Contributors wanted for metabolism modeling project

[ruphos]

Hey folks,

TL;DR - know java and want to join in on an ongoing computation bio project? Check out MOST: https://github.com/dennisegen/MOST

I've been at ISMB in Long Beach the past few days and it's been pretty awesome. During one of the SIGs, Dennis Egen presented on a project he's working on with some folks at Rutgers called MOST: Metabolic Optimization and Simulation Tool. It's a tool that is designed to model e. coli in silico, so you can run simulations to get an idea of what would be most effective for an actual experiment. It sounds really cool. The project is open source, though currently using privately licensed software for the optimization portion. They hope to move towards a fully open source project soon, but Gurobi is currently outperforming all other comers.

In any case, the core algorithms are set, but they're working on putting the actual application framework and flow together and would love some help. It was emphasized that overall project stage is in alpha, so there is going to be some not-so-pretty code in the repository that will be overhauled before it is finalized. If you're curious about the algorithm behind the project, they were recently published in Bioinformatics (http://bioinformatics.oxfordjournals.org/content/28/12/1619). If you do not have access to the journal, email me off list and I can send you the article.

Hope some of you find this interesting and decide to help out!

--
"And if ye cannot be saints of knowledge, then be at least its warriors."
-- Friedrich Nietzsche

[Stephanie]

Hi. I know java (web developer by trade) and I am interested in participating! Sounds exciting. Who should I get in contact with?

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[Matthias Bock]

You know about Copasi and biographer ?

biographer also contains a simulator.

 

Cheers, Matthias