Open source molecular modeling–finally?

My Bio SmartBrief newsletter today had a reference to a paper in a rather…um…obscure journal. Maybe it is just something I have missed over the years, but the Journal of the Royal Society Interface has really just never come across my desk before. Nevertheless, Wired seems to think this software is finally meeting our needs in biological modeling. Finally?

The open-source software movement has finally met the world of biological modeling.

Both a language and a program, “little b” gives systems biologists an infrastructure for building and sharing models of cellular activity.

Ok–this may be fabulous software. I’ll have a look. But to say that this is the one we have been holding our breath for is rather presumptuous. I’m not paying $49 for the paper, so I can’t assess it from the text. I will go and evaluate it at the developer’s site. For software evaluation I do read the papers (unless they cost $49), but I don’t believe anything until I kick the tires quite a bit anyway.

But from the breathless Wired article I can’t see why this is the solution rather than GenMapp, or BiologicalNetworks, or Cytoscape, or NAViGaTOR, or VisANT or….the half a dozen other that we are looking at for tutorial development. Or the ones I intend to learn about at the ISSB meeting in Sweden next month. The choice of tutorials there had me stumped on which ones I could fit into my schedule.

This Wired line about the image they show cracked me up:

Image: Detail from a gene regulation network, courtesy of PNAS. Wouldn’t it be great not to have to duplicate this in every new model?

Um….I can reproduce most of that now with about 10 different tools. If I wanted to do it quickly with stored information I could go to MINT and check out the curated interaction data and their very cool MINT Viewer (you can watch me do that in a movie here). Well, except it doesn’t show a picture of the Golgi in the background. Is that what’s new–despite that being from some unreferenced PNAS paper that may have nothing to do with this software? I would bet if I asked most of these teams would let me load up a cell graphic in the background, or I could create a network and layer it in with my image editing software. But I don’t think that’s it.

I hope little b is great. But like most software in this field there are other options–and some tools are right for some tasks, others are right for other tasks, even when they are in the same space. As we say in the blogosphere, YMMV {your mileage may vary}.