straindesign
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klamt-lab
StrainDesign is a python package for the computational design of metabolic networks and based on COBRApy
Hi, I got the following problem running plot_flux_space function on the iMM904 model (no modification from the BiGG). Am I missing any argument? Thank you in advance and beautiful module!...
Trying to calculate de gMCS of iJN1463 I get the following error, I think the issue starts when SD tries to trim some GPRs that exceeds the character limit. WARNING:root:...
Hi, StrainDesign has worked very well for me when used on basic stoichiometric genome-scale models (e.g. iML1515). However, I am encountering problems when I try to use it on an...
This could reduce the number of computations necessary for producing the production envelope. For yield-dimensions, this could be more complex or even impossible, since yield spaces can be non-convex.
The network compression needs java. This is a potential future break point of the pipeline. Maybe implement the python compression routine instead.
enhancement, see title
Enforce some set of constraints also in the dual problems of OptKnock, RobustKnock and OptCouple. Then, for instance, someone could use the OptKnock module to enforce pGCP only under anaerobic...
Some models, e.g., iCHOv1 from Bigg, do not have GPR rules in DNF form. Improve the handling of such models. ``` import logging logging.basicConfig(level=logging.INFO) import straindesign as sd import cobra...