[Cdd-commits] r588 - in projects/med/trunk/debian-med: debian tasks

[CDD Subversion Commit]

Author: tille
Date: Mon Mar 10 10:06:13 2008
New Revision: 588

Modified:
   projects/med/trunk/debian-med/debian/changelog
   projects/med/trunk/debian-med/tasks/bio
Log:
Added most prospective packages from static pages


Modified: projects/med/trunk/debian-med/debian/changelog
==============================================================================
--- projects/med/trunk/debian-med/debian/changelog	(original)
+++ projects/med/trunk/debian-med/debian/changelog	Mon Mar 10 10:06:13 2008
@@ -3,11 +3,13 @@
   * tasks/bio:
     - Added emboss-kaptain as prospective package
     - Added agdbnet as prospective package
-    - Added autodock
+    - Added autodock, exonerate
     - Suggests biococoa.app: Only suggests because status is
       questionable
     - Removed bugsx which is not really biology related
     - Added gamgi as prospective package
+    - Moved unoffical and prospective packages from static
+      web pages to tasks file
   * tasks/bio-dev:
     - Added aceperl as prospective package
     - Added libgff-perl as prospective package

Modified: projects/med/trunk/debian-med/tasks/bio
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio	(original)
+++ projects/med/trunk/debian-med/tasks/bio	Mon Mar 10 10:06:13 2008
@@ -39,7 +39,7 @@
 
 Depends: dialign-t
 
-Depends: glam2
+Depends: glam2, exonerate
 
 Depends: autodock, autogrid
 Why: This is just in SVN and hopefully an upload will happen soon.
@@ -390,3 +390,166 @@
 Pkg-Description: general atomistic modelling graphic interface
  GAMGI provides a graphical user interface for the handling
  of molecular structures.
+
+Depends: bioconductor
+Homepage: http://www.bioconductor.org/
+Responsible: Steffen Moeller <moeller at debian.org>
+License: GPL/LGPL
+Pkg-URL: http://bioinformatics.pzr.uni-rostock.de/~moeller/debian/bioconductor/
+Pkg-Description: analysis and comprehension of genomic data
+ Bioconductor is an open source and open development software project
+ to provide tools for the analysis and comprehension of genomic data.
+ .
+ The Bioconductor core team is based primarily at the Biostatistics Unit of
+ the Dana Farber Cancer Institute at the Harvard Medical School/Harvard School
+ of Public Health. Other members come from various US and international
+ institutions.
+ .
+ The broad goals of the projects are to
+  * provide access to a wide range of powerful statistical and graphical methods
+    for the analysis of genomic data;
+  * facilitate the integration of biological metadata in the analysis of
+    experimental data: e.g. literature data from PubMed, annotation data from
+    LocusLink;
+  * allow the rapid development of extensible, scalable, and interoperable
+    software;
+  * promote high-quality documentation and reproducible research;
+  * provide training in computational and statistical methods for the analysis
+    of genomic data.
+
+Depends: biomart
+Homepage: http://www.ebi.ac.uk/biomart/
+Responsible: Steffen Moeller <moeller at debian.org>
+License: GPL
+Pkg-URL: http://bioinformatics.pzr.uni-rostock.de/~moeller/debian/martj/
+Pkg-Description: distributed data integration system for biological data
+ BioMart is a simple, distributed data integration system with
+ powerful query capabilities. The BioMart data model has been applied
+ to the following data sources: UniProt Proteomes, Macromolecular
+ Structure Database (MSD), Ensembl, Vega, and dbSNP.
+       
+Depends: cluster3
+Homepage: http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/software.htm#ctv
+Responsible: Steffen Moeller <moeller at debian.org>
+License: non-free
+Pkg-URL: http://bioinformatics.pzr.uni-rostock.de/~moeller/debian/cluster3/
+Pkg-Description: find clustering solutions for genome data
+ Cluster 3.0 is an enhanced version of Cluster, which was originally
+ developed by Michael Eisen while at Stanford University. The main
+ improvement consists of the k-means algorithm, which now includes
+ multiple trials to find the best clustering solution. This is crucial
+ for the k-means algorithm to be reliable. The routine for self-organizing
+ maps was extended to include 2D rectangular geometries. The Euclidean
+ distance and the city-block distance were added to the available
+ measures of similarity.
+
+Depends: jmol
+Homepage: http://jmol.sourceforge.net/
+Responsible:
+License: LGPL
+Pkg-URL: http://debian.wgdd.de/debian/dists/unstable/contrib/binary-all/science/
+Pkg-Description: molecule viewer
+ Jmol is a free, open source molecule viewer for students, educators,
+ and researchers in chemistry and biochemistry.
+  * The JmolApplet is a web browser applet that can be integrated into web pages.
+  * The Jmol application is a standalone Java application that runs on the
+    desktop.
+  * The JmolViewer is a development tool kit that can be integrated into other
+    Java applications.
+
+Depends: jtreeview
+Homepage: http://jtreeview.sourceforge.net/
+Responsible: Steffen Moeller <moeller at debian.org>
+License: GPL
+Pkg-URL: http://bioinformatics.pzr.uni-rostock.de/~moeller/debian/treeview/
+Pkg-Description: viewer for microarray data
+ Java TreeView is an extensible viewer for microarray data in
+ PCL or CDT format.
+
+Depends: smile
+Homepage: http://www-igm.univ-mlv.fr/~marsan/smile_english.html
+Responsible: Steffen Moeller <moeller at debian.org>
+License: GPL
+Pkg-URL: http://bioinformatics.pzr.uni-rostock.de/~moeller/debian/smile/
+Pkg-Description: infer motifs in a set of sequences
+ SMILE is a tool that infers motifs in a set of sequences, according to some
+ criteria. It was first made to infer exceptional sites as binding sites in
+ DNA sequences. Since the 1.4 version, it allows to infer motifs written on
+ any alphabet (even degenerate) in any kind of sequences.
+ .
+ The specificity of SMILE is to allow to deal with what we call structured
+ motifs, which are motifs associated by some distance constraints.
+
+Depends: cactus
+Homepage: http://www.cactuscode.org/Community/Biology.html
+License: GPL
+Pkg-Description:
+ Cactus is an open source problem solving environment designed for scientists
+ and engineers. Its modular structure easily enables parallel computation
+ across different architectures and collaborative code development between
+ different groups.
+ .
+ Cactus provides easy access to many cutting edge software technologies being
+ developed in the academic research community, including the Globus
+ Metacomputing Toolkit, HDF5 parallel file I/O, the PETSc scientific library,
+ adaptive mesh refinement, web interfaces, and advanced visualization tools.
+
+Depends: contralign
+Homepage: http://contra.stanford.edu/contralign/
+License: Public Domain
+Pkg-Description: parameter learning framework for protein pairwise sequence alignment
+ CONTRAlign is an extensible and fully automatic parameter learning
+ framework for protein pairwise sequence alignment based on pair
+ conditional random fields. The CONTRAlign framework enables the
+ development of feature-rich alignment models which generalize well to
+ previously unseen sequences and avoid overfitting by controlling model
+ complexity through regularization.
+
+Depends: galaxy
+Homepage: http://g2.trac.bx.psu.edu/
+License: MIT
+Pkg-Description: manipulate sequences and annotation files
+ Galaxy is a web-based tool allowing users to perform operations which
+ are usually done with command-line interface. Using galaxy, one can
+ manipulate sequences and annotation files in many formats. Galaxy has
+ strong ties with the UCSC genome browser, and makes it easy to
+ visualise modified annotation files as a custom track.
+
+Depends: genographer
+Homepage: http://hordeum.oscs.montana.edu/genographer/
+License: GPL
+Pkg-Description: read data and reconstruct them into a gel image
+ This program will read in data from an ABI 3700, 3100, 377 or 373,
+ CEQ 2000 or SCF and reconstruct them into a gel image which is
+ straightened and sized. Bins can be defined easily and viewed as
+ thumbnails, which allows for a fairly quick and easy way of scoring a gel.
+ .
+ The program is written in Java and uses the Java 1.3 API. Therefore,
+ it should run on any machine that can run java.
+
+Depends: molekel
+Homepage: http://bioinformatics.org/molekel/wiki/Main/HomePage
+License: GPL
+Pkg-Description: multiplatform molecular visualization
+ Molekel is an opensource (GPL) multiplatform molecular visualization
+ program being developed at the Swiss National Supercomputing Centre
+ (CSCS).
+
+Depends: pftools
+Homepage: ftp://us.expasy.org/databases/prosite/tools/ps_scan/sources
+License: GPL
+Pkg-Description: tools to handle patterns from PROSITE
+ ps_scan is a perl program used to scan one or several patterns, rules
+ and/or profiles from PROSITE against one or several protein sequences
+ in Swiss-Prot or FASTA format. It requires two compiled external
+ programs from the PFTOOLS, which are also distributed with the sources.
+
+Depends: 
+Homepage: 
+License: GPL
+Pkg-Description:
+
+Depends: 
+Homepage: 
+License: GPL
+Pkg-Description: