Author: plessy Date: 2012-02-18 01:23:39 +0000 (Sat, 18 Feb 2012) New Revision: 9702
Modified: trunk/packages/R/r-cran-qvalue/trunk/debian/upstream trunk/packages/R/r-cran-rocr/trunk/debian/upstream trunk/packages/R/r-other-bio3d/trunk/debian/upstream trunk/packages/R/r-other-mott-happy/trunk/debian/upstream trunk/packages/adun.app/trunk/debian/upstream trunk/packages/alien-hunter/trunk/debian/upstream trunk/packages/altree/trunk/debian/upstream trunk/packages/autodock-vina/trunk/debian/upstream trunk/packages/autodocksuite/trunk/debian/upstream trunk/packages/biomaj/trunk/debian/upstream trunk/packages/bioperl/trunk/debian/upstream trunk/packages/blat/trunk/debian/upstream trunk/packages/cd-hit/trunk/debian/upstream trunk/packages/circos/trunk/debian/upstream trunk/packages/clonalframe/trunk/debian/upstream trunk/packages/clustalo/trunk/debian/upstream trunk/packages/coils/trunk/debian/upstream trunk/packages/dialign-t/trunk/debian/upstream trunk/packages/dialign/trunk/debian/upstream trunk/packages/epigrass/trunk/debian/upstream trunk/packages/exonerate/trunk/debian/upstream trunk/packages/gassst/trunk/debian/upstream trunk/packages/glam2/trunk/debian/upstream trunk/packages/hmmer/trunk/debian/upstream trunk/packages/infernal/trunk/debian/upstream trunk/packages/kalign/trunk/debian/upstream trunk/packages/last-align/trunk/debian/upstream trunk/packages/libhmsbeagle/trunk/debian/upstream trunk/packages/libtfbs-perl/trunk/debian/upstream trunk/packages/mafft/trunk/debian/upstream trunk/packages/maq/trunk/debian/upstream trunk/packages/maude/trunk/debian/upstream trunk/packages/melting/trunk/debian/upstream trunk/packages/mgltools/autodocktools/trunk/debian/upstream trunk/packages/mothur/trunk/debian/upstream trunk/packages/mustang/trunk/debian/upstream trunk/packages/phy-spread/trunk/debian/upstream trunk/packages/poa/trunk/debian/upstream trunk/packages/primer3/trunk/debian/upstream trunk/packages/probalign/trunk/debian/upstream trunk/packages/probcons/trunk/debian/upstream trunk/packages/proda/trunk/debian/upstream trunk/packages/python-pynast/trunk/debian/upstream trunk/packages/qiime/trunk/debian/upstream trunk/packages/raster3d/trunk/debian/upstream trunk/packages/raxml/trunk/debian/upstream trunk/packages/rnahybrid/trunk/debian/upstream trunk/packages/rostlab/libzerg-perl/trunk/debian/upstream trunk/packages/rostlab/libzerg/trunk/debian/upstream trunk/packages/seqan/trunk/debian/upstream trunk/packages/sigma-align/trunk/debian/upstream trunk/packages/t-coffee/trunk/debian/upstream trunk/packages/tm-align/trunk/debian/upstream trunk/packages/transtermhp/trunk/debian/upstream trunk/packages/velvet/trunk/debian/upstream Log: debian/upstream: Moved DOI and PMID to the Reference namespace. Modified: trunk/packages/R/r-cran-qvalue/trunk/debian/upstream =================================================================== --- trunk/packages/R/r-cran-qvalue/trunk/debian/upstream 2012-02-18 01:17:47 UTC (rev 9701) +++ trunk/packages/R/r-cran-qvalue/trunk/debian/upstream 2012-02-18 01:23:39 UTC (rev 9702) @@ -1,10 +1,10 @@ Bioconductor: http://www.bioconductor.org/packages/bioc/html/qvalue.html Contact: John D. Storey <jstorey at u.washington.edu> CRAN: http://cran.r-project.org/web/packages/qvalue/ -DOI: 10.1073/pnas.1530509100 +Reference-DOI: 10.1073/pnas.1530509100 Homepage: http://cran.r-project.org/web/packages/qvalue/ Name: qvalue -PMID: 12883005 +Reference-PMID: 12883005 Reference: article: John D.Storey08052003 author: Storey, John D. and Tibshirani, Robert Modified: trunk/packages/R/r-cran-rocr/trunk/debian/upstream =================================================================== --- trunk/packages/R/r-cran-rocr/trunk/debian/upstream 2012-02-18 01:17:47 UTC (rev 9701) +++ trunk/packages/R/r-cran-rocr/trunk/debian/upstream 2012-02-18 01:23:39 UTC (rev 9702) @@ -1,11 +1,11 @@ Contact: - Tobias Sing <[email protected]> - Oliver Sander <[email protected]> -DOI: 10.1093/bioinformatics/bti623 +Reference-DOI: 10.1093/bioinformatics/bti623 Gallery: http://rocr.bioinf.mpi-sb.mpg.de/rocr_gallery.html Homepage: http://rocr.bioinf.mpi-sb.mpg.de Name: ROCR -PMID: 16096348 +Reference-PMID: 16096348 Reference: | author: Sing, Tobias and Sander, Oliver and Beerenwinkel, Niko and Lengauer, Thomas title: ROCR: visualizing classifier performance in R Modified: trunk/packages/R/r-other-bio3d/trunk/debian/upstream =================================================================== --- trunk/packages/R/r-other-bio3d/trunk/debian/upstream 2012-02-18 01:17:47 UTC (rev 9701) +++ trunk/packages/R/r-other-bio3d/trunk/debian/upstream 2012-02-18 01:23:39 UTC (rev 9702) @@ -1,9 +1,9 @@ Contact: Barry Grant <[email protected]> -DOI: 10.1093/bioinformatics/btl461 +Reference-DOI: 10.1093/bioinformatics/btl461 Gallery: http://mccammon.ucsd.edu/~bgrant/bio3d/gallery/gallery.html Homepage: http://mccammon.ucsd.edu/~bgrant/bio3d/ Name: Bio3D -PMID: 16940322 +Reference-PMID: 16940322 Reference: author: Grant, Barry J. and Rodrigues, Ana P. C. and ElSawy, Karim M. and McCammon, J. Andrew and Caves, Leo S. D. title: Bio3d: an R package for the comparative analysis of protein structures Modified: trunk/packages/R/r-other-mott-happy/trunk/debian/upstream =================================================================== --- trunk/packages/R/r-other-mott-happy/trunk/debian/upstream 2012-02-18 01:17:47 UTC (rev 9701) +++ trunk/packages/R/r-other-mott-happy/trunk/debian/upstream 2012-02-18 01:23:39 UTC (rev 9702) @@ -1,8 +1,8 @@ Contact: Richard Mott <[email protected]> -DOI: 10.1073/pnas.230304397 +Reference-DOI: 10.1073/pnas.230304397 Homepage: http://www.well.ox.ac.uk/happy/happyR Name: HAPPY -PMID: 11050180 +Reference-PMID: 11050180 Reference: author: Mott, Richard and Talbot, Christopher J. and Turri, Maria G. and Collins, Allan C. and Flint, Jonathan title: A method for fine mapping quantitative trait loci in outbred animal stocks Modified: trunk/packages/adun.app/trunk/debian/upstream =================================================================== --- trunk/packages/adun.app/trunk/debian/upstream 2012-02-18 01:17:47 UTC (rev 9701) +++ trunk/packages/adun.app/trunk/debian/upstream 2012-02-18 01:23:39 UTC (rev 9702) @@ -1,8 +1,8 @@ Archive: Gna -DOI: 10.1002/jcc.20312 +Reference-DOI: 10.1002/jcc.20312 Homepage: http://diana.imim.es/Adun Name: Adun -PMID: 16175583 +Reference-PMID: 16175583 Reference: Author: Michael A. Johnston, Ignacio Fdez. Galván and Jordi Villà-Freixa Title: Framework-based design of a new all-purpose molecular simulation application: The Adun simulator Modified: trunk/packages/alien-hunter/trunk/debian/upstream =================================================================== --- trunk/packages/alien-hunter/trunk/debian/upstream 2012-02-18 01:17:47 UTC (rev 9701) +++ trunk/packages/alien-hunter/trunk/debian/upstream 2012-02-18 01:23:39 UTC (rev 9702) @@ -1,8 +1,8 @@ Contact : George Vernikos <[email protected]> -DOI: 10.1093/bioinformatics/btl369 +Reference-DOI: 10.1093/bioinformatics/btl369 Homepage: http://www.sanger.ac.uk/resources/software/alien_hunter.html Name: Alien_hunter -PMID: 16837528 +Reference-PMID: 16837528 Reference: author: Vernikos, Georgios S. and Parkhill, Julian title: Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands Modified: trunk/packages/altree/trunk/debian/upstream =================================================================== --- trunk/packages/altree/trunk/debian/upstream 2012-02-18 01:17:47 UTC (rev 9701) +++ trunk/packages/altree/trunk/debian/upstream 2012-02-18 01:23:39 UTC (rev 9702) @@ -1,8 +1,8 @@ Contact: Claire Bardel <[email protected]> -DOI: 10.1093/bioinformatics/btl131 +Reference-DOI: 10.1093/bioinformatics/btl131 Homepage: http://claire.bardel.free.fr/software.html Name: ALTree -PMID: 16595555 +Reference-PMID: 16595555 Reference-Author: Bardel, Claire and Danjean, Vincent and Genin, Emmanuelle Reference-Journal: Bioinformatics Reference-Number: 11 Modified: trunk/packages/autodock-vina/trunk/debian/upstream =================================================================== --- trunk/packages/autodock-vina/trunk/debian/upstream 2012-02-18 01:17:47 UTC (rev 9701) +++ trunk/packages/autodock-vina/trunk/debian/upstream 2012-02-18 01:23:39 UTC (rev 9702) @@ -1,5 +1,5 @@ Contact: Oleg Trott <[email protected]> -DOI: 10.1002/jcc.21334 +Reference-DOI: 10.1002/jcc.21334 Homepage: http://vina.scripps.edu Name: AutoDock Vina Reference: Modified: trunk/packages/autodocksuite/trunk/debian/upstream =================================================================== --- trunk/packages/autodocksuite/trunk/debian/upstream 2012-02-18 01:17:47 UTC (rev 9701) +++ trunk/packages/autodocksuite/trunk/debian/upstream 2012-02-18 01:23:39 UTC (rev 9702) @@ -1,8 +1,8 @@ Donation: http://autodock.scripps.edu/downloads/autodock-registration/autodock-4-2-download-page/ -DOI: 10.1002/jcc.21256 +Reference-DOI: 10.1002/jcc.21256 Homepage: http://autodock.scripps.edu/ Name: AutoDock -PMID: 19399780 +Reference-PMID: 19399780 Reference: Author: Garrett M. Morris, Ruth Huey, William Lindstrom, Michel F. Sanner, Richard K. Belew, David S. Goodsell and Arthur J. Olson. Title: AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility Modified: trunk/packages/biomaj/trunk/debian/upstream =================================================================== --- trunk/packages/biomaj/trunk/debian/upstream 2012-02-18 01:17:47 UTC (rev 9701) +++ trunk/packages/biomaj/trunk/debian/upstream 2012-02-18 01:23:39 UTC (rev 9702) @@ -1,4 +1,4 @@ -DOI: 10.1093/bioinformatics/btn325 +Reference-DOI: 10.1093/bioinformatics/btn325 Homepage: http://biomaj.genouest.org Reference: Author: Olivier Filangi, Yoann Beausse, Anthony Assi, Ludovic Legrand, Jean-Marc Larré, Véronique Martin, Olivier Collin, Christophe Caron, Hugues Leroy and David Allouche Modified: trunk/packages/bioperl/trunk/debian/upstream =================================================================== --- trunk/packages/bioperl/trunk/debian/upstream 2012-02-18 01:17:47 UTC (rev 9701) +++ trunk/packages/bioperl/trunk/debian/upstream 2012-02-18 01:23:39 UTC (rev 9702) @@ -1,9 +1,9 @@ Bug-Database: https://redmine.open-bio.org/projects/bioperl Contact: Bioperl developers <[email protected]> -DOI: 10.1101/gr.361602 +Reference-DOI: 10.1101/gr.361602 Homepage: http://www.bioperl.org/ Name: BioPerl -PMID: 12368254 +Reference-PMID: 12368254 Reference: author: > J.E. Stajich and D. Block and K. Boulez and S.E. Brenner Modified: trunk/packages/blat/trunk/debian/upstream =================================================================== --- trunk/packages/blat/trunk/debian/upstream 2012-02-18 01:17:47 UTC (rev 9701) +++ trunk/packages/blat/trunk/debian/upstream 2012-02-18 01:23:39 UTC (rev 9702) @@ -1,12 +1,12 @@ NAME: BLAT Reference: - author = Kent, W. James - title = BLAT—The BLAST-Like Alignment Tool - journal = Genome Research - volume = 12 - number = 4 - pages = 656-664 - doi = 10.1101/gr.229202 - year = 2002 - URL = http://genome.cshlp.org/content/12/4/656.abstract - eprint = http://genome.cshlp.org/content/12/4/656.full.pdf+html + author: Kent, W. James + title: BLAT—The BLAST-Like Alignment Tool + journal: Genome Research + volume: 12 + number: 4 + pages: 656-664 + doi: 10.1101/gr.229202 + year: 2002 + URL: http://genome.cshlp.org/content/12/4/656.abstract + eprint: http://genome.cshlp.org/content/12/4/656.full.pdf+html Modified: trunk/packages/cd-hit/trunk/debian/upstream =================================================================== --- trunk/packages/cd-hit/trunk/debian/upstream 2012-02-18 01:17:47 UTC (rev 9701) +++ trunk/packages/cd-hit/trunk/debian/upstream 2012-02-18 01:23:39 UTC (rev 9702) @@ -1,8 +1,8 @@ Contact: Weizhong Li <[email protected]> -DOI: 10.1093/bioinformatics/btl158 +Reference-DOI: 10.1093/bioinformatics/btl158 Homepage: http://weizhong-lab.ucsd.edu/cd-hit/ Name: CD-HIT -PMID: 16731699 +Reference-PMID: 16731699 Reference: author: Weizhong Li, Adam Godzik title: Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Modified: trunk/packages/circos/trunk/debian/upstream =================================================================== --- trunk/packages/circos/trunk/debian/upstream 2012-02-18 01:17:47 UTC (rev 9701) +++ trunk/packages/circos/trunk/debian/upstream 2012-02-18 01:23:39 UTC (rev 9702) @@ -1,4 +1,4 @@ -DOI: 10.1101/gr.092759.109 +Reference-DOI: 10.1101/gr.092759.109 Homepage: http://circos.ca/ Reference: Author: Martin I Krzywinski, Jacqueline E Schein, Inanc Birol, Joseph Connors, Randy Gascoyne, Doug Horsman, Steven J Jones, and Marco A Marra Modified: trunk/packages/clonalframe/trunk/debian/upstream =================================================================== --- trunk/packages/clonalframe/trunk/debian/upstream 2012-02-18 01:17:47 UTC (rev 9701) +++ trunk/packages/clonalframe/trunk/debian/upstream 2012-02-18 01:23:39 UTC (rev 9702) @@ -1,5 +1,5 @@ Contact: Xavier Didelot <[email protected]> -DOI: 10.1534/genetics.106.063305 +Reference-DOI: 10.1534/genetics.106.063305 Homepage: http://www.xavierdidelot.xtreemhost.com/clonalframe.htm Name: ClonalFrame Reference: Modified: trunk/packages/clustalo/trunk/debian/upstream =================================================================== --- trunk/packages/clustalo/trunk/debian/upstream 2012-02-18 01:17:47 UTC (rev 9701) +++ trunk/packages/clustalo/trunk/debian/upstream 2012-02-18 01:23:39 UTC (rev 9702) @@ -1,8 +1,8 @@ Contact: Fabian Sievers (UCD Dublin, Ireland) -DOI: 10.1038/msb.2011.75 +Reference-DOI: 10.1038/msb.2011.75 Homepage: http://www.clustal.org/omega/ Name: Clustal Omega -PMID: 21988835 +Reference-PMID: 21988835 Reference: author: Fabian Sievers, Andreas Wilm, David Dineen, Toby J Gibson, Kevin Karplus, Weizhong Li, Rodrigo Lopez, Hamish McWilliam, Michael Remmert, Johannes Söding, Julie D Thompson and Desmond G Higgins title: Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega Modified: trunk/packages/coils/trunk/debian/upstream =================================================================== --- trunk/packages/coils/trunk/debian/upstream 2012-02-18 01:17:47 UTC (rev 9701) +++ trunk/packages/coils/trunk/debian/upstream 2012-02-18 01:23:39 UTC (rev 9702) @@ -1,6 +1,6 @@ Homepage: http://www.russelllab.org/cgi-bin/coils/coils-svr.pl Name: Coils -PMID: 2031185 +Reference-PMID: 2031185 Reference: Author: A. Lupas, M. Van Dyke, and J. Stock Title: Predicting coiled coils from protein sequences Modified: trunk/packages/dialign/trunk/debian/upstream =================================================================== --- trunk/packages/dialign/trunk/debian/upstream 2012-02-18 01:17:47 UTC (rev 9701) +++ trunk/packages/dialign/trunk/debian/upstream 2012-02-18 01:23:39 UTC (rev 9702) @@ -1,7 +1,7 @@ -DOI: 10.1093/bioinformatics/15.3.211 +Reference-DOI: 10.1093/bioinformatics/15.3.211 Name: DIALIGN Homepage: http://dialign.gobics.de/ -PMID: 10222408 +Reference-PMID: 10222408 Reference: Author: Morgenstern, B Title: DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment Modified: trunk/packages/dialign-t/trunk/debian/upstream =================================================================== --- trunk/packages/dialign-t/trunk/debian/upstream 2012-02-18 01:17:47 UTC (rev 9701) +++ trunk/packages/dialign-t/trunk/debian/upstream 2012-02-18 01:23:39 UTC (rev 9702) @@ -1,7 +1,7 @@ Contact: Amarendran R. Subramanian <[email protected]> -DOI: 10.1186/1748-7188-3-6 +Reference-DOI: 10.1186/1748-7188-3-6 Homepage: http://dialign-tx.gobics.de/ -PMID: 18505568 +Reference-PMID: 18505568 Name: DIALIGN-T Reference: AUTHOR: Subramanian, Amarendran and Kaufmann, Michael and Morgenstern, Burkhard Modified: trunk/packages/epigrass/trunk/debian/upstream =================================================================== --- trunk/packages/epigrass/trunk/debian/upstream 2012-02-18 01:17:47 UTC (rev 9701) +++ trunk/packages/epigrass/trunk/debian/upstream 2012-02-18 01:23:39 UTC (rev 9702) @@ -1,18 +1,16 @@ Contact: Flavio Codeco Coelho <[email protected]> -DOI: 10.1186/1751-0473-3-3 Homepage: http://epigrass.sourceforge.net/ Name: EpiGrass Watch: http://pypi.python.org/packages/source/e/epigrass/epigrass-(.*).tar.gz -PMID: 18302744 Reference: author: Coelho, Flavio and Cruz, Oswaldo and Codeco, Claudia + DOI: 10.1186/1751-0473-3-3 title: Epigrass: a tool to study disease spread in complex networks journal: Source Code for Biology and Medicine volume: 3 year: 2008 number: 1 pages: 3 + PMID: 18302744 URL: http://www.scfbm.org/content/3/1/3 ISSN: 1751-0473 -} - Modified: trunk/packages/exonerate/trunk/debian/upstream =================================================================== --- trunk/packages/exonerate/trunk/debian/upstream 2012-02-18 01:17:47 UTC (rev 9701) +++ trunk/packages/exonerate/trunk/debian/upstream 2012-02-18 01:23:39 UTC (rev 9702) @@ -1,8 +1,8 @@ Contact: Guy St.C. Slater <guy AT ebi.ac.uk> -DOI: 10.1186/1471-2105-6-31 +Reference-DOI: 10.1186/1471-2105-6-31 Name: Exonerate Homepage: http://www.ebi.ac.uk/~guy/exonerate/ -PMID: 15713233 +Reference-PMID: 15713233 Reference: Author: Slater, Guy and Birney, Ewan Title: Automated generation of heuristics for biological sequence comparison Modified: trunk/packages/gassst/trunk/debian/upstream =================================================================== --- trunk/packages/gassst/trunk/debian/upstream 2012-02-18 01:17:47 UTC (rev 9701) +++ trunk/packages/gassst/trunk/debian/upstream 2012-02-18 01:23:39 UTC (rev 9702) @@ -1,5 +1,5 @@ Contact: Dominique Lavanier <[email protected]> -DOI: 10.1093/bioinformatics/btq485 +Reference-DOI: 10.1093/bioinformatics/btq485 Homepage: http://www.irisa.fr/symbiose/projects/gassst/ Name: GASSST Reference: Modified: trunk/packages/glam2/trunk/debian/upstream =================================================================== --- trunk/packages/glam2/trunk/debian/upstream 2012-02-18 01:17:47 UTC (rev 9701) +++ trunk/packages/glam2/trunk/debian/upstream 2012-02-18 01:23:39 UTC (rev 9702) @@ -1,8 +1,8 @@ Contact: Martin C Frith <[email protected]> and Timothy L Bailey <[email protected]> -DOI: 10.1371/journal.pcbi.1000071 +Reference-DOI: 10.1371/journal.pcbi.1000071 Homepage: http://bioinformatics.org.au/glam2/ Name: GLAM2 -PMID: 18437229 +Reference-PMID: 18437229 Reference: author: Frith, Martin C. AND Saunders, Neil F. W. AND Kobe, Bostjan AND Bailey, Timothy L. journal: PLoS Comput Biol Modified: trunk/packages/hmmer/trunk/debian/upstream =================================================================== --- trunk/packages/hmmer/trunk/debian/upstream 2012-02-18 01:17:47 UTC (rev 9701) +++ trunk/packages/hmmer/trunk/debian/upstream 2012-02-18 01:23:39 UTC (rev 9702) @@ -1,8 +1,8 @@ Contact: http://selab.janelia.org/people/eddys/contact.html -DOI: 10.1093/bioinformatics/14.9.755 +Reference-DOI: 10.1093/bioinformatics/14.9.755 Name: HMMER Homepage: http://hmmer.janelia.org -PMID: 9918945 +Reference-PMID: 9918945 Reference: Author: Eddy, SR Title: Profile hidden Markov models Modified: trunk/packages/infernal/trunk/debian/upstream =================================================================== --- trunk/packages/infernal/trunk/debian/upstream 2012-02-18 01:17:47 UTC (rev 9701) +++ trunk/packages/infernal/trunk/debian/upstream 2012-02-18 01:23:39 UTC (rev 9702) @@ -1,6 +1,6 @@ -DOI: 10.1093/bioinformatics/btp157 +Reference-DOI: 10.1093/bioinformatics/btp157 Homepage: http://infernal.janelia.org/ -PMID: 19307242 +Reference-PMID: 19307242 Reference: author: Nawrocki, Eric P. and Kolbe, Diana L. and Eddy, Sean R. title: Infernal 1.0: inference of RNA alignments Modified: trunk/packages/kalign/trunk/debian/upstream =================================================================== --- trunk/packages/kalign/trunk/debian/upstream 2012-02-18 01:17:47 UTC (rev 9701) +++ trunk/packages/kalign/trunk/debian/upstream 2012-02-18 01:23:39 UTC (rev 9702) @@ -1,8 +1,8 @@ Contact: Timo Lassmann <[email protected]> -DOI: 10.1093/nar/gkn1006 +Reference-DOI: 10.1093/nar/gkn1006 Name: Kalign Homepage: http://msa.cgb.ki.se -PMID: 19103665 +Reference-PMID: 19103665 Reference: Author: Lassmann, Timo and Frings, Oliver and Sonnhammer, Erik L. L. Journal: Nucl. Acids Res. Modified: trunk/packages/last-align/trunk/debian/upstream =================================================================== --- trunk/packages/last-align/trunk/debian/upstream 2012-02-18 01:17:47 UTC (rev 9701) +++ trunk/packages/last-align/trunk/debian/upstream 2012-02-18 01:23:39 UTC (rev 9702) @@ -1,8 +1,8 @@ Contact: last (ATmark) cbrc (dot) jp -DOI: 10.1093/nar/gkq010 +Reference-DOI: 10.1093/nar/gkq010 Name: LAST Homepage: http://last.cbrc.jp/ -PMID: 20110255 +Reference-PMID: 20110255 Reference: author: Frith, Martin C. and Wan, Raymond and Horton, Paul title: Incorporating sequence quality data into alignment improves DNA read mapping Modified: trunk/packages/libhmsbeagle/trunk/debian/upstream =================================================================== --- trunk/packages/libhmsbeagle/trunk/debian/upstream 2012-02-18 01:17:47 UTC (rev 9701) +++ trunk/packages/libhmsbeagle/trunk/debian/upstream 2012-02-18 01:23:39 UTC (rev 9702) @@ -1,8 +1,8 @@ Contact: Andrew Rambaut <[email protected]> -DOI: 10.1093/sysbio/syr100 +Reference-DOI: 10.1093/sysbio/syr100 Homepage: http://code.google.com/p/beagle-lib Name: beagle-lib -PMID: 21963610 +Reference-PMID: 21963610 Reference: author: Daniel L. Ayres, Aaron Darling, Derrick J. Zwickl, Peter Beerli, Mark T. Holder, Paul O. Lewis, John P. Huelsenbeck, Fredrik Ronquist, David L. Swofford, Michael P. Cummings, Andrew Rambaut and Marc A. Suchard title: BEAGLE: an Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics Modified: trunk/packages/libtfbs-perl/trunk/debian/upstream =================================================================== --- trunk/packages/libtfbs-perl/trunk/debian/upstream 2012-02-18 01:17:47 UTC (rev 9701) +++ trunk/packages/libtfbs-perl/trunk/debian/upstream 2012-02-18 01:23:39 UTC (rev 9702) @@ -1,8 +1,8 @@ Contact: Boris.Lenhard at bccs.uib.no -DOI: 10.1093/bioinformatics/18.8.1135 +Reference-DOI: 10.1093/bioinformatics/18.8.1135 Homepage: http://tfbs.genereg.net/ Name: TFBS -PMID: 12176838 +Reference-PMID: 12176838 Reference-Journal: Bioinformatics Reference-Title: TFBS: Computational framework for transcription factor binding site analysis Reference-Authors: Lenhard, Boris and Wasserman, Wyeth W. Modified: trunk/packages/mafft/trunk/debian/upstream =================================================================== --- trunk/packages/mafft/trunk/debian/upstream 2012-02-18 01:17:47 UTC (rev 9701) +++ trunk/packages/mafft/trunk/debian/upstream 2012-02-18 01:23:39 UTC (rev 9702) @@ -1,8 +1,8 @@ Contact: Kazutaka Katoh <[email protected]> -DOI: 10.1093/bib/bbn013 +Reference-DOI: 10.1093/bib/bbn013 Name: MAFFT Homepage: http://mafft.cbrc.jp/alignment/software/ -PMID: 18372315 +Reference-PMID: 18372315 Reference-Author: Katoh, Kazutaka and Toh, Hiroyuki Reference-Journal: Brief Bioinform Reference-Number: 4 Modified: trunk/packages/maq/trunk/debian/upstream =================================================================== --- trunk/packages/maq/trunk/debian/upstream 2012-02-18 01:17:47 UTC (rev 9701) +++ trunk/packages/maq/trunk/debian/upstream 2012-02-18 01:23:39 UTC (rev 9702) @@ -1,10 +1,10 @@ Archive: SourceForge Contact: Heng Li <[email protected]> -DOI: 10.1101/gr.078212.108 +Reference-DOI: 10.1101/gr.078212.108 FAQ: http://maq.sourceforge.net/faq.shtml Name: Maq Homepage: http://maq.sourceforge.net/ -PMID: 18714091 +Reference-PMID: 18714091 Reference: author: Li, Heng and Ruan, Jue and Durbin, Richard title: Mapping short DNA sequencing reads and calling variants using mapping quality scores Modified: trunk/packages/maude/trunk/debian/upstream =================================================================== --- trunk/packages/maude/trunk/debian/upstream 2012-02-18 01:17:47 UTC (rev 9701) +++ trunk/packages/maude/trunk/debian/upstream 2012-02-18 01:23:39 UTC (rev 9702) @@ -1,5 +1,5 @@ Contact: Richard J. Wagner -DOI: 10.1145/272991.272995 +Reference-DOI: 10.1145/272991.272995 Homepage: http://www-personal.umich.edu/~wagnerr/MersenneTwister.html Name: Mersenne Twister Random Number Generator Reference: Modified: trunk/packages/melting/trunk/debian/upstream =================================================================== --- trunk/packages/melting/trunk/debian/upstream 2012-02-18 01:17:47 UTC (rev 9701) +++ trunk/packages/melting/trunk/debian/upstream 2012-02-18 01:23:39 UTC (rev 9702) @@ -1,8 +1,8 @@ Contact: Nicolas Le Novère <[email protected]> -DOI: 10.1093/bioinformatics/17.12.1226 +Reference-DOI: 10.1093/bioinformatics/17.12.1226 Homepage: http://www.ebi.ac.uk/compneur-srv/melting/ Name: MELTING -PMID: 11751232 +Reference-PMID: 11751232 Reference: author: Le Novère, Nicolas title: MELTING, computing the melting temperature of nucleic acid duplex Modified: trunk/packages/mgltools/autodocktools/trunk/debian/upstream =================================================================== --- trunk/packages/mgltools/autodocktools/trunk/debian/upstream 2012-02-18 01:17:47 UTC (rev 9701) +++ trunk/packages/mgltools/autodocktools/trunk/debian/upstream 2012-02-18 01:23:39 UTC (rev 9702) @@ -1,8 +1,8 @@ Donation: http://autodock.scripps.edu/downloads/autodock-registration/autodock-4-2-download-page/ -DOI: 10.1002/jcc.21256 +Reference-DOI: 10.1002/jcc.21256 Homepage: http://autodock.scripps.edu/ Name: AutoDockTools -PMID: 19399780 +Reference-PMID: 19399780 Reference: Author: Garrett M. Morris, Ruth Huey, William Lindstrom, Michel F. Sanner, Richard K. Belew, David S. Goodsell and Arthur J. Olson. Title: AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility Modified: trunk/packages/mothur/trunk/debian/upstream =================================================================== --- trunk/packages/mothur/trunk/debian/upstream 2012-02-18 01:17:47 UTC (rev 9701) +++ trunk/packages/mothur/trunk/debian/upstream 2012-02-18 01:23:39 UTC (rev 9702) @@ -1,7 +1,7 @@ Contact: Patrick D. Schloss <[email protected]> -DOI: 10.1128/AEM.01541-09 +Reference-DOI: 10.1128/AEM.01541-09 Homepage: http://www.mothur.org -PMID: 19801464 +Reference-PMID: 19801464 Name: Mothur Reference: AUTHOR: Schloss, P.D., et al. Modified: trunk/packages/mustang/trunk/debian/upstream =================================================================== --- trunk/packages/mustang/trunk/debian/upstream 2012-02-18 01:17:47 UTC (rev 9701) +++ trunk/packages/mustang/trunk/debian/upstream 2012-02-18 01:23:39 UTC (rev 9702) @@ -1,8 +1,8 @@ Contact: Arun S. Konagurthu (http://www.csse.unimelb.edu.au/~arun) -DOI: 10.1002/prot.20921 +Reference-DOI: 10.1002/prot.20921 Homepage: http://www.cs.mu.oz.au/~arun/mustang/ Name: MUSTANG -PMID: 16736488 +Reference-PMID: 16736488 Reference: Author: Arun S. Konagurthu, James C. Whisstock, Peter J. Stuckey and Arthur M. Lesk Title: MUSTANG: A multiple structural alignment algorithm Modified: trunk/packages/phy-spread/trunk/debian/upstream =================================================================== --- trunk/packages/phy-spread/trunk/debian/upstream 2012-02-18 01:17:47 UTC (rev 9701) +++ trunk/packages/phy-spread/trunk/debian/upstream 2012-02-18 01:23:39 UTC (rev 9702) @@ -1,8 +1,8 @@ Contact: Filip Bielejec <[email protected]> -DOI: 10.1093/bioinformatics/btr481 +Reference-DOI: 10.1093/bioinformatics/btr481 Homepage: http://www.kuleuven.be/aidslab/phylogeography/SPREAD.html Name: SPREAD -PMID: 21911333 +Reference-PMID: 21911333 Reference: author: Filip Bielejec, Andrew Rambaut, Marc A. Suchard and Philippe Lemey title: SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics Modified: trunk/packages/poa/trunk/debian/upstream =================================================================== --- trunk/packages/poa/trunk/debian/upstream 2012-02-18 01:17:47 UTC (rev 9701) +++ trunk/packages/poa/trunk/debian/upstream 2012-02-18 01:23:39 UTC (rev 9702) @@ -1,8 +1,8 @@ Contact: Christopher Lee <[email protected]> -DOI: 10.1093/bioinformatics/bth126 +Reference-DOI: 10.1093/bioinformatics/bth126 Homepage: http://www.bioinformatics.ucla.edu/poa Name: POA -PMID: 14962922 +Reference-PMID: 14962922 Reference: author: Grasso, Catherine and Lee, Christopher title: Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problems Modified: trunk/packages/primer3/trunk/debian/upstream =================================================================== --- trunk/packages/primer3/trunk/debian/upstream 2012-02-18 01:17:47 UTC (rev 9701) +++ trunk/packages/primer3/trunk/debian/upstream 2012-02-18 01:23:39 UTC (rev 9702) @@ -1,7 +1,7 @@ Contact: Steve Rozen (http://purl.com/STEVEROZEN/) Homepage: http://primer3.sourceforge.net Name: Primer3 -PMID: 10547847 +Reference-PMID: 10547847 Reference: Author: Steve Rozen and Helen J. Skaletsky Year: 2000 Modified: trunk/packages/probalign/trunk/debian/upstream =================================================================== --- trunk/packages/probalign/trunk/debian/upstream 2012-02-18 01:17:47 UTC (rev 9701) +++ trunk/packages/probalign/trunk/debian/upstream 2012-02-18 01:23:39 UTC (rev 9702) @@ -1,7 +1,7 @@ Contact: Usman Roshan <[email protected]> -DOI: 10.1093/bioinformatics/btl472 +Reference-DOI: 10.1093/bioinformatics/btl472 Homepage: http://cs.njit.edu/usman/probalign/ -PMID: 16954142 +Reference-PMID: 16954142 Name: Probalign Reference: AUTHOR: Usman Roshan, Dennis R. Livesay Modified: trunk/packages/probcons/trunk/debian/upstream =================================================================== --- trunk/packages/probcons/trunk/debian/upstream 2012-02-18 01:17:47 UTC (rev 9701) +++ trunk/packages/probcons/trunk/debian/upstream 2012-02-18 01:23:39 UTC (rev 9702) @@ -1,8 +1,8 @@ Contact: Chuong Do <[email protected]> -DOI: 10.1101/gr.2821705 +Reference-DOI: 10.1101/gr.2821705 Homepage: http://probcons.stanford.edu/ Name: ProbCons -PMID: 15687296 +Reference-PMID: 15687296 Reference: author: Do, Chuong B. and Mahabhashyam, Mahathi S.P. and Brudno, Michael and Batzoglou, Serafim title: ProbCons: Probabilistic consistency-based multiple sequence alignment Modified: trunk/packages/proda/trunk/debian/upstream =================================================================== --- trunk/packages/proda/trunk/debian/upstream 2012-02-18 01:17:47 UTC (rev 9701) +++ trunk/packages/proda/trunk/debian/upstream 2012-02-18 01:23:39 UTC (rev 9702) @@ -1,7 +1,7 @@ -DOI: 10.1093/nar/gkl511 +Reference-DOI: 10.1093/nar/gkl511 Name: ProDA Homepage: http://proda.stanford.edu/ -PMID: 17068081 +Reference-PMID: 17068081 Reference: author: Phuong, Tu Minh and Do, Chuong B. and Edgar, Robert C. and Batzoglou, Serafim title: Multiple alignment of protein sequences with repeats and rearrangements Modified: trunk/packages/python-pynast/trunk/debian/upstream =================================================================== --- trunk/packages/python-pynast/trunk/debian/upstream 2012-02-18 01:17:47 UTC (rev 9701) +++ trunk/packages/python-pynast/trunk/debian/upstream 2012-02-18 01:23:39 UTC (rev 9702) @@ -1,7 +1,7 @@ Name: PyNAST Homepage: http://pynast.sourceforge.net/ -DOI: 10.1093/bioinformatics/btp636 -PMID: 19914921 +Reference-DOI: 10.1093/bioinformatics/btp636 +Reference-PMID: 19914921 Reference: Author: J. Gregory Caporaso, Kyle Bittinger, Frederic D. Bushman, Todd Z. DeSantis, Gary L. Andersen, and Rob Knight Title: PyNAST: a flexible tool for aligning sequences to a template alignment Modified: trunk/packages/qiime/trunk/debian/upstream =================================================================== --- trunk/packages/qiime/trunk/debian/upstream 2012-02-18 01:17:47 UTC (rev 9701) +++ trunk/packages/qiime/trunk/debian/upstream 2012-02-18 01:23:39 UTC (rev 9702) @@ -1,7 +1,7 @@ Name: QIIME Homepage: http://www.qiime.org/ -DOI: 10.1038/nmeth.f.303 -PMID: 20383131 +Reference-DOI: 10.1038/nmeth.f.303 +Reference-PMID: 20383131 Reference: Author: Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R. Title: QIIME allows analysis of high-throughput community sequencing data Modified: trunk/packages/raster3d/trunk/debian/upstream =================================================================== --- trunk/packages/raster3d/trunk/debian/upstream 2012-02-18 01:17:47 UTC (rev 9701) +++ trunk/packages/raster3d/trunk/debian/upstream 2012-02-18 01:23:39 UTC (rev 9702) @@ -1,6 +1,6 @@ Homepage: http://skuld.bmsc.washington.edu/raster3d/ Name: Raster3D -PMID: 18488322 +Reference-PMID: 18488322 Reference: Article: MerrittBacon1997 Author: Merritt, E.A. and Bacon, D.J. Modified: trunk/packages/raxml/trunk/debian/upstream =================================================================== --- trunk/packages/raxml/trunk/debian/upstream 2012-02-18 01:17:47 UTC (rev 9701) +++ trunk/packages/raxml/trunk/debian/upstream 2012-02-18 01:23:39 UTC (rev 9702) @@ -1,8 +1,8 @@ Contact: Alexandros Stamatakis <[email protected]> -DOI: 10.1093/bioinformatics/btl446 +Reference-DOI: 10.1093/bioinformatics/btl446 Homepage: http://wwwkramer.in.tum.de/exelixis/software.html Name: RAxML -PMID: 16928733 +Reference-PMID: 16928733 Reference: author: 16928733 title: RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models Modified: trunk/packages/rnahybrid/trunk/debian/upstream =================================================================== --- trunk/packages/rnahybrid/trunk/debian/upstream 2012-02-18 01:17:47 UTC (rev 9701) +++ trunk/packages/rnahybrid/trunk/debian/upstream 2012-02-18 01:23:39 UTC (rev 9702) @@ -1,7 +1,7 @@ -DOI: 10.1261/rna.5248604 +Reference-DOI: 10.1261/rna.5248604 Homepage: http://bibiserv.techfak.uni-bielefeld.de/rnahybrid Name: RNAhybrid -PMID: 15383676 +Reference-PMID: 15383676 Reference: author: REHMSMEIER, MARC and STEFFEN, PETER and HÖCHSMANN, MATTHIAS and GIEGERICH, ROBERT title: Fast and effective prediction of microRNA/target duplexes Modified: trunk/packages/rostlab/libzerg/trunk/debian/upstream =================================================================== --- trunk/packages/rostlab/libzerg/trunk/debian/upstream 2012-02-18 01:17:47 UTC (rev 9701) +++ trunk/packages/rostlab/libzerg/trunk/debian/upstream 2012-02-18 01:23:39 UTC (rev 9702) @@ -1,5 +1,5 @@ Contact: Apuã Paquola <[email protected]> -DOI: 10.1093/bioinformatics/btg122 +Reference-DOI: 10.1093/bioinformatics/btg122 Homepage: http://code.google.com/p/libzerg/ Name: libzerg Reference: Modified: trunk/packages/rostlab/libzerg-perl/trunk/debian/upstream =================================================================== --- trunk/packages/rostlab/libzerg-perl/trunk/debian/upstream 2012-02-18 01:17:47 UTC (rev 9701) +++ trunk/packages/rostlab/libzerg-perl/trunk/debian/upstream 2012-02-18 01:23:39 UTC (rev 9702) @@ -1,5 +1,5 @@ Contact: Apuã Paquola <[email protected]> -DOI: 10.1093/bioinformatics/btg122 +Reference-DOI: 10.1093/bioinformatics/btg122 Homepage: http://code.google.com/p/libzerg/ Name: libzerg-perl Reference: Modified: trunk/packages/seqan/trunk/debian/upstream =================================================================== --- trunk/packages/seqan/trunk/debian/upstream 2012-02-18 01:17:47 UTC (rev 9701) +++ trunk/packages/seqan/trunk/debian/upstream 2012-02-18 01:23:39 UTC (rev 9702) @@ -1,9 +1,9 @@ Contact: SeqAn Team (http://www.seqan.de/contact-us.html) -DOI: 10.1186/1471-2105-9-11 +Reference-DOI: 10.1186/1471-2105-9-11 Donate: http://www.seqan.de/ Homepage: http://www.seqan.de/ Name: SeqAn -PMID: 18184432 +Reference-PMID: 18184432 Reference: AUTHOR: Doring, Andreas and Weese, David and Rausch, Tobias and Reinert, Knut TITLE: SeqAn An efficient, generic C++ library for sequence analysis Modified: trunk/packages/sigma-align/trunk/debian/upstream =================================================================== --- trunk/packages/sigma-align/trunk/debian/upstream 2012-02-18 01:17:47 UTC (rev 9701) +++ trunk/packages/sigma-align/trunk/debian/upstream 2012-02-18 01:23:39 UTC (rev 9702) @@ -1,7 +1,7 @@ Contact: Rahul Siddharthan <rsidd AT imsc.res.in> -DOI: 10.1186/1471-2105-7-143 +Reference-DOI: 10.1186/1471-2105-7-143 Homepage: http://www.imsc.res.in/~rsidd/sigma/ -PMID: 16542424 +Reference-PMID: 16542424 Name: Sigma Reference: AUTHOR: Siddharthan, Rahul Modified: trunk/packages/t-coffee/trunk/debian/upstream =================================================================== --- trunk/packages/t-coffee/trunk/debian/upstream 2012-02-18 01:17:47 UTC (rev 9701) +++ trunk/packages/t-coffee/trunk/debian/upstream 2012-02-18 01:23:39 UTC (rev 9702) @@ -1,8 +1,8 @@ Contact: Cédric Notredame <[email protected]> -DOI: 10.1006/jmbi.2000.4042 +Reference-DOI: 10.1006/jmbi.2000.4042 Name: T-Coffee Homepage: http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html -PMID: 10964570 +Reference-PMID: 10964570 Reference-Author: Cédric Notredame and Desmond G. Higgins and Jaap Heringa Reference-Journal: Journal of Molecular Biology Reference-Number: 1 Modified: trunk/packages/tm-align/trunk/debian/upstream =================================================================== --- trunk/packages/tm-align/trunk/debian/upstream 2012-02-18 01:17:47 UTC (rev 9701) +++ trunk/packages/tm-align/trunk/debian/upstream 2012-02-18 01:23:39 UTC (rev 9702) @@ -1,7 +1,7 @@ Contact: Yang Zhang <[email protected]> -DOI: 10.1093/nar/gki524 +Reference-DOI: 10.1093/nar/gki524 Homepage: http://zhanglab.ccmb.med.umich.edu/TM-align/ -PMID: 15849316 +Reference-PMID: 15849316 Name: TM-align & TM-score Reference: AUTHOR: Y. Zhang, J. Skolnick Modified: trunk/packages/transtermhp/trunk/debian/upstream =================================================================== --- trunk/packages/transtermhp/trunk/debian/upstream 2012-02-18 01:17:47 UTC (rev 9701) +++ trunk/packages/transtermhp/trunk/debian/upstream 2012-02-18 01:23:39 UTC (rev 9702) @@ -1,7 +1,7 @@ Contact: Carl Kingsford <[email protected]> -DOI: 10.1186/gb-2007-8-2-r22 +Reference-DOI: 10.1186/gb-2007-8-2-r22 Homepage: http://transterm.cbcb.umd.edu/ -PMID: 17313685 +Reference-PMID: 17313685 Name: TransTermHP Reference: AUTHOR: C. Kingsford, K. Ayanbule, S.L. Salzberg Modified: trunk/packages/velvet/trunk/debian/upstream =================================================================== --- trunk/packages/velvet/trunk/debian/upstream 2012-02-18 01:17:47 UTC (rev 9701) +++ trunk/packages/velvet/trunk/debian/upstream 2012-02-18 01:23:39 UTC (rev 9702) @@ -1,8 +1,8 @@ Contact: Daniel Zerbino <[email protected]> -DOI: 10.1101/gr.074492.107 +Reference-DOI: 10.1101/gr.074492.107 Homepage: http://www.ebi.ac.uk/~zerbino/velvet/ Name: Velvet -PMID: 18349386 +Reference-PMID: 18349386 Reference: author: Zerbino, Daniel R. and Birney, Ewan title: Velvet: Algorithms for de novo short read assembly using de Bruijn graphs _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
