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Genome annotation@BioDec: python all over the place.

Description

The talk will briefly describe BioDec’s genome annotation pipeline, which has been internally evolved for ten years to annotate mammalian, bacterial, and viral genomes at the protein level. Everything we built is coded in Python: the machine-learning annotation engine, the middleware and the data visualization interface. A software that would have been extremely difficult to create, for a tiny shop as BioDec, without leveraging the language itself and projects such as BioPython, Scipy, Plone, and Web2py. We will try to distill some of the lessons that we learned from more than ten years of experience dealing with machine-learning-intensive applications and large data sets with open-source software and Python.

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