[Baypiggies] Bioinformatics Python Programmer

Anna Ravenscroft annaraven at gmail.com
Sat Oct 10 23:25:31 CEST 2009

On Sat, Oct 10, 2009 at 10:51 AM, Glen Jarvis <glen at glenjarvis.com> wrote:
> Wow! This is *such* a big topic. Although it's impossible to squeeze two
> semesters of classwork into an hour, I could definitely speak on it, but I'd
> have to keep it on "just the basics"... I'd also drag one of my peers from
> work in to do this talk (he has a degree both in Microbiology and in
> Computer Science and can field a lot of the questions)....
> We could do a tech talk which answered just the self-evaluation questions I
> sent in a recent email and did some very basic BioPython and webqueries. I
> know BioPython has fallen out of favor in the past few years, but it's great
> for doing things like iterating through FASTA sequences, getting sequence
> lengths, converting from one sequence format to another, etc. And, it's very
> simple to use - which makes it a great fundamental tool for a basic tech
> talk. I saw at least two people who were much more qualified than I was on
> this list - I'd happily speak with them. My topics, however, would assume
> the audience has zero Biological background.
> If there's an interest, I could certainly try to put something together. I
> guess the fundamental question is, how many people would really be
> interested?  Especially since this is 95% basic science and the programming
> is dead simple (iterating through a sequence and getting some results). We
> don't have the science to do more complex programming examples.
> We could also do a basic demo of Pymol too - but that would be showing
> pretty 3D models of molecules (proteins in our case) using a tool that's
> already created.
> I could do this starting January -- but again, I'm not certain how
> interested our entire group would be since it's heavy on the science you
> need to understand as background and very light on the actual
> python/programming.


I think it sounds delightful! Both the basics with BioPython and the
intro to Pymol. If not everyone is interested, that's okay. There's
plenty of talks that not *everyone* is interested in.

I am the mother of all things and all things shall wear a sweater!

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