I presented journal club today on the paper:
Pandya, C., Brown, S., Pieper, U., Šali, A., Dunaway-Mariano, D., Babbitt, P. C., et al. (2013). Consequences of domain insertion on sequence-structure divergence in a superfold. PNAS, 110(36), E3381–7. PMID:23959887
They look at structural diversity in the HAD superfamily, which consists of a Rossmann fold plus 0-2 large domain insertions. This leads to some interesting conclusions about how the inserted domain changes the structure of the core domain. For instance, the interface between the two domains is relatively similar regardless of what cap domain is inserted, yet more distant portions show definite patterns.
It is often difficult to make strong conclusions about fold space due to the large divergence within folds, which obscures the evolutionary signal. Pandya et. al strike a nice balance between well-supported claims about this single superfamily, and more speculative general hypotheses about evolution and protein fold space.
My slides are available on SlideShare.
I’m quite proud of my recently-released Castle Panic game pieces. Castle Panic is a great game, and it is fun to have some sturdy walls and towers to replace the flimsy cardboard ones it comes with. I spent a long time figuring out how to use Sketchup for the 3D models and figuring out how to get my printer to make good-looking bricks. The design is CC-BY, and can be downloaded from thingiverse.
Last summer, my boss Phil Bourne brought up an interesting problem for science. Wikipedia is the first place most people look for information, and yet most scientific research can only be found in scientific journals. Experts rarely have time or desire to move this information onto Wikipedia, where it will be accessible to the general public. Phil credits this to a lack of incentives for academics—the pressure to publish in peer-reviewed journals leaves no time for other kinds of writing.
His solution as Editor-in-Chief of PLoS Computational Biology is to start publishing Wikipedia pages. Or rather, to publish a new kind of article called a Topic Page that is suitable for broad audiences and will be published simultaneously on PLoS Comp Biol and Wikipedia. I thought this was a great idea, and Andreas Prlić and I volunteered to be guinea pigs.
Today, I am happy to announce the publication of the first Topic Page. “Circular Permutation in Proteins”. It is peer reviewed and indexed by PubMed. It also appears as the Wikipedia page Circular permutation in proteins. In the past few hours there have already been edits by 5 people. I am excited to see how the Wikipedia community will improve my humble article. The PLoS PDF looks nice, but it is already outdated. In contrast, the Wikipedia version feels very much alive.
It was fun to be a part of the process of starting a new method of publishing. One of the problems we had is that while PLoS Comp Biol is an open-access journal, it has a slightly different license from Wikipedia. So I had to set up a wiki of our own on which to draft Topic Pages. I now know far more about administering a website than I did from my comparatively simple other websites (such as this blog). I also liked drafting a paper on a wiki. It’s easy to collaborate with someone else (although not real-time, like Google Docs), and the markup syntax is powerful but intuitive. I would consider drafting other scientific papers on wikis in the future.
Finally, here’s a few links if you found this interesting:
On June 7th I officially passed my qualifying exam. It consisted of a written report and an oral presentation. Many thanks to my committee: Ruben Abagyan, Pat Jennings, and Andy MacCammon.
I attend a lot of seminars as a grad student. Most of these include free food, which is both a blessing and a curse. A typical week for me:
|Monday||No seminars on Mondays, ever. Get lunch from the taco truck which parks just outside my window.|
|Tuesday ||Bourne Journal Club. Papa John’s sausage & pepperoni pizza.|
|Wednesday ||Mass spec seminar. Papa John’s sausage & pepperoni pizza.|
|Thursday ||Bioinformatics seminar. Papa John’s sausage & pepperoni pizza, cookies, or faculty lunch (depends on week).|
|Friday ||Pevzner Journal Club. Costco sandwiches. Usually free beer at a happy hour (CS, BMS, Pharmacy, or our lab, depending on week).|
Not exactly balanced, but it’s difficult to say no to free food!