[Cdd-commits] r503 - in projects/med/trunk/debian-med: debian tasks

CDD Subversion Commit noreply at alioth.debian.org
Mon Dec 17 21:45:08 UTC 2007 

Author: tille
Date: Mon Dec 17 21:45:07 2007
New Revision: 503

Modified:
   projects/med/trunk/debian-med/debian/changelog
   projects/med/trunk/debian-med/tasks/bio
   projects/med/trunk/debian-med/tasks/imaging
   projects/med/trunk/debian-med/tasks/imaging-dev
Log:
Added 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	Mon Dec 17 21:45:07 2007
@@ -3,11 +3,14 @@
   * New upstream version
   * Standards-Version: 3.7.3 (no changes needed)
   * Added Vcs-Browser / Vcs-Svn tags
-  * tasks/imaging: Added Dr. Jekyll as prospective package
-  * tasks/imaging(-dev): libvolpack1(-dev),
-    odin as prospective package
+  * tasks/imaging: Added Dr. Jekyll and libvista2 as
+    prospective package
+  * tasks/imaging(-dev): odin and libvista2-dev as
+    prospective package
   * tasks/bio: Added ballview as prospective package
   * tasks/bio-dev: Added BioClipse as prospective package
+  * tasks/bio: dialign-t is now official package - removed
+    Pkg-Description
 
  -- Andreas Tille <tille at debian.org>  Sun, 09 Dec 2007 11:43:52 +0100
 

Modified: projects/med/trunk/debian-med/tasks/bio
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio	(original)
+++ projects/med/trunk/debian-med/tasks/bio	Mon Dec 17 21:45:07 2007
@@ -39,26 +39,6 @@
 Why:         Other packages (Non-free, thus only suggested).
 
 Depends: dialign-t
-Homepage: http://dialign-t.gobics.de/
-Responsible: Charles Plessy <charles-debian-nospam at plessy.org>
-License: LGPL
-WNPP: 445983
-Pkg-Description: Segment-based multiple sequence alignment
- DIALIGN-T is a command line tool to perform multiple alignment of protein or
- DNA sequences. It is a complete reimplementation of the segment-base approach
- including several new improvements and heuristics that significantly enhance
- the quality of the output alignments compared to DIALIGN 2.2. For pairwise
- alignment, DIALIGN-T uses a fragment-chaining algorithm that favours chains of
- low-scoring local alignments over isolated high-scoring fragments. For
- multiple alignment, DIALIGN-T uses an improved greedy procedure that is less
- sensitive to spurious local sequence similarities.  DIALIGN-T has been
- published in Amarendran R. Subramanian, Jan Weyer-Menkhoff, Michael Kaufmann,
- Burkhard Morgenstern: DIALIGN-T: An improved algorithm for segment-based
- multiple sequence alignment. BMC Bioinformatics 2005, 6:66.
- .
- DIALIGN-T is needed by dm_coffee, a special mode of t_coffee prepared
- especially for Debian, in which non-free alignment software was replaced by
- free alternatives.
 
 Depends: tm-align
 Homepage: http://zhang.bioinformatics.ku.edu/TM-align/
@@ -123,3 +103,21 @@
  It provides an extensive set of data structures as well as classes
  for Molecular Mechanics, advanced solvation methods, comparison and
  analysis of protein structures, file import/export, and visualization.
+
+Depends: raxml
+Homepage: http://icwww.epfl.ch/~stamatak/index-Dateien/Page443.htm
+License: GPL
+Pkg-Description: Randomized Axelerated Maximum Likelihood
+ RAxML is a program for sequential and parallel Maximum Likelihood-based
+ inference of large phylogenetic trees. It has originally been derived
+ from fastDNAml.
+
+Depends: axparafit
+Homepage: http://icwww.epfl.ch/~stamatak/AxParafit.html
+License: GPL
+Pkg-Description: optimized statistical analysis of host-parasite coevolution
+ AxParafit is a highly optimized version of Pierre Legendre's Parafit
+ program for statistical analysis of host-parasite coevolution.
+ AxParafit has been parallelized with MPI (Message Passing Interface)
+ for compute clusters and was used to carry out the largest
+ co-evolutionary analysis to date for the paper describing the software.

Modified: projects/med/trunk/debian-med/tasks/imaging
==============================================================================
--- projects/med/trunk/debian-med/tasks/imaging	(original)
+++ projects/med/trunk/debian-med/tasks/imaging	Mon Dec 17 21:45:07 2007
@@ -11,6 +11,8 @@
 
 Depends: libfslio0, libniftiio1, nifti-bin, dicomnifti, libvolpack1
 
+Depends: aeskulap
+
 Depends: bioimagesuite
 Homepage: http://www.bioimagesuite.org/
 License: GPL
@@ -28,18 +30,6 @@
  BioImage Suite was developed at Yale University and has been
  extensively used at different labs at Yale since 2004.
 
-Depends: aeskulap
-Homepage: http://www.nongnu.org/aeskulap/
-Pkg-URL: http://www.bms-austria.com/~pipelka/aeskulap/breezy/aeskulap_0.2.1-2_i386.deb
-License: GPL
-WNPP: 451946
-Pkg-Description: medical DICOM image viewer
- It is able to load a series of special images stored in the DICOM
- format for review. Additionally Aeskulap is able to query and fetch
- DICOM images from archive nodes (also called PACS) over the network.
- The goal of this project is to create a full open source replacement
- for commercially available DICOM viewers.
-
 Depends: dr_jekyll
 Homepage: http://drjekyll.sourceforge.net
 License: GPL
@@ -49,5 +39,22 @@
  Voxel elements (=voxels) and pixel ("picture element") are viewed
  as data sets and can be processed by this program as kind of
  a final polishing process.
-Why: Hint givven ba Petter Reinholdtsen 
+Why: Hint given by Petter Reinholdtsen 
 
+Depends: libvista2
+Homepage: http://mia.sourceforge.net/
+License: GPL
+Pkg-Description: software environment for computer vision research
+ Vista is a software environment for computer vision research. It is
+ designed to support not only images, but also edge sets, camera models,
+ and more complex  data structures. Vista includes libraries of common
+ computer vision and image  processing algorithms. It is written in
+ ANSI C, for UNIX platforms running X Windows, and it is freely available.
+ The original development was done  at University of British Columbia
+ (http://www.cs.ubc.ca/nest/lci/vista/vista.html).
+ .
+ Because the development was stalled by the original authors the
+ development continued in the "Tools for Medical Image Analysis"
+ framework (http://mia.sourceforge.net/) which is maintained by
+ Max Planck Institute of Cognitive Neuroscience
+ (http://www.cns.mpg.de/).

Modified: projects/med/trunk/debian-med/tasks/imaging-dev
==============================================================================
--- projects/med/trunk/debian-med/tasks/imaging-dev	(original)
+++ projects/med/trunk/debian-med/tasks/imaging-dev	Mon Dec 17 21:45:07 2007
@@ -27,3 +27,23 @@
  parallel imaging with GRAPPA reconstruction, two-dimensional pulses
  and field-map-based distortion corrections.
 
+Depends: libvista2-dev
+Homepage: http://mia.sourceforge.net/
+License: GPL
+Pkg-Description: software environment for computer vision research
+ Vista is a software environment for computer vision research. It is
+ designed to support not only images, but also edge sets, camera models,
+ and more complex  data structures. Vista includes libraries of common
+ computer vision and image  processing algorithms. It is written in
+ ANSI C, for UNIX platforms running X Windows, and it is freely available.
+ The original development was done  at University of British Columbia
+ (http://www.cs.ubc.ca/nest/lci/vista/vista.html).
+ .
+ Because the development was stalled by the original authors the
+ development continued in the "Tools for Medical Image Analysis"
+ framework (http://mia.sourceforge.net/) which is maintained by
+ Max Planck Institute of Cognitive Neuroscience
+ (http://www.cns.mpg.de/).
+ .
+ This is the development package.
+

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