[Blends-commit] r1857 - projects/med/trunk/debian-med/tasks

Fri Aug 28 11:56:04 UTC 2009

Author: moeller
Date: Fri Aug 28 11:56:04 2009
New Revision: 1857
URL: http://svn.debian.org/viewsvn/blends?rev=1857&view=rev

Log:
Series of references added.


Modified:
   projects/med/trunk/debian-med/tasks/bio
   projects/med/trunk/debian-med/tasks/bio-dev

Modified: projects/med/trunk/debian-med/tasks/bio
URL: http://svn.debian.org/viewsvn/blends/projects/med/trunk/debian-med/tasks/bio?rev=1857&view=diff&r1=1857&r2=1856&p1=projects/med/trunk/debian-med/tasks/bio&p2=projects/med/trunk/debian-med/tasks/bio
==============================================================================

--- projects/med/trunk/debian-med/tasks/bio	(original)
+++ projects/med/trunk/debian-med/tasks/bio	Fri Aug 28 11:56:04 2009
@@ -23,12 +23,30 @@
 
 X-Begin-Category: Sequence alignments and related programs.
 
-Depends:     amap-align, blast2, boxshade, gff2aplot, hmmer, kalign, mafft, mummer, muscle, sim4, sibsim4, t-coffee, wise, exonerate
+Depends:     amap-align, blast2, boxshade, gff2aplot, hmmer, kalign, mafft, mummer, muscle, sim4, sibsim4, t-coffee, wise
+
+Depends: hmmer
+Published-Title: Multiple Alignment Using Hidden Markov Models.
+Published-Authors: S. R. Eddy.
+Published-In: Proc. Third Int. Conf. Intelligent Systems for Molecular Biology, 114-120.
+Published-Year: 1995
+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
+X-Published-doi: 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
@@ -65,7 +83,14 @@
 Published-In: BMC Bioinformatics 16;7:143
 Published-Year: 2006
 
-Depends:     emboss, embassy-domalign, embassy-domainatrix
+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
 Suggests:    emboss-explorer
 Why:         The EMBOSS sequence analysis suite and its galaxy.
 
@@ -152,7 +177,7 @@
 Enhanced-By: autogrid
 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-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
@@ -173,7 +198,7 @@
          would hide them from the tasks and bugs list as well from the sectioning in
          http://qa.debian.org/developer.php?login=debian-med-packaging@lists.alioth.debian.org&ordering=3
          so they are mentioned here in addition to autodocktools.
-Published-Title: AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility.
+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

Modified: projects/med/trunk/debian-med/tasks/bio-dev
URL: http://svn.debian.org/viewsvn/blends/projects/med/trunk/debian-med/tasks/bio-dev?rev=1857&view=diff&r1=1857&r2=1856&p1=projects/med/trunk/debian-med/tasks/bio-dev&p2=projects/med/trunk/debian-med/tasks/bio-dev
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio-dev	(original)
+++ projects/med/trunk/debian-med/tasks/bio-dev	Fri Aug 28 11:56:04 2009
@@ -20,6 +20,11 @@
      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: libbio-ruby
 

