veyepar: antiSMASH: Searching for New Antibiotics Using Open Source Tools

Author(s):	Kai Blin
Location	Caro
Date	jan Tue 17	Days Raw Files
Start	13:20	First Raw Start	error-in-template
Duration	0:50:00	Offset	None
End	14:10	Last Raw End
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http://lca2012.linux.org.au/schedule/75/view_talk
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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 the genetic potential to synthesize antibiotics and other interesting small-molecular substances in bacteria and fungi. By combining existing Open Source tools with re-implementations 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.

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