Re: Molekel becomes free (GPL licensed)? (fwd)
Le Mon, Jan 29, 2007 at 04:07:15PM +0100, Daniel Leidert a écrit :
> Am Montag, den 29.01.2007, 09:00 +0100 schrieb Andreas Tille:
>
> [GPLed Molekel]
> > something for our TODO-List, IMHO.
>
> http://lists.alioth.debian.org/pipermail/debichem-devel/2007-January/000009.html
Dear all, dear Tobias,
I have added Molekel (and BALLview by the way) to our microbio.wml page.
I also moved some officialised packages to the proper section. The patch
is attached to this mail. Tobias, can you commit it ?
Have a nice week-end
--
Charles Plessy
http://charles.plessy.org
Wako, Saitama, Japan
? microbio.wml.65
? microbio.wml.diff
? practice.wml.diff
? practice.wml.new
Index: microbio.wml
===================================================================
RCS file: /cvs/webwml/webwml/english/devel/debian-med/microbio.wml,v
retrieving revision 1.67
diff -u -r1.67 microbio.wml
--- microbio.wml 17 Jan 2007 19:57:14 -0000 1.67
+++ microbio.wml 4 Feb 2007 08:39:23 -0000
@@ -13,6 +13,19 @@
</h2>
+<project name="Amap"
+ url="http://bio.math.berkeley.edu/amap/";
+ license="Public Domain">
+ AMAP is a command line tool to perform multiple alignment of peptidic
+ sequences. It utilizes posterior decoding, and a sequence-annealing
+ alignment, instead of the traditional progressive alignment method. It
+ is the only alignment program that allows to control the sensitivity /
+ specificity tradeoff. It is based on the ProbCons source code, but
+ uses alignment metric accuracy and eliminates the consistency
+ transformation.
+</project>
+
+
<project name="ARB"
url="http://www.arb-home.de/";
license="<non-free />"
@@ -367,6 +380,49 @@
</project>
+<project name="POA"
+ url="http://sourceforge.net/projects/poamsa/";
+ license="GPL">
+ POA is Partial Order Alignment, a fast program for multiple sequence
+ alignment in bioinformatics. Its advantages are speed, scalability,
+ sensitivity, and the superior ability to handle branching / indels in
+ the alignment.
+</project>
+
+
+<project name="Primer3"
+ url="http://frodo.wi.mit.edu/primer3/primer3_code.html";
+ license="<free />"
+ deb="http://packages.debian.org/unstable/science/primer3/";>
+ <p>
+ Primer3 picks primers for polymerase chain reactions, considering as
+ criteria:
+ </p>
+ <ul>
+ <li>oligonucleotide melting temperature, size, GC content,
+ and primer-dimer possibilities</li>
+ <li>PCR product size</li>
+ <li>positional constraints within the source sequence</li>
+ <li>miscellaneous other constraints</li>
+ </ul>
+ <p>
+ All of these criteria are user-specifiable as constraints, and
+ some are specifiable as terms in an objective function that
+ characterizes an optimal primer pair.
+ </p>
+</project>
+
+
+<project name="ProAlign"
+ url="http://evol-linux1.ulb.ac.be/ueg/ProAlign/";
+ license="GPL">
+ ProAlign includes a graphical interface allowing to (i) perform
+ alignments of nucleotide or amino-acid sequences, (ii) view the
+ quality of solutions, (iii) filter the unreliable alignment regions
+ and (iv) export alignments to other softwares.
+</project>
+
+
<project name="ProbCons"
url="http://probcons.stanford.edu/";
license="Public domain"
@@ -488,6 +544,22 @@
types; more detailed output about polyadenylation sites.
</project>
+
+<project name="Sigma"
+ url="http://www.imsc.res.in/~rsidd/sigma/";
+ license="GPL">
+ Sigma (<q>Simple greedy multiple alignment</q>) is an alignment program
+ with a new algorithm and scoring scheme designed specifically for
+ non-coding DNA sequence. Sigma uses a strategy of seeking the best
+ possible gapless local alignments (a strategy earlier used by
+ DiAlign), at each step making the best possible alignment consistent
+ with existing alignments, and scores the significance of the alignment
+ based on the lengths of the aligned fragments and a background model
+ which may be supplied or estimated from an auxiliary file of
+ intergenic DNA.
+</project>
+
+
<project name="T-Coffee"
url="http://igs-server.cnrs-mrs.fr/~cnotred/Projects_home_page/t_coffee_home_page.html";
license="GPL"
@@ -565,6 +637,22 @@
</h2>
+<project name="BALLView"
+ url="http://www.ballview.org/";
+ license="LGPL"
+ deb="http://mentors.debian.net/debian/pool/main/b/ballview/ballview_1.2-1.dsc";>
+ BALLView is an extensible viewer for bio-molecular structures. It
+ provides all standard models and offers rich functionality for
+ molecular modeling and simulation, including molecular mechanics
+ methods (AMBER and CHARMM force fields), continuum electrostatics
+ methods employing a Finite-Difference Poisson Boltzmann solver, and
+ secondary structure calculation. Since BALLView is based on BALL (the
+ Biochemical ALgorithms Library), it is easily extensible on the level
+ of C++ code and it has an Python interface to allow interactive rapid
+ prototyping.
+</project>
+
+
<project name="Bioconductor"
url="http://www.bioconductor.org/";
license="GPL/LGPL"
@@ -699,29 +787,6 @@
</project>
-<project name="Primer3"
- url="http://frodo.wi.mit.edu/primer3/primer3_code.html";
- license="<free />"
- deb="http://bioinformatics.pzr.uni-rostock.de/~moeller/debian/primer3/";>
- <p>
- Primer3 picks primers for polymerase chain reactions, considering as
- criteria:
- </p>
- <ul>
- <li>oligonucleotide melting temperature, size, GC content,
- and primer-dimer possibilities</li>
- <li>PCR product size</li>
- <li>positional constraints within the source sequence</li>
- <li>miscellaneous other constraints</li>
- </ul>
- <p>
- All of these criteria are user-specifiable as constraints, and
- some are specifiable as terms in an objective function that
- characterizes an optimal primer pair.
- </p>
-</project>
-
-
<project name="SMILE"
url="http://www-igm.univ-mlv.fr/~marsan/smile_english.html";
license="GPL"
@@ -767,19 +832,6 @@
</h2>
-<project name="Amap"
- url="http://bio.math.berkeley.edu/amap/";
- license="Public Domain">
- AMAP is a command line tool to perform multiple alignment of peptidic
- sequences. It utilizes posterior decoding, and a sequence-annealing
- alignment, instead of the traditional progressive alignment method. It
- is the only alignment program that allows to control the sensitivity /
- specificity tradeoff. It is based on the ProbCons source code, but
- uses alignment metric accuracy and eliminates the consistency
- transformation.
-</project>
-
-
<project name="Cactus"
url="http://www.cactuscode.org/Community/Biology.html";
license="GPL">
@@ -828,13 +880,12 @@
</project>
-<project name="POA"
- url="http://sourceforge.net/projects/poamsa/";
+<project name="Molekel"
+ url="http://bioinformatics.org/molekel/wiki/Main/HomePage";
license="GPL">
- POA is Partial Order Alignment, a fast program for multiple sequence
- alignment in bioinformatics. Its advantages are speed, scalability,
- sensitivity, and the superior ability to handle branching / indels in
- the alignment.
+ Molekel is an opensource (GPL) multiplatform molecular visualization
+ program being developed at the Swiss National Supercomputing Centre
+ (CSCS).
</project>
@@ -848,31 +899,6 @@
</project>
-<project name="ProAlign"
- url="http://evol-linux1.ulb.ac.be/ueg/ProAlign/";
- license="GPL">
- ProAlign includes a graphical interface allowing to (i) perform
- alignments of nucleotide or amino-acid sequences, (ii) view the
- quality of solutions, (iii) filter the unreliable alignment regions
- and (iv) export alignments to other softwares.
-</project>
-
-
-<project name="Sigma"
- url="http://www.imsc.res.in/~rsidd/sigma/";
- license="GPL">
- Sigma (<q>Simple greedy multiple alignment</q>) is an alignment program
- with a new algorithm and scoring scheme designed specifically for
- non-coding DNA sequence. Sigma uses a strategy of seeking the best
- possible gapless local alignments (a strategy earlier used by
- DiAlign), at each step making the best possible alignment consistent
- with existing alignments, and scores the significance of the alignment
- based on the lengths of the aligned fragments and a background model
- which may be supplied or estimated from an auxiliary file of
- intergenic DNA.
-</project>
-
-
<project name="Staden"
url="http://staden.sourceforge.net/";
license="BSD">
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