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Biologie - Biocomputing

PAGES WEB

La Station de Biologie Marine de Concarneau

Le museum national d'Histoire naturelle

<http://cimbad.mnhn.fr/mnhn/conc/>

Biomethodes

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/>

Phylogeny and Reconstructing Phylogenetic Trees

Reconstruction Algorithms

<http://babbage.clarku.edu/~djoyce/java/Phyltree/reconstruction.html>

Phylogenetic tree - Wikipedia

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>

PhyloCode

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>

Methods of Phylogenetic Tree Reconstruction

<http://www-hto.usc.edu/~cbmp/2002/PhylogeneticAnalysis/methods.html>

Bioinformatics in the CSE Department

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/>

PAGES WEB UNIVERSITÉS

Bioknoppix

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

Webiologie

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/>

The Tree of Life Project

<http://tolweb.org/tree/>

O|B|F Open Bioinformatics Foundation

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/>

Société Française de Microbiologie

<http://www.sfm.asso.fr/>

ALGORITHMES

UPGMA

Fred Opperdoes

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

CompLearn

Rudi Cilibrasi

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/>

newicktree

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

Biopython

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

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/>

PISE - Pasteur Institute Software Environment

a tool to generate Web interfaces for Molecular Biology programs

Catherine Letondal, Pasteur Institute.

<http://www.pasteur.fr/recherche/unites/sis/Pise/>

The NCBI C++ Toolkit Book

ftp

<http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit.chapter.ch_getcode>

JAVA

BioJava

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.

BioJava tutoriel

<http://biojava.org/>

PERL

BioPerl

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

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

Theory of evolution

<http://www.ucmp.berkeley.edu/history/evotheory.html>

THÈSES - THESIS

Banque des monographies SVT

Ecole Pratique des Hautes Etudes

<http://www.ephe.univ-montp2.fr/menu_html/monographies_html/monographies.html>

DOCUMENTS - PAPERS

Laboratory for Molecular Science

Papers From LMS

DNA Computation - Self-assembly -

<http://www.usc.edu/dept/molecular-science/fm-papers.htm>

COURS - COURSES

Sequence comparison

Christian Charras - Thierry Lecroq

<http://www-igm.univ-mlv.fr/~lecroq/seqcomp/>

Génétique

Introduction générale et notions de base

Premier Cycle Sur Mesure

<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>

Algorithms in Molecular Biology

Richard Karp, Larry Ruzzo, Martin Tompa

<http://www.cs.washington.edu/education/courses/590bi/96w/>

TUTORIELS - TUTORIALS

Scientific Computation WS 2001/2002

Gaston Gonnet

<http://linneus20.ethz.ch:8080/wsrscript.html>

Phylogenetic Trees

Peer Itsik

<http://www.math.tau.ac.il/~rshamir/algmb/00/scribe00/html/lec08/lec08.html>

UPGMA

<http://pubmlst.org/software/analysis/start/manual/upgma.shtml>

ARTICLES

L'explosion des mathématique

SMF société Mathématique de France

De l'ADN à la théorie des noeuds Nguyen Cam Chi et Hoang Ngoc Minh

<http://smf.emath.fr/Publications/ExplosionDesMathematiques/>

PLoS BIOLOGY

<http://www.plosbiology.org/plosonline/?request=index-html>

BIOGRAPHIES

Ernst Haeckel (1834-1919)

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

Phylogénie

<liens_phylo.html>

bookmarks pour la bioinformatique

Catherine Mathé

<http://genopole.toulouse.inra.fr/~mathe/liens_bioinfo.html>

VSNS BioComputing Division Multiple Alignment Resource Page

This page was developed for the GNA-VSNS Biocomputing course

<http://merlin.bcm.tmc.edu:8001/bcdusa/Curric/MulAli/welcome.html>

Pedro's BioMolecular Research Tools

A Collection of WWW Links to Information and Services Useful to Molecular Biologists

<http://www.biophys.uni-duesseldorf.de/BioNet/Pedro/research_tools.html>

Actualités

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