[Cdd-commits] r604 - in projects/med/trunk/debian-med: debian tasks

[CDD Subversion Commit]

Author: tille
Date: Thu Mar 13 13:05:08 2008
New Revision: 604

Modified:
   projects/med/trunk/debian-med/debian/changelog
   projects/med/trunk/debian-med/tasks/bio
   projects/med/trunk/debian-med/tasks/bio-dev
Log:
More prospective packages


Modified: projects/med/trunk/debian-med/debian/changelog
==============================================================================
--- projects/med/trunk/debian-med/debian/changelog	(original)
+++ projects/med/trunk/debian-med/debian/changelog	Thu Mar 13 13:05:08 2008
@@ -9,6 +9,7 @@
   * tasks/bio
     - Added prospective projects where Steffen Möller started some
       packaging work
+    - Suggests: texlive-latex-extra (because of TeXShade)
   * tasks/tools
     - Added mssstest
 

Modified: projects/med/trunk/debian-med/tasks/bio
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio	(original)
+++ projects/med/trunk/debian-med/tasks/bio	Thu Mar 13 13:05:08 2008
@@ -26,7 +26,7 @@
 Depends:     plasmidomics
 Why:         Presentation
 
-Suggests:    texlive-science
+Suggests:    texlive-science, texlive-latex-extra
 Why:         This is only recommended to not necessarily flood the system with TeX
              packages - perhaps target for -doc?
 
@@ -669,3 +669,15 @@
  from protein sequences. The algorithm was published in
  Lupas, van Dyke & Stock, Predicting coiled coils from
  protein sequences Science, 252, 1162-1164, 1991.
+
+Depends: haploview
+Homepage: http://www.broad.mit.edu/mpg/haploview/
+Responsible: Steffen Moeller <moeller at debian.org>
+WNPP: 311421
+License: DFSG free
+Pkg-URL: http://svn.debian.org/wsvn/debian-med/trunk/packages/haploview/trunk/?rev=0&sc=0
+Pkg-Description: Analysis and visualization of LD and haplotype maps
+ This tools assists in the analysis of the nucleotide
+ variation in a population. Such investigations are performed
+ to determine genes and genetic pathways that are associated
+ with diseases. This is an early stage in the quest for new drugs.

Modified: 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	Thu Mar 13 13:05:08 2008
@@ -141,3 +141,37 @@
  Limma is an essential package of the bioconductor.org effort to
  investigate gene expression data from microarrays with the
  statistical package R.
+
+Depends: libtfbs-perl
+Homepage: http://forkhead.cgb.ki.se/TFBS/
+Responsible: Steffen Moeller <moeller at debian.org>
+WNPP: 320777
+License: artistic
+Pkg-URL: http://svn.debian.org/wsvn/debian-med/trunk/packages/tfbs/trunk/?rev=0&sc=0
+Pkg-Description: Perl extension for scanning a DNA sequences for TFBS
+ TFBS Perl OO modules implement classes for the representation of objects
+ encountered in analysis of protein-binding sites in DNA sequences.The
+ objects defined by TFBS classes include:
+  * pattern definition objects, currently position specific score matrices
+    (raw frequency, information content and position weight matrices)with
+    methods for interconversion between matrix types, sequence searching
+    with a matrix profile, sequence 'logo' drawing and matrix manipulation;
+  * a composite object representing a set of position specific score
+    matrices, with methods for the identification of motifs within DNA
+    sequences with the set of profiles from its member matrices;
+  * methods for searching pairwise alignments for patterns conserved
+    in both sequences (phylogenetic footprinting) defined for both matrix
+    profile and composite (matrix set) objects;
+  * an object representing DNA binding site sequence, and an object
+    representing sets of DNA binding sequences, with methods and helper
+    classes to facilitate scanning, filtering and statistical analyses;
+  * an object representing a pair of DNA binding site sequences, and an
+    object representing a set of such pairs, for storage, manipulation and
+    analysis of phylogenetic footprinting searches;
+  * database interfaces to relational, flat file and WWW database of
+    position-specifc score matrices, with methods for searching existing
+    databases, as well as creating new ones containing user-defined matrices.
+  * interfaces to matrix pattern generating programs
+ .
+ The modules within the TFBS set are fully integrated and compatible with
+ Bioperl.