[Collab-qa-commits] r2283 - in packages-metadata: c d g h l n p r
Charles Plessy
plessy at alioth.debian.org
Tue May 8 03:00:31 UTC 2012
Author: plessy
Date: 2012-05-08 03:00:31 +0000 (Tue, 08 May 2012)
New Revision: 2283
Added:
packages-metadata/c/cp2k.upstream
packages-metadata/p/python-cogent.upstream
packages-metadata/p/python-pynast.copyright
packages-metadata/p/python-pynast.upstream
Modified:
packages-metadata/c/circos.upstream
packages-metadata/c/coils.upstream
packages-metadata/d/disulfinder.upstream
packages-metadata/g/gausssum.upstream
packages-metadata/g/gspiceui.copyright
packages-metadata/h/hhsuite.upstream
packages-metadata/l/last-align.copyright
packages-metadata/l/libsbml.upstream
packages-metadata/l/libzerg-perl.upstream
packages-metadata/l/libzerg.upstream
packages-metadata/n/ncbi-tools6.upstream
packages-metadata/p/pixelmed.copyright
packages-metadata/p/profphd.upstream
packages-metadata/p/pymvpa.upstream
packages-metadata/r/rnahybrid.upstream
Log:
Daily automatic umegaya push
Modified: packages-metadata/c/circos.upstream
===================================================================
--- packages-metadata/c/circos.upstream 2012-05-07 22:12:18 UTC (rev 2282)
+++ packages-metadata/c/circos.upstream 2012-05-08 03:00:31 UTC (rev 2283)
@@ -1,6 +1,6 @@
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
+ Author: Martin I Krzywinski and Jacqueline E Schein and Inanc Birol and Joseph Connors and Randy Gascoyne and Doug Horsman and Steven J Jones and Marco A Marra
Title: >
Circos: An information aesthetic for comparative genomics
Journal: Genome Research
Modified: packages-metadata/c/coils.upstream
===================================================================
--- packages-metadata/c/coils.upstream 2012-05-07 22:12:18 UTC (rev 2282)
+++ packages-metadata/c/coils.upstream 2012-05-08 03:00:31 UTC (rev 2283)
@@ -1,7 +1,7 @@
Homepage: http://www.russelllab.org/cgi-bin/coils/coils-svr.pl
Name: Coils
Reference:
- Author: A. Lupas, M. Van Dyke, and J. Stock
+ Author: Andrei Lupas and Marc Van Dyke and Jeff Stock
Title: Predicting coiled coils from protein sequences
Journal: Science
Volume: 252
Added: packages-metadata/c/cp2k.upstream
===================================================================
--- packages-metadata/c/cp2k.upstream (rev 0)
+++ packages-metadata/c/cp2k.upstream 2012-05-08 03:00:31 UTC (rev 2283)
@@ -0,0 +1,63 @@
+Name: CP2K
+Homepage: http://www.cp2k.org
+Other-References: http://manual.cp2k.org/trunk/references.html
+Repository-Browse: http://cp2k.svn.sourceforge.net/viewvc/cp2k/trunk/cp2k/
+Reference:
+ - Title: "CP2K version 2.2.426 (Release Version), the CP2K developers group: http://www.cp2k.org"
+ Year: 2011
+ URL: http://www.cp2k.org
+ - Author: VandeVondele, J and Krack, M and Mohamed, F and Parrinello, M and Chassaing, T and Hutter, J
+ Title: "QUICKSTEP: Fast and accurate density functional calculations using a mixed Gaussian and plane waves approach"
+ Journal: Comp. Phys. Comm.
+ Year: 2005
+ Volume: 167
+ Number: 2
+ Pages: 103-128
+ DOI: 10.1016/j.cpc.2004.12.014
+ URL: http://www.sciencedirect.com/science/article/pii/S0010465505000615
+ - Author: Kuhne, TD and Krack, M and Mohamed, FR and Parrinello, M
+ Title: "Efficient and accurate Car-Parrinello-like approach to Born-Oppenheimer molecular dynamics"
+ Journal: Phys. Rev. Lett.
+ Year: 2007
+ Volume: 98
+ Number: 6
+ Pages: 066401
+ DOI: 10.1103/PhysRevLett.98.066401
+ URL: http://prl.aps.org/abstract/PRL/v98/i6/e066401
+ - Author: Lippert, G and Hutter, J and Parrinello, M
+ Title: "A hybrid Gaussian and plane wave density functional scheme"
+ Journal: Mol. Phys.
+ Year: 1997
+ Volume: 92
+ Number: 3
+ Pages: 447-487
+ DOI: 10.1080/002689797170220
+ URL: http://www.tandfonline.com/doi/abs/10.1080/002689797170220
+ - Author: Lippert, G and Hutter, J and Parrinello, M
+ Title: "The Gaussian and augmented-plane-wave density functional method for ab initio molecular dynamics simulations"
+ Journal: Theo. Chem. Acc.
+ Year: 1999
+ Volume: 103
+ Number: 2
+ Pages: 124-140
+ DOI: 10.1007/s002140050523
+ URL: http://www.springerlink.com/content/7f52yxb1qy4nqawb/
+ - Author: Guidon, M and Schiffmann, F and Hutter, J and VandeVondele, J
+ Title: "Ab initio molecular dynamics using hybrid density functionals"
+ Journal: J. Chem. Phys.
+ Year: 2008
+ Volume: 128
+ Number: 21
+ Pages: 214104
+ DOI: 10.1063/1.2931945
+ URL: http://jcp.aip.org/resource/1/jcpsa6/v128/i21/p214104_s1
+ - Author: Krack, M and Parrinello, M
+ Title: "All-electron ab-initio molecular dynamics"
+ Journal: Phys. Chem. Chem. Phys.
+ Year: 2000
+ Volume: 2
+ Number: 10
+ Pages: 2105-2112
+ DOI: 10.1039/b001167n
+ URL: http://pubs.rsc.org/en/Content/ArticleLanding/2000/CP/b001167n
+ Eprint: http://pubs.rsc.org/en/content/articlepdf/2000/cp/b001167n
Modified: packages-metadata/d/disulfinder.upstream
===================================================================
--- packages-metadata/d/disulfinder.upstream 2012-05-07 22:12:18 UTC (rev 2282)
+++ packages-metadata/d/disulfinder.upstream 2012-05-08 03:00:31 UTC (rev 2283)
@@ -10,7 +10,7 @@
URL: http://www.ncbi.nlm.nih.gov/pubmed/16844986
PMID: 16844986
- Comment: For the disulphide connectivity predictor
- Author: Vullo, Alessandro, and Frasconi, Paolo
+ Author: Alessandro Vullo and Paolo Frasconi
Title: Disulfide connectivity prediction using recursive neural networks and evolutionary information.
Journal: Bioinformatics
Volume: 20
@@ -20,14 +20,14 @@
Month: March
PMID: 15033872
- Comment: For the cystein bonding state predictor
- Author: A. Ceroni, P. Frasconi, A. Passerini and A. Vullo
+ Author: A. Ceroni and P. Frasconi and A. Passerini and A. Vullo
Title: Predicting the Disulfide Bonding State of Cysteines with Combinations of Kernel Machines
Journal: Journal of VLSI Signal Processing
Volume: 35
Pages: 287-295
Year: 2003
- Comment: For the cystein bonding state predictor
- Author: P. Frasconi, A. Passerini and A. Vullo
+ Author: P. Frasconi and A. Passerini and A. Vullo
Title: A Two-Stage SVM Architecture for Predicting the Disulfide Bonding State of Cysteines
Journal: Proc. IEEE Workshop on Neural Networks for Signal Processing
Pages: 25-34
Modified: packages-metadata/g/gausssum.upstream
===================================================================
--- packages-metadata/g/gausssum.upstream 2012-05-07 22:12:18 UTC (rev 2282)
+++ packages-metadata/g/gausssum.upstream 2012-05-08 03:00:31 UTC (rev 2283)
@@ -1,6 +1,6 @@
Name: GaussSum
Reference:
- - Author: Noel M. O'Boyle, Adam L. Tenderholt, Karol M. Langner
+ - Author: Noel M. O'Boyle and Adam L. Tenderholt and Karol M. Langner
Title: "cclib: A library for package-independent computational chemistry algorithms"
Journal: J. Comp. Chem.
Year: 2008
Modified: packages-metadata/g/gspiceui.copyright
===================================================================
--- packages-metadata/g/gspiceui.copyright 2012-05-07 22:12:18 UTC (rev 2282)
+++ packages-metadata/g/gspiceui.copyright 2012-05-08 03:00:31 UTC (rev 2283)
@@ -1,21 +1,32 @@
-This package was debianized by Gudjon I. Gudjonsson <gudjon at gudjon.org> on
-Sat, 25 Aug 2007 13:20:22 +0200.
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Source: ftp://ftp.geda.seul.org/pub/geda/dist/
-It was downloaded from
- ftp://ftp.geda.seul.org/pub/geda/dist/
+Files: *
+Copyright: 2003-2011 Mike Waters <M.Waters at bom.gov.au>
+License: GPL-2
-Upstream Author:
- Mike Waters <M.Waters at bom.gov.au>
+Files: debian/*
+Copyright: 2007-2012 Gudjon I. Gudjonsson <gudjon at gudjon.org>
+License: GPL-2
-Copyright:
- Copyright © 2003-2006 Mike Waters
+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
+ version 2.
+ .
+ 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 package; if not, write to the Free
+ Software Foundation, Inc., 51 Franklin St, Fifth Floor,
+ Boston, MA 02110-1301 USA
+ .
+ On Debian systems, the full text of the GNU General Public
+ License version 2 can be found in the file
+ `/usr/share/common-licenses/GPL-2'.
-License:
- GNU GENERAL PUBLIC LICENSE
- Version 2, June 1991
-
- On Debian systems, the complete text of the GNU General
- Public License can be found in `/usr/share/common-licenses/GPL'.
-
-The Debian packaging is © 2007, Gudjon I. Gudjonsson <gudjon at gudjon.org> and
-is licensed under the GPL, see `/usr/share/common-licenses/GPL'.
Modified: packages-metadata/h/hhsuite.upstream
===================================================================
--- packages-metadata/h/hhsuite.upstream 2012-05-07 22:12:18 UTC (rev 2282)
+++ packages-metadata/h/hhsuite.upstream 2012-05-08 03:00:31 UTC (rev 2283)
@@ -2,7 +2,7 @@
Contact: Andreas Hauser <hauser at genzentrum.lmu.de>
Homepage: http://toolkit.genzentrum.lmu.de/hhblits
Reference:
- - Author: Remmert M., Biegert A., Hauser A., and Soding J.
+ - Author: Michael Remmert and Andreas Biegert and Andreas Hauser and Johannes Söding
Title: 'HHblits: Lightning-fast iterative protein sequence searching by HMM-HMM alignment.'
Journal: Nat. Methods
DOI: 10.1038/NMETH.1818
@@ -12,7 +12,7 @@
Pages: 173-175
URL: http://www.nature.com/nmeth/journal/v9/n2/full/nmeth.1818.html
PMID: 22198341
- - Author: Söding J.
+ - Author: Johannes Söding
Title: Protein homology detection by HMM-HMM comparison.
Journal: Bioinformatics
Volume: 21
Modified: packages-metadata/l/last-align.copyright
===================================================================
--- packages-metadata/l/last-align.copyright 2012-05-07 22:12:18 UTC (rev 2282)
+++ packages-metadata/l/last-align.copyright 2012-05-08 03:00:31 UTC (rev 2283)
@@ -1,5 +1,5 @@
Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Source: http://last.cbrc.jp/archive/last-189.zip
+Source: http://last.cbrc.jp/archive/
License: GPL-3+
LAST combines GPL-3+ and public domain programs, and links to libc6, libgcc1
and libstdc++6. Its effective license as a whole is therefore GPL-3+.
Modified: packages-metadata/l/libsbml.upstream
===================================================================
--- packages-metadata/l/libsbml.upstream 2012-05-07 22:12:18 UTC (rev 2282)
+++ packages-metadata/l/libsbml.upstream 2012-05-08 03:00:31 UTC (rev 2283)
@@ -1,7 +1,7 @@
Contact: sbml-team at caltech.edu
Name: libSBML
Reference:
- Author: Bornstein, B. J., Keating, S. M., Jouraku, A., and Hucka M.
+ Author: Bornstein, B. J. and Keating, S. M. and Jouraku, A. and Hucka M.
Title: "LibSBML: An API Library for SBML"
Journal: Bioinformatics
Volume: 24
Modified: packages-metadata/l/libzerg-perl.upstream
===================================================================
--- packages-metadata/l/libzerg-perl.upstream 2012-05-07 22:12:18 UTC (rev 2282)
+++ packages-metadata/l/libzerg-perl.upstream 2012-05-08 03:00:31 UTC (rev 2283)
@@ -2,14 +2,14 @@
Homepage: http://code.google.com/p/libzerg/
Name: libzerg-perl
Reference:
- author: Paquola, Apuã C M, Machado, Abimael A, Reis, Eduardo M, Da Silva, Aline M, and Verjovski-Almeida, Sergio
- title: >
- Zerg: a very fast BLAST parser library.
+ author: Paquola, Apuã C M and Machado, Abimael A and Reis, Eduardo M and Da Silva, Aline M and Verjovski-Almeida, Sergio
+ title: "Zerg: a very fast BLAST parser library"
journal: Bioinformatics
volume: 19
number: 8
pages: 1035-6
year: 2003
+ URL: http://bioinformatics.oxfordjournals.org/content/19/8/1035.short
+ eprint: http://bioinformatics.oxfordjournals.org/content/19/8/1035.full.pdf+html
DOI: 10.1093/bioinformatics/btg122
- URL: http://code.google.com/p/libzerg/
PMID: 12761068
Modified: packages-metadata/l/libzerg.upstream
===================================================================
--- packages-metadata/l/libzerg.upstream 2012-05-07 22:12:18 UTC (rev 2282)
+++ packages-metadata/l/libzerg.upstream 2012-05-08 03:00:31 UTC (rev 2283)
@@ -1,14 +1,15 @@
Contact: Apuã Paquola <apuapaquola at gmail.com>
-Reference-DOI: 10.1093/bioinformatics/btg122
Homepage: http://code.google.com/p/libzerg/
Name: libzerg
Reference:
- author: Paquola, Apuã C M, Machado, Abimael A, Reis, Eduardo M, Da Silva, Aline M, and Verjovski-Almeida, Sergio
- title: "Zerg: a very fast BLAST parser library."
+ author: Paquola, Apuã C M and Machado, Abimael A and Reis, Eduardo M and Da Silva, Aline M and Verjovski-Almeida, Sergio
+ title: "Zerg: a very fast BLAST parser library"
journal: Bioinformatics
volume: 19
number: 8
pages: 1035-6
year: 2003
- URL: http://www.ncbi.nlm.nih.gov/pubmed/12761068
+ URL: http://bioinformatics.oxfordjournals.org/content/19/8/1035.short
+ eprint: http://bioinformatics.oxfordjournals.org/content/19/8/1035.full.pdf+html
+ DOI: 10.1093/bioinformatics/btg122
PMID: 12761068
Modified: packages-metadata/n/ncbi-tools6.upstream
===================================================================
--- packages-metadata/n/ncbi-tools6.upstream 2012-05-07 22:12:18 UTC (rev 2282)
+++ packages-metadata/n/ncbi-tools6.upstream 2012-05-08 03:00:31 UTC (rev 2283)
@@ -1,5 +1,5 @@
Reference:
- - Author: Stephen F. Altschul, Warren Gish, Webb Miller, Eugene W. Myers, David J. Lipman
+ - Author: Stephen F. Altschul and Warren Gish and Webb Miller and Eugene W. Myers and David J. Lipman
Title: Basic local alignment search tool
Journal: Journal of Molecular Biology
Volume: 215
@@ -10,7 +10,7 @@
DOI: 10.1016/S0022-2836(05)80360-2
URL: http://www.sciencedirect.com/science/article/pii/S0022283605803602
Debian-Package: blast2
- - Author: Christine Gemünd, Chenna Ramu, Brigitte Altenberg-Greulich, and Toby J. Gibsona
+ - Author: Christine Gemünd and Chenna Ramu and Brigitte Altenberg-Greulich and Toby J. Gibsona
Title: "Gene2EST: a BLAST2 server for searching expressed sequence tag (EST) databases with eukaryotic gene-sized queries"
Journal: Nucleic Acids Res
Year: 2001
Modified: packages-metadata/p/pixelmed.copyright
===================================================================
--- packages-metadata/p/pixelmed.copyright 2012-05-07 22:12:18 UTC (rev 2282)
+++ packages-metadata/p/pixelmed.copyright 2012-05-08 03:00:31 UTC (rev 2283)
@@ -34,7 +34,6 @@
applicable local, state, national or international regulations.
Files: debian/*
-Copyright:
- Copyright 2009-2012, Mathieu Malaterre <malat at debian.org>
+Copyright: 2009-2012, Mathieu Malaterre <malat at debian.org>
License: BSD
Same as above
Modified: packages-metadata/p/profphd.upstream
===================================================================
--- packages-metadata/p/profphd.upstream 2012-05-07 22:12:18 UTC (rev 2282)
+++ packages-metadata/p/profphd.upstream 2012-05-08 03:00:31 UTC (rev 2283)
@@ -18,7 +18,7 @@
Year: 1994
URL: http://www.ncbi.nlm.nih.gov/pubmed/7892171
PMID: 7892171
- - Author: Rost, B., Casadio, R., Fariselli, P., and Sander, C.
+ - Author: Rost, B. and Casadio, R. and Fariselli, P. and Sander, C.
Title: 'Transmembrane helices predicted at 95% accuracy.'
Journal: Protein Sci
Volume: 4
Modified: packages-metadata/p/pymvpa.upstream
===================================================================
--- packages-metadata/p/pymvpa.upstream 2012-05-07 22:12:18 UTC (rev 2282)
+++ packages-metadata/p/pymvpa.upstream 2012-05-08 03:00:31 UTC (rev 2283)
@@ -1,6 +1,6 @@
Name: pymvpa
Reference:
- - Author: Michael Hanke and Yaroslav O. Halchenko and Per B. Sederberg and Stephen Jos{\'e} Hanson and James V. Haxby and Stefan Pollmann
+ - Author: Michael Hanke and Yaroslav O. Halchenko and Per B. Sederberg and Stephen José Hanson and James V. Haxby and Stefan Pollmann
Title: 'PyMVPA: A Python toolbox for multivariate pattern analysis of fMRI data'
Journal: Neuroinformatics
Volume: 7
@@ -10,3 +10,4 @@
URL: http://dx.doi.org/10.1007/s12021-008-9041-y
DOI: 10.1007/s12021-008-9041-y
PMID: 19184561
+ eprint: http://www.springerlink.com/content/n4jm3533pw2661q3/fulltext.pdf
Added: packages-metadata/p/python-cogent.upstream
===================================================================
--- packages-metadata/p/python-cogent.upstream (rev 0)
+++ packages-metadata/p/python-cogent.upstream 2012-05-08 03:00:31 UTC (rev 2283)
@@ -0,0 +1,12 @@
+Reference:
+ Author: Knight, Rob and Maxwell, Peter and Birmingham, Amanda and Carnes, Jason and Caporaso, J Gregory and Easton, Brett C and Eaton, Michael and Hamady, Micah and Lindsay, Helen and Liu, Zongzhi and Lozupone, Catherine and McDonald, Daniel and Robeson, Michael and Sammut, Raymond and Smit, Sandra and Wakefield, Matthew J and Widmann, Jeremy and Wikman, Shandy and Wilson, Stephanie and Ying, Hua and Huttley, Gavin A
+ Title: "PyCogent: a toolkit for making sense from sequence"
+ Journal: Genome Biology
+ Year: 2007
+ Volume: 8
+ Number: 8
+ Pages: R171
+ DOI: 10.1186/gb-2007-8-8-r171
+ PMID: 17708774
+ URL: http://genomebiology.com/2007/8/8/R171
+ eprint: http://genomebiology.com/content/pdf/gb-2007-8-8-r171.pdf
Added: packages-metadata/p/python-pynast.copyright
===================================================================
--- packages-metadata/p/python-pynast.copyright (rev 0)
+++ packages-metadata/p/python-pynast.copyright 2012-05-08 03:00:31 UTC (rev 2283)
@@ -0,0 +1,35 @@
+Format: http://dep.debian.net/deps/dep5/
+Upstream-Name: PyNAST
+Upstream-Contact: Greg Caporaso <gregcaporaso at gmail.com>, Rob Knight <rob at spot.colorado.edu>
+Source: http://pynast.sorceforge.net
+
+Files: *
+Copyright: © 2010, The PyNAST Project
+ Greg Caporaso <gregcaporaso at gmail.com>
+ Kyle Bittinger
+ Rob Knight <rob at spot.colorado.edu>
+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 package; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+ .
+ On Debian systems, the full text of the GNU General Public License
+ version 2 can be found in the file `/usr/share/common-licenses/GPL-2'.
+
+Files: debian/*
+Copyright: © 2010 Sri Girish Srinivasa Murthy <srigirish at evolbio.mpg.de>,
+ © 2011 Steffen Moeller <moeller at debian.org>,
+ Tim Booth <tbooth at ceh.ac.uk>,
+ Andreas Tille <tille at debian.org>
+License: GPL-2
+ Same as the software itself.
Added: packages-metadata/p/python-pynast.upstream
===================================================================
--- packages-metadata/p/python-pynast.upstream (rev 0)
+++ packages-metadata/p/python-pynast.upstream 2012-05-08 03:00:31 UTC (rev 2283)
@@ -0,0 +1,13 @@
+Name: PyNAST
+Homepage: http://pynast.sourceforge.net/
+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
+ Journal: Bioinformatics
+ Volume: 26
+ Pages: 266-267.
+ Year: 2010
+ DOI: 10.1093/bioinformatics/btp636
+ PMID: 19914921
+ URL: http://bioinformatics.oxfordjournals.org/content/26/2/266.long
Modified: packages-metadata/r/rnahybrid.upstream
===================================================================
--- packages-metadata/r/rnahybrid.upstream 2012-05-07 22:12:18 UTC (rev 2282)
+++ packages-metadata/r/rnahybrid.upstream 2012-05-08 03:00:31 UTC (rev 2283)
@@ -1,7 +1,7 @@
Homepage: http://bibiserv.techfak.uni-bielefeld.de/rnahybrid
Name: RNAhybrid
Reference:
- author: Marc Rehmsmeier, Peter Steffen, Matthias Höchsmann, and Robert Giegerich
+ author: Marc Rehmsmeier and Peter Steffen and Matthias Höchsmann and Robert Giegerich
title: Fast and effective prediction of microRNA/target duplexes
journal: RNA
volume: 10
More information about the Collab-qa-commits
mailing list