biolib Pjotr Prins

generic C/C++ libraries for Bio::* projects. esp for data IO/parsing/interpretation

In <language of choice> bind <generic C implementation> using SWIG with Biolib

Limited pool of bioinf programmers and being spread too thin across diff language specific projects. Shared stuff good cos less duplication, more people testing code etc. Inexplicable picture of young girl. Man with beard.

Bioperl on Github. Uses Cmake (as opposed to autoconf? – modular, resolves complex dependencies) and SWIG (rules for generating code, DRY, pattern matching, multi-language support (>20))

Year One:
Staden sequencer trace files
GSL (GNU Science Library)
Rlib R stuff
R/qtl quant genetics
Libsequence sequence analysis
Bio++ sequence analysis

Automated API doc
more libs (Emboss, NCBI)
more languages
Bio* integration (CPAN, Ruby gems etc)
Distribute as packages

NB: BoF session at 16.50

Note to self: SAMtools?

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