Biopython project update at BOSC 2012

Not so hot off the presses, here are the slides from the talk I gave this summer at the Bioinformatics Open Source Conference (BOSC), a satellite conference of Intelligent Systems for Molecular Biology (ISMB). Since Peter Cock wasn't able to make it out to California this year, he suggested I fill in.

In addition to the usual coverage of new features, a big theme this year was the recurring successes we've had bring in new core developers via Google Summer of Code.

Biopython Project Update (BOSC 2012) from Eric Talevich

Jan Aerts has also posted the rest of the BOSC 2012 slides.

Python workshop #2: Biopython

As promised, here are the slides from Monday's Biopython programming workshop:

Biopython programming workshop at UGA

View more presentations from Eric Talevich.

This was another 2-hour session, with a short snack break in the middle this time -- which was also a nice opportunity to ask everyone about the pacing, and see if who's been following along with the examples in IPython (versus staring at a BSOD or lolcats -- which I didn't notice any of).

This went well:

• Pacing
• Using IPython to inspect objects and display documentation -- this lets some people "read ahead" and perhaps answer their own minor questions, leading to other, better questions
• The general introductory pattern of:
  1. Demonstrate how to import a module and instantiate the basic class
  2. Review, in English, the core features of the module and why they exist
  3. Walk through a short script that uses real data to accomplish some simple but useful task(s)
  4. Display the result, completing the mental pipeline of input -> transformation -> output

Room for improvement:

• I didn't always execute the final draft of each example, so there were a couple typos -- inconvenient for those following along in Python. (I've fixed them in the slides here.)
  
• Consequently, I didn't have an output file to show at the end of each example -- so I had to describe or draft one on the spot.
• The PDB module was the coolest part of the workshop, and I rushed it a bit. I was afraid the visitors from Genetics and Plant Bio would be bored with it, but I don't think they were, and the Bioinformatics folks were left wanting more.

I'm planning to host both Python workshops again in the next academic year, either 1 per semester (as it was this year) or both each semester, maybe 2 weeks apart. The Biopython workshop in particular will be different next time because Bio.Phylo will finally be included with the main Biopython distribution -- evolution is cool, and more of the pretty is always a good thing to have in a programming workshop.

Python workshop #1, now on SlideShare

Last November I hosted a workshop on basic Python programming at UGA. The attendees were mostly from the bioinformatics department, but this workshop didn't go into science at all -- just practical Python usage. Today I finally got around to cleaning up the slides and uploading them to SlideShare:

Python workshop #1 at UGA

View more presentations from etalevich.

It looks like LaTeX Beamer and SlideShare's PDF/Flash converter don't play well together. Meh, it's still easy enough to read.

I'm working on a Biopython-specific followup right now for a workshop on Monday, 2/22. I'll post that here when it's done, too, with reasonable haste.