Cells are tiny chemical robots hacked together through billions of years of evolution. Usually, when you want to understand how a robot works, you read its source code. The closest thing cells have to source, however, is a kind of interpreted byte-code called DNA. Reading and understanding this code (which is sometimes brilliant, sometimes kludgey, and never commented) is a major task in modern biology.
Luckily, there is currently way more sequenced DNA than we know what to do with. Approximately 150 billion bases of DNA have been sequenced as of late 2012, and this volume is expected to double by 2014. This data, if printed and bound, would run to sixty thousand volumes: clearly, no human being could ever read even 1% of it, much less use it to discover new biological knowledge. Our only hope for dealing with this deluge is to develop artificial intelligence to help us do science, or even do it for us. This is already happening. How?
In this workshop we'll explore some fundamental techniques in computational genomics, focusing on the lowly _E. coli_ bacterium. We'll start from scratch: after a crash course in molecular biology, we'll download an _E. coli_ genome and begin to analyze it with our own code, so that everything we do can be replicated from the comfort of your own basement. We'll develop algorithms for finding genes and predicting their expression levels, and by the end of the session we'll have added some comments and documentation to the _E. coli_ code base. We'll be writing code in Python, and all source will be available during the session. Please BYO Laptop (if you have one)
Some knowledge of Python may be helpful, but there are no prerequisites, except interest. This session is meant to give the coder (or would-be coder) with little experience in bioinformatics a taste of what its about, in a fun way.
This happens on Friday, Feb 15th at 7:00 pm. We are asking for a donation, whatever you deem appropriate, so that BUGSS can continue to do this kind of thing. No this is not NPR. (I think they have a 501(C)(3). We're still working on ours) This is the BUGSS lab.
Your guide, Patrick O'Neill, is a graduate student in the Erill Lab at UMBC, where he applies machine learning and biophysics to the study of gene regulation in bacteria. He once crashed a supercomputer.
Please RSVP here.
BUGSS is a 501(C)3 charity. Please help keep BUGSS going!