Comments (4)
Sorry, I forgot to mention that you'll need to pull the latest cobrapy commits in order to run prototype 41.
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OK. Moving in the right direction.
I didn't have Gurobi installed. Is it necessary here? I can install it.
Traceback (most recent call last):
File "prototype_41.py", line 552, in <module>
compiled_expressions=expressions, debug=False, solver = 'gurobi')
File "/Users/zaking/sharedrepos/minime/minime/solve/algorithms.py", line 54, in binary_search
solver = get_ME_solver(solver)
File "/Users/zaking/sharedrepos/minime/minime/solve/algorithms.py", line 34, in get_ME_solver
return solver_dict[solver]
KeyError: 'gurobi'
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No it's not necessary. You can delete that argument and it'll use soplex. Gurobi is just faster, though inaccurate. We use it for quickly determining growth/no growth for debugging.
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awesome. it worked!
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Related Issues (18)
- build_ME_model.ipynb PFL reaction change HOT 2
- Missing add_modification_data
- compute GC fraction from genbank (automate the process for other organisms)
- Reimplement DNA replication reaction HOT 1
- Reduce number of global_info fields HOT 1
- biomass_allocation piechart key errors HOT 2
- biomass_allocation.py get_by_id problem HOT 2
- ME model can change the objective function? HOT 2
- glycyl misspelled in keffs.json
- Add compartments to all model metabolites
- EG10544-MONOMER_mod_palmitate HOT 1
- how to obtain Keff for metabolic enzymes HOT 1
- circular import: minime.core.MEReactions.MetabolicReaction
- Blocked reactions
- remove dashes HOT 1
- Remaining model errors
- import scripts error
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