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Biologie - Biocomputing
| SOMMAIRE | Pages Web | Web Edu. | Associations | Algorithmes | Logiciels | Utilitaires |
| Java | Perl | Données | Théorie | ThÈses | Papiers | Cours | Tutoriels |
| Articles | Biographies | Liens |
| Java | Perl | Données | Théorie | ThÈses | Papiers | Cours | Tutoriels |
| Articles | Biographies | Liens |
PAGES WEB
<http://cimbad.mnhn.fr/mnhn/conc/>Biomethodes' mission is to conceive, produce and sell a new generation of highly competitive biomolecular tools for genetic engineering which derive from its unique technological platform.
<http://www.biomethodes.com/>
Reconstruction Algorithms
<http://babbage.clarku.edu/~djoyce/java/Phyltree/reconstruction.html>
A phylogenetic tree is a tree showing the evolutionary interrelationships between various species or other entities that are believed to have a common ancestor. A phylogenetic tree is a form of cladogram.
<http://en.wikipedia.org/wiki/Phylogenetic_tree>
The PhyloCode is a formal set of rules governing phylogenetic nomenclature. It is designed to name the parts of the tree of life by explicit reference to phylogeny.
The first international meeting on phylogenetic nomenclature is scheduled for July 6-9, 2004 in Paris.
<http://www.ohiou.edu/phylocode/index.html>
<http://www-hto.usc.edu/~cbmp/2002/PhylogeneticAnalysis/methods.html>
The Department of Computer Science and Engineering is involved in several major initiatives in bioinformatics, specifically in the area of computational life science.
NIH working definition of bioinformatics and computational biology developed by the BISTIC Definition Committee and released on July 17, 2000.
<http://www.cse.sc.edu/research/bioinformatics/index.html>
Freshwater Shrimp in the Aquarium Description And General Information For the Interested Hobbyist
by Joe Anderson
<http://www.thekrib.com/Fish/Shrimp/>
EDUCATION
is a customized distribution of Knoppix Linux Live CD. With this distrubution you just boot from the CD and you have a fully functional Linux OS distribution with open source applications targeted for the molecular biologist. Beside using some RAM, Bioknoppix doesn't touch the host computer, being ideal for demonstrations, molecular biology students, workshops, etc.
Carlos M Rodriguez University of Puerto Rico
<http://bioknoppix.hpcf.upr.edu/>
ASSOCIATIONS
Ce site est consacré à la vulgarisation de la biologie. Il a pour ambition d'aborder tous les thèmes de façon à faire un tour d'horizon des connaissances actuelles.
<http://www.webiologie.org/>
<http://tolweb.org/tree/>
The foundation grew out of the volunteer projects Bioperl, BioJava and Biopython and was formally incorporated in order to handle our modest requirements of hardware ownership, domain name management and funding for conferences and workshops.
<http://www.open-bio.org/>
<http://www.sfm.asso.fr/>
ALGORITHMES
Construction of a distance tree using clustering with the Unweighted Pair Group Method with Arithmatic Mean (UPGMA).
<http://www.icp.ucl.ac.be/~opperd/private/upgma.html>
Calculation of phylogenetic tree using UPGMA & Fitch-Margoliash methods
<http://uwadmnweb.uwyo.edu/zoology/mcdonald/molmark/Demos/UPGMA/UPGMA.html>
LOGICIELS - SOFTWARES
this method is so general that it requires no background knowledge about any particular classification. There are no domain-specific parameters to set and only a handful of general settings. Just feed and run.
<http://complearn.sourceforge.net/>
by GEORGE SAVVA
newicktree LaTeX package that allows the easy drawing of Newick (New Hampshire) format phylogenetic trees, by providing a high level interface to the PSTricks package.
<http://cbr.jic.ac.uk/dicks/software/newicktree/index.html>
OUTILS - TOOLS
It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics.
<http://www.biopython.org/>
BioRuby project aims to implement an integrated environment for Bioinformatics with Ruby language. Design philosophy of the BioRuby library is KISS (keep it simple and stupid) to maximize the usability and the efficiency for biologists as a daily tool. The project was started in Japan and supported by University of Tokyo (Human Genome Center), Kyoto University (Bioinformatics Center) and the Open Bio Foundation.
<http://www.bioruby.org/>
a tool to generate Web interfaces for Molecular Biology programs
<http://www.pasteur.fr/recherche/unites/sis/Pise/>
<http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit.chapter.ch_getcode>
JAVA
is an open-source project dedicated to providing a Java framework for processing biological data. It include objects for manipulating sequences, file parsers, DAS client and server suport, access to BioSQL and Ensembl databases, and powerful analysis and statistical routines including a dynamic programming toolkit.
<http://biojava.org/>
PERL
The Bioperl server provides an online resource for modules, scripts, and web links for developers of Perl-based software for life science research. We can also provide web, FTP and CVS space for individuals and organizations wishing to distribute or otherwise make freely available standalone scripts & code.
<http://www.bioperl.org/>
DONNÉES - DATAS
Ensembl is a joint project between EMBL - EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on metazoan genomes. Ensembl is primarily funded by the Wellcome Trust.
This site provides free access to all the data and software from the Ensembl project. Click on the species buttons to the right to browse the data.
<http://www.ensembl.org/>
THÉORIE - THEORY
<http://www.ucmp.berkeley.edu/history/evotheory.html>
THÈSES - THESIS
Ecole Pratique des Hautes Etudes
<http://www.ephe.univ-montp2.fr/menu_html/monographies_html/monographies.html>
DOCUMENTS - PAPERS
Papers From LMS
DNA Computation - Self-assembly -
<http://www.usc.edu/dept/molecular-science/fm-papers.htm>
COURS - COURSES
Christian Charras - Thierry Lecroq
<http://www-igm.univ-mlv.fr/~lecroq/seqcomp/>
Introduction générale et notions de base
<http://commedia.campus.univ-poitiers.fr/biologie/introgen/index.htm>
Cours de biologie et des liens vers des cours de bio
<http://jc.goncalves.free.fr/index.htm>
Richard Karp, Larry Ruzzo, Martin Tompa
<http://www.cs.washington.edu/education/courses/590bi/96w/>
TUTORIELS - TUTORIALS - TUTORS
Gaston Gonnet
<http://linneus20.ethz.ch:8080/wsrscript.html>
Peer Itsik
<http://www.math.tau.ac.il/~rshamir/algmb/00/scribe00/html/lec08/lec08.html>
<http://pubmlst.org/software/analysis/start/manual/upgma.shtml>
ARTICLES
De l'ADN à la théorie des noeuds Nguyen Cam Chi et Hoang Ngoc Minh
<http://smf.emath.fr/Publications/ExplosionDesMathematiques/>
<http://www.plosbiology.org/plosonline/?request=index-html>
BIOGRAPHIES
Ernst Haeckel, much like Herbert Spencer, was always quotable, even when wrong. Although best known for the famous statement "ontogeny recapitulates phylogeny", he also coined many words commonly used by biologists today, such as phylum, phylogeny, and ecology. On the other hand, Haeckel also stated that "politics is applied biology", a quote used by Nazi propagandists. The Nazi party, rather unfortunately, used not only Haeckel's quotes, but also Haeckel's justifications for racism, nationalism and social darwinism.
<http://www.ucmp.berkeley.edu/history/haeckel.html>
LIENS - LINKS
<liens_phylo.html>Catherine Mathé
<http://genopole.toulouse.inra.fr/~mathe/liens_bioinfo.html>
This page was developed for the GNA-VSNS Biocomputing course
<http://merlin.bcm.tmc.edu:8001/bcdusa/Curric/MulAli/welcome.html>
A Collection of WWW Links to Information and Services Useful to Molecular Biologists
<http://www.biophys.uni-duesseldorf.de/BioNet/Pedro/research_tools.html>
| SOMMAIRE | Pages Web | Web Edu. | Associations | Algorithmes | Logiciels | Utilitaires |
| Java | Perl | Données | Théorie | ThÈses | Papiers | Cours | Tutoriels |
| Articles | Biographies | Liens |
| Java | Perl | Données | Théorie | ThÈses | Papiers | Cours | Tutoriels |
| Articles | Biographies | Liens |
| Accueil | Plan du site | Bloc notes | Jeux | Graphes | Combinatoire | Arithmétique | Algèbre |
| Analyse | Probabilités | Automates | Informatique | Divers | Lycée |
| Analyse | Probabilités | Automates | Informatique | Divers | Lycée |
Advertising :
If you see a reference in one of the files that is not linked, and you know of a link address to the appropriate document,
please send me mail, and I will include the link in the document. Thanks very much in advance.
Avertissement : Le classement par catégories est approximatif. Certains liens se retrouvent dans des rubriques différentes et sur plusieurs pages. Les commentaires sont généralement des courts extraits des pages référencées. Il est possible que certains liens nécessitent une mise à jour.
Tous commentaires ou remarques sont les bienvenus, vous pouvez les adresser à :
Les mises à jour demandées sont réalisées dès que possible et, sauf si c'est nécessaire, aucun message de réponse n'est expédié. Merci de m'écrire.
Copyright © 1999-2012 Jean-Paul Davalan - Reproduction interdite.
Avertissement : Le classement par catégories est approximatif. Certains liens se retrouvent dans des rubriques différentes et sur plusieurs pages. Les commentaires sont généralement des courts extraits des pages référencées. Il est possible que certains liens nécessitent une mise à jour.
Tous commentaires ou remarques sont les bienvenus, vous pouvez les adresser à :
Les mises à jour demandées sont réalisées dès que possible et, sauf si c'est nécessaire, aucun message de réponse n'est expédié. Merci de m'écrire.
Copyright © 1999-2012 Jean-Paul Davalan - Reproduction interdite.