antiSMASH: Searching for New Antibiotics Using Open Source Tools
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Ever since Alexander Fleming discovered the first antibiotic being produced by
a Penicillium mould in 1928, scientists have been searching bacteria and fungi
for new substances to combat infectious diseases. In the last 40 years however,
only few new substances have been discovered that actually reached the market.
In the arms race between bacteria developing new resistances and humanity
developing new antibiotics, a more organized approach on drug discovery can
keep us from falling behind. With the advent of high throughput genetic
sequencing, a large number of bacterial genome sequences have become available
for analysis. Rather than testing every candidate strain for antimicrobial
activity and then painstakingly isolating and characterizing the substance
causing this activity, it has now become viable to predict the substances a
bacterium can produce using computer-based prediction algorithms.

antiSMASH is an Open Source pipeline that combines all published methods for
predicting antibiotics and other interesting small-molecular substances
produced by bacteria and fungi from their genomic sequence. By combining
existing Open Source tools with reimplementation of published but proprietary
prediction methods, antiSMASH manages to provide life scientists with a
user-friendly web interface and publication-quality illustrations.

This talk will present to the interested non-biologist how the whole process of
going from sequence information to prediction of produced antibiotics is done,
requiring as little previous knowledge in mathematics and biology as possible.
The author will also talk about the differences in developing Open Source
software in an academic environment as compared to traditional OSS development.



Bio
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Kai Blin is a computational biologist by trade and Open Source developer by
passion. During the day he is helping to identify new antibiotics to combat
diseases. Being more of a network and systems programmer in his spare time,
the Samba Team member feels lucky to be able to also work on Open Source
software on his day job.