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cdanielmachado / carveme

CarveMe: genome-scale metabolic model reconstruction
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CPLEX Optimizer is not available for free for academia #55

Closed famosab closed 3 years ago

famosab commented 5 years ago

I tried following the links given in the docs but had to find out that IBM does not offer their academic deal for the CPLEX Optimizer software anymore. I asked them for sponsoring for my work but since this is crucial for CarveMe to run, it should be indicated in the README.

famosab commented 5 years ago

Changing the default solver in the config file to gurobi worked for me. Gurobi provides an academic license.

cdanielmachado commented 5 years ago

Did your reconstructions run successfully with gurobi?

Although, in theory, we support both I found gurobi to be slower and fail more often to find the optimal solution. All the benchmarks on model quality have been run on cplex only.

famosab commented 5 years ago

Gurobi worked for the one genome I tested it with.

However IBM told me that they plan to bring back the academic version but this make take some months.

cdanielmachado commented 5 years ago

Thanks, that's good to know. I will keep CPLEX as the preferred solver since I haven't properly tested the pipeline using Gurobi so far.

If anyone encounters the same problem I would recommend to try to get an installer for one of the previous versions that were still supported by the academic initiative (I think the latest was 12.8).

InesHo commented 5 years ago

Just for your information: I installed the ILOG CPLEX Optimizer (12.9) today using the academic licence IBM provides.

cdanielmachado commented 3 years ago

I have just downloaded the latest version of CPLEX, it continues to be free for academic users.