Daniel Machado

Failed to load universal_model.json

10

Trying to load the latest `universal_model.json` file from BiGG returns the following error: ``` ~/opt/miniconda3/envs/py37/lib/python3.7/site-packages/cobra/core/object.py in annotation(self, annotation) 48 def annotation(self, annotation): 49 if not isinstance(annotation, dict): ---> 50 raise...

Incorrect calculations

1

The calculations displayed are incorrect, and this seems to affect the final score as well. 

Missing GPRs

18

**memote** gives an error for all intracellular reactions without GPRs. However, it is not clear to me why a GPR should be mandatory. Maybe there could be evidence for the...

Universal subsystems

1

Universal reactions currently do not have subsystems associated. One can inspect the model-specific reactions to obtain the respective subsystem. However, differences in nomenclature across models make it difficult to come...

To anyone having this problem, please use the flag "--flavor bigg" when running smetana. The problem is the way the exchange reactions are calculated. If we know the models use...

Changing variable bounds during reoptimization

9

I am trying to solve an LP problem multiple times, where both the objective coefficients and the bounds of the variables may get modified between iterations. Something of the form:...