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cdanielmachado / carveme

CarveMe: genome-scale metabolic model reconstruction
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glpk solver support #82

Closed mmp3 closed 4 years ago

mmp3 commented 4 years ago

I see that glpk is not supported by framed since the November 2017 release, and carveme is built on top of framed, so carveme is also unable to use glpk.

Is there any inherent difficulty to providing a solver interface for glpk, or was glpk support discontinued only because of lack of time, labor, interest, or importance?

Any warnings or advice for someone who were to attempt to re-introduce a solver interface for glpk?

cdanielmachado commented 4 years ago

The framed library is now deprecated and was replaced with reframed, which I also maintain. My plan is to make the next release of carveme depend on reframed instead.

The support for glpk was dropped for multiple reasons, including lack of interest. On the other hand, reframed now supports optlang, and therefore supports any solver available in optlang including glpk.

However, I don't believe GLPK can handle the large MILP problem generated by CarveMe. I have plans to explore SoPlex, but have not done so yet due to lack of time.

I would, of course, welcome any feedback and contributions if you would like to try any different solver configuration in CarveMe.