[Blends-commit] r3246 - in /projects/med/trunk/debian-med/tasks: bio bio-dev bio-ngs bio-phylogeny imaging
tille at users.alioth.debian.org
tille at users.alioth.debian.org
Mon Apr 2 14:06:08 UTC 2012
Author: tille
Date: Mon Apr 2 14:06:07 2012
New Revision: 3246
URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=3246
Log:
Automatically removed those Published-* fields from tasks files that are identical strings in UDD and thus not used. Comparison of other fields will be done in a next step. (automatic replacement also cleaned up some trailing spaces)
Modified:
projects/med/trunk/debian-med/tasks/bio
projects/med/trunk/debian-med/tasks/bio-dev
projects/med/trunk/debian-med/tasks/bio-ngs
projects/med/trunk/debian-med/tasks/bio-phylogeny
projects/med/trunk/debian-med/tasks/imaging
Modified: projects/med/trunk/debian-med/tasks/bio
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/tasks/bio?rev=3246&op=diff
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio (original)
+++ projects/med/trunk/debian-med/tasks/bio Mon Apr 2 14:06:07 2012
@@ -26,7 +26,6 @@
X-Published-Authors: FIXME
X-Published-Title: FIXME
Published-In: Computer Applications in the Bioscience 12:357-358
-Published-Year: 1996
Depends: figtree
@@ -57,26 +56,16 @@
Depends: maqview
Depends: bwa
-Published-Title: Fast and accurate short read alignment with Burrows-Wheeler transform
-Published-Authors: Li, Heng and Durbin, Richard
Published-In: Bioinformatics 25(14):1754-1760
-Published-Year: 2009
-Published-URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/14/1754
Depends: mummer
-Published-Title: Versatile and open software for comparing large genomes
Published-Authors: Stefan Kurtz, Adam Phillippy, Arthur L. Delcher, Michael Smoot, Martin Shumway, Corina Antonescu, Steven L. Salzberg
Published-In: Genome Biol. 5(2):R12
-Published-Year: 2004
Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/14759262
-Published-DOI: 10.1186/gb-2004-5-2-r12
-Published-PubMed: 14759262
Depends: blast2
-Published-Title: Basic local alignment search tool
Published-Authors: S.F. Altschul, W. Gish, W. Miller, E.W. Myers, D.J. Lipman
Published-In: J Mol Biol. 215(3):403-410
-Published-Year: 1990
Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/2231712
Depends: mafft
@@ -91,9 +80,7 @@
Published-Title: T-Coffee: A novel method for multiple sequence alignments
Published-Authors: C. Notredame, D. Higgins, J. Heringa
Published-In: Journal of Molecular Biology 302(1):205-217
-Published-Year: 2000
Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/10964570
-Published-PubMed: 10964570
Remark: Do not update to version 9.0
Version 9.0 contains non-free code. See http://bugs.debian.org/649263.
@@ -113,43 +100,33 @@
Published-URL: ftp://selab.janelia.org/pub/publications/Eddy95b/Eddy95b-preprint.pdf
Depends: exonerate
-Published-Title: Automated generation of heuristics for biological sequence comparison
Published-Authors: G.C. Slater, E. Birney
Published-In: BMC Bioinformatics 6:31
-Published-Year: 2005
Published-URL: http://www.biomedcentral.com/1471-2105/6/31/abstract
-Published-doi: 10.1186/1471-2105-6-31
Depends: dialign
Published-Authors: Burkhard Morgenstern
Published-Title: DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment.
Published-In: Bioinformatics 15(3):211-218
-Published-Year: 1999
Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/10222408
Depends: dialign-tx
Published-Authors: Amarendran R. Subramanian, Michael Kaufmann, Burkhard Morgenstern
Published-Title: Improvement of the segment-based approach for multiple sequence alignment by combining greedy and progressive alignment strategies
Published-In: Algorithms for Molecular Biology 3:6
-Published-Year: 2008
Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/18505568
Depends: poa
Published-Authors: C. Grasso, C. Lee
-Published-Title: Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problems
Published-In: Bioinformatics 20(10):1546-1556.
-Published-Year: 2004
Depends: probcons
Published-Authors: C. B. Do, M. S. P. Mahabhashyam, M. Brudno, S. Batzoglou
Published-In: Genome Research 15: 330-340
-Published-Year: 2005
Depends: proda
Published-Authors: T. M. Phuong, C. B. Do, R. C. Edgar, S. Batzoglou
-Published-Title: Multiple alignment of protein sequences with repeats and rearrangements
Published-In: Nucleic Acids Research 34(20), 5932-5942
-Published-Year: 2006
Depends: seaview
@@ -157,13 +134,11 @@
X-Published-Authors: FIXME
X-Published-Title: FIXME
Published-In: BMC Bioinformatics 16;7:143
-Published-Year: 2006
Depends: emboss
Published-Authors: P. Rice, I. Longden, A. Bleasby
Published-Title: EMBOSS: the European Molecular Biology Open Software Suite.
Published-In: Trends Genet., 16(6):276-277
-Published-Year: 2000
Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/10827456
Depends: embassy-domalign, embassy-domainatrix, embassy-domsearch, embassy-phylip
@@ -177,9 +152,7 @@
Depends: clustalw
Published-Authors: M. Larkin, et al.
-Published-Title: Clustal W and Clustal X version 2.0
Published-In: Bioinformatics 23(21):2947-2948
-Published-Year: 2007
Depends: clustalw-mpi
Comment: Originally the dependency was clustalw | clustalw-mpi but currently it is
@@ -203,17 +176,13 @@
X-Begin-Category: Analysis of RNA sequences.
Depends: infernal
-Published-Authors: Nawrocki, Eric P. and Kolbe, Diana L. and Eddy, Sean R.
-Published-Title: Infernal 1.0: inference of RNA alignments
Published-In: Bioinformatics 15;25(10):1335-7
-Published-Year: 2009
Published-URL: http://bioinformatics.oxfordjournals.org/cgi/content/full/25/10/1335
Depends: rnahybrid
Published-Authors: Marc Rehmsmeier, Peter Steffen, Matthias Höchsmann, Robert Giegerich
Published-Title: Fast and effective prediction of microRNA/target duplexes RNA
Published-In: 10:1507-1517
-Published-Year: 2004
X-Category: Target duplex prediction
X-End-Category: Analysis of RNA sequences.
@@ -224,9 +193,7 @@
Published-Title: Framework Based Design of a New All-Purpose Molecular Simulation Application: The Adun Simulator
Published-Authors: M.A. Johnston, I.F. Galván, J. Villà -Freixa
Published-In: J. Comp. Chem
-Published-Year: 2005
Published-URL: http://www3.interscience.wiley.com/cgi-bin/abstract/112094040/ABSTRACT
-Published-DOI: 10.1002/jcc.20312
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
@@ -259,25 +226,18 @@
Depends: melting
Published-Authors: Nicolas Le Novère
-Published-Title: MELTING, computing the melting temperature of nucleic acid duplex
Published-In: Bioinformatics, 17: S.1226-1227
-Published-Year: 2001
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
-Published-Authors: Aerts J & Veenendaal T.
-Published-Title: MIPE - a XML-format to facilitate the storage and exchange of PCR-related data
Published-In: Online Journal of Bioinformatics 6(2): 114-120
-Published-Year: 2005
Depends: primer3
Published-Authors: S. Rozen, H. Skaletsky
-Published-Title: Primer3 on the WWW for general users and for biologist programmers
Published-In: Methods Mol Biol. 132:365-86
-Published-Year: 2000
X-End-Category: Tools for the molecular biologist.
@@ -298,8 +258,6 @@
Published-Title: Discovering sequence motifs with arbitrary insertions and deletions
Published-Authors: MC Frith, NFW Saunders, B Kobe, TL Bailey
Published-In: PLoS Computational Biology
-Published-Year: 2008
-Published-DOI: 10.1371/journal.pcbi.1000071
Depends: raster3d
@@ -308,12 +266,9 @@
Depends: autodock
Registration: http://autodock.scripps.edu/downloads/autodock-registration
Why: Molecular modelling and molecular dynamics.
-Published-Title: AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
Published-Authors: G.M. Morris, R. Huey, W. Lindstrom, M.F. Sanner, R.K. Belew, D.S. Goodsell, A.J. Olson
Published-In: J. Comput. Chem.
-Published-Year: 2009
Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/19399780
-Published-Pubmed: 19399780
Depends: autogrid
@@ -328,17 +283,13 @@
so they are mentioned here in addition to autodocktools.
.
This was changed by adding Enhances field to the packages in question.
-Published-Title: AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
Published-Authors: G.M. Morris, R. Huey, W. Lindstrom, M.F. Sanner, R.K. Belew, D.S. Goodsell, A.J. Olson
Published-In: J. Comput. Chem.
-Published-Year: 2009
Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/19399780
Depends: mustang
Published-Authors: A. S. Konagurthu, J. C. Whisstock, P. J. Stuckey, A. M. Lesk
-Published-Title: MUSTANG: A multiple structural alignment algorithm
Published-In: Proteins: Structure, Function, and Bioinformatics. 64(3):559-574
-Published-Year: 2006
Depends: theseus
@@ -349,19 +300,13 @@
Depends: gassst
Depends: r-bioc-hilbertvis
-Published-Authors: Simon Anders
Published-Title: Visualization of genomic data with the Hilbert curve
Published-In: Bioinformatics 25(10):1231-1235
-Published-Year: 2009
-Published-DOI: 10.1093/bioinformatics/btp152
Remark: It would be interesting to package HilbertVisGUI (see below) as well.
Depends: r-other-mott-happy
Published-Authors: Richard Mott, Christopher J. Talbot, Maria G. Turri, Allan C. Collins, Jonathan Flint
-Published-Title: A method for fine mapping quantitative trait loci in outbred animal stocks
Published-In: Proc. Natl. Acad. Sci. USA
-Published-Year: 2000
-Published-DOI: 10.1073/pnas.230304397
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.
@@ -369,11 +314,8 @@
Depends: seq-gen
Depends: mira-assembler
-Published-Title: Using the miraEST Assembler for Reliable and Automated mRNA Transcript Assembly and SNP Detection in Sequenced ESTs
Published-Authors: Chevreux B, Pfisterer T, Drescher B, Driesel AJ, Müller WE, Wetter T, Suhai S.
Published-In: Genome Res. Jun;14(6):1147-59.
-Published-Year: 2004
-Published-doi: 10.1101/gr.1917404
Published-URL: http://pubmed.org/15140833
Depends: bagphenotype
@@ -395,10 +337,7 @@
revisiting the Salmonella pathogenicity islands
Published-Authors: GS Vernikos and J. Parkhill
Published-In: Bioinformatics
-Published-Year: 2006
Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/16837528
-Published-DOI: 10.1093/bioinformatics/btl369
-Published-PubMed: 16837528
Suggests: seqan-apps
@@ -407,10 +346,8 @@
Depends: gentle
Depends: gmap
-Published-Title: GMAP: a genomic mapping and alignment program for mRNA and EST sequences
Published-Authors: Thomas D. Wu, Colin K. Watanabe
Published-In: Bioinformatics
-Published-Year: 2005
Published-URL: http://bioinformatics.oupjournals.org/cgi/content/full/21/9/1859
Depends: igv
@@ -434,11 +371,7 @@
Depends: clonalframe
Depends: jellyfish
-Published-Title: A fast, lock-free approach for efficient parallel counting of occurrences of k-mers
-Published-Authors: Guillaume Marcais and Carl Kingsford
Published-In: Bioinformatics
-Published-Year: 2011
-Published-DOI: 10.1093/bioinformatics/btr011
Depends: r-other-genabel
Homepage: http://mga.bionet.nsc.ru/nlru/GenABEL/
@@ -496,7 +429,6 @@
Published-Title: BALLView: a tool for research and education in molecular modeling.
Published-Authors: A. Moll, A. Hildebrandt, H.P.Lenhof, O. Kohlbacher
Published-In: Bioinformatics, 22(3):365-6
-Published-Year: 2006
Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/16332707
Depends: pynast
@@ -517,12 +449,7 @@
Depends: cufflinks
X-References_in_debian_upstream: yes
-Published-Authors: Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, Salzberg SL, Wold B, Pachter L.
-Published-Title: Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
Published-In: Nature Biotechnology
-Published-DOI: doi:10.1038/nbt.1621
-Published-URL: http://www.nature.com/nbt/journal/v28/n5/full/nbt.1621.html
-Published-Year: 2010
Depends: r-bioc-cummerbund
@@ -1788,7 +1715,6 @@
Published-Title: BEAST: Bayesian evolutionary analysis by sampling trees
Published-Authors: A. J. Drummond, A. Rambaut
Published-In: BMC Evolutionary Biology
-Published-Year: 2007
Published-URL: http://www.biomedcentral.com/1471-2148/7/214/abstract
Published-DOI: 10.1186/1471-2148-7-214
Published-PubMed: 17996036
@@ -2961,7 +2887,6 @@
Published-Title: Searching for SNPs with cloud computing
Published-Authors: Ben Langmead, Michael Schatz, Jimmy Lin, Mihai Pop, Steven Salzberg
Published-In: Genome Biology
-Published-Year: 2009
Published-URL: http://genomebiology.com/2009/10/11/R134
Published-DOI: 10.1186/gb-2009-10-11-r134
@@ -3002,15 +2927,10 @@
Published-Authors: Christopher Quince, Anders Lanzen, Russell J Davenport and Peter J Turnbaugh
Published-Title: Removing Noise From Pyrosequenced Amplicons
Published-In: BMC Bioinformatics
-Published-Year: 2001
Published-DOI: 12:38doi:10.1186/1471-2105-12-38
Depends: disulfinder
-Published-Title: DISULFIND: a disulfide bonding state and cysteine connectivity prediction server.
-Published-Authors: A. Ceroni and A. Passerini and A. Vullo and P. Frasconi
Published-In: Nucleic Acids Res. 34:W177-81
-Published-Year: 2006
-Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/16844986
Published-PubMed: 19378139
Suggests: circos
@@ -3027,7 +2947,6 @@
Published-In: BMC Bioinformatics
Published-DOI: doi:10.1186/1471-2105-5-59
Published-URL: http://www.biomedcentral.com/1471-2105/5/59/abstract
-Published-Year: 2004
Depends: vcftools
@@ -3445,7 +3364,6 @@
Published-Title: Tandem repeats finder: a program to analyze DNA sequences
Published-Authors: G. Benson
Published-In: Nucleic Acids Research
-Published-Year: 1999
Depends: rmblast
Homepage: http://tandem.bu.edu/trf/trf.html
Modified: projects/med/trunk/debian-med/tasks/bio-dev
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/tasks/bio-dev?rev=3246&op=diff
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio-dev (original)
+++ projects/med/trunk/debian-med/tasks/bio-dev Mon Apr 2 14:06:07 2012
@@ -20,10 +20,7 @@
beeing forced to deinstall med-bio-dev as well
Depends: python-biopython
-Published-Authors: P.J. Cock, T. Antao, J.T. Chang, B.A. Chapman, C.J. Cox, A. Dalke, I. Friedberg, T. Hamelryck, F. Kauff, B. Wilczynski, M.J. de Hoon
-Published-Title: Biopython: freely available Python tools for computational molecular biology and bioinformatics
Published-In: Bioinformatics, 25(11):1422-1423
-Published-Year: 2009
Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/19304878
Depends: python-cogent
@@ -32,11 +29,7 @@
Depends: libbiojava-java
Published-Authors: R.C.G. Holland, T. Down, M. Pocock, A. Prlić, D. Huen, K. James, S. Foisy, A. Dräger, A. Yates, M. Heuer, M.J. Schreiber
-Published-Title: BioJava: an Open-Source Framework for Bioinformatics
Published-In: Bioinformatics 24(18):2096-2097
-Published-Year: 2008
-Published-URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btn397
-Published-DOI: 10.1093/bioinformatics/btn397
Depends: libqsearch-dev
@@ -51,7 +44,7 @@
Depends: libtfbs-perl
-Depends: libgo-perl
+Depends: libgo-perl
Depends: r-cran-genetics, r-cran-haplo.stats
@@ -191,7 +184,7 @@
Vcs-Browser: http://git.debian.org/?p=debian-med/pysam.git
Pkg-Description: interface for the SAM/BAM sequence alignment and mapping format
Pysam is a python module for reading and manipulating Samfiles. It's a
- lightweight wrapper of the samtools C-API.
+ lightweight wrapper of the samtools C-API.
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.
Modified: projects/med/trunk/debian-med/tasks/bio-ngs
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/tasks/bio-ngs?rev=3246&op=diff
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio-ngs (original)
+++ projects/med/trunk/debian-med/tasks/bio-ngs Mon Apr 2 14:06:07 2012
@@ -34,11 +34,8 @@
Depends: mira-assembler
X-References_in_debian_upstream: yes
-Published-Title: Using the miraEST Assembler for Reliable and Automated mRNA Transcript Assembly and SNP Detection in Sequenced ESTs
Published-Authors: Chevreux B, Pfisterer T, Drescher B, Driesel AJ, Müller WE, Wetter T, Suhai S.
Published-In: Genome Res. Jun;14(6):1147-59.
-Published-Year: 2004
-Published-doi: 10.1101/gr.1917404
Published-URL: http://pubmed.org/15140833
Depends: ssaha2
@@ -102,43 +99,43 @@
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
+ 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
+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
+ (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
+ 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
+ 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,
+ 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
+ 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
+ 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
+ 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.
Modified: projects/med/trunk/debian-med/tasks/bio-phylogeny
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/tasks/bio-phylogeny?rev=3246&op=diff
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio-phylogeny (original)
+++ projects/med/trunk/debian-med/tasks/bio-phylogeny Mon Apr 2 14:06:07 2012
@@ -32,7 +32,6 @@
X-Published-Authors: FIXME
X-Published-Title: FIXME
Published-In: Computer Applications in the Bioscience 12:357-358
-Published-Year: 1996
X-End-Category: Phylogenetic analysis
@@ -50,9 +49,7 @@
Published-Title: T-Coffee: A novel method for multiple sequence alignments
Published-Authors: C. Notredame, D. Higgins, J. Heringa
Published-In: Journal of Molecular Biology 302(1):205-217
-Published-Year: 2000
Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/10964570
-Published-PubMed: 10964570
Depends: kalign
Published-Title: Kalign--an accurate and fast multiple sequence alignment algorithm
@@ -70,43 +67,33 @@
Published-URL: ftp://selab.janelia.org/pub/publications/Eddy95b/Eddy95b-preprint.pdf
Depends: exonerate
-Published-Title: Automated generation of heuristics for biological sequence comparison
Published-Authors: G.C. Slater, E. Birney
Published-In: BMC Bioinformatics 6:31
-Published-Year: 2005
Published-URL: http://www.biomedcentral.com/1471-2105/6/31/abstract
-Published-doi: 10.1186/1471-2105-6-31
Depends: dialign
Published-Authors: Burkhard Morgenstern
Published-Title: DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment.
Published-In: Bioinformatics 15(3):211-218
-Published-Year: 1999
Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/10222408
Depends: dialign-tx
Published-Authors: Amarendran R. Subramanian, Michael Kaufmann, Burkhard Morgenstern
Published-Title: Improvement of the segment-based approach for multiple sequence alignment by combining greedy and progressive alignment strategies
Published-In: Algorithms for Molecular Biology 3:6
-Published-Year: 2008
Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/18505568
Depends: poa
Published-Authors: C. Grasso, C. Lee
-Published-Title: Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problems
Published-In: Bioinformatics 20(10):1546-1556.
-Published-Year: 2004
Depends: probcons
Published-Authors: C. B. Do, M. S. P. Mahabhashyam, M. Brudno, S. Batzoglou
Published-In: Genome Research 15: 330-340
-Published-Year: 2005
Depends: proda
Published-Authors: T. M. Phuong, C. B. Do, R. C. Edgar, S. Batzoglou
-Published-Title: Multiple alignment of protein sequences with repeats and rearrangements
Published-In: Nucleic Acids Research 34(20), 5932-5942
-Published-Year: 2006
Depends: seaview
Published-Authors: N. Galtier, M. Gouy, C. Gautier
@@ -118,13 +105,10 @@
X-Published-Authors: FIXME
X-Published-Title: FIXME
Published-In: BMC Bioinformatics 16;7:143
-Published-Year: 2006
Depends: gmap
-Published-Title: GMAP: a genomic mapping and alignment program for mRNA and EST sequences
Published-Authors: Thomas D. Wu, Colin K. Watanabe
Published-In: Bioinformatics
-Published-Year: 2005
Published-URL: http://bioinformatics.oupjournals.org/cgi/content/full/21/9/1859
Depends: clustalx
@@ -132,9 +116,7 @@
Depends: clustalw
Published-Authors: M. Larkin, et al.
-Published-Title: Clustal W and Clustal X version 2.0
Published-In: Bioinformatics 23(21):2947-2948
-Published-Year: 2007
Depends: clustalw-mpi
Comment: Originally the dependency was clustalw | clustalw-mpi but currently it is
@@ -143,9 +125,7 @@
Depends: mustang
Published-Authors: A. S. Konagurthu, J. C. Whisstock, P. J. Stuckey, A. M. Lesk
-Published-Title: MUSTANG: A multiple structural alignment algorithm
Published-In: Proteins: Structure, Function, and Bioinformatics. 64(3):559-574
-Published-Year: 2006
X-End-Category: Sequence alignments and related programs.
@@ -280,7 +260,6 @@
Published-Title: BEAST: Bayesian evolutionary analysis by sampling trees
Published-Authors: A. J. Drummond, A. Rambaut
Published-In: BMC Evolutionary Biology
-Published-Year: 2007
Published-URL: http://www.biomedcentral.com/1471-2148/7/214/abstract
Published-DOI: 10.1186/1471-2148-7-214
Published-PubMed: 17996036
@@ -323,7 +302,7 @@
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
+ that the DT weights are very gross
Depends: prottest
License: GPL, MIT
Modified: projects/med/trunk/debian-med/tasks/imaging
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/tasks/imaging?rev=3246&op=diff
==============================================================================
--- projects/med/trunk/debian-med/tasks/imaging (original)
+++ projects/med/trunk/debian-med/tasks/imaging Mon Apr 2 14:06:07 2012
@@ -868,7 +868,6 @@
Published-Authors: S. Klein, M. Staring, K. Murphy, M.A. Viergever, J.P.W. Pluim
Published-In: IEEE Transactions on Medical Imaging, vol. 29, no. 1, pp. 196 - 205
Published-Title: elastix: a toolbox for intensity based medical image registration
-Published-Year: 2010
Registration: http://elastix.isi.uu.nl/download.php
; Added by blends-inject 0.0.6. [Please note here if modified manually]
@@ -1187,7 +1186,7 @@
License: GPL
Pkg-Description: coming standard LIMS for microscopy images
OMERO is client-server software for visualisation, management and
- analysis of biological microscope images.
+ analysis of biological microscope images.
X-Comment: More image viewers might be listed in the Fed-Med project:
http://fedoraproject.org/wiki/Medical_Imaging
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