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Bioinformatics. 2012 Apr 1;28(7):1035-7. doi: 10.1093/bioinformatics/bts080. Epub 2012 Feb 12.

Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics.

Author information

  • 1Integrative Biology Program, Istituto Nazionale Genetica Molecolare, Milan 20122, Italy. bonnal@ingm.org

Abstract

SUMMARY:

Biogem provides a software development environment for the Ruby programming language, which encourages community-based software development for bioinformatics while lowering the barrier to entry and encouraging best practices. Biogem, with its targeted modular and decentralized approach, software generator, tools and tight web integration, is an improved general model for scaling up collaborative open source software development in bioinformatics.

AVAILABILITY:

Biogem and modules are free and are OSS. Biogem runs on all systems that support recent versions of Ruby, including Linux, Mac OS X and Windows. Further information at http://www.biogems.info. A tutorial is available at http://www.biogems.info/howto.html

CONTACT:

bonnal@ingm.org.

PMID:
22332238
[PubMed - indexed for MEDLINE]
PMCID:
PMC3315718
Free PMC Article

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