[Cdd-commits] r1094 - projects/med/trunk/debian-med/tasks

[CDD Subversion Commit]

Author: tille
Date: Tue Sep 23 08:40:58 2008
New Revision: 1094

Modified:
   projects/med/trunk/debian-med/tasks/bio
   projects/med/trunk/debian-med/tasks/physics
Log:
Added gate to physics and some more biolinux projects to bio


Modified: projects/med/trunk/debian-med/tasks/bio
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio	(original)
+++ projects/med/trunk/debian-med/tasks/bio	Tue Sep 23 08:40:58 2008
@@ -2773,3 +2773,44 @@
  .
  This package is included into BioLinux distribution
  http://envgen.nox.ac.uk/biolinux.html
+
+Depends: rbs-finder
+Homepage: http://www.genomics.jhu.edu/RBSfinder/
+License: not specified
+Responsible: BioLinux - Stewart Houten <shou at ceh.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: find ribosome binding sites(RBS)
+ The program implements an algorithm to find ribosome binding
+ sites(RBS) in the upstream regions of the genes annotated by
+ Glimmer2, GeneMark, or other prokaryotic gene finders.  If there is
+ no RBS-like patterns in this region, program searches for a start
+ codon having a RBS-like pattern ,in the same reading frame upstream
+ or downstream and relocates start codon accordingly.
+ .
+ You can find more detailed information at
+ http://nbc11.biologie.uni-kl.de/docbook/doc_userguide_bioinformatics_server/chunk/ch01s06.html
+ .
+ This package is included into BioLinux distribution
+ http://envgen.nox.ac.uk/biolinux.html
+
+Depends: recombine
+Homepage: http://evolution.genetics.washington.edu/lamarc/recombine.html
+License: not specified
+Responsible: BioLinux - Nathan S Haigh <n.haigh at sheffield.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: effective population size of populations
+ RECOMBINE fits a model which has a single population of constant size
+ with a single recombination rate across all sites. It can accomodate
+ either plain DNA or RNA data or SNP (Single Nucleotide Polymorphism)
+ data. It estimates 4Nu and r, where N is the effective population
+ size, u is the neutral mutation rate per site, and r is the ratio of
+ the per-site recombination rate to the per-site mutation rate.
+ .
+ The homepage contains the explicite link: "We are no longer
+ supporting RECOMBINE as its functions can be done just as well by
+ LAMARC and it's easier for us to support just one program. You may
+ still want the paper, however."  So this is actually no target for
+ the Debian Med distribution but just a hint for users about the
+ existence of this program and the even better alternative even if
+ BioLinux distribution http://envgen.nox.ac.uk/biolinux.html contains
+ a package.

Modified: projects/med/trunk/debian-med/tasks/physics
==============================================================================
--- projects/med/trunk/debian-med/tasks/physics	(original)
+++ projects/med/trunk/debian-med/tasks/physics	Tue Sep 23 08:40:58 2008
@@ -53,3 +53,20 @@
     Simulink.
   * BioProFeed (bioprofeed)
   * BCIx (bcix)
+
+Depends: gate
+Homepage: http://www.opengatecollaboration.org
+License: LGPL
+WNPP: 431425
+Responsible: Nicolas Spalinger <nicolas.spalinger at healthgrid.org>
+Pkg-Description: Geant4 Application for Emission Tomography
+ GATE incorporates the Geant4 libraries in a modular, versatile, and
+ scripted simulation toolkit which is adapted to the field of nuclear
+ medicine both in PET (Positron Emission Tomography) and SPECT (Single
+ Photon Emission Computer Tomography). It allows the accurate description
+ of time-dependent phenomena such as source or detector movement and
+ source decay kinetics. The ability to synchronize all time-dependent
+ components allows a coherent description of the acquisition process. It
+ makes it possible to perform realistic simulations of data acquisitions
+ in time.
+