[Cdd-commits] r605 - projects/med/trunk/debian-med/tasks
CDD Subversion Commit
noreply at alioth.debian.org
Thu Mar 13 13:38:14 UTC 2008
Author: tille
Date: Thu Mar 13 13:38:13 2008
New Revision: 605
Modified:
projects/med/trunk/debian-med/tasks/bio
projects/med/trunk/debian-med/tasks/bio-dev
projects/med/trunk/debian-med/tasks/epi
projects/med/trunk/debian-med/tasks/imaging
projects/med/trunk/debian-med/tasks/imaging-dev
projects/med/trunk/debian-med/tasks/physics
Log:
Removed blanks at end of lines that sometimes confuse parsing tools
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 13:38:13 2008
@@ -13,7 +13,7 @@
Why: Genetics
Depends: amap-align, blast2, boxshade, dialign, gff2aplot, emboss, hmmer,
- kalign, mummer, muscle, poa, probcons, proda,
+ kalign, mummer, muscle, poa, probcons, proda,
seaview, sim4, sibsim4, sigma-align, t-coffee, wise, exonerate
Why: Sequence alignments and related programs.
@@ -80,8 +80,8 @@
Depends: cytoscape
Homepage: http://cytoscape.org/
Responsible: Mike Smoot <mes at aescon.com>
-License:
-WNPP:
+License: LGPL
+WNPP: 465331
Pkg-Description: visualizing molecular interaction networks
Cytoscape is a bioinformatics software platform for visualizing molecular
interaction networks and integrating these interactions with gene expression
@@ -110,9 +110,7 @@
Depends: raxml
Homepage: http://icwww.epfl.ch/~stamatak/index-Dateien/Page443.htm
-Responsible:
License: GPL
-WNPP:
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
@@ -136,22 +134,20 @@
Depends: axpcoords
Homepage: http://icwww.epfl.ch/~stamatak/AxParafit.html
-Responsible:
+Responsible: David Paleino <d.paleino at gmail.com>
License: GPL
WNPP: 464323
Pkg-Description: LAPACK-based implementation of DistPCoA
- AxPcoords is a fast, LAPACK-based implementation of DistPCoA (see
+ AxPcoords is a fast, LAPACK-based implementation of DistPCoA (see
http://www.bio.umontreal.ca/Casgrain/en/labo/distpcoa.html)
- which is another program by Pierre Legendre, it conducts a principal
+ which is another program by Pierre Legendre, it conducts a principal
coordinates analysis.
- This program is required for the pipeline that conducts a full host-parasite
+ This program is required for the pipeline that conducts a full host-parasite
co-phylogenetic analysis in combination with AxParafit.
Depends: copycat
Homepage: http://www-ab.informatik.uni-tuebingen.de/software/copycat/welcome.html
-Responsible:
License: Use of the program is free for academic purposes at an academic institute. For all other uses, please contact the authors.
-WNPP:
Pkg-Description: fast access to cophylogenetic analyses
CopyCat provides an easy and fast access to cophylogenetic analyses.
It incorporates a wrapper for the program ParaFit, which conducts a
@@ -283,7 +279,7 @@
Homepage: http://asap.ahabs.wisc.edu/mauve/
Responsible: Andreas Tille <tille at debian.org>
License: GPL
-WNPP:
+WNPP:
Pkg-Description: multiple genome alignment
Mauve is a system for efficiently constructing multiple genome alignments
in the presence of large-scale evolutionary events such as rearrangement
@@ -313,7 +309,6 @@
Homepage: http://asap.ahabs.wisc.edu/software/asap/
Responsible: Andreas Tille <tille at debian.org>
License: GPL
-WNPP:
Pkg-Description: organize the data associated with a genome
Developments in genome-wide approaches to biological research have
yielded greatly increased quantities of data, necessitating the cooperation
@@ -629,7 +624,7 @@
Debian. The analysis itself is performed with AutoDock, which was
recently made available under the GPL.
.
- Upstream is very supportive but their binary-only libraries are of a
+ Upstream is very supportive but their binary-only libraries are of a
third party. This set of tools is well known across biochemistry and
computational/structural biology.
@@ -652,7 +647,7 @@
The core part of the system, E-Cell Simulation Environment version 3,
allows many components driven by multiple algorithms with different
timescales to coexist.
- .
+ .
E-Cell System consists of the following three major parts:
* E-Cell Simulation Environment (or E-Cell SE)
* E-Cell Modeling Environment (or E-Cell ME)
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 13:38:13 2008
@@ -45,9 +45,7 @@
Depends: bioclipse
Homepage: http://www.bioclipse.net/
-Responsible:
License: Eclipse Public License (EPL) + exception
-WNPP:
Pkg-Description: platform for chemo- and bioinformatics based on Eclipse
The Bioclipse project is aimed at creating a Java-based, open source,
visual platform for chemo- and bioinformatics based on the Eclipse
@@ -64,7 +62,7 @@
updated on upcoming features, releases, new plugins etc, please register
for the mailing list bioclipse-announce. The development is best
followed on the Bioclipse Wiki where we document the progress and
- ideas of the development on a daily basis.
+ ideas of the development on a daily basis.
Depends: aceperl
Homepage: http://stein.cshl.org/AcePerl/
@@ -108,7 +106,7 @@
is efficient, requiring a maximum of only 16 bytes per base of the largest
input sequence, and this data can be stored externally (i.e. on disk) to
further reduce memory requirements.
-
+
Depends: libbio-das-perl
Homepage: http://www.biodas.org/
Responsible: Steffen Moeller <moeller at debian.org>
Modified: projects/med/trunk/debian-med/tasks/epi
==============================================================================
--- projects/med/trunk/debian-med/tasks/epi (original)
+++ projects/med/trunk/debian-med/tasks/epi Thu Mar 13 13:38:13 2008
@@ -9,7 +9,6 @@
Homepage: http://www.netepi.org/
Responsible: Andreas Tille <tille at debian.org>
License: free
-WNPP:
Pkg-Description: network-enabled tools for epidemiology and public health practice
NetEpi, which is short for "Network-enabled Epidemiology", is a collaborative
project to create a suite of free, open source software tools for epidemiology
@@ -33,7 +32,6 @@
Homepage: http://www.netepi.org/
Responsible: Andreas Tille <tille at debian.org>
License: free
-WNPP:
Pkg-Description: network-enabled tools for epidemiology and public health practice
NetEpi, which is short for "Network-enabled Epidemiology", is a collaborative
project to create a suite of free, open source software tools for epidemiology
Modified: projects/med/trunk/debian-med/tasks/imaging
==============================================================================
--- projects/med/trunk/debian-med/tasks/imaging (original)
+++ projects/med/trunk/debian-med/tasks/imaging Thu Mar 13 13:38:13 2008
@@ -15,9 +15,7 @@
Depends: bioimagesuite
Homepage: http://www.bioimagesuite.org/
-Responsible:
License: GPL
-WNPP:
Pkg-Description: integrated image analysis software suite
BioImage Suite has extensive capabilities for both neuro/cardiac
and abdominal image analysis and state of the art visualization.
@@ -34,26 +32,22 @@
.
There is a forum at BioImage Suite site for discussion of
compiling it from source and packaging issues at
- http://research.yale.edu/bioimagesuite/forum/index.php?board=12.0
+ http://research.yale.edu/bioimagesuite/forum/index.php?board=12.0
Depends: drjekyll
Homepage: http://drjekyll.sourceforge.net
-Responsible:
License: GPL
-WNPP:
Pkg-Description: interactive voxel editor for viewing and editing three-dimensional images
It is specifically aimed at postprocessing of segmented datasets,
- but offers some functionality for raw data as well.
+ but offers some functionality for raw data as well.
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 given by Petter Reinholdtsen
+Why: Hint given by Petter Reinholdtsen
Depends: libvista2
Homepage: http://mia.sourceforge.net/
-Responsible:
License: GPL
-WNPP:
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,
@@ -71,15 +65,13 @@
Depends: dcm4che
Homepage: http://www.dcm4che.org/
-Responsible:
License: LGPL, MPL, Apache, other (also non-free)
-WNPP:
Pkg-Description: collection of open source applications and utilities healthcare enterprise
At the core of the dcm4che project is a robust implementation of the
DICOM standard. The dcm4che-1.x DICOM toolkit is used in many production
applications across the world, while the current (2.x) version of the
toolkit has been re-architected for high performance and flexibility.
- .
+ .
Also contained within the dcm4che project is dcm4chee (the extra 'e'
stands for 'enterprise'). dcm4chee is an Image Manager/Image Archive
(according to IHE). The application contains the DICOM, HL7 services
@@ -104,7 +96,7 @@
Homepage: http://neuroimaging.scipy.org/
License: Free
Pkg-Description: development platform for neuroimaging research
- Python-based development platform for neuroimaging research. Please see
+ Python-based development platform for neuroimaging research. Please see
https://cirl.berkeley.edu/view/Grants/BrainPySummary for a description of
the various subprojects.
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 Thu Mar 13 13:38:13 2008
@@ -1,6 +1,6 @@
Task: Imaging Development
Description: Debian-Med packages for medical image development
- This meta package will install Debian packages which might be useful
+ This meta package will install Debian packages which might be useful
for developing applications for medical image processing.
Depends: ctn-dev, cimg-dev, libminc0-dev | libminc-dev, libmdc2-dev
@@ -17,9 +17,7 @@
Depends: odin
Homepage: http://od1n.sourceforge.net/
-Responsible:
License: GPL
-WNPP:
Pkg-Description: simulate and run magnetic resonance sequences
C++ software framework to develop, simulate and run magnetic resonance
sequences.
@@ -30,9 +28,7 @@
Depends: libvista2-dev
Homepage: http://mia.sourceforge.net/
-Responsible:
License: GPL
-WNPP:
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,
Modified: projects/med/trunk/debian-med/tasks/physics
==============================================================================
--- projects/med/trunk/debian-med/tasks/physics (original)
+++ projects/med/trunk/debian-med/tasks/physics Thu Mar 13 13:38:13 2008
@@ -14,7 +14,7 @@
Suggests: paw-demos
-Depends: octave | octave2.1,
+Depends: octave | octave2.1
Depends: r-base | r-base-core
Why: "r-base" is a meta package and it is better to have a default
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