[Cdd-commits] r296 - projects/med/trunk/menu/bio-dev

[Andreas Tille]

Author: tille
Date: Fri Sep 17 00:21:58 2004
New Revision: 296

Added:
   projects/med/trunk/menu/bio-dev/
   projects/med/trunk/menu/bio-dev/biomode.txt
   projects/med/trunk/menu/bio-dev/bioperl.txt
   projects/med/trunk/menu/bio-dev/libncbi6-dev.menu
   projects/med/trunk/menu/bio-dev/libvibrant6-dev.txt
   projects/med/trunk/menu/bio-dev/mcl.txt
Log:
Further 0.8.9 merge


Added: projects/med/trunk/menu/bio-dev/biomode.txt
==============================================================================
--- (empty file)
+++ projects/med/trunk/menu/bio-dev/biomode.txt	Fri Sep 17 00:21:58 2004
@@ -0,0 +1,11 @@
+BioMode: Emacs mode to edit genetic data
+
+Some information about Biomode from the Debian-Med project.
+
+    It provides you several interesting commands to take the antiparallel
+    of a region, convert it using readseq, runs blast on it, etc.
+
+This package is not really installed by the med-bio package but it is
+suggested.  That means if you are comfortable with the powerful editor
+Emacs you might wish to install also the biomode package and make use
+of it by typing "M-x biomode".

Added: projects/med/trunk/menu/bio-dev/bioperl.txt
==============================================================================
--- (empty file)
+++ projects/med/trunk/menu/bio-dev/bioperl.txt	Fri Sep 17 00:21:58 2004
@@ -0,0 +1,13 @@
+Bioperl: Perl tools for computational molecular biology
+
+Some information about Bioperl from the Debian-Med project.
+
+ The Bioperl project is a coordinated effort to collect computational methods
+ routinely used in bioinformatics into a set of standard CPAN-style,
+ well-documented, and freely available Perl modules.
+
+The Homepage is http://bio.perl.org/
+
+You can get a good overview by the main manpage:
+
+       man bioperl

Added: projects/med/trunk/menu/bio-dev/libncbi6-dev.menu
==============================================================================
--- (empty file)
+++ projects/med/trunk/menu/bio-dev/libncbi6-dev.menu	Fri Sep 17 00:21:58 2004
@@ -0,0 +1,4 @@
+?package(libncbi6-dev):command="/usr/bin/vibrate /usr/bin/asntool" needs="X11" \
+	section="Med/Biology development" title="asntool" hints="Biology" icon="/usr/share/pixmaps/asntool.xpm"
+?package(libncbi6-dev):command="/usr/bin/vibrate /usr/bin/errhdr" needs="X11" \
+	section="Med/Biology development" title="errhdr" hints="Biology" icon="/usr/share/pixmaps/ncbilogo.xpm"

Added: projects/med/trunk/menu/bio-dev/libvibrant6-dev.txt
==============================================================================
--- (empty file)
+++ projects/med/trunk/menu/bio-dev/libvibrant6-dev.txt	Fri Sep 17 00:21:58 2004
@@ -0,0 +1,13 @@
+libvibrant6-dev: NCBI libraries for graphic biology applications
+                 (development files)
+
+Some information about libvibrant6-dev from the Debian-Med project.
+
+ Vibrant allows you to develop portable (Motif, MS-Windows, Mac-OS) graphic
+ biological applications.
+  
+The Homepage is http://www.ncbi.nlm.nih.gov/
+
+You can get a good overview by reading
+
+       zless /usr/share/doc/libvibrant6-dev/README.gz

Added: projects/med/trunk/menu/bio-dev/mcl.txt
==============================================================================
--- (empty file)
+++ projects/med/trunk/menu/bio-dev/mcl.txt	Fri Sep 17 00:21:58 2004
@@ -0,0 +1,33 @@
+MCL: Markov Cluster algorithm
+
+Some information about mcl from the Debian-Med project.
+
+ The MCL package is an implementation of the MCL algorithm, and offers
+ utilities for manipulating sparse matrices (the essential data
+ structure in the MCL algorithm) and conducting cluster experiments.
+ 
+ MCL is currently being used in sciences like biology (protein family
+ detection, genomics), computer sciense (node clustering in
+ Peer-to-Peer networks), and linguistics (text analysis).
+
+ Homepage: http://micans.org/mcl/
+	
+An overview about the various tools are given by the following manpages:
+
+     man mcx
+     man clmimac
+     man clmmate
+     man clmmeet
+     man clmformat
+     man clmdist
+     man clminfo
+     man mcxconvert
+     man mcxassemble
+     man mcxmap
+     man mcxsubs
+     man mcxarray
+     man mcxdeblast
+     man mclblastline
+     man mcl
+     man clmresidue
+     man mclpipeline