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

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.

Fig. 1.

Biogem eases publication of new bioinformatics Ruby software modules on the Internet, in a few steps. (1) The software generator creates the directory layout and files for a new software module named ‘foo’. (2) The developer writes or modifies source code and (3) quickly and easily publishes the source code and module online, for others to read, install and use. Collaboration (4) is facilitated by publishing source code and changes to navigationable websites. Then the workflow continues again at (2). The http://biogems.info website tracks published modules. Popularity of each published module is tracked, as well as source code changes, updates, bugs and issues. Unlike with the practise of publishing scientific papers, collaboration on software often comes post factum, i.e. after original publishing of a software module. Therefore, it pays to publish software modules early and often. This is reflected in the Biogem workflow.