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Practical Innovation at BioCon 2003


BioPerl: Reality vs. Myth
Nathan Goodman

Track: Toolkits
Date: Tuesday, February 04
Time: 2:15pm - 3:00pm
Location: California Ballroom C

Open source. Community software. Hackathons. All great sentiments, but do they really work? A lot of groups are developing open source community software­-all those BioXxxs­-but is anyone using this stuff? And is any good?

Goodman’s group at the Institute for Systems Biology (ISB) decided to take the plunge and use BioPerl for a real project. At ISB, open source is regarded as a key element of the academic mission. ISB releases its own software as open source and prefers to use open source in developing that software. How could ISB espouse this philosophy and ignore the significant open source developments of BioPerl and the other BioXxxs?

The choice of BioPerl vs. the other Bios was based on two beliefs: (1) Perl is the preferred programming language of the field; and (2) the folks behind BioPerl have a very convincing track record.

Goodman describes his team’s experiences with BioPerl--the bad along with the good, including issues with performance, documentation, and code quality. BioPerl is far from a comprehensive bioinformatics toolkit, but it does provide a lot of useful functionality. It’s definitely a package ISB will keep on using!

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