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brianjamesschmidt / gim3e

Gene Inactivation Moderated by Metabolism, Metabolomics, and Expression (COBRApy)
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gim3e examples not working #9

Open migp11 opened 6 years ago

migp11 commented 6 years ago

Hi,

I'm trying to use gim3e in a research project to integrate expression data of cancer cell lines into Recon2. However, I've found this package to be very outdated and not compatible with the new versions of cobrapy. I've already started to refactor part of the code but is becoming very hard and thus I wonder if you have a more updated version or if you are planning to release a new version soon? Thank you! Best

Miguel

brianjamesschmidt commented 6 years ago

Hi Miguel,

It is great to hear GIM3E might be useful for you. As you can tell, I haven’t been keeping this up-to-date with the COBRApy updates. Ali was nice enough to push a few updates to keep up with COBRApy development for a while. If you use any 0.2.x version, I used 0.2.1, it should be compatible with the last GIM3E version I posted before Ali started updating. The version with commits on 11/30/13 should work: https://github.com/brianjamesschmidt/gim3e/commit/562adda89efbc8007470db03618c31a2fb1aaf5a

That may not be helpful. Sorry right now I don't have a new release in development that I'm planning to commit soon! I've been engaged lately with ODE-based QSP modeling and have been working on a whole new set of applications, data, models & algorithms. There hasn't been much free time or resources to update GIM3E at present.

Please also send me an e-mail if you want to discuss additional options offline.

Best regards, Brian