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@coltonlloyd coltonlloyd released this 24 Mar 20:58
· 10 commits to master since this release
v0.0.8
162deac

Adds support for Docker

  • Dockerfiles added which can install COBRAme, ECOLIme, solvemepy, soplex_cython and a compiled version of qMINOS and SoPlex. It also installs all of the dependencies and builds iJL1678b-ME

  • A Docker image containing all of the above can now be obtained from DockerHub .

  • Fixes #23

Adds compartments to ME-model JSONs and refactored JSON saving/loading scripts

  • Fixes #21
  • Save/load full ME-model with:
from cobrame.io.json import save_json_me_model, load_json_me_model
save_json_me_model(me_model, '[save_loc]/model.json')
new_me_model = load_json_me_model('[save_loc]/model.json')
  • Save/load reduced versino of ME-model with:
from cobrame.io.json import save_reduced_json_me_model, load_reduced_json_me_model
save_reduced_json_me_model(me_model, '[save_loc]/model.json')
new_me_model = load_reduced_json_me_model('[save_loc]/model.json')

Mass is no longer a property of model metabolites

  • Now uses formula_weight and calculates mass based on formula
  • Fixes #22

Additional changes

  • Updated documentation to include examples of coupling constraint derivations
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