[Blends-commit] r3394 - /projects/med/trunk/debian-med/tasks/bio

[tille at users.alioth.debian.org]

Author: tille
Date: Tue Jun  5 17:19:10 2012
New Revision: 3394

URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=3394
Log:
Remove redundant infoprmation about plato

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

Modified: projects/med/trunk/debian-med/tasks/bio
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/tasks/bio?rev=3394&op=diff
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio (original)
+++ projects/med/trunk/debian-med/tasks/bio Tue Jun  5 17:19:10 2012
@@ -394,6 +394,8 @@
  .
  Check with authors about licensing, they adopted code from clustalw which is now
  free.  Thus a change might be possible
+
+Depends: plato
 
 Depends: proalign
 
@@ -2734,50 +2736,6 @@
  .
  The reaper module is used underneath the http://genenetwork.org site.
 
-Depends: plato
-Homepage: https://chgr.mc.vanderbilt.edu/plato
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/plato/trunk/
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/plato/trunk
-License: GPL-2+
-Pkg-Description: Analysis, translation, and organization of large-scale genetic data
- PLATO is an acronym for "PLatform for the Analysis, Translation,
- and Organization of large-scale data".  Recent technological advances
- enable the study of hundreds of thousands of human single-nucleotide
- polymorphisms at the population level. Because strategies for analyzing
- these data have not kept pace with the laboratory methods that generate
- the data, it is unlikely that these advances will immediately lead to
- an improved understanding of the genetic contribution to common human
- disease and drug response. Currently, no single analytical method
- allows us to extract all available information from a whole-genome
- association study. In fact, no single method can be optimal for all
- datasets, especially when the genetic architecture for diseases can
- vary substantially, as is certainly the case. Therefore, an integrative
- platform is needed to accommodate multiple analytical methods for
- analysis as we learn more about genetic architecture. As a result,
- we are developing a system for the analysis of genome-wide association
- data that will incorporate several analytical approaches as filters to
- allow a scientist to choose whatever analytical methods they wish to
- apply. PLATO (PLatform for the Analysis, Translation, and Organization
- of large-scale data) will incorporate a number of filters to select
- the important SNPs in a genome-wide association study.
- .
- Whole-genome Association Study Pipeline (WASP) has recently been
- absorbed into PLATO. WASP was designed to aid in retrieving, evaluating,
- formatting, and analyzing genotypic and clinical data from the latest
- large-scale genotyping studies. WASP implements a battery of quality
- control procedures to assess the data. Among the currently available
- procedures are the examination of marker and sample genotyping
- efficiency, allele frequency calculations, checks of Mendelian error
- (if applicable) and gender discrepancies (based on available chromosome X
- and Y genotypes), and tests of Hardy-Weinberg Equilibrium. Additionally,
- WASP can retrieve and format data for other software programs such as the
- Graphical Representation of Relationships (GRR) program, or STRUCTURE,
- and depending on the nature of the samples and the depth of examination
- the user desires to pursue. Beyond the quality control aspect of this
- application, WASP can perform standard tests of association using the
- Transmission Disequilibrium Test TDT for family-based datasets and the
- chi-square test of association for case-control datasets.
-
 Depends: sequenceconverter.app
 Homepage: http://bioinformatics.org/biococoa/
 License: GPL