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### Use Case
Often for perfusion and metabolic modeling, different systems of differential algebraic equations are included as reaction terms to represent kinetic components of overall metabolism. Of…
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It suggests using a docker container but doesn't link to dockerhub and the actual .py files seem to be absent
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Dear Francisco
I'm working on a project where I wish to use MAGs to create a community GEM (6 species). The MAGs will be obtained from somewhere else, and I want to use that data to create the mod…
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### **Glycolysis**
- **Accuracy**: The model correctly represents glycolysis occurring in the cytoplasm, where each glucose molecule is converted into two pyruvate molecules, yielding a net gain of…
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Thermodynamics constraints are rather important in metabolic modeling.
If not considered, they would lead to thermodynamically infeasible/implausible flux loops within flux sample.
*Loopless* spa…
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Add stage for illustrating adding Rhea IDs to metabolic conversions in Advanced Modeling track
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This is an issue I think is due to updates in `cobra`. With `cobra` version 0.21.0 `create_smoment_model_reaction_wise_with_sbml()` runs in a reasonable amount of time. However, once I use an environm…
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COBRA Models Module folder -> COBRA Models Module Python Files folder -> where could I find iAB_RBC_283.metabolism.json?
I could only find iAB_RBC_283.json in BIGG
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## Target functionality
tINIT is an (umbrella name for an) algorithm that obtains a subset of a genome-scale metabolic model based on the gene expression (typically in healthy/diseased bulk tissue …
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Currently, for metabolic flux analysis, MFAPipe models the independent fluxes of the reaction network as the independent variables of the regression. Hence, the values of the independent fluxes are fi…