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">