigma-align Depends: gmap Depends: clustalx Why: Sequence alignments and related programs (Non-free, thus only suggested). Depends: clustalw | clustalw-mpi Depends: mustang X-End-Category: Sequence alignments and related programs. X-Begin-Category: Models of nucleotide/amino acid evolution Depends: phyml X-End-Category: Models of nucleotide/amino acid evolution Depends: beast-mcmc Depends: tm-align Depends: mrbayes Depends: figtree Depends: populations X-Mark: Packages in Vcs - Information about these is queried from UDD as well Depends: proalign Depends: prottest Depends: treeview Depends: phylowin Homepage: http://pbil.univ-lyon1.fr/software/phylowin.html WNPP: 395840 License: unknown Pkg-Description: Graphical interface for molecular phylogenetic inference Phylo_win is a graphical colour interface for molecular phylogenetic inference. It performs neighbor-joining, parsimony and maximum likelihood methods and bootstrap with any of them. Many distances can be used including Jukes & Cantor, Kimura, Tajima & Nei, HKY, Galtier & Gouy (1995), LogDet for nucleotidic sequences, Poisson correction for protein sequences, Ka and Ks for codon sequences. Species and sites to include in the analysis are selected by mouse. Reconstructed trees can be drawn, edited, printed, stored and evaluated according to numerous criteria. . This program uses sources files from the Phylip program, which forbids its use for profit. Therfore, Phylo_win will unfortunately have to be distributed in contrib or non-free. Remark: Issuer of previous ITP said: Because I could never figure out the license of Phylo_win, and because the upstream authors released SeaView 4, which provides similar functionalities, I will not package Phylo_win. . Probably it makes sense to remove this project from the prospective packages list. Depends: gbioseq Homepage: http://www.bioinformatics.org/project/?group_id=94 License: GPL Pkg-Description: DNA sequence editor for Linux gBioSeq is in an early stage of development, but it is already running. The goal is to provide an easy to use software to edit DNA sequences under Linux, Windows, MacOsX, using GTK C# (Mono). Depends: phpphylotree Homepage: http://www.bioinformatics.org/project/?group_id=372 License: GPL Pkg-Description: draw phylogenetic trees PhpPhylotree is a web application that is able to draw phylogenetic trees. It produces an SVG (Scalable Vector Graphic) file from phylip/newick tree files. Depends: jstreeview Homepage: http://www.sanger.ac.uk/Users/lh3/treeview.shtml License: MIT/X11 Language: JavaScript Pkg-Description: Editor for Phylogenetic Trees A concise viewer/editor for phylogenetic trees in the Newick format. The core functions are written in JavaScript, using the canvas tag proposed by HTML 5. No server side support is needed for rendering the picture and therefore you can grab this page together with knhx.js and canvastext.js to locally view your trees in a supported web browser. . The source can be downloaded at http://www.sanger.ac.uk/Users/lh3/download/jstreeview.zip Depends: treetime Homepage: http://treetime.linhi.com/ License: GPL Pkg-Description: Bayesian sampling of phylogenetic trees from molecular data TreeTime is controlled by input files in nexus format and does bayesian sampling of phylogenetic trees from these data. Depends: jmodeltest Homepage: http://darwin.uvigo.es/software/jmodeltest.html License: GPL Pkg-Description: phylogenetic model averaging JModelTest is a tool to carry out statistical selection of best-fit models of nucleotide substitution. It implements five different model selection strategies: hierarchical and dynamical likelihood ratio tests (hLRT and dLRT), Akaike and Bayesian information criteria (AIC and BIC), and a decision theory method (DT). It also provides estimates of model selection uncertainty, parameter importances and model-averaged parameter estimates, including model-averaged phylogenies. Please note that the DT weights are very gross Depends: forester Depends: patristic Language: Java Depends: phy-spread | spread-phy debian-med-1.13.2ubuntu3/tasks/imaging0000664000000000000000000013250712124332225014470 0ustar Task: Imaging Description: Debian Med imaging packages This metapackage will install Debian packages which might be useful in medical image processing. . It installs several packages supporting DICOM (Digital Imaging and Communications in Medicine) which is the de-facto standard for medical image management. The standard defines data structures and services for the exchange of medical images and related information. The latest release has been published in 2008 and consists of 18 parts. . For more information, you can visit the NEMA homepage http://medical.nema.org/ . . The status of the official DICOM base standard plus all the supplements and correction items are summarized at David Clunie's webpage: http://www.dclunie.com/dicom-status/status.html where you'll find direct links to the most recent yearly edition ftp://medical.nema.org/medical/dicom/2008/ . Depends: amide, ctsim, ctn, dicomnifti, imagej, minc-tools, medcon, python-nifti, xmedcon, dcmtk Suggests: imagemagick, pngquant, imview Depends: nifti-bin Depends: aeskulap Depends: fsl Registration: http://www.fmrib.ox.ac.uk/fsldownloads/ Published-Title: FSL Published-Authors: Mark Jenkinson and Christian F. Beckmann, and Timothy E. J. Behrens and Mark W. Woolrich and Stephen M. Smith Published-In: NeuroImage, 62:782-790 Published-Year: 2012 Published-DOI: 10.1016/j.neuroimage.2011.09.015 Depends: fslview Published-Title: Advances in functional and structural MR image analysis and implementation as FSL Published-Authors: S.M. Smith, M. Jenkinson, M.W. Woolrich, C.F. Beckmann, T.E.J. Behrens, H. Johansen-Berg, P.R. Bannister, M. De Luca, I. Drobnjak, D.E. Flitney, R. Niazy, J. Saunders, J. Vickers, Y. Zhang, N. De Stefano, J.M. Brady, P.M. Matthews Published-In: NeuroImage, 23:208-219 Published-Year: 2004 Published-DOI: 10.1016/j.neuroimage.2004.07.051 Depends: via-bin Depends: gwyddion Depends: sofa-apps Depends: python-mvpa Why: Suggested by maintainer Michael Hanke Depends: python-nipy Why: Although listed in -dev task, it also has a strong focus on interactive data analysis. ; Added by blends-inject 0.0.4. [Please note here if modified manually] Depends: python-nipype Why: Although listed in -dev task, it also has a strong focus on interactive data analysis. Published-Authors: SS Ghosh, C Burns, D Clark, K Gorgolewski, YO Halchenko, C Madison, R Tungaraza, KJ Millman Published-In: 16th Annual Meeting of the Organization for Human Brain Mapping Published-Title: Nipype: Opensource platform for unified and replicable interaction with existing neuroimaging tools Published-URL: https://github.com/satra/ohbm2010/raw/master/NIPYPE/POSTER/poster_nipype.pdf Published-Year: 2010 Recommends: python-nitime Why: Although listed in -dev task, it also has a strong focus on interactive data analysis. Depends: caret Registration: http://brainmap.wustl.edu/register.html Published-Title: An Integrated Software Suite for Surface-based Analyses of Cerebral Cortex Published-Authors: David C. Van Essen, Heather A. Drury, James Dickson, John Harwell, Donna Hanlon, Charles H. Anderson Published-In: Journal of American Medical Informatics Association, 8(5): 443-459 Published-Year: 2001 Published-URL: http://www.pubmedcentral.nih.gov/articlerender.fcgi?pubmedid=11522765 Depends: libgdcm-tools Depends: slicer Depends: lipsia Published-Title: Lipsia—a new software system for the evaluation of functional magnetic resonance images of the human brain Published-Authors: Gabriele Lohmann, Karsten Müller, Volker Bosch, Heiko Mentzel, Sven Hessler, Lin Chen, S. Zysset, D. Yves von Cramon Published-In: Computerized Medical Imaging and Graphics, 25: 449-457 Published-Year: 2001 Published-URL: http://www.medicalimagingandgraphics.com/article/S0895-6111(01)00008-8 Published-DOI: 10.1016/S0895-6111(01)00008-8 Depends: dicom3tools Depends: imagevis3d Depends: odin Published-Title: ODIN: Object-oriented development interface for NMR Published-Authors: Thies H. Jochimsen, Michael von Mengershausen Published-In: Journal of Magnetic Resonance 170:67-78 Published-Year: 2004 Published-URL: http://od1n.sourceforge.net/odin.pdf Depends: dicomscope Depends: pixelmed-java Depends: vmtk Depends: gofigure2 Depends: ginkgocadx Depends: openslide-tools Depends: volview Depends: conquest-dicom-server Suggests: paraview Depends: camitk-imp Depends: crea Depends: orthanc Depends: bioimagesuite Remark: Contact to upstream There is a forum at BioImage Suite site for discussion of compiling it from source and packaging issues at http://research.yale.edu/bioimagesuite/forum/index.php?board=12.0 Depends: drjekyll Homepage: http://drjekyll.sourceforge.net License: GPL Pkg-Description: interactive voxel editor for viewing and editing three-dimensional images It is specifically aimed at postprocessing of segmented datasets, but offers some functionality for raw data as well. Voxel elements (=voxels) and pixel ("picture element") are viewed as data sets and can be processed by this program as kind of a final polishing process. Why: Hint given by Petter Reinholdtsen Depends: libdcm4che-java Remark: Needs jai_imageio as prerequsite Building the package using the packaging code in SVN works up to a point were jai_imageio.jar is required. For the status of packaging this prerequisite see the Debian Java mailing list at http://lists.debian.org/debian-java/2011/04/msg00045.html Depends: dcm4chee Homepage: http://www.dcm4che.org/ License: LGPL, MPL, Apache, other (also non-free) Pkg-Description: Clinical Image and Object Management (enterprise) Contained within the dcm4che project is dcm4chee (the extra 'e' stands for 'enterprise'). dcm4chee is an Image Manager/Image Archive (according to IHE). The application contains the DICOM, HL7 services and interfaces that are required to provide storage, retrieval, and workflow to a healthcare environment. dcm4chee is pre-packaged and deployed within the JBoss application server. By taking advantage of many JBoss features (JMS, EJB, Servlet Engine, etc.), and assuming the role of several IHE actors for the sake of interoperability, the application provides many robust and scalable services. Depends: piano Homepage: http://mbi.dkfz-heidelberg.de/mbi/software/ License: BSD Pkg-Description: medical image processing library for surgical planning Piano is a library containing roughly 75 algorithms and tools for multi-dimensional medical image processing, analysis and visualization. It is used in the field of surgical planning. Depends: mesa-test-tools Homepage: http://ihedoc.wustl.edu/mesasoftware/ License: free Pkg-Description: IHE Test Software for Radiology The MESA software release which is available at http://ihedoc.wustl.edu/mesasoftware/10.15.0/dist/ provides several tools that might cover a wide range of applications for Integrating the Healthcare Enterprise (IHE) testing. . Another important element of the IHE testing process is the set of software tools HIMSS and RSNA have commissioned. Developed by the Electronic Radiology Laboratory at the Mallinckrodt Institute of Radiology, Washington University of St. Louis, the MESA tools are designed for use by participating companies in implementing IHE capabilities in their systems and preparing for the Connectathon. Their purpose is to provide communication partners, test data and test plans to allow organizations to provide a baseline level of testing as they implement the IHE Technical Framework. These tools are made available to participants during the period of an IHE demonstration year and are then released into the public domain at the end of that cycle. The latest version of the MESA Test Tools available in the public domain can be found here. . This kind of software is definitively valuable for information systems vendors and imaging systems vendors. . Because the CTN Debian package is based on an upstream dead project these tools should have a high priority for packaging because the CTN homepage http://erl.wustl.edu/research/dicom/ctn.html says: "The CTN software is also embedded within the MESA tools. The version of CTN software in those tools does not have a separate release number but is more current than version 3.0.6." Depends: devide Homepage: http://code.google.com/p/devide/ License: BSD WNPP: 509110 Responsible: Mathieu Malaterre Pkg-Description: Delft Visualization and Image processing Development Environment DeVIDE, or the Delft Visualization and Image processing Development Environment, is a Python-based dataflow application builder that enables the rapid prototyping of medical visualization and image processing applications via visual programming. In other words, by visually connecting functional blocks (think Yahoo pipes), you can create cool visualizations. . See the DeVIDE website at http://visualisation.tudelft.nl/Projects/DeVIDE Depends: dicom4j Homepage: http://dicom4j.sourceforge.net/ License: GPL Pkg-Description: Java framework for Dicom Java framework for Dicom Depends: opendicom.net Homepage: http://opendicom.sourceforge.net/ License: LGPL Responsible: Albert Gnandt Pkg-URL: http://ubuntu.mi.hs-heilbronn.de/other/opendicom Pkg-Description: API to DICOM in C# for Mono The openDICOM.NET project implements a new approach towards DICOM (Digital Imaging and Communications in Medicine) libraries. DICOM is a worldwide standard in Medical IT and is provided by the National Electrical Manufacturers Association (NEMA). This standard specifies the way medical images and meta data like study or patient related data is stored and communicated over different digital medias. Thus, DICOM is a binary protocol and data format. . The openDICOM# Class Library, main part of the openDICOM.NET project, provides an API to DICOM in C# for Mono and the .NET Framework. It is a completely new implementation of DICOM. In contrast to other similar libraries the intention of this implementation is to provide a clean classification with support of unidirectional DICOM data streaming. Another implemented goal is the support of DICOM as XML. This is not standard conform but very use- and powerful within software development, storage and manipulation. Currently, full read support of DICOM output stream and full write support to XML is supposed to be provided. The entire DICOM content can be accessed as sequence or as tree of class instances. Latter is the default representation of DICOM content by the library. . The openDICOM.NET Utils are a collection of console tools for working with the needed data dictionaries in different data formats (binary and textual), query of ACR-NEMA (prior DICOM standard) and DICOM files and transcoding them into image formats like JPEG and XML files. These utils are written in C# for Mono and the .NET Framework and are using the openDICOM# API for processing. . The openDICOM.NET Navigator recapitulates the openDICOM.NET Utils in form of a GTK# GUI. It provides different views with focus on DICOM data sets and visualization. Connectivity to GIMP is also given for single image processing purpose as well as the possibility to run through multi-frame images like a movie. . The openDICOM.NET Beagle Filter Plugin increases the usability of ACR-NEMA and DICOM query within your desktop. It makes DICOM content overall indexable for retrieval. The Beagle search engine relies on Mono/.NET and works in the background of your system, but is able to detect content changes in realtime (depending on your configuration). . All GUI applications focus the popular GNOME desktop, but are 100% platform independent by relying on Mono. Depends: afni Homepage: http://afni.nimh.nih.gov/ WNPP: 409849 Responsible: NeuroDebian Team License: GPL Pkg-URL: http://neuro.debian.net/pkgs/afni.html Pkg-Description: environment for processing and displaying functional MRI data AFNI is an environment for processing and displaying functional MRI data. It provides a complete analysis toolchain, including 3D cortical surface models, and mapping of volumetric data (SUMA). In addition to its own format AFNI understands the NIfTI format and is therefore easily usable in combination with FSL and Freesurfer. Published-Title: AFNI: Software for analysis and visualization of functional magnetic resonance neuroimages Published-Authors: Robert W. Cox Published-In: Computers and Biomedical Research, 29:162-173 Published-Year: 1996 Published-URL: http://afni.nimh.nih.gov/pub/dist/doc/papers/afni_paper1.pdf Depends: blox Homepage: http://sourceforge.net/projects/blox/ License: GPL Pkg-Description: medical imaging and visualization program The purpose of the project is to develop a quantitative medical imaging and visualization program for use on brain MR, DTI and MRS data. It is a joint project of the Kennedy Krieger Institute and the Johns Hopkins University, Psychiatric Neuroimaging Lab (http://pni.med.jhu.edu/methods/morph.htm). Depends: ecg2png X-Homepage-old: http://www.cardiothink.com/downloads Homepage: http://www.freshports.org/graphics/ecg2png/ License: GPL Pkg-Description: convert scanned electrocardiograms into PNG format This program is designed to convert scanned 12-lead electrocardiograms into PNG format and a web-friendly image size. It assumes that the electrocardiogram (ECG) is printed with a black line on white paper with a red grid. . The problems this program is designed to solve are (1) an ECG scanned at relatively high resolution (300 to 600 dots per inch) imposes a substantial load on the web browser because it contains about 6 million pixels which may require 18 to 24 MB of RAM to store for display. Also, (2) typical scanners convert a clean paper ECG into a multitude of colors, include green and blue. The resulting file cannot be compressed efficiently because it does not contain as much redundancy, and thus takes more time to transmit over low-speed network connections. Remark: Homepage vanished The homepage of this project that used to be at http://www.cardiothink.com/downloads/ecg2png/ vanished but the source can be downloaded fro instance from http://www.freshports.org/graphics/ecg2png/ . Depends: kradview Depends: opensourcepacs Homepage: http://www.mii.ucla.edu/index.php/MainSite:OpenSourcePacsHome License: GPL WNPP: 509113 Responsible: Mathieu Malaterre Pkg-Description: medical image referral, archiving, routing and viewing system OpenSourcePACS is a free, open source image referral, archiving, routing and viewing system. It adds functionality beyond conventional PACS by integrating wet read functions, implemented through DICOM Presentation State and Structured Reporting standards. . In its first release, OpenSourcePACS delivers a complete wet read system, enabling an imaging clinic or hospital to offer its services over the web to physicians within or outside the institution. In future releases, we hope to incorporate more RIS (dictation, transcription, and reporting) functionality. . OpenSourcePACS is a product of the UCLA Medical Imaging Informatics group (http://www.mii.ucla.edu/). Suggests: visit Homepage: http://www.llnl.gov/visit/ WNPP: 395573 License: 3-clause BSD license with additional disclaimers Pkg-Description: visualization and graphical analysis tool for viewing scientific data VisIt is a free interactive parallel visualization and graphical analysis tool for viewing scientific data. Users can quickly generate visualizations from their data, animate them through time, manipulate them, and save the resulting images for presentations. VisIt contains a rich set of visualization features so that you can view your data in a variety of ways. It can be used to visualize scalar and vector fields defined on two- and three-dimensional (2D and 3D) structured and unstructured meshes. . VisIt was designed to handle very large data set sizes in the terascale range and yet can also handle small data sets in the kilobyte range. Depends: mni-autoreg Homepage: http://www.bic.mni.mcgill.ca/software/mni_autoreg/ License: no-free, but GPLed parts Responsible: NeuroDebian Team Pkg-URL: http://apsy.gse.uni-magdeburg.de/debian/pool/contrib/m/mni-autoreg-model/ Pkg-Description: MNI average brain (305 MRI) stereotaxic registration model This package provides a version of the MNI Average Brain (an average of 305 T1-weighted MRI scans, linearly transformed to Talairach space) specially adapted for use with the MNI Linear Registration Package. . * average_305.mnc - a version of the average MRI that covers the whole brain (unlike the original Talairach atlas), sampled with 1mm cubic voxels * average_305_mask.mnc - a mask of the brain in average_305.mnc * average_305_headmask.mnc - another mask, required for nonlinear mode Depends: mni-n3 Homepage: http://www.bic.mni.mcgill.ca/software/N3/ License: BSDish Responsible: NeuroDebian Team Pkg-URL: http://mentors.debian.net/debian/pool/main/m/mni-n3/ Pkg-Description: MNI Non-parametric Non-uniformity Normalization MNI Non-parametric Non-uniformity Normalization (N3). This package provides the 'nu_correct' tool for unsupervised correction of radio frequency (RF) field inhomogenities in MR volumes. Two packages are provided: * mni-n3 - provides 'nu_correct' * libebtks-dev - MNI support library with numerical types and algorithms Depends: brainvisa Homepage: http://brainvisa.info/ License: Free? (CeCill License) Pkg-Description: image processing factory for MR images BrainVISA is a software, which embodies an image processing factory. A simple control panel allows the user to trigger some sequences of treatments on series of images. These treatments are performed by calls to command lines provided by different laboratories. These command lines, hence, are the building blocks on which are built the assembly lines of the factory. BrainVISA is distributed with a toolbox of building blocks dedicated to the segmentation of T1-weighted MR images. The product of the main assembly line made up from this toolbox is the following: grey/white classification for Voxel Based Morphometry, Meshes of each hemisphere surface for visualization purpose, Spherical meshes of each hemisphere white matter surface, a graph of the cortical folds, a labeling of the cortical folds according to a nomenclature of the main sulci. Depends: maris Homepage: http://maris.homelinux.org/ License: GPL Pkg-Description: package suite for Radiological Workflow The MARiS Project goal is to realize a package suite for Radiological Workflow using Open Source tools and technologies in according with IHE guidelines. The architecture of the single packages is based on the concept of IHE actor: this is very useful to develop a system that is an ensemble of single pieces that cooperate together using IHE profiles. Depends: micromanager Pkg-URL: http://mentors.debian.net/package/micromanager Remark: Partially problematic licenses Unfortunately there is a pile of dirty licenses involved so I'm not sure this is ready for Debian yet. Some of the code cannot be given out and some drivers require kernel modules to be built. You have to sign NDAs to get access to all the code. Suggests: mrisim Homepage: http://packages.bic.mni.mcgill.ca/tgz/ Responsible: NeuroDebian Team License: BSD-like Pkg-Description: simulator for magnetic resonance imaging data mrisim is a simple Magnetic Resonance Imaging (MRI) simulation program which produces MINC volumes from a segmented and labelled brain phantom. It allows intrinsic tissue parameters (T1, T2...) and pulse sequence parameters (TR, TE ...) to be specified and then produces simulated images with noise. Currently, no artifacts are implemented. Depends: fiji Homepage: http://pacific.mpi-cbg.de/ Responsible: Mark Longair Pkg-URL: http://pacific.mpi-cbg.de/wiki/index.php/Downloads Pkg-Description: The Fiji image processing suite (based on ImageJ) Fiji is a project aiming at simplifying: * the installation of ImageJ * the usage of ImageJ * the usage of specific, powerful ImageJ plugins * the development of plugins using ImageJ Remark: About packaging status the authors said: See the thread on the Debian Med mailing list at: http://lists.debian.org/debian-med/2009/04/msg00059.html - We've been working to get rid of, or replace, any remaining non-DFSG licensed plugins, but there's at least one left. The bug for tracking this is here: http://pacific.mpi-cbg.de/cgi-bin/bugzilla/show_bug.cgi?id=19 - At the moment Fiji depends on sun-java6 rather than openjdk. - The packages are rather large at the moment (about 35MiB). This is mostly due to bundling various components with Fiji that could be satisfied as dependencies in Debian, such as junit, jruby, etc. but I haven't had time to work on separating those out. - Fiji uses a modified version of ImageJA (which again is bundled into the fiji package) rather than depending on the imagej Debian package created by people on this list. - One of the aims of Fiji was to make Benjamin Schmid's Java3D-based 3D viewer plugin work out-of-the-box, since people often had trouble installing it manually. At the time when I first made these packages there were no java3d packages in Debian, but now that these are in sid we should eventually be able to switch to using those. Depends: cdmedicpacs Homepage: http://cdmedicpacsweb.sourceforge.net/ License: GPL2 Pkg-URL: http://sourceforge.net/projects/cdmedicpacsweb/files/ Pkg-Description: web interface to PACS to access DICOM study images Web based PACS (Picture Archiving and Communication System) to access DICOM studies images, in an easy and quick manner. . * Easy configuration of PACS nodes (AE,IP,Port) , status, statistics of storage form web interface. * Dynamic web page generation from DICOM data +- prospective preparation when system is idle. * Automatic video(mp4/gif) generation from Heart MRI at Patient’s heart bit frame rate and XA at 15 fps. * Still images in jpeg with Window/Level from DICOM header when present or with Histogram algorithm. * Possibility on large Studies of still images to make a single mp4 for Series instead of a bunch of jpeg. * Easy web deletion of Series/Studies and auto deletion (Study date/DB insertion) for temporal PACS. * Good DICOM interaction with Diagnostic Modalities and commercial DICOM Viewers/Work Stations. * Good DICOM interaction with free DICOM Viewers Aeskulap Depends: stir Homepage: http://stir.sourceforge.net/ License: GPL Pkg-Description: Software for Tomographic Image Reconstruction STIR is Open Source software for use in tomographic imaging. Its aim is to provide a Multi-Platform Object-Oriented framework for all data manipulations in tomographic imaging. Currently, the emphasis is on (iterative) image reconstruction in PET, but other application areas and imaging modalities can and might be added. . STIR is the successor of the PARAPET software library which was the result of a (European Union funded) collaboration between 6 different partners, the PARAPET project.. Remark: Even if this is GPLed software the download requires registration. Depends: openelectrophy Homepage: http://neuralensemble.org/trac/OpenElectrophy License: Cecill v2 (GPL-compatible) Language: Python Responsible: NeuroDebian Team WNPP: 556552 Pkg-URL: http://neuro.debian.net/pkgs/openelectrophy.html Published-In: Frontiers in Neuroinformatics, 3:14 Published-Year: 2009 Published-DOI: 10.3389/neuro.11.014.2009 Pkg-Description: data analysis framework for intra- and extra-cellular recordings This package provide a library und GUI for analyzing electrophysiological data. The data handling and storage uses a MySQL-server. The package is written in pure Python. Depends: invesalius X-Screenshot: http://dl.dropbox.com/u/4053278/invesalius_trac/screenshots/invesalius3_promed_0446_bone.png Pkg-URL: http://svn.softwarepublico.gov.br/trac/invesalius/wiki/downloads/3.0-beta-1#GNULinux Remark: Dependency from SIGAR The package depends from SIGAR which needs to be packaged first. This is discussed at http://lists.debian.org/debian-med/2010/03/msg00025.html. Comment: Several related R packages are listed at CRAN: http://cran.r-project.org/web/views/MedicalImaging.html Depends: mricron Published-Title: Improving lesion-symptom mapping Published-Authors: Chris Rorden, Hans-Otto Karnath, Leonardo Bonilha Published-In: Journal of Cognitive Neuroscience, 19: 1081-1088 Published-Year: 2007 Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/17583985 Depends: voxbo Registration: http://voxbo.org/usage.html Depends: mrtrix Published-Title: Robust determination of the fibre orientation distribution in diffusion MRI: Non-negativity constrained super-resolved spherical deconvolution Published-Authors: J-Donald Tournier, Fernando Calamantea, Alan Connelly Published-In: NeuroImage, 35: 1459-1472 Published-Year: 2007 Published-DOI: 10.1016/j.neuroimage.2007.02.016 Depends: ants Published-Title: The optimal template effect in hippocampus studies of diseased populations Published-Authors: Brian B. Avants, Paul Yushkevich, John Pluta, David Minkoff, Marc Korczykowski, John Detre and James C. Gee Published-In: NeuroImage, 49: 2457-2466 Published-Year: 2010 Published-DOI: 10.1016/j.neuroimage.2009.09.062 X-Institution: UCLA Center for Computation Biology Depends: itksnap Depends: mriconvert Depends: mia-tools, mialmpick ; Added by blends-inject 0.0.7. [Please note here if modified manually] Suggests: connectomeviewer Published-Authors: Gerhard S, Daducci A, Lemkaddem A, Meuli R, Thiran J-P and Hagmann P Published-DOI: 10.3389/fninf.2011.00003 Published-In: Front. Neuroinform. 5:3 Published-Title: The Connectome Viewer Toolkit: An open source framework to manage, analyze, and visualize connectomes Published-Year: 2011 ; Added by blends-inject 0.0.7. [Now official package] Depends: sigviewer Depends: tifffile Depends: mni-icbm152-nlin-2009 Homepage: http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009 License: custom, DFSG-compliant Responsible: NeuroDebian Team Pkg-Description: MNI stereotaxic space human brain template This is an unbiased standard magnetic resonance imaging template volume for the normal human population. It has been created by the Montreal Neurological Institute (MNI) using anatomical data from the International Consortium for Brain Mapping (ICBM). . The package provides a 1x1x1 mm and 0.5x0.5x0.5 mm resolution templates (hemissphere-symetric and asymetric non-linearily co-registered versions), some including T1w, T2w, PDw modalities, T2 relaxometry, and tissue probability maps. In addition, it contains a lobe atlas, and masks for brain, eyes and face. Published-Authors: V.S. Fonov, A.C. Evans, R.C. McKinstry, C.R. Almli and D.L. Collins Published-Title: Unbiased nonlinear average age-appropriate brain templates from birth to adulthood. Published-In: NeuroImage, 47, Supplement 1: 102 Published-Year: 2009 Remark: This package is waiting for the Debian data package archive to become available. Depends: mni-colin27-nifti Homepage: http://packages.bic.mni.mcgill.ca/tgz/ License: custom, DFSG-compliant Responsible: NeuroDebian Team Pkg-URL: http://neuro.debian.net/pkgs/mni-colin27-nifti.html Pkg-Description: Talairach stereotaxic space template This template MRI volume was created from 27 T1-weighted MRI scans of a single individual that have been transformed into the Talairach stereotaxic space. The anatomical image is complemented by a brain and a head mask. All images are in 1x1x1 mm resolution. . This package provides the template in NIfTI format. Published-Authors: C.J. Holmes, R. Hoge, L. Collins, R. Woods, A.W. Toga, A.C. Evans Published-Title: Enhancement of MR images using registration for signal averaging. Published-In: J Comput Assist Tomogr, 22: 324-333 Published-Year: 1998 Remark: This package is waiting for the Debian data package archive to become available. Depends: mipav Homepage: http://mipav.cit.nih.gov/ License: custom, non-free, closed-source (DFSG-compliant version promised) Responsible: NeuroDebian Team WNPP: 587645 Pkg-URL: http://neuro.debian.net/pkgs/mipav.html Pkg-Description: quantitative analysis and visualization of medical images The MIPAV (Medical Image Processing, Analysis, and Visualization) application enables quantitative analysis and visualization of medical images of numerous modalities such as PET, MRI, CT, or microscopy. Using MIPAV's standard user-interface and analysis tools, researchers at remote sites can easily share research data and analyses, thereby enhancing their ability to research, diagnose, monitor, and treat medical disorders. MIPAV provides an interface for plug-ins and serves as the foundation for other projects (e.g. JIST). . This package provides downloader/installer for non-redistributable closed-source version of MIPAV and a convenience startup wrapper. You will have a choice of reviewing the license and accepting or declining it upon installation. Published-Authors: M.J. McAuliffe, F.M Lalonde, D. McGarry, W. Gandler, K. Csaky, B.L Trus Published-Title: Medical Image Processing, Analysis & Visualization In Clinical Research Published-In: IEEE Computer-based Medical Systems (CBMS) Published-Year: 2001 Depends: jist Homepage: http://www.nitrc.org/projects/jist/ License: LGPL Responsible: NeuroDebian Team WNPP: 587820 Pkg-URL: http://neuro.debian.net/pkgs/jist.html Pkg-Description: Java Image Science Toolkit Java Image Science Toolkit (JIST) provides a native Java-based imaging processing environment similar to the ITK/VTK paradigm. Initially developed as an extension to MIPAV (CIT, NIH, Bethesda, MD), the JIST processing infrastructure provides automated GUI generation for application plug-ins, graphical layout tools, and command line interfaces. Published-Authors: B.C. Lucas, J.A. Bogovic, A. Carass, P.-L. Bazin, J.L. Prince, D. Pham, B.A. Landman Published-Title: The Java Image Science Toolkit (JIST) for Rapid Prototyping and Publishing of Neuroimaging Software. Published-In: Neuroinformatics 8, 5-17 Published-Year: 2010 Depends: openmeeg-tools Published-Authors: Alexandre Gramfort, Théodore Papadopoulo, Emmanuel Olivi, Maureen Clerc Published-In: BioMedical Engineering OnLine 45:9 Published-Title: OpenMEEG: opensource software for quasistatic bioelectromagnetics Published-URL: http://www.biomedical-engineering-online.com/content/9/1/45 Published-Year: 2010 Depends: jemris License: GPL-2+ Responsible: NeuroDebian Team WNPP: 590469 Homepage: http://www.jemris.org/ Pkg-Description: high performance computing MRI simulator JEMRIS, which stands for "Juelich Extensible MRI Simulator", is a general simulator of MRI (Magnetic Resonance Imaging) data. The general process of simulation consists of preparation by choice or implementation of sequence, sample and coil setup and the invocation of the simulation run itself. Published-Authors: Tony Stöcker, Kaveh Vahedipour, Daniel Pflugfelder, N. Jon Shah Published-Title: High-performance computing MRI simulations Published-In: Magnetic Resonance in Medicine Published-Year: 2010 Published-DOI: 10.1002/mrm.22406 Depends: insightapplications Language: C++, Python, Tcl Depends: tempo Homepage: http://code.google.com/p/tempo/ License: BSD Language: C++, Qt Pkg-Description: 3D visualization of brain electrical activity TEMPO is open source software for 3D visualization of brain electrical activity. TEMPO accepts EEG file in standard EDF format and creates animated sequence of topographic maps. Topographic maps are generated over 3D head model and user is able to navigate around head and examine maps from different viewpoints. Most mapping parameters are adjustable through appropriate graphical user interface controls. Also, individual topographic maps could be saved in PNG format for future examination or publishing. Remark: Packaged for OpenSuSE http://en.opensuse.org/TEMPO Depends: dti-query Homepage: http://graphics.stanford.edu/projects/dti/software/index.html License: MIT Language: C++ Pkg-Description: dynamic queries of the white matter brain pathways This application allows neuroscientists to place and interactively manipulate box-shaped regions (or volumes of interest) to selectively display pathways that pass through specific anatomical areas. A simple and extensible query language allows for arbitrary combinations of these queries using Boolean logic operators. Queries can be further restricted by numerical path properties such as length, mean fractional anisotropy, and mean curvature. Remark: Depends on RAPID library that is available under non-commercial licensing terms. ; Added by blends-inject 0.0.5. [Please note here if modified manually] Suggests: eeglab Homepage: http://sccn.ucsd.edu/eeglab Language: C, Matlab/Octave WNPP: 605739 Responsible: NeuroDebian Team License: GPL-2+ Pkg-Description: toolbox for processing and visualization of electrophysiological data EEGLAB is an interactive Matlab toolbox for processing continuous and event-related EEG, MEG and other electrophysiological data incorporating independent component analysis (ICA), time/frequency analysis, artifact rejection, event-related statistics, and several useful modes of visualization of the averaged and single-trial data. Published-Authors: Delorme A and Makeig S Published-In: Journal of Neuroscience Methods 134:9-21 Published-Title: EEGLAB: an open source toolbox for analysis of single-trial EEG dynamics Published-Year: 2004 Registration: http://sccn.ucsd.edu/eeglab/install.html Suggests: elastix Registration: http://elastix.isi.uu.nl/download.php ; Added by blends-inject 0.0.6. [Please note here if modified manually] Suggests: pyxid Homepage: https://github.com/cedrus-opensource/pyxid Language: Python WNPP: 607213 License: BSD-3 Pkg-Description: interfacing with Cedrus XID and StimTracker devices pyxid is a Python library for interfacing with Cedrus XID (eXperiment Interface Device) and StimTracker devices. XID devices are used in software such as SuperLab, Presentation, and ePrime for receiving input as part of stimulus/response testing experiments. . pyxid handles all of the low level device handling for XID devices in python projects. Recommends: python-dipy Why: Although listed in -dev task, it also has a strong focus on interactive data analysis. Published-Authors: Garyfallidis E, Brett M, Tsiaras V, Vogiatzis G, Nimmo-Smith I Published-In: Proc. Intl. Soc. Mag. Reson. Med. 18 Published-Title: Identification of corresponding tracks in diffusion MRI tractographies Published-Year: 2010 Depends: plastimatch Depends: medisnap Homepage: http://medisnap.sourceforge.net/ License: GPL-3 Pkg-Description: photograph, manage, view, compare, document and archive medical photos Photograph, manage, view, compare, document and archive medical photos fully integrated into doctor's practice systems. Take a photo and immediately see how the picture gets archived to your current patient automatically. * direct support for Olympus E-System cameras * network support * fully integrated via GDT interface into many medical software systems * organise photos by patients effectively * define your own localisations * compare photos of healing processes at different times * work time-optimized and effective, photos automatically get added and archived under the current patient in your system * easily print selected photos and archive or give them to your patients Depends: gimias Homepage: http://www.gimias.org/ X-SF-URL: http://gimias.sourceforge.net License: BSD-like Pkg-Description: Graphical Interface for Medical Image Analysis and Simulation GIMIAS is a workflow-oriented environment for solving advanced biomedical image computing and individualized simulation problems, which is extensible through the development of problem-specific plug-ins. In addition, GIMIAS provides an open source framework for efficient development of research and clinical software prototypes integrating contributions from the Physiome community while allowing business-friendly technology transfer and commercial product development. X-Comment: See http://lists.debian.org/debian-med/2011/02/msg00031.html Dependencies: ANN/ BOOST-1.45.0/ CGNS/ cmakeMacros/ CMGUI/ CXXTEST/ DCMTK-3.5.4/ EXPAT/ HDF5/ ITK-3.20/ LIBELF/ LOG4CPLUS/ MITK_SVN2/ NETGEN-4.5/ PCRE-8.01/ SLICER/ SLICERAPPS/ TinyXml/ VTK-5.6.1/ WXMATHPLOT-0.1.0/ WXWIDGETS-2.8.10/ XERCES-3.0.1/ ZLIB/ ; Added by blends-inject 0.0.7. [Please note here if modified manually] Suggests: dtitk Homepage: http://www.nitrc.org/projects/dtitk Language: C++ WNPP: 612619 License: GPL-3+ Pkg-Description: DTI spatial normalization and atlas construction toolkit DTI-TK is a spatial normalization & atlas construction toolkit, designed from ground up to support the manipulation of diffusion-tensor images (DTI) with special cares taken to respect the tensorial nature of the data. It implements a state-of-the-art registration algorithm that drives the alignment of white matter (WM) tracts by matching the orientation of the underlying fiber bundle at each voxel. The algorithm has been shown to both improve WM tract alignment and to enhance the power of statistical inference in clinical settings. The key features include: . - NIfTI support for scalar, vector and DTI volumes - tool chains for manipulating DTI volumes: resampling, smoothing, warping, registration & visualization - pipelines for WM morphometry: spatial normalization & atlas construction for population-based studies - built-in cluster-computing support - interoperability with other major DTI tools: AFNI, Camino, DTIStudio & FSL Published-Authors: H Zhang, P A Yushkevich, D C Alexander, and J C Gee Published-DOI: 10.1016/j.media.2006.06.004 Published-In: Medical Image Analysis - Special Issue: The Eighth International Conference on Medical Imaging and Computer Assisted intervention - MICCAI 2005, 10(5):764-785 Published-Title: Deformable registration of diffusion tensor MR images with explicit orientation optimization Published-Year: 2006 ; Added by blends-inject 0.0.7. [Please note here if modified manually] Suggests: openwalnut Homepage: http://berkeley.informatik.uni-leipzig.de/trac/ow-public/ Language: C++ WNPP: 613419 License: LGPL-3+ Pkg-Description: multi-modal medical and brain data visualization OpenWalnut is an open source tool for multi-modal medical and brain data visualization. Its universality allows it to be easily extended and used in a large variety of application cases. It is both, a tool for the scientific user and a powerful framework for the visualization researcher. Published-Authors: Sebastian Eichelbaum, Mario Hlawitschka, Alexander Wiebel, Gerik Scheuermann Published-In: Werner Benger et al., editors, Proceedings of 6th High-End Visualization Workshop. Lehmanns Published-Title: OpenWalnut - An Open-Source Visualization System Published-Year: 2010 ; Added by blends-inject 0.0.7. [Please note here if modified manually] Suggests: miview Why: Seems to be quite neat Homepage: http://www.gbooksoft.com/ Language: C++ License: GPL-3+ Pkg-Description: Medical Images viewer and converter MIView features - DICOM files browser - volume rendering - reads DICOM v3, NEMA/ACR, Papyrus, Jpeg, GIF, bitmap, TIFF, Analyze 7.5, and Nifti1 files - can convert to raster (jpeg, bitmap, etc) and Analyze/Nifti1 Remark: At the moment available only for Windows, but author says there should be no major showstoppers to build it on Linux -- just needs building infrastructure Depends: mayam Language: Java ; Added by blends-inject 0.0.7. [extra information removed because package uploaded to Debian] Suggests: cmtk ; Added by blends-inject 0.0.7. [extra information removed because obtained from Vcs] Suggests: freesurfer Registration: http://surfer.nmr.mgh.harvard.edu/fswiki/Registration Remark: The 'tktools' (tkmedit, tksurfer and tkregister2) under the CorTechs license are not readily redistributable thus excluded. . Here you can see a list where Freesurfer was cited http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferMethodsCitation ; Added by blends-inject 0.0.7. [Please note here if modified manually] Suggests: xnat Homepage: http://www.xnat.org Language: java WNPP: 629143 License: XNAT SLA Pkg-Description: platform for data management and productivity tasks in neuroimaging The primary functionality of XNAT is to provide a place to store and control access to neuroimaging data. This includes sophisticated user control, search and retrieval, and archiving capabilities. As open-source software, XNAT also supports a wide variety of research-based processing pipelines, and is able to link up with supercomputer processing power to dramatically shorten image processing time. Published-Authors: Marcus, D.S., Olsen T., Ramaratnam M., and Buckner, R.L. Published-In: Neuroinformatics 5(1): 11-34 Published-Title: The Extensible Neuroimaging Archive Toolkit (XNAT): An informatics platform for managing, exploring, and sharing neuroimaging data. Published-Year: 2007 Registration: http://www.xnat.org/download-xnat.html ; Added by blends-inject 0.0.7. [Removed unneeded publication data] Depends: biosig-tools ; Added by blends-inject 0.0.7. [Please note here if modified manually] Suggests: isis Why: IO layer for Lipsia and maybe soon Odin. Homepage: http://isis-group.github.com/isis/ Language: C++ WNPP: 633677 Responsible: NeuroDebian Team License: GPL-2+ Pkg-Description: I/O framework for neuroimaging data This framework aids access of and conversion between various established neuro-imaging data formats, like Nifti, Analyze, DICOM and VISTA. ISIS is extensible with plugins to add support for additional data formats. ; Added by blends-inject 0.0.7. [Please note here if modified manually] Suggests: pymeg Homepage: https://github.com/badbytes/pymeg/wiki Language: Python License: GPL-3 Pkg-Description: suite for analysis of magnetoencephalography (MEG) data PyMEG is a project in Python to do various neuroimaging processing with magnetoencephalography (MEG) data. The purpose of this project, is to create a suite of functions to do MEG analysis in Python. Remark: Needs DFSG-ification. According to the author is not yet ready for the use by mortals -- wasn't released yet. ; Added by blends-inject 0.0.7. [Please note here if modified manually] Suggests: stabilitycalc Homepage: https://github.com/bbfrederick/stabilitycalc Language: Python Responsible: NeuroDebian Team License: BSD Vcs-Git: https://github.com/bbfrederick/stabilitycalc.git Pkg-URL: http://neuro.debian.net/pkgs/stabilitycalc.html Pkg-Description: evaluate fMRI scanner stability Command-line tools to calculate numerous fMRI scanner stability metrics, based on the FBIRN quality assurance test protocal. Any 4D volumetric timeseries image in NIfTI format is support input. Output is a rich HTML report. ; Added by blends-inject 0.0.7. [Please note here if modified manually] Suggests: pysurfer Homepage: http://pysurfer.github.com/ Language: Python WNPP: 641345 Responsible: NeuroDebian Team License: BSD-3 Pkg-Description: visualize Freesurfer's data in Python This is a Python package for visualization and interaction with cortical surface representations of neuroimaging data from Freesurfer. It extends Mayavi’s powerful visualization engine with a high-level interface for working with MRI and MEG data. . PySurfer offers both a command-line interface designed to broadly replicate Freesurfer’s Tksurfer program as well as a Python library for writing scripts to efficiently explore complex datasets. Depends: dicoogle Depends: cellprofiler Depends: bioimagexd Depends: omero Homepage: http://www.openmicroscopy.org License: GPL Pkg-Description: coming standard LIMS for microscopy images OMERO is client-server software for visualisation, management and analysis of biological microscope images. X-Comment: More image viewers might be listed in the Fed-Med project: http://fedoraproject.org/wiki/Medical_Imaging ; Added by blends-inject 0.0.7. [Please note here if modified manually] Suggests: hid Homepage: http://www.nitrc.org/projects/hid Language: java License: BSD, BIRN Pkg-Description: database management system for clinical imaging The Human Imaging Database (HID) is an extensible database management system developed to handle the increasingly large and diverse datasets collected as part of the MBIRN and FBIRN collaboratories and throughout clinical imaging communities at large. Published-Authors: Keator, D.B.; Grethe, J.S.; Marcus, D.; Ozyurt, B.; Gadde, S.; Murphy, S.; Pieper, S.; Greve, D.;Notestine, R.; Bockholt, H.J.; Papadopoulos, P. Published-In: IEEE Transactions on Information Technology in Biomedicine, 12 (2) Published-Title: A National Human Neuroimaging Collaboratory Enabled By The Biomedical Informatics Research Network (BIRN) Published-Year: 2008 Registration: http://www.nitrc.org/account/register.php Depends: king Suggests: incf-nidash-oneclick-clients Homepage: http://xnat.incf.org/ License: BSD Language: Python Pkg-Description: utility for pushing DICOM data to the INCF datasharing server A command line utility for anonymizing and sending DICOM data to the XNAT image database at the International Neuroinformatics Coordinating Facility (INCF). This tool is maintained by the INCF NeuroImaging DataSharing (NIDASH) task force. Responsible: NeuroDebian Team Vcs-Git: https://github.com/INCF/one_click.git Vcs-Browser: https://github.com/INCF/one_click debian-med-1.13.2ubuntu3/tasks/dental0000664000000000000000000000113612124332225014315 0ustar Task: Dental Description: Debian Med packages related to dental practice This metapackage contains dependencies for a collection of software which might be helpful for dentists to manage their practice. Depends: openmolar Homepage: https://launchpad.net/openmolar License: GPL-3+ WNPP: 564285 Responsible: David Paleino Language: Python Pkg-URL: https://launchpad.net/~rowinggolfer/+archive/ppa Pkg-Description: dental practice management software More customisable software for dental practices, and ultimately, patients of those practices. Depends: imagetooth Depends: entangle debian-med-1.13.2ubuntu3/tasks/physics0000664000000000000000000001122612124332225014531 0ustar Task: Physics Description: Debian Med packages for medical physicists This metapackage contains dependencies for a collection of software and documentation which is useful for medical physicists in radiation oncology, diagnostics imaging and related fields. Depends: paw++ Why: Just depend from the user friendly version because it is easier to povide a menu item Depends: paw Why: This is for the purists with exactly the same functionality as paw++ Suggests: paw-demos Depends: octave Depends: r-base X-Comment: removed " | r-base-core" which desturbs tasks page and does not harm to just use the metapackage in the dependency list Why: "r-base" is a metapackage and it is better to have a default alternative -- Dirk Eddelbuettel Depends: biosig Homepage: http://biosig.sf.net License: GPL WNPP: 251868 Responsible: NeuroDebian Team Pkg-Description: library for biomedical signal processing BioSig is an open source software library for biomedical signal processing, featuring for example the analysis of biosignals such as the electroencephalogram (EEG), electrocorticogram (ECoG), electrocardiogram (ECG), electrooculogram (EOG), electromyogram (EMG), respiration, and so on. Major application areas are: Neuroinformatics, brain-computer interfaces, neurophysiology, psychology, cardiovascular systems and sleep research. The aim of the BioSig project is to foster research in biomedical signal processing by providing open source software tools for many different applications. Generally, many concerns have to be addressed in this scientific field. BioSig handles this by providing solutions for data acquisition, artifact processing, quality control, feature extraction, classification, modeling, data visualization, and so on. . BioSig consists of some (more or less) coherent parts, for more details take a look at the project page: * BioSig for Octave and Matlab (biosig4octmat): A toolbox for Octave and Matlab with powerful data import and export filters, feature extraction algorithms, classification methods, and a powerful viewing and scoring software. * BioSig for C/C++ (biosig4c++) containing: reading and writing routines for different biosignal data formats. - libbiosig - a library for reading and writing of a number of data formats. libbiosig is used by save2gdf, mexSLOAD and SigViewer - save2gdf - a converter between different data formats, and can be used to show the header information - mexSLOAD is a MEX-interface for loading biosignal data into Octave (its much faster than the pure M-tools from biosig4octmat). It requires Octave-headers and libbiosig * SigViewer (sigviewer): A stand-alone viewing and scoring software for biosignals (especially for EEG signals) based on C++ and the platform-independent GUI toolkit Qt 4. * rtsBCI (rtsbci): A real-time BCI system implemented in Matlab and Simulink. * BioProFeed (bioprofeed) * BCIx (bcix) Published-Title: BioSig: A Free and Open Source Software Library for BCI Research Published-Authors: 10.1109/MC.2008.407 Published-In: Computer, 41(10): 44-50 Published-Year: 2008 Published-URL: http://hci.tugraz.at/~schloegl/publications/Schloegl2007_BCI_Software.pdf Published-DOI: 10.3389/neuro.11.003.2009 X-Institution: Institute for Human-Computer Interfaces, University of Technology Graz Depends: gate Homepage: http://www.opengatecollaboration.org License: LGPL WNPP: 431425 Responsible: Nicolas Spalinger Pkg-Description: Geant4 Application for Emission Tomography GATE incorporates the Geant4 libraries in a modular, versatile, and scripted simulation toolkit which is adapted to the field of nuclear medicine both in PET (Positron Emission Tomography) and SPECT (Single Photon Emission Computer Tomography). It allows the accurate description of time-dependent phenomena such as source or detector movement and source decay kinetics. The ability to synchronize all time-dependent components allows a coherent description of the acquisition process. It makes it possible to perform realistic simulations of data acquisitions in time. ; Added by blends-inject 0.0.6. [Please note here if modified manually] Suggests: openvibe Homepage: http://openvibe.inria.fr Language: C++ WNPP: 580247 License: LGPL Pkg-Description: platform for the design, test and use of BCI OpenViBE enables to design, test and use Brain-Computer Interfaces (BCI). OpenViBE is a software for real-time neurosciences (that is, for real-time processing of brain signals). It can be used to acquire, filter, process, classify and visualize brain signals in real time. debian-med-1.13.2ubuntu3/tasks/bio-ngs0000664000000000000000000001243312124332225014406 0ustar Task: Next Generation Sequencing Metapackage: false Description: Debian Med bioinformatics applications usable in Next Generation Sequencing It aims at gettting packages which specializes in alignment of sequences produced by next generation sequencing. Comment: Do not build a metapackage because it is not clear in how far this set of packages is complete regarding NGS. Depends: bedtools, bwa, bowtie, fastx-toolkit, filo, last-align, maq, picard-tools, r-bioc-edger, r-bioc-hilbertvis, samtools, sra-toolkit, ssake, tabix, tophat, vcftools, velvet Depends: mothur Depends: qiime Depends: cufflinks Depends: mira-assembler X-Mark: Prospective packages are starting here. X-Mark: Packages in Vcs - Information about these is queried from UDD as well Depends: mosaik-aligner Depends: ssaha2 Homepage: http://www.sanger.ac.uk/resources/software/ssaha2/ License: to be clarified Pkg-Description: pairwise sequence alignment program SSAHA2 (Sequence Search and Alignment by Hashing Algorithm) is a pairwise sequence alignment program designed for the efficient mapping of sequencing reads onto genomic reference sequences. SSAHA2 reads of most sequencing platforms (ABI-Sanger, Roche 454, Illumina-Solexa) and a range of output formats (SAM, CIGAR, PSL etc.) are supported. A pile-up pipeline for analysis and genotype calling is available as a separate package. Published-Title: SSAHA: a fast search method for large DNA databases. Published-Authors: Ning Z, Cox AJ and Mullikin JC Published-In: Genome research 2001;11;10;1725-9 Published-doi: 10.1101/gr.194201 Depends: forge Homepage: http://combiol.org/forge/ License: Apache 2.0 Pkg-Description: genome assembler for mixed read types Forge Genome Assembler is a parallel, MPI based genome assembler for mixed read types. . Forge is a classic "Overlap layout consensus" genome assembler written by Darren Platt and Dirk Evers. Implemented in C++ and using the parallel MPI library, it runs on one or more machines in a network and can scale to very large numbers of reads provided there is enough collective memory on the machines used. It generates a full consensus alignment of all reads, can handle mixtures of sanger, 454 and illumina reads. There is some support for solid color space and it includes built in tools for vector trimming and contamination screening. . Forge and was originally developed at Exelixis and they have kindly agreed to place the software which underwent much subsequent development outside Exelixis, into the public domain. Forge works with most of the common MPI implementations. Remark: Competitor to MIRA2 and wgs-assembler This package was requested by William Spooner as a competitor to MIRA2 and wgs-assembler. Depends: uc-echo Homepage: http://uc-echo.sourceforge.net/ License: BSD License Pkg-Description: error correction algorithm designed for short-reads from next-generation sequencing ECHO is an error correction algorithm designed for short-reads from next-generation sequencing platforms such as Illumina's Genome Analyzer II. The algorithm uses a Bayesian framework to improve the quality of the reads in a given data set by employing maximum a posteriori estimation. Depends: annovar Homepage: http://www.openbioinformatics.org/annovar/ License: Open Source for non-profit Pkg-Description: annotate genetic variants detected from diverse genomes ANNOVAR is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, as well as mouse, worm, fly, yeast and many others). Given a list of variants with chromosome, start position, end position, reference nucleotide and observed nucleotides, ANNOVAR can perform: . 1. Gene-based annotation: identify whether SNPs or CNVs cause protein coding changes and the amino acids that are affected. Users can flexibly use RefSeq genes, UCSC genes, ENSEMBL genes, GENCODE genes, or many other gene definition systems. 2. Region-based annotations: identify variants in specific genomic regions, for example, conserved regions among 44 species, predicted transcription factor binding sites, segmental duplication regions, GWAS hits, database of genomic variants, DNAse I hypersensitivity sites, ENCODE H3K4Me1/H3K4Me3/H3K27Ac/CTCF sites, ChIP-Seq peaks, RNA-Seq peaks, or many other annotations on genomic intervals. 3. Filter-based annotation: identify variants that are reported in dbSNP, or identify the subset of common SNPs (MAF>1%) in the 1000 Genome Project, or identify subset of non-synonymous SNPs with SIFT score>0.05, or many other annotations on specific mutations. 4. Other functionalities: Retrieve the nucleotide sequence in any user-specific genomic positions in batch, identify a candidate gene list for Mendelian diseases from exome data, identify a list of SNPs from 1000 Genomes that are in strong LD with a GWAS hit, and many other creative utilities. . In a modern desktop computer (3GHz Intel Xeon CPU, 8Gb memory), for 4.7 million variants, ANNOVAR requires ~4 minutes to perform gene-based functional annotation, or ~15 minutes to perform stepwise "variants reduction" procedure, making it practical to handle hundreds of human genomes in a day. debian-med-1.13.2ubuntu3/AUTHORS0000664000000000000000000000004112124332225013040 0ustar Andreas Tille debian-med-1.13.2ubuntu3/debian/0000775000000000000000000000000012323033136013217 5ustar debian-med-1.13.2ubuntu3/debian/upstream0000664000000000000000000000077612124332225015014 0ustar Reference: - AUTHOR: Steffen Moller and Hajo Krabbenhoft and Andreas Tille and David Paleino and Alan Williams and Katy Wolstencroft and Carole Goble and Richard Holland and Dominique Belhachemi and Charles Plessy TITLE: Community-driven computational biology with Debian Linux. JOURNAL: BMC Bioinformatics VOLUME: 11 YEAR: 2010 NUMBER: Suppl 12 PAGES: S5 URL: "http://www.biomedcentral.com/1471-2105/11/S12/S5" DOI: 10.1186/1471-2105-11-S12-S5 PMID: 21210984 ISSN: 1471-2105 debian-med-1.13.2ubuntu3/debian/source/0000775000000000000000000000000012124332546014525 5ustar debian-med-1.13.2ubuntu3/debian/source/format0000664000000000000000000000000412124332225015724 0ustar 1.0 debian-med-1.13.2ubuntu3/debian/copyright0000664000000000000000000000027612124332225015157 0ustar This package is Copyright 2004-2009 by Andreas Tille This software is licensed under the GPL. On Debian systems, the GPL can be found at /usr/share/common-licenses/GPL. debian-med-1.13.2ubuntu3/debian/med-config.postinst.stub0000664000000000000000000000035612124332225020014 0ustar #!/bin/sh -e # if apt-get hook of med-common package remains it might lead to # creating user menus twice. So get rid of this not needed file. if [ -e /etc/apt/apt.conf.d/90med-common ] ; then rm /etc/apt/apt.conf.d/90med-common fi debian-med-1.13.2ubuntu3/debian/changelog0000664000000000000000000005146612323033132015101 0ustar debian-med (1.13.2ubuntu3) trusty; urgency=medium * s/libgenome-1.3-0-dev/libgenome-1.3/ due to changes in libegnome, this should resolve NBS. -- Dimitri John Ledkov Mon, 14 Apr 2014 20:26:18 +0100 debian-med (1.13.2ubuntu2) saucy; urgency=low * s/pixelmed-java/libpixelmed-java/ due to changes in pixelmed packaging - update debian/control -- Micah Gersten Mon, 22 Jul 2013 22:47:59 -0500 debian-med (1.13.2ubuntu1) raring; urgency=low * Merge from Debian unstable. Remaining changes: - sources.list.quantal → sources.list.raring - regenerate debian/control. - Change libteem1-dev in Recommends to libteem-dev for libteem1-dev -> libteem-dev transition. -- Vibhav Pant Tue, 26 Mar 2013 13:52:45 +0530 debian-med (1.13.2) unstable; urgency=low * Build-Depends: blends-dev (>= 0.6.16.2) * Added dependency in imaging-dev: libopenigtlink1-dev -- Andreas Tille Thu, 20 Dec 2012 09:13:33 +0100 debian-med (1.13.1ubuntu1) raring; urgency=low * Merge from Debian unstable (LP: #1089907). Remaining changes: - sources.list.quantal → sources.list.raring - regenerate debian/control. - Change libteem1-dev in Recommends to libteem-dev for libteem1-dev -> libteem-dev transition. -- Vibhav Pant Thu, 13 Dec 2012 18:19:52 +0530 debian-med (1.13.1) unstable; urgency=low * Revert name change from med-pharmacy -> med-pharma Closes: #694424 -- Andreas Tille Tue, 27 Nov 2012 17:37:26 +0100 debian-med (1.13ubuntu1) raring; urgency=low * Merge from Debian unstable. Remaining changes: - sources.list.quantal → sources.list.raring - regenerate debian/control. - Change libteem1-dev in Recommends to libteem-dev for libteem1-dev -> libteem-dev transition. -- Bhavani Shankar Wed, 05 Dec 2012 21:30:26 +0530 debian-med (1.13) unstable; urgency=low * med-rehabilitation: sitplus is back to testing - regenerate dependencies * Some new prospective packages in tasks -- Andreas Tille Wed, 07 Nov 2012 11:39:29 +0100 debian-med (1.12) unstable; urgency=low * debian/control: Usual changes of dependency based on the resolving of new packages in Debian as specified in the tasks files * config/control: Enhanced readability and spelling of long description * Added dependencies due to packages progressing to testing after last upload Bio: r-cran-genabel, gentle, dssp, neobio, fasttree Bio-dev: libbiojava3-java, libai-fann-perl, librg-blast-parser-perl, libsort-key-top-perl, libhmsbeagle-dev Imaging: ants, king Practice: freediams, freemedforms-freedata, freemedforms-emr * Removed dependencies due to packages removed from testing Bio: gassst (removed in #689957) Rehabilitation: sitplus (lacking build-depends in testing, see #680798) * Renamed metapackages: med-pharmacy -> med-pharma * Add debian/med-*.lintian-overrides to prevent false positives about homepage links -- Andreas Tille Mon, 05 Nov 2012 15:52:59 +0100 debian-med (1.11ubuntu2) quantal; urgency=low * debian/control: - Change libteem1-dev in Recommends to libteem-dev for libteem1-dev -> libteem-dev transition. (LP: #1019485) -- Vibhav Pant Sat, 30 Jun 2012 09:46:02 +0530 debian-med (1.11ubuntu1) quantal; urgency=low * Merge from Debian unstable. Remaining changes: - sources.list.precise → sources.list.quantal - regenerate debian/control. -- Bhavani Shankar Tue, 01 May 2012 20:19:01 +0530 debian-med (1.11) unstable; urgency=low * debian/control(.stub): Standards-Version: 3.9.3 (no changes needed) * debian/control: Usual changes of dependency based on the resolving of new packages in Debian as specified in the tasks files * tasks/physics: s/octave3.2/octave/ Closes: #667588 -- Andreas Tille Thu, 05 Apr 2012 08:30:44 +0200 debian-med (1.10ubuntu1) precise; urgency=low * sources.list.oneiric → sources.list.precise * regenerate debian/control. -- Charlie Smotherman Tue, 27 Dec 2011 11:14:18 -0500 debian-med (1.10) unstable; urgency=low * tasks/oncology: Fix typo Closes: #647987 * tasks/dental: Fullfilled dependency imagetooth results in new metapackage med-dental -- Andreas Tille Fri, 16 Dec 2011 13:25:18 +0100 debian-med (1.9) unstable; urgency=low * Standards-Version: 3.9.2 (no changes needed) * Do not create med-cms metapackage any more because the only Dependency is dropped from testing / unstable * New tasks bio-ngs + bio-phylogeny which are actual subsets of med-bio created but not turned into metapackages for this release * New task oncology - packaging dependencies is in preparation * Several new Dependencies created by Blends tools * Fixed Vcs fields -- Andreas Tille Mon, 18 Jul 2011 10:32:39 +0200 debian-med (1.8) unstable; urgency=low [Steffen Möller] * Added task cloud: Cloud computing image for Debian Med [Andreas Tille] * config/control: Depends: blends-common (>= 0.6.15) * debian/control.stub: Build-Depends-Indep: blends-dev (>= 0.6.15) which provides postrm / preinst scripts for each metapackage to enable handling failed-upgrade Closes: ##603853 -- Andreas Tille Thu, 18 Nov 2010 08:16:45 +0100 debian-med (1.7) unstable; urgency=low * Rebuild against blends-dev >= 0.6.14 to prevent accessint internet at package build time * Standards-Version: 3.9.1 (no changes needed) * tasks/imaging-dev: Revcent version of vtk to make sure vtk migration will be not blocked by Debian Med * config/control: - Do not mention mention med-cms any more because the package will not be created any more. The only dependency in Debian zope-zms was removed. - Add med-psychology and med-statistics -- Andreas Tille Wed, 04 Aug 2010 12:43:09 +0200 debian-med (1.6) unstable; urgency=low * Rebuild against blends-dev >= 0.6.12. This results in using a prerm script instead of postrm which ensures that blends-common is installed while this script is running * Standards-Version: 3.8.4 (no changes needed) * debian/oldchangelogs: removed old stuff -- Andreas Tille Thu, 18 Mar 2010 10:07:26 +0100 debian-med (1.5) unstable; urgency=low * Depend from blends-common >= 0.6.9 and explain in NEWS.Debian that no attempt to take over any CDD related configuration Closes: #562553 -- Andreas Tille Mon, 18 Jan 2010 22:22:05 +0100 debian-med (1.4) unstable; urgency=low * Several new dependencies in Metapackages * Depend from blends-common >= 0.6.8 Closes: #562553 * No need to Build-Depends from debhelper because blends-dev does depend from it * Several new package -- Andreas Tille Mon, 28 Dec 2009 08:58:27 +0100 debian-med (1.3) unstable; urgency=low * tasks/physics: Enhanced information about biosig * tasks/*: Several changes and additional information for a lot of prospective packages; a certain amount of packages is now available as official packages * debian/control.stub: - Fixed Vcs-Svn (missing svn/) * Replaced some remaining "cdd" strings in the docs by "blends" * Standards-Version: 3.8.3 (no changes needed) * config/control: Depends: blends-common (>= 0.6.6) Closes: #542656 -- Andreas Tille Fri, 21 Aug 2009 14:09:18 +0200 debian-med (1.2) unstable; urgency=low [ Andreas Tille ] * Bumped policy to 3.8.1 and make use of the new feature that debian/control allows comment lines starting with # with no preceding whitespace. [Policy paragraph 5.2] * debhelper (>=7) * Added med-statistics * tasks/bio: Replaced biococoa.app by sequenceconverter.app * tasks/bio-dev: Added libbiococoa-dev * Build-Depends: blends-dev (0.6.3) to make sure no useless metapackages with no dependency available in Debian will be created * tasks.ctl: Added missing tasks; tasks data, his, laboratory which do not yet feature an existing depenency in Debian were set to priority-none. [ Michael Hanke ] * Added ODIN to imaging task. * Added VIA to the imaging task. * Updated LIPSIA item to ppoint to the packaging VCS and note ITP. -- Andreas Tille Mon, 30 Mar 2009 07:56:56 +0200 debian-med (1.1) experimental; urgency=low * Make use of blends-dev instead of cdd-dev * Versioned build depends from blends-dev >= 0.6.1 because this also supports dist experimental * Adapted Vcs fields to new location (cdd -> blends) * tasks/practice: Depends: aeskulap * Added link to tasks page in long description of med-tasks (thanks to James Busser for the hint) * tasks/*: several updates of newly uploaded packages and prospective packages -- Andreas Tille Tue, 06 Jan 2009 10:01:49 +0100 debian-med (1.0) unstable; urgency=low * tasks/bio-dev - Added libgenome - Added libmems as prospective package - Moved bioconductor from bio to bio-dev - Added prospective projects where Steffen Möller started some packaging work - libqsearch -> libqsearch-dev * tasks/bio - Added prospective projects where Steffen Möller started some packaging work - Suggests: texlive-latex-extra (because of TeXShade) - Removed line breaks in Dependencies, because cdd-gen-control is not compliant to RFC 822 and requires '\' at the end of lines to continue parsing the tasks files. To simply circumvent this problem the relevant lines were concatenated to not miss the dependencies in the resulting control file - Renamed dialign-t to dialign-tx * tasks/tools - Added mssstest - Added wgerman-medical, hunspell-de-med (remark: these are not really tools but we have no better section, typesetting might be an option but does also fit not really good) * tasks/imaging - Added prospective packages from static page * tasks/imaging-dev - Removed libgtkimreg - Added libvtk5 - Added prospective packages from static page - libminc0-dev | libminc-dev -> libminc-dev - insighttoolkit -> insighttoolkit3 * tasks/physics - octave | octave2.1 -> octave3.0 * debian/control.stub: XS-DM-Upload-Allowed -> DM-Upload-Allowed * Standards-Version: 3.8.0 (no changes needed) * Fixed typing of Debian Med: sed -i 's/Debian-Med/Debian Med/' * -- Andreas Tille Mon, 30 Jun 2008 09:59:37 +0200 debian-med (0.17) unstable; urgency=low * tasks/bio: - Added emboss-kaptain as prospective package - Added agdbnet as prospective package - Added autodock, exonerate - Suggests biococoa.app: Only suggests because status is questionable - Removed bugsx which is not really biology related - Added gamgi as prospective package - Moved unoffical and prospective packages from static web pages to tasks file * tasks/bio-dev: - Added aceperl as prospective package - Added libgff-perl as prospective package - Added Recommends: libqsearch * tasks/imaging - Removed paul - pngquant: Recommends -> Suggests - Added gdmc as prospective package - Added dicom4j as prospective package * tasks/epi: New meta package: med-epi for epidemiology research * tasks/tools: - Moved NetEpi prospective package to epi where it really belongs to - Added pondus * Removed remark about recommended and suggested packages from description or meta packages * Build-Depends-Indep: cdd-dev (>= 0.5.0) which ensures that the source tarball is builded properly and no network access is neede to build the package Closes: #470271 -- Andreas Tille Wed, 20 Feb 2008 13:31:25 +0100 debian-med (0.16) unstable; urgency=low * New upstream version * Standards-Version: 3.7.3 (no changes needed) * Added Vcs-Browser / Vcs-Svn tags * tasks/imaging: - Added Dr. Jekyll, libvista2 and dcm4che as prospective package - Fixed minc and nifti library depends - odin, gwyddion and many more as prospective package - Removed libfslio1, libniftiio0 which are only available in Etch - Suggests: Imview * tasks/imaging-dev: - libvista2-dev as prospective package - Fixed minc-dev and nifti-dev library depends - Removed libniftiio0-dev which is only available in Etch * tasks/bio - Added ballview and mustang as prospective packages - dialign-t is now official package - removed long description - Added glam2 as prospective package - textopo is now in texlilve-science, decreased this from Recommends to Suggests to not spoil systems with whole texlive installation * tasks/bio-dev: Added BioClipse as prospective package Pkg-Description * tasks/practice: - Added Mirth as prospective package - Fixed libchipcard depends * Debian-Med packaging policy: - Maintainer: Debian-Med Packaging Team - XS-DM-Upload-Allowed: yes - Uploaders: Andreas Tille - Vcs-Browser, Vcs-Svn * Increased mozilla-biofox from Suggests to Recommends. Installation of firefox as Dependency of this package should be no real problem. * Increased bugsx from Suggests to Recommends. It is automatically decreased to Suggests by cdd-gen-control so there is no need to decrease it in the tasks file. * Make tasks files compliant with rfc822 to be able to use python-debian tools successfully. That means basically to have exactly one Depends/Recommends/Suggest per paragraph so the fix was to insert some newlines and remove '\' in end of lines * tasks/tools: Fixed description * tasks/practice: tinyheb as prospective package * Increased Build-Dep version cdd-dev (>= 0.4.7) because 0.4.5 and 0.4.6 are broken * config/control: med-config Depends cdd-common (>= 0.4.7) -- Andreas Tille Tue, 19 Feb 2008 17:07:36 +0100 debian-med (0.15) unstable; urgency=low * med-imaging-dev: Added Depends: libinsighttoolkit-dev Suggests: insighttoolkit-examples * med-imaging(-dev): Depend from libniftiio1(-dev) instead of libniftiio0(-dev) Closes: #448903 * Increased Build-Dep version cdd-dev (>= 0.4.4) * Standards-Version: 3.7.3 (no changes needed) * Added several prospective packages in tasks -- Andreas Tille Sun, 07 Oct 2007 18:25:56 +0200 debian-med (0.14) unstable; urgency=low * Builded using new cdd-dev 0.4 - med-common is now renamed to med-config - additional package med-tasks * med-bio: added emboss * med-imaging: amide, dicomnifti, imagej, python-nifti decreased paul from Recommends to Suggests * med-imaging-dev: cimg-dev decreased libgtkimreg-dev from Recommends to Suggests * med-practice: libchipcard3c1, libchipcard3d0 -- Andreas Tille Sat, 11 Aug 2007 17:50:29 +0200 debian-med (0.13) unstable; urgency=low * Removed entry for gnumed-client-debug because this package does not exist any more. Removed gnumed-client menu as well because this should be builded automatically from menu entry inside gnumed-client package Closes: #429217 * Added several packages to med-bio and reordering the task to specific fields * Imaging: Added dicomnifti * Enhanced long description of med-common * Remove header from po.stub/de.po because cdd-dev will add another one -- Andreas Tille Thu, 28 Jun 2007 16:23:36 +0200 debian-med (0.12) unstable; urgency=low * Changed med-practice menu Closes: #385584 Use menu entry for gnumed-client-debug that regards #389932. Note: gnumed-client-debug is not in the med-practice dependency list but it is suggested by gnumed-client. So *if* the package is installed at the box then an additional menu item occures correctly in the Debian-Med menu. If it is not installed, only gnumed-client is shown in the menu. * med-bio: Added alternative to tree-puzzle as tree-ppuzzle * Drop med-dent because odontolinux was removed from Debian * med-bio: Added poa Moved vrom Suggests to Depends: seaview (now really free) Suggests: wise-doc * med-imaging: Depends: libfslio0, libniftiio0, nifti-bin Suggests: * med-imaging-dev: Depends: libfslio0-dev, libniftiio0-dev Suggests: libnifti-doc -- Andreas Tille Thu, 14 Sep 2006 15:28:51 +0200 debian-med (0.11) unstable; urgency=low * bugsx to from Depends to Suggets because this package moved to non-free Closes: #383265 * Standards-Version: 3.7.2 Build-Depends: debhelper * med-bio: Depends: gromacs, dialign, kalign, probcons, wise, amap-align, biosquid Suggests: mozilla-biofox * debian/compat: 5 * Uploaders: Debian-Med Packaging Team -- Andreas Tille Wed, 16 Aug 2006 10:07:41 +0200 debian-med (0.10.1) unstable; urgency=low * Make med-common depend from ${misc:Depends} Closes: #331797 * Now med-practice really depends from gnumed-client which is now awailable at Debian mirror -- Andreas Tille Wed, 5 Oct 2005 07:55:13 +0200 debian-med (0.10) unstable; urgency=low * Rebuilded with cdd-dev 0.3.11 (and increased versioned dependency because 0.3.10 created broken *.dsc file) Closes: #328428 * Standards-Version: 3.6.2 (no changes necessary) * Added dependencies: med-bio: mipe, sim4, perlprimer med-bio-dev: libbio-ruby * Addes meta package: med-practice -- Andreas Tille Sun, 25 Sep 2005 21:14:47 +0200 debian-med (0.9) unstable; urgency=low * Removed gnutrion from tools because it was removed from Debian at all * Rebuilded with cdd-dev 0.3.10 version * med-bio: Depends: muscle, gff2aplot, t-coffee, gff2ps, gdpc Suggests: arb * med-bio-dev Recommends: libvibrant6-dev Why: libmotif-dev conflicts lesstif-dev, so if someone wants to install libmotif-dev it must be possible to deinstall libvibrant6-dev without beeing forced to deinstall med-bio-dev as well Depends: python-biopython * med-imaging: paul now Recommends not Depends Depends: dcmtk Recommends: pngquant * med-tools: Depends: cycle Suggests: cl-pubmed Strong dependency would cost installing a large amount of Common Lisp tools which in most cases is not worth the effort * Added user menu entries: bio/gff2aplot.txt, bio/gff2ps.txt, bio/muscle.txt, bio/t-coffee.txt, bio/boxshade.txt, bio-dev/python-biopython.txt, imaging/dcmtk.txt * Added charset to debian/po.stub/de.po -- Andreas Tille Sun, 24 Oct 2004 20:59:03 +0200 debian-med (0.8.9) experimental; urgency=low * New upstream version which now uses the features of cdd-dev 0.3.9 * Exclude .svn dirs in dist target of debian/rules -- Andreas Tille Fri, 16 Jul 2004 11:33:21 +0200 debian-med (0.8.3) unstable; urgency=high * Rebuilded again against cdd-dev 0.3.4 which really closes the mentioned bug. * Urgency set to high because it *really* fixes a grave bug. -- Andreas Tille Thu, 15 Jul 2004 10:59:25 +0200 debian-med (0.8.2) unstable; urgency=high * Rebuilded with cdd-dev 0.3.3 which closes a grave bug (which was reassigned to cdd-dev and thus it is not closed in this changelog). * Please make sure that all ${HOME}/.menu/cdd-menu files or ${HOME}/.menu/med-* files are removed - they will not be needed any more. -- Andreas Tille Wed, 14 Jul 2004 21:42:24 +0200 debian-med (0.8.1) unstable; urgency=low * Adjust versioned dependency of med-common from cdd-common Closes: #258373 -- Andreas Tille Fri, 9 Jul 2004 09:18:49 +0200 debian-med (0.8) unstable; urgency=low * Added med-physics, med-pharmacy, med-bio-dev * Overworked menus of meta packages -- Andreas Tille Fri, 4 Jun 2004 14:44:36 +0200 debian-med (0.7) unstable; urgency=low * Switched to new version of cdd package (0.3) which has many enhancements (no really important changes to the Debian-Med stuff except that the packages have to be rebuilded with cdd-dev). * New cdd-dev package cares for versioned dependency on med-common Closes: #244903 -- Andreas Tille Tue, 20 Apr 2004 11:21:16 +0200 debian-med (0.6) unstable; urgency=medium * Took over Debian-Edu method to build metapackages from one common source. The changelogs of the previous single meta package sources can be found in the source package under debian/oldchangelogs. -- Andreas Tille Mon, 22 Mar 2004 19:21:55 +0100 debian-med-1.13.2ubuntu3/debian/med-imaging.lintian-overrides0000664000000000000000000000032112124332225020751 0ustar # The link inside the description is no homepage replacement but rather a reference # for more detailed information about the topic med-imaging: description-possibly-contains-homepage http://medical.nema.org/ debian-med-1.13.2ubuntu3/debian/med-bio.lintian-overrides0000664000000000000000000000026412124332225020115 0ustar # The *.html files are just simple helpers for the user menu entries and # should not be used in doc-base-registration med-bio: possible-documentation-but-no-doc-base-registration debian-med-1.13.2ubuntu3/debian/control0000664000000000000000000004110212323032575014626 0ustar # This file is autogenerated via make -f debian/rules dist. Do not edit! Source: debian-med Section: misc Priority: extra Maintainer: Ubuntu Developers XSBC-Original-Maintainer: Debian Med Packaging Team DM-Upload-Allowed: yes Uploaders: Andreas Tille Build-Depends-Indep: blends-dev (>= 0.6.16.2) Standards-Version: 3.9.3 Vcs-Browser: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/ Vcs-Svn: svn://svn.debian.org/blends/projects/med/trunk/debian-med/ Package: med-tasks Architecture: all Depends: tasksel Description: Debian Med tasks for tasksel This package provides Debian Med tasks in tasksel. . These tasks are described in detail at http://debian-med.alioth.debian.org/tasks/ Package: med-config Architecture: all Depends: adduser, ${misc:Depends}, menu, blends-common (>= 0.6.15) Conflicts: med-common Replaces: med-common Provides: med-common Description: Debian Med general config package This package provides the basic infrastructure of all metapackages assembled by the Debian Med team. . This metapackage provides common features shared between the different metapackages of the project. Moreover it introduces a method to handle a 'med' system users group using debconf. . The Debian Med Project include metapackages for different tasks, which are: * applications for microbiological research and support for development of biological applications * cloud computing in microbiological research * drug databases * dental surgery practice * epidemiology and medical statistics * image processing and support for imaging application development * pharmacological research * radiation oncology, diagnostic imaging and related fields * medical practice * psychological research and practice * rehabilitation * typesetting and publishing * miscellaneous tools . Each task is represented by a metapackage. Metapackages do not contain executable programs, but rather dependencies from other packages. This way you will conveniently get all free medical software which is available for Debian by simply installing the relevant metapackage Package: med-bio Architecture: all Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version}) Recommends: abacas, acedb-other, acedb-other-belvu, acedb-other-dotter, adun.app, alien-hunter, altree, amap-align, ampliconnoise, autodock, autodock-vina, autogrid, ballview, bedtools, biomaj, blast2, bowtie, bowtie2, boxshade, bwa, cd-hit, clonalframe, clustalo, clustalw, clustalx, dialign, dialign-tx, disulfinder, dotur, dssp, embassy-domainatrix, embassy-domalign, embassy-domsearch, emboss, exonerate, fastdnaml, fastlink, fasttree, fastx-toolkit, ffindex, figtree, filo, gamgi, garlic, gbrowse, gdpc, gentle, gff2aplot, gff2ps, ghemical, glam2, grinder, gromacs, hhsuite, hmmer, infernal, jalview, jellyfish, jmol, kalign, last-align, librg-utils-perl, loki, mafft, maq, maqview, massxpert, melting, mipe, mira-assembler, mlv-smile, mothur, mrbayes, mummer, muscle, mustang, ncbi-blast+, ncbi-epcr, ncbi-tools-bin, ncbi-tools-x11, ncoils, neobio, njplot, perlprimer, phyml, picard-tools, plasmidomics, plink, poa, populations, primer3, probalign, probcons, proda, profnet-bval, profnet-chop, profnet-con, profnet-isis, profnet-md, profnet-norsnet, profnet-prof, profnet-snapfun, profphd, profphd-net, profphd-utils, proftmb, pymol, pynast, python-cogent, qiime, r-bioc-cummerbund, r-bioc-hilbertvis, r-cran-genabel, r-cran-qtl, r-other-bio3d, r-other-mott-happy, rasmol, raster3d, raxml, readseq, reprof, rnahybrid, samtools, sibsim4, sigma-align, sim4, squizz, sra-toolkit, ssake, staden-io-lib-utils, t-coffee, tabix, theseus, tigr-glimmer, tm-align, transtermhp, tree-puzzle | tree-ppuzzle, treeviewx, vcftools, velvet, wise Suggests: abyss, act, amos-assembler, amoscmp, anfo, apollo, arachne, arb, artemis, asap, augustus, autodocktools, axparafit, axpcoords, bagphenotype, bambus, bamtools, beads, beast-mcmc, big-blast, bigsdb, blimps-utils, blixem, btk-core, cactus, caftools, cain, cap3, cdbfasta, cdna-db, cinema, circos, clonalorigin, clustalw-mpi, cluster3, cmap, coalesce, codonw, compclust, concavity, conservation-code, contralign, coot, copycat, crossbow, cufflinks, cytoscape, das-proserver, dazzle, decipher, e-hive, ecell, edtsurf, eigensoft, elph, embassy-phylip, emboss-explorer, ensembl, est-db, estferret, estscan, exalt, excavator, fas, fasta, fastqc, figaro, finex, fluctuate, forester, forge, galaxy, gassst, gbioseq, gbrowse-syn, genemark, genesplicer, genetrack, genezilla, genographer, genometools, glimmerhmm, gmap, gmv, grogui, haploview, hawkeye, hexamer, hilbertvisgui, hmmer2, igv, jbrowse, jigsaw, jstreeview, kempbasu, lagan, lamarc, logol-bin, logomat-m, ltrsift, lucy, macs, mage2tab, maker2, martj, maude, mauvealigner, maxd, melting-gui, meme, mesquite, metarep, microbiomeutil, migrate, minimus, mirbase, mobyle, molekel, mosaik-aligner, mozilla-biofox, mpsqed, msatfinder, mugsy, mummergpu, murasaki, mview, ncbi-seg, ngila, norsnet, norsp, nw-align, oases, obo-edit, oligoarrayaux, omegamap, operondb, pal2nal, paml, partigene, patman, patristic, pcma, pdb2pqr, pfaat, pftools, phagefinder, phpphylotree, phy-spread, phylip, phylographer, phyloviz-core, phylowin, plato, prank, predictnls, predictprotein, proalign, profbval, profisis, profit, prot4est, pscan-tfbs, psipred, pyrophosphate-tools, python-orange, python-rdkit, python-reaper, qtlcart, r-ape, r-other-valdar-bagphenotype.library, raccoon, ray-denovoassembler, rbs-finder, rdp-classifier, recombine, repeatmasker, rmblast, roche454ace2caf, rose, rosetta, sap, seaview, seq-gen, seqan-apps, seqtk, sequenceconverter.app, sga, sift, smalt, snap, snpeff, soapdenovo, spice, splitstree, spread-phy, sra-sdk, ssaha, strap, tacg, taverna, taxinspector, tetra, tigr-assembler, tigr-glimmer-mg, tophat, trace2dbest, tracetuner, treebuilder3d, treetime, treeview, tripal, trnascan-se, twain, ugene, uniprime, vegan, vienna-rna, vmd, wgs-assembler, x-tandem-pipeline, zalign, zodiac-zeden Description: Debian Med micro-biology packages This metapackage will install Debian packages related to molecular biology, structural biology and bioinformatics for use in life sciences. Package: med-bio-dev Architecture: all Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version}) Recommends: bioperl, bioperl-run, biosquid, libace-perl, libai-fann-perl, libbio-graphics-perl, libbio-mage-perl, libbio-mage-utils-perl, libbio-primerdesigner-perl, libbiococoa-dev, libbiojava-java, libbiojava3-java, libchado-perl, libffindex0-dev, libgenome-1.3-dev, libgo-perl, libhmsbeagle-dev, libjebl2-java, libncbi6-dev, libpal-java, librg-blast-parser-perl, librg-reprof-bundle-perl, librostlab-blast-doc, librostlab-blast0-dev, librostlab-doc, librostlab3-dev, libsort-key-top-perl, libsrf-dev, libstaden-read-dev, libtfbs-perl, libvibrant6-dev, libzerg-perl, libzerg0-dev, mcl, python-biopython, python-cogent, r-bioc-biobase, r-cran-genetics, r-cran-haplo.stats, ruby-bio, seqan-dev Suggests: bioclipse, biostrings, iranges, libbamtools-dev, libbio-das-perl, libforester-java, libgbfp-dev, libgenometools0-dev, libgff-perl, libmems-1.5-1, libnhgri-blastall-perl, libopenmm4-dev, libqsearch-dev, librcsb-core-wrapper0-dev, libsbml5-dev, libswarm2-dev, octace-bioinfo, octave-bioinfo, python-biom-format, python-librcsb-core-wrapper, python-mmtk, python-pysam, r-bioc-biocgenerics, r-cran-rocr Description: Debian Med packages for development of micro-biology applications This metapackage will install Debian packages which might be helpful for development of applications for micro-biological research. Package: med-cloud Architecture: all Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version}) Recommends: autodock, clustalw, python-cogent, raster3d Suggests: bagphenotype, clustalw-mpi, r-other-valdar-bagphenotype.library Description: Debian Med bioinformatics applications usable in cloud computing This metapackage will install Debian packages related to molecular biology, structural biology and bioinformatics for use in life sciences, that do not depend on graphical toolkits and therefore can fit on system images for use in cloud computing clusters, where space can be limited. Package: med-data Architecture: all Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version}) Recommends: freediams, freemedforms-freedata, python-hl7 Suggests: drugref.org Description: Debian Med drug databases This metapackage will install free drug databases and related applications. The database can be accessed by any EMR using the application. Package: med-dental Architecture: all Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version}) Recommends: imagetooth Suggests: entangle, openmolar Description: Debian Med packages related to dental practice This metapackage contains dependencies for a collection of software which might be helpful for dentists to manage their practice. Package: med-epi Architecture: all Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version}) Recommends: epigrass, r-cran-diagnosismed, r-cran-epi, r-cran-epibasix, r-cran-epicalc, r-cran-epir, r-cran-epitools Suggests: netepi-analysis, netepi-collection, r-cran-msm, r-cran-surveillance, repast Description: Debian Med epidemiology related packages This metapackage will install tools that are useful in epidemiological research. Several packages making use of the GNU R data language for statistical investigation. It might be a good idea to read the paper "A short introduction to R for Epidemiology" at http://staff.pubhealth.ku.dk/%7Ebxc/Epi/R-intro.pdf Package: med-imaging Architecture: all Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version}) Recommends: aeskulap, amide, ants, biosig-tools, caret, ctn, ctsim, dcmtk, dicom3tools, dicomnifti, dicomscope, ginkgocadx, gofigure2, gwyddion, imagej, imagevis3d, itksnap, king, libgdcm-tools, medcon, minc-tools, mriconvert, mricron, mrtrix, nifti-bin, odin, openmeeg-tools, openslide-tools, libpixelmed-java, plastimatch, python-dipy, python-mvpa, python-nifti, python-nipy, python-nipype, python-nitime, sigviewer, sofa-apps, tifffile, via-bin, volview, voxbo, xmedcon Suggests: afni, bioimagesuite, bioimagexd, blox, brainvisa, camitk-imp, cdmedicpacs, cellprofiler, cmtk, connectomeviewer, conquest-dicom-server, crea, dcm4chee, devide, dicom4j, dicoogle, drjekyll, dti-query, dtitk, ecg2png, eeglab, elastix, fiji, freesurfer, fsl, fslview, gimias, hid, imagemagick, imview, incf-nidash-oneclick-clients, insightapplications, invesalius, isis, jemris, jist, kradview, libdcm4che-java, lipsia, maris, mayam, medisnap, mesa-test-tools, mia-tools, mialmpick, micromanager, mipav, miview, mni-autoreg, mni-colin27-nifti, mni-icbm152-nlin-2009, mni-n3, mrisim, omero, opendicom.net, openelectrophy, opensourcepacs, openwalnut, orthanc, paraview, piano, pngquant, pymeg, pysurfer, pyxid, slicer, stabilitycalc, stir, tempo, visit, vmtk, xnat Description: Debian Med imaging packages This metapackage will install Debian packages which might be useful in medical image processing. . It installs several packages supporting DICOM (Digital Imaging and Communications in Medicine) which is the de-facto standard for medical image management. The standard defines data structures and services for the exchange of medical images and related information. The latest release has been published in 2008 and consists of 18 parts. . For more information, you can visit the NEMA homepage http://medical.nema.org/ . . The status of the official DICOM base standard plus all the supplements and correction items are summarized at David Clunie's webpage: http://www.dclunie.com/dicom-status/status.html where you'll find direct links to the most recent yearly edition ftp://medical.nema.org/medical/dicom/2008/ . Package: med-imaging-dev Architecture: all Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version}) Recommends: cimg-dev, ctn-dev, gmic, libactiviz.net-cil, libbiosig-dev, libcv-dev, libgdcm2-dev, libgdf-dev, libgiftiio-dev, libigstk4-dev, libinsighttoolkit3-dev, libmdc2-dev, libminc-dev, libnifti-dev, libopenigtlink1-dev, libopenmeeg-dev, libopenslide-dev, libvia-dev, libvolpack1-dev, libvtk5-dev, libvxl1-dev, odin, python-cfflib, python-dicom, python-dipy, python-gdcm, python-mvpa, python-nibabel, python-nipy, python-nipype, python-nitime, python-pyxnat Suggests: emokit, igstk-examples, insighttoolkit3-examples, libbio-formats-java, libcamitk3-dev, libctk-dev, libeegdev-dev, libmia-2.0-dev, libmni-perllib-perl, libnifti-doc, libopenslide-java, libteem-dev, libvistaio-dev, libvtk5.4, libxdffileio-dev, octave-dicom, python-casmoothing, python-libavg, python-openslide Description: Debian Med packages for medical image development This metapackage will install Debian packages which might be useful for developing applications for medical image processing. Package: med-oncology Architecture: all Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version}) Recommends: dicompyler Suggests: planunc, uw-prism Description: Debian Med packages for oncology This metapackage will install tools that are useful for radiation oncology. Package: med-pharmacy Architecture: all Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version}) Recommends: chemtool Suggests: raccoon Description: Debian Med packages for pharmaceutical research This metapackage contains dependencies for a collection of software and documentation which is useful for pharmaceutical research. Package: med-physics Architecture: all Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version}) Recommends: octave, paw, paw++, r-base Suggests: biosig, gate, openvibe, paw-demos Description: Debian Med packages for medical physicists This metapackage contains dependencies for a collection of software and documentation which is useful for medical physicists in radiation oncology, diagnostics imaging and related fields. Package: med-practice Architecture: all Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version}) Recommends: clinica, freediams, freemedforms-emr, ginkgocadx, gnumed-client, gnumed-server, libchipcard-tools, r-cran-medadherence Suggests: clearhealth, elementalclinic, elexis, entangle, freeb, freeicd, freemed, freeshim, libctapimkt0, medintux, mirrormed, mirth, openemr, openpms, openrep, proteus, qrisk2, remitt, resmedicinae, sqlclinic, thera-pi, tinyheb Description: Debian Med packages for practice management This metapackage contains dependencies for a collection of software which might be helpful for practitioners to manage their practice. Package: med-psychology Architecture: all Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version}) Recommends: praat, psignifit, psychopy, python-pyepl, r-cran-foreign, r-cran-psy Suggests: miscpsycho, psignifit3, psych, psychometric, psychotree, psyphy, science-psychophysics, visionegg Description: Debian Med packages for psychology This metapackage contains dependencies for a collection of software which might be helpful for psychological research. Package: med-rehabilitation Architecture: all Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version}) Recommends: sitplus Suggests: aghermann Description: Debian Med packages for rehabilitation technologies This metapackage will install tools that are useful for rehabilitation and therapy. Package: med-statistics Architecture: all Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version}) Recommends: r-bioc-edger, r-bioc-limma, r-bioc-qvalue, r-cran-pvclust, r-cran-randomforest Suggests: r-cran-beeswarm, science-statistics Description: Debian Med statistics This metapackage will install packages which are helpful to do statistics with a special focus on tasks in medical care. Package: med-tools Architecture: all Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version}) Recommends: edfbrowser, hunspell-de-med, pcalendar, pondus, quitcount, wgerman-medical, workrave Suggests: cl-pubmed, cycle, entangle, hunspell-en-med, mencal, mssstest, python-clips Description: Debian Med several tools This metapackage will install tools for several purposes in health care. Currently it contains some simple programs for Personal Health. Package: med-typesetting Architecture: all Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version}) Recommends: king, texlive-latex-extra, texlive-science Suggests: biber, bibus, jabref-plugin-oo, kbibtex, referencer Description: Debian Med support for typesetting and publishing This metapackage will install Debian packages that might be helpful for typesetting and publishing in medical care and structural biology. debian-med-1.13.2ubuntu3/debian/control.stub0000664000000000000000000000121712124332225015577 0ustar Source: debian-med Section: misc Priority: extra Maintainer: Debian Med Packaging Team DM-Upload-Allowed: yes Uploaders: Andreas Tille Build-Depends-Indep: blends-dev (>= 0.6.16.2) Standards-Version: 3.9.3 Vcs-Browser: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/ Vcs-Svn: svn://svn.debian.org/blends/projects/med/trunk/debian-med/ Package: med-tasks Architecture: all Depends: tasksel Description: Debian Med tasks for tasksel This package provides Debian Med tasks in tasksel. . These tasks are described in detail at http://debian-med.alioth.debian.org/tasks/ debian-med-1.13.2ubuntu3/debian/rules0000775000000000000000000000007012124332225014274 0ustar #!/usr/bin/make -f include /usr/share/blends-dev/rules debian-med-1.13.2ubuntu3/debian/compat0000664000000000000000000000000212124332225014415 0ustar 7 debian-med-1.13.2ubuntu3/debian/med-tasks.lintian-overrides0000664000000000000000000000034112124332225020465 0ustar # The link inside the description is no homepage replacement but rather a reference # for more detailed information about the topic med-tasks: description-possibly-contains-homepage http://debian-med.alioth.debian.org/tasks/ debian-med-1.13.2ubuntu3/debian/med-epi.lintian-overrides0000664000000000000000000000035012124332225020115 0ustar # The link inside the description is no homepage replacement but rather a reference # for more detailed information about the topic med-epi: description-possibly-contains-homepage http://staff.pubhealth.ku.dk/%7Ebxc/Epi/R-intro.pdf debian-med-1.13.2ubuntu3/Makefile0000775000000000000000000000052612124332225013443 0ustar #!/usr/bin/make -f BLENDMAKEFILE=/usr/share/blends-dev/Makefile CheckBLENDMakefile := $(shell if [ -e $(BLENDMAKEFILE) ] ; then echo 1 ; else echo 0 ; fi) ifeq ($(CheckBLENDMakefile),1) include $(BLENDMAKEFILE) else err := $(shell echo "$(BLENDMAKEFILE) is missing. Please install blends-dev package!") endif dummy: @echo $(err)