Create a Biogem!
Creating a Biogem is easy. New biogems get added monthly!
Biogem provides a set of tools for those Bioinformaticans who want to start coding an application, or a library for using/extending BioRuby's core library and sharing the code as a gem through rubygems.org. Biogems are automatically listed at biogems.info when the gem is pushed to rubygems.org, using the biogem tool, and the name of the gem starts with bio- (bio dash), e.g. bio-fasta or bio-gff3.
Biogem aims to encourage open source software development, and provide tools to support bazaar programming. In our interpretation:
- Every good work of software starts by scratching a developer's personal itch
- Release source code early and often
- With enough users, almost every problem is quickly known, and a fix obvious
- Many heads are inevitably better than one
- Good programmers know what to write. Great ones know what to rewrite (and reuse)
We suggest for bioinformatics
- Use Ruby and Biogem software generation, or do not repeat yourself (DRY)!
- Use the foreign function interface (FFI) for performance
- Use unit tests and specifications (RSpec) for both agility and robustness
- Biogem README
- Create a Biogem!
- Hacking the Biogem tool (DRY)!
- Source code for Biogem
- Source code for the biogems.info website
Other important links