Today I attended a virtual journal club. Organized by Stephen Larson of OpenWorm (I talked about that very cool 3D worm project in a tip of the week a while back), it also included a few folks from OpenWorm, and two of the authors of the paper: Jonathan Karr and Jayodita Sanghvi. Jonathan’s cat also showed up at one point .
Stephen did a part in the beginning that was a presentation of the main features of the paper, and the context of the work in biology today. I think he had quite a similar take on it to what I was describing in my tip this week: modeling types of papers cause a bit of drama and resistance in the biology community; and that this relied on so much previous work in hundreds of publications and lots of curated databases. But he also stressed the importance of this work in moving this field forward.
The discussion part was terrific. We covered standards in system biology (they aren’t quite ready to accommodate this work), how this can help other modelers think through the issues (especially those with larger genomes), how much characterization of the biology you need before you do this, how much of a cell system this actually captures, and more. There was a part about making this more of a community of “open cell” like OpenWorm. But the response from the authors/grad students was interesting: it’s really not up to them. If that was to happen, it would have to be supported and nurtured and that’s not what they are charged with. It hits on the issue of support for computational tools and our ability to build on existing stuff. It was an important point.
Anyway, the video is available and you can watch. It’s over an hour long, but if you are working on cell modeling I think it would be worth your time. It also might offer students some guidance on potential areas that need to be picked up after this if you are looking for projects.
I really enjoyed the virtual journal club idea and format. There should be more of these. It would be great if publishers would support some of them.
EDIT: Just wanted to note that the original meeting invitation has links to the video, also to the slides Stephen used, and some other handy stuff (like the paper and supplements) https://plus.google.com/events/c1hs4k76d0mc5d6n03b4rneh0ro/117948341754627144949