debian/0000755000000000000000000000000012021420464007161 5ustar debian/README.Debian0000644000000000000000000000365011576401577011250 0ustar profnet ======= profnet_* binaries are neural network implementations in Fortran. Due to the original design of the code, a specific binary is compiled for each particular network architecture, changing certain constants in the source code. Therefore, there is a binary for every network architecture used. Note: certain array structures are intentionally indexed out of bounds in some of the binaries! Q: Why so many binary packages? ------------------------------- There are a handful of prediction methods built around each of the binary profnet packages. Each depends on the matching profnet binary package. Each prediction method requires a different neural network architecture and therefore - due to the design of the code - a different binary. Binaries are compiled with constants set to the architecture of the network and are therefore not reusable for other architectures. To further develop the code beyond regular maintenance for compiler and architecture updates is not planned since a complete reimplementation of these networks with a neural network library is already underway. Publications of predictors that use these neural networks --------------------------------------------------------- Note: this list contains references only to the secondary structure and accessibility predictor (profnet-prof and profphd-net). References for the other methods are provided in the man pages of the respective methods' predictor commands, e.g. profbval(1). * Rost, B. and Sander, C. (1994a). Combining evolutionary information and neural networks to predict protein secondary structure. Proteins, 19(1), 55-72. * Rost, B. and Sander, C. (1994b). Conservation and prediction of solvent accessibility in protein families. Proteins, 20(3), 216-26. * Rost, B., Casadio, R., Fariselli, P., and Sander, C. (1995). Transmembrane helices predicted at 95 Protein Sci, 4(3), 521-33. -- Laszlo Kajan Tue, 14 Jun 2011 18:50:52 +0200 debian/watch0000644000000000000000000000007711575107474010236 0ustar version=3 ftp://rostlab.org/profnet/profnet-([0-9.]+)\.tar\.gz debian/rules0000755000000000000000000000512411664720730010256 0ustar #!/usr/bin/make -f # -*- makefile -*- # Sample debian/rules that uses debhelper. # This file was originally written by Joey Hess and Craig Small. # As a special exception, when this file is copied by dh-make into a # dh-make output file, you may use that output file without restriction. # This special exception was added by Craig Small in version 0.37 of dh-make. # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 build: build-arch build-indep build-arch: build-stamp build-indep: build-stamp build-stamp: dh_testdir @echo "******************" @echo "** M A K E **" @echo "******************" # Add here commands to compile the package. make patch make #docbook-to-man debian/profnet.sgml > profnet.1 touch $@ clean: dh_testdir dh_testroot rm -f build-stamp configure-stamp # Add here commands to clean up after the build process. $(MAKE) clean dh_clean install: build dh_testdir dh_testroot dh_prep dh_installdirs @echo "*******************" @echo "** I N S T A L L **" @echo "*******************" # Add here commands to install the package into debian/profnet. $(MAKE) DESTDIR=$(CURDIR)/debian/profnet-bval prefix=/usr install-bval $(MAKE) DESTDIR=$(CURDIR)/debian/profnet-chop prefix=/usr install-chop $(MAKE) DESTDIR=$(CURDIR)/debian/profnet-con prefix=/usr install-con $(MAKE) DESTDIR=$(CURDIR)/debian/profnet-isis prefix=/usr install-isis $(MAKE) DESTDIR=$(CURDIR)/debian/profnet-md prefix=/usr install-md $(MAKE) DESTDIR=$(CURDIR)/debian/profnet-norsnet prefix=/usr install-norsnet $(MAKE) DESTDIR=$(CURDIR)/debian/profnet-prof prefix=/usr install-prof $(MAKE) DESTDIR=$(CURDIR)/debian/profnet-snapfun prefix=/usr install-snapfun $(MAKE) DESTDIR=$(CURDIR)/debian/profphd-net prefix=/usr install-phd # Build architecture-independent files here. binary-indep: build install # We have nothing to do by default. # Build architecture-dependent files here. binary-arch: build install dh_testdir dh_testroot dh_installchangelogs ChangeLog dh_installdocs dh_installexamples # dh_install # dh_installmenu # dh_installdebconf # dh_installlogrotate # dh_installemacsen # dh_installpam # dh_installmime # dh_python # dh_installinit # dh_installcron # dh_installinfo dh_installman dh_link dh_strip --dbg-package=profnet-dbg dh_compress dh_fixperms # dh_perl # dh_makeshlibs dh_installdeb dh_shlibdeps for i in $$(sed -n '/^Package:/s/^.* //p' debian/control); do \ cat debian/substvars >> debian/$$i.substvars; \ done; dh_gencontrol dh_md5sums dh_builddeb binary: binary-indep binary-arch .PHONY: build clean binary-indep binary-arch binary install configure debian/substvars0000644000000000000000000000061411576403251011152 0ustar Description=Profnet is a component of the prediction methods that make up the${Newline}Predict Protein service by the lab of Burkhard Rost. It provides the neural${Newline}network component to a variety of predictors that perform protein feature${Newline}prediction directly from sequence. This neural network implementation has${Newline}to be compiled for every different network architecture. debian/changelog0000644000000000000000000001056312021420426011036 0ustar profnet (1.0.22-1) unstable; urgency=low * added build-arch and build-indep recommended targets * Demoted Recommends: not-yet-existent (in Debian) packages to Suggests:. * New upstream release. -- Laszlo Kajan Mon, 28 Nov 2011 15:51:23 +0100 profnet (1.0.21-1) unstable; urgency=low * New upstream release -- Laszlo Kajan Tue, 21 Jun 2011 16:15:37 +0200 profnet (1.0.20-2) unstable; urgency=low * added copyright info for Guy Yachdav and Laszlo Kajan; fixed description lines in debian/control -- Laszlo Kajan Thu, 16 Jun 2011 17:41:46 +0000 profnet (1.0.20-1) unstable; urgency=low * New upstream release * Removed -Werror patch - upstream does not need it any more * Explained the reason for the many binary packages in README.Debian * Added profnet-dbg package with debugging symbols -- Laszlo Kajan Tue, 14 Jun 2011 18:50:52 +0200 profnet (1.0.19-4) stable; urgency=low * build for Debian unstable -- Laszlo Kajan Sun, 12 Jun 2011 19:39:32 +0200 profnet (1.0.19-3) stable; urgency=low * build for Debian squeeze -- Laszlo Kajan Fri, 25 Feb 2011 18:48:41 +0100 profnet (1.0.19-2) stable; urgency=low * profnet-chop -- Laszlo Kajan Wed, 12 May 2010 20:07:24 +0200 profnet (1.0.19-1) stable; urgency=low * New upstream release -- Laszlo Kajan Wed, 12 May 2010 20:07:24 +0200 profnet (1.0.18-2) stable; urgency=low * Another attempt at profnet_md -- Laszlo Kajan Wed, 17 Mar 2010 16:23:34 +0100 profnet (1.0.18-1) stable; urgency=low * New upstream release -- Laszlo Kajan Wed, 17 Mar 2010 16:23:34 +0100 profnet (1.0.17-1) stable; urgency=low * New upstream release with profnet_isis -- Laszlo Kajan Fri, 26 Feb 2010 11:25:32 +0100 profnet (1.0.16-3) stable; urgency=low * profnet depends on profnet-con -- Laszlo Kajan Tue, 23 Feb 2010 10:55:09 +0100 profnet (1.0.16-2) stable; urgency=low * profnet_con -- Laszlo Kajan Tue, 23 Feb 2010 10:55:09 +0100 profnet (1.0.16-1) stable; urgency=low * New upstream release -- Laszlo Kajan Tue, 23 Feb 2010 10:55:09 +0100 profnet (1.0.15-1) stable; urgency=low * New upstream release -- Laszlo Kajan Wed, 17 Feb 2010 11:52:06 +0100 profnet (1.0.14-1) stable; urgency=low * New upstream release -- Laszlo Kajan Thu, 11 Feb 2010 13:06:40 +0100 profnet (1.0.13-1) stable; urgency=low * New upstream release -- Laszlo Kajan Wed, 10 Feb 2010 18:01:02 +0100 profnet (1.0.12-1) unstable; urgency=low * New upstream release -- Laszlo Kajan Tue, 05 Jan 2010 18:09:16 +0100 profnet (1.0.11-1) unstable; urgency=low * New upstream release -- Laszlo Kajan Fri, 18 Dec 2009 22:20:36 +0100 profnet (1.0.10-1) unstable; urgency=low * New upstream release -- Laszlo Kajan Thu, 17 Dec 2009 18:24:02 +0100 profnet (1.0.8-1) unstable; urgency=low * New upstream release -- Laszlo Kajan Tue, 15 Dec 2009 09:17:13 +0100 profnet (1.0.7-1) unstable; urgency=low * New upstream release -- Laszlo Kajan Thu, 10 Dec 2009 13:55:34 +0100 profnet (1.0.6-1) unstable; urgency=low * (unstable) New upstream release -- Guy Yachdav Wed, 09 Dec 2009 14:32:49 +0100 profnet (1.0.5-1) unstable; urgency=low * New upstream release. -- Guy Yachdav Wed, 09 Dec 2009 13:11:39 +0100 profnet (1.0.4-1) unstable; urgency=low * New upstream release -- Guy Yachdav Tue, 08 Dec 2009 16:21:27 +0100 profnet (1.0.3-1) unstable; urgency=low * New upstream release -- Guy Yachdav Wed, 02 Dec 2009 12:00:57 +0100 profnet (1.0.2-1) unstable; urgency=low * New upstream release -- Guy Yachdav Mon, 30 Nov 2009 18:23:31 +0100 profnet (1.0.1-1) unstable; urgency=low * New upstream release -- Guy Yachdav Mon, 30 Nov 2009 16:04:11 +0100 profnet (1.0.0) unstable; urgency=low * Initial release. -- Guy Yachdav Mon, 30 Nov 2009 14:50:26 +0100 debian/control0000644000000000000000000000633512021420426010571 0ustar Source: profnet Section: science Priority: extra Maintainer: Debian Med Packaging Team Uploaders: Guy Yachdav , Laszlo Kajan Build-Depends: debhelper (>= 7), gfortran, rsync Standards-Version: 3.9.2 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/rostlab/profnet/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/rostlab/profnet/trunk/ DM-Upload-Allowed: yes Homepage: http://www.predictprotein.org/ Package: profnet-bval Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Suggests: profbval Description: neural network architecture for profbval ${Description} . This package contains the neural network architecture for profbval. Package: profnet-chop Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Suggests: profchop Description: neural network architecture for profchop ${Description} . This package contains the neural network architecture for profchop. Package: profnet-con Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Suggests: profcon Description: neural network architecture for profcon ${Description} . This package contains the neural network architecture for profcon. Package: profnet-isis Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Suggests: profisis Description: neural network architecture for profisis ${Description} . This package contains the neural network architecture for profisis. Package: profnet-md Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Suggests: metadisorder Description: neural network architecture for metadisorder ${Description} . This package contains the neural network architecture for metadisorder. Package: profnet-norsnet Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Suggests: norsnet Description: neural network architecture for norsnet ${Description} . This package contains the neural network architecture for norsnet. Package: profnet-prof Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Suggests: profphd Description: neural network architecture for profacc ${Description} . This package contains the neural network architecture for profsec and profacc. Package: profnet-snapfun Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Suggests: snapfun Description: neural network architecture for snapfun ${Description} . This package contains the neural network architecture for snapfun. Package: profphd-net Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Suggests: profphd Description: neural network architecture for profphd ${Description} . This package contains the neural network architecture for profphd. Package: profnet-dbg Section: debug Architecture: any Depends: ${misc:Depends}, profnet-bval (= ${binary:Version}), profnet-chop (= ${binary:Version}), profnet-con (= ${binary:Version}), profnet-isis (= ${binary:Version}), profnet-md (= ${binary:Version}), profnet-norsnet (= ${binary:Version}), profnet-prof (= ${binary:Version}), profnet-snapfun (= ${binary:Version}), profphd-net (= ${binary:Version}) Description: debug files for profnet packages ${Description} . This package contains the stripped debugging symbols for profnet binaries. debian/compat0000644000000000000000000000000211575106147010373 0ustar 7 debian/copyright0000644000000000000000000000322412021420426011113 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: profnet Upstream-Contact: assistant@rostlab.org Source: ftp://rostlab.org/profnet Files: debian/* Copyright: 2009 Guy Yachdav 2012 Laszlo Kajan License: GPL-2+ Files: * Copyright: Copyright (C) 1998-2011 by Burkhard Rost EMBL CUBIC (Columbia University, NY, USA) LION Biosciences (Heidelberg, DE) . Copyright (C) 2009-2011 by Laszlo Kajan Technical University Munich (Munich, DE) . Copyright (C) 2009-2011 by Guy Yachdav CUBIC (Columbia University, NY, USA) Technical University Munich (Munich, DE) License: GPL-2+ License: GPL-2+ 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, see . . On Debian systems, the complete text of the GNU General Public License version 2 can be found in `/usr/share/common-licenses/GPL-2'. debian/patches/0000755000000000000000000000000012021420464010610 5ustar debian/patches/series0000644000000000000000000000000011575713342012030 0ustar debian/source/0000755000000000000000000000000012021420463010460 5ustar debian/source/format0000644000000000000000000000001411575174053011704 0ustar 3.0 (quilt)