Open Bioinformatics Foundation
Encyclopedia
The Open Bioinformatics Foundation is a non profit, volunteer run organization focused on supporting open source
programming in bioinformatics
.
The mission of the foundation is to support development of open source toolkits for bioinformatics, organize and run the Bioinformatics Open Source Conference, and generally assist in the development and promotion of open source software development in the life sciences.
The foundation hosts servers for mailing lists, websites, and code repositories for the following open source projects:
Open source
The term open source describes practices in production and development that promote access to the end product's source materials. Some consider open source a philosophy, others consider it a pragmatic methodology...
programming in bioinformatics
Bioinformatics
Bioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...
.
The mission of the foundation is to support development of open source toolkits for bioinformatics, organize and run the Bioinformatics Open Source Conference, and generally assist in the development and promotion of open source software development in the life sciences.
The foundation hosts servers for mailing lists, websites, and code repositories for the following open source projects:
- BioDAS (see: http://www.biodas.org/) - XML Infrastructure for exchanging genome annotations
- BioJavaBioJavaThe BioJava Project is an open source project dedicated to providing Java tools for processing biological data. This includes include objects for manipulating sequences, protein structures, file parsers, CORBA interoperability, DAS, access to AceDB, dynamic programming, and simple statistical...
- Java toolkit - BioMOBYBioMOBYBioMOBY is a registry of web services used in bioinformatics. It allows interoperability between biological data hosts and analytical services by annotating services with terms taken from standard ontologies.- The BioMOBY project :...
- Data and application execution through web services - BioPerlBioPerlBioPerl is a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. It has played an integral role in the Human Genome Project....
- Perl toolkit - BioPipe - Pipelines and workflow project for creating bioinformatics protocol
- BioPythonBioPythonThe Biopython Project is an international association of developers of freely available Python tools for computational molecular biology, as well as bioinformatics.-References:*refer to the Biopython website for other , and a list of over one hundred ....
- Python toolkit - BioRubyBioRubyBioRuby is a package of Open Source Ruby code, with classes for DNA and protein sequence analysis, alignment, database parsing, and other Bioinformatics tools. Recently, tools for structural biology have been added.-External links:* ,*...
- Ruby toolkit - BioPHPBioPHPBioPHP is a package of Open Source PHP code, with classes for DNA and protein sequence analysis, alignment, database parsing, and other Bioinformatics tools.-External links:**...
- BioSQL - RDBMS Database schema for storing sequences, annotations, taxa data.
- OBDA (see: http://obda.open-bio.org/) - a standard for sequence data access locally, remotely, and via RDBMS
- EMBOSSEMBOSSEMBOSS is an acronym for European Molecular Biology Open Software Suite. EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology and bioinformatics user community...
- Sequence analysis toolkit.
See also
- List of Open Source Bioinformatics software
- BioinformaticsBioinformaticsBioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...
- Bioinformatics.org http://www.bioinformatics.org
- GMODGeneric Model Organism DatabaseThe Generic Model Organism Database Project began as an effort to create reusable software tools for developing Model Organism Databases . MODs describe genome and other information about important experimental organisms in the life sciences...
http://www.gmod.org - BioC# — Biolibrary for C#