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BioSystemsUM / MEWpy

Metabolic Engineering Workbench
https://mewpy.readthedocs.io
GNU General Public License v3.0
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Error in (from mewpy.regulation.optram import OptRamProblem, load_optram) #3

Closed jinb88187 closed 4 years ago

jinb88187 commented 4 years ago

Hi, I see the following error:

~\anaconda3\lib\site-packages\mewpy\simulation\cobra.py in 4 from cobra.core.model import Model 5 from cobra.core.solution import Solution ----> 6 from geckopy.gecko import GeckoModel 7 from cobra.flux_analysis import pfba, moma, room 8 from mewpy.simulation import SimulationMethod, SStatus

ModuleNotFoundError: No module named 'geckopy'

Thanks.

vmspereira commented 4 years ago

Hi,

You need to install geckopy (pip install geckopy) to use the original GECKO model implementation by Benjamin Sanchez. As a side note, if the optimization time is an important factor, you should preferably use the MEWpy implementation. MEWpy implementation uses REFRAMED for phenotype simulations while geckopy uses COBRApy which is considerably slower.

Thank you.