本帖最后由 redcat 于 2012-2-25 18:01 编辑
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Bioperl.org
http://www.bioperl.org
The Bioperl Project is an international association of developers of open source Perl tools for bioinformatics, genomics and life science research. The Bioperl server provides an online resource for modules, scripts, and web links.
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AceDB
http://www.acedb.org
A hierarchical database system for displaying genomic data (originally C. elegans), suitable also for displaying other scientific data.
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Bielefeld University Bioinformatics Server
http://bibiserv.techfak.uni-bielefeld.de
BiBiServ supports Internet-based collaborative research, software development and distance education in bioinformatics.
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BioJava.org
http://biojava.org
The BioJava Project is an open-source project dedicated to providing Java tools for processing biological data.
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BioLisp.org
http://nostoc.stanford.edu/Docs
BioLisp.org is a public resource supporting scientists who use Lisp to develop intelligent applications in the biological sciences. We collect and disseminate Lisp biocomputing code, and gather pointers to Lisp and other Intelligent BioComputing methods.
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BioPHP
http://www.biophp.org
An open source project to develop PHP code and scripts for biocomputing. A wiki-like service allows collaboration between developers.
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BioPython
http://www.biopython.org
The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology.
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BioQuery
http://www.bioquery.org
Tools that searches multiple biomedical databases from your desktop.
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BioRuby
http://bioruby.org
BioRuby project aims to implement an integrated environment for Bioinformatics with Ruby language.
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BioWarehouse Database Integration System
http://biowarehouse.ai.sri.com
Integrates multiple public bioinformatics databases into a single relational database system within a common bioinformatics schema.
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Bionconductor
http://www.bioconductor.org
The Bioconductor project produces an open source software framework that will assist biologists and statisticians working in bioinformatics, with primary emphasis on inference using DNA microarrays, built mostly using R.
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Brainwave Biosolutions
http://www.brainwave.in
Bioinformatics Company focused on the development of data mining products, databases, visualization and analysis tools.
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Cell Electrophysiology Simulation Environment (CESE)
http://cese.sourceforge.net
A framework to perform electrophysiological simulations. Useful for simulations of action potentials, individual ionic currents, and changes in ionic concentrations.
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DW Computing
http://www.dwcomputing.com
Web design, computer sales, and custom programming, including bioinformatics.
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Daggoo
http://www.daggoo.net
Daggoo helps biologists create automated analyses workflows using existing web services. Includes a video of the project.
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Dynamite
http://www.ebi.ac.uk/Dynamite
Code generator for writing dynamic programming programs.
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High Throughput Screening Tools
http://www.htstools.com
Analytical tools and SQL scripts that solve common problems in drug discovery.
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InterMine
http://www.intermine.org
A general-purpose object-oriented data warehouse system developed as part of the FlyMine project and made available as stand-alone open-source software.
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MolTalk
http://www.moltalk.org
Software development for structural bioinformatics. Runs on Unix, Windows and MacOSX.
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The National Cancer Institute's Center for Bioinformatics produces the caCORE infrastructure, an open-source enterprise architecture for cancer informatics.
http://ncicb.nci.nih.gov/NCICB/infrastructure">NCICB Core Infrastructure
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NeoBio
http://neobio.sourceforge.net
An open source library of Java bioinformatics algorithms. The current version consists mainly of sequence alignment algorithms such as Needleman- Wunsch and Smith-Waterman.
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PISE
http://www.pasteur.fr/recherche/unites/sis/Pise
Given an abstract definition of a program's parameters, PISE can generate various types of interface from the configuration module.
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Pathway Tools
http://bioinformatics.ai.sri.com/ptools
Predict metabolic pathways from genomes and graphically depict pathways. Visualize gene expression data on a metabolic pathway map. Generate a metabolic wall chart. Includes a genome browser and support for transcriptional regulatory networks.
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Phylogenetic Analysis Library
http://www.cebl.auckland.ac.nz/pal-project
PAL library is a Java toolkit for determining evolutionary trends.
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Sight
http://bioinformatics.org/jSight
Extendable parallel system for automatic genome analysis. Software for analysing all potential genes in a defined genome region. Given two marker names, can output reports of genomic features between them. Features for converting between naming systems, sequence retrieval, E-PCR, gene prediction, similarity search, protein pattern search, and report formatting. Written in Java.
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The BioSharp Project
http://biosharp.sourceforge.net
BioSharp is an open-source project to provide a framework for processing biological data using C# and other .net languages.
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Guide to running this programming language. Library contains programs to compute pairwise alignments, phylogenetic trees, multiple sequence alignments, and to make secondary structure predictions.
http://www.inf.ethz.ch/personal/ ... l/DarwinManual.html">The Darwin Manual
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A set of software tools that filter, format, and merge data in tabular or common biological formats. Organized as a classified collection of Perl one-liners.
http://sysbio.harvard.edu/csb/resources/computational/scriptome">The Scriptome
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The Systems Biology Markup Language
http://sbml.org
Information on the SBML project which helps develop a variety of software packages for SBML, a computer-readable format for representing models of biochemical reaction networks in software.
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The XEMBL Project
http://www.ebi.ac.uk/xembl
XEMBL provides access to the EMBL/GenBank/DDBJ Nucleotide Sequence Database, providing output in various XML standards.
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发表于 2012-2-25 17:22:13