Hello world!

Yes, I admit. Caught red-handed. I too am contributing to the ever-expanding Blogosphere. Recent events have triggered me to actually do something that was on the someday/maybe list for the longest time. This is the result.

What recent events am I talking about? Why, I thought you’d never ask. I’m going to participate in this year’s Google Summer of Code!

My project is entitled “Visual history of biological pathways“. I’d like to explain that a bit.

I’m a PhD student, and my research involves something called Biological pathways. Biological Pathways are simply drawings of processes that take place within a Cell, for example, you could have an Insulin Signalling Pathway that schematically shows how Insulin activates the Insulin Receptor in the cell membrane, which in turn activates Ras / MAP-K proteins which in turn activate many other enzymes and glucose transporters which eventually leads to uptake of glucose from the blood.

Representing pathways as simple drawings can be a useful research tool. My contribution to all this has been the development (together with fellow PhD student Thomas Kelder) of PathVisio, a pathway creation and editing program written in Java. It’s currently in Beta.

At the same time, the research group where I work, BiGCaT Bioinformatics, was setting up a collaboration with the GenMAPP group at UCSF, San Francisco. GenMAPP was officially accepted as a Mentoring organization, and they asked me and Thomas to apply. I’m really excited about this, this is a great opportunity for me for two reasons: through the summer of code I can work closer together with the people at UCSF, plus I get to be part of a really cool open source event.

Recently at GenMAPP they started something called WikiPathways (no prizes for guessing what that is). WikiPathways is what my Summer Project is all about. Basically it boils down to this: I think WikiPathways needs a history feature, so that you can easily see what other people have changed. Although this may seem at first like a minor detail, I think it is of immense psychological value for any wiki-like system.

One thing is for sure, It’s going to be a very interesting summer!


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