> > Bio-* Programming Tools

Bio-* Programming Tools

This section contains links that include information on software development tools, such as BioJava and BioPerl. Other application programming interfaces (API) which are specifically designed for processing biological data are also listed here.

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Found 18 links

Displaying 15 links

BioconductorTool Content

http://www.bioconductor.org/

Computer Related > Bio-* Programming Tools
Computer Related > Math and Statistics
Expression > Transcript Expression Analysis

Bioconductor is an open source and open development software project that aims to provide access to a wide range of powerful statistical and graphical methods for the analysis of genomic data.

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tagsalgorithms biological models computational biology computer simulation database management systems dna probes dna sequence analysis gene expression profiling gene expression regulation information dissemination nucleic acid sequence homology oligonucleotide array sequence analysis reproducibility of results sequence alignment signal transduction transcription factors

BioDASResource Content

http://biodas.org/

Computer Related > Bio-* Programming Tools

This site is the center of development of an Open Source system for exchanging annotations on genomic sequence data.

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tagsbase sequence computational biology computer terminals genetic databases human genome humans reference values
setsOpen Bioinformatics Foundation

BioJavaTool Content

http://www.biojava.org/

Computer Related > Bio-* Programming Tools
Computer Related > Java

The BioJava Project is an open-source project dedicated to providing Java tools for processing biological data.

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tagscomputational biology computer systems humans programming languages
setsOpen Bioinformatics Foundation

BioMobyTool Content

http://biomoby.org/

Computer Related > Bio-* Programming Tools

BioMOBY is an international research project involving biological data hosts, biological data service providers, and coders whose aim is to explore various methodologies for biological data representation, distribution, and discovery.

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tagsdatabase management systems humans international cooperation nucleic acid databases
setsOpen Bioinformatics Foundation

BioPaxResource Content

http://www.biopax.org/

Computer Related > Bio-* Programming Tools

The BioPAX web site provides information about a collaborative effort to create a data exchange format for biological pathways.

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tagscomputational biology information dissemination metabolic networks and pathways programming languages signal transduction

BioPerlTool Content

http://www.bioperl.org/

Computer Related > Bio-* Programming Tools
Computer Related > PERL

The BioPerl Project is an international association of developers of open source Perl tools for bioinformatics, genomics and life science research.

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tagsalgorithms animals biological science disciplines computational biology computer systems database management systems genetic databases humans online systems programming languages software design systems integration
setsOpen Bioinformatics Foundation

BioPerl courseResource Content

http://www.pasteur.fr/recherche/unites/sis/formation/bioperl/

Computer Related > Bio-* Programming Tools
Computer Related > PERL

Great tutorial for those interested in the bioperl group of modules.

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BioPHPTool Content

http://www.biophp.org/

Computer Related > Bio-* Programming Tools
Computer Related > PHP

Open Source PHP code for bioinformatics. Includes functions and minitools (copy and paste one page scripts for basic tasks in bioinformatics. A wiki-like service allows modification and improvement of code.

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BioPythonTool Content

http://biopython.org/

Computer Related > Bio-* Programming Tools

The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology.

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tagscomputational biology computer simulation computer systems database management systems humans macromolecular substances molecular models programming languages protein conformation protein databases
setsOpen Bioinformatics Foundation

BioRubyTool Content

http://bioruby.org/

Computer Related > Bio-* Programming Tools

The BioRuby project aims to implement an integrated environment for bioinformatics with Ruby.

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setsOpen Bioinformatics Foundation

CCTTool Content

http://sourceforge.net/projects/orb-cct

Computer Related > Bio-* Programming Tools

CCT (Current Comparative Table) is a software package that you can install and set-up on your own system to help you to maintain and search databases.

NAR Web Server Issue 2005
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tagscomputational biology genomics nucleic acid databases protein databases

Ensembl APITool Content

http://ensembl.org/info/data/api.html

Computer Related > Bio-* Programming Tools

Ensembl is a freely available software system for genomic analysis. The documentation page at Ensembl is the best place to get information on the Ensembl application programming interface (API). In particular, the tutorial document includes lots of examples of scripts and exercises for you to try.

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Human Ageing Genomic ResourcesResource Content

http://genomics.senescence.info/index.html

Computer Related > Bio-* Programming Tools
Human Genome > Other Resources

The Human Ageing Genomic Resources (HAGR) website provides tools and curated databases relevant to the genetics of human ageing. GenAge is a database of genes related to human ageing, and AnAge is a multi-species database facilitating the comparative biology of ageing. The Ageing Research Computational Tools (ARCT) is a collection of Perl modules to assist comparative genomics research.

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NCBI C++ toolkitTool Content

http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=toolkit.TOC&...

Computer Related > Bio-* Programming Tools
Computer Related > C/C++

The NCBI C++ Toolkit is a collection of C++ modules developed by the NCBI for writing bioinformatics software and applications.

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setsNational Center for Biotechnology Information (NCBI)

Open Bioinformatics FoundationResource Content

http://www.open-bio.org/

Computer Related > Bio-* Programming Tools
Education > Community

The Open Bioinformatics Foundation is a non profit, volunteer run organization focused on supporting open source programming in bioinformatics.

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external linksLink on Twitter
setsOpen Bioinformatics Foundation

Tags associated with subcategory 'Computer Related/Bio-* Programming Tools'

computational biology Open Bioinformatics Foundation database management systems programming languages humans computer systems dna probes dna sequence analysis software design systems integration online systems gene expression profiling gene expression regulation transcription factors genomics nucleic acid databases signal transduction sequence alignment information dissemination nucleic acid sequence homology oligonucleotide array sequence analysis reproducibility of results genetic databases protein databases chemical models controlled vocabulary computer simulation biological models algorithms metabolic networks and pathways base sequence animals biological science disciplines international cooperation National Center for Biotechnology Information (NCBI) protein conformation computer terminals human genome reference values molecular models macromolecular substances documentation factual databases metabolism terminology as topic