Jonathan Robinson

This might be a matter of opinion, but I agree with @matthiaskoenig that the calculation of the overall score could use another look - at least with regard to some...

> Running `solveLP(built_model)` also gives a zero value of the objective value. If this is the case, then I have two additional questions @manas-kohli (sorry if they have been asked...

@edkerk I have never used `randomSampling` with Human-GEM or Human-GEM-derived models, but I took a look at the code to see what could be happening. For me, when using Gurobi,...

Thanks for spotting this. Though I guess now we would abbreviate the compartment as `[e]` rather than `[s]`.

Another option instead of making them into params is to code their paths relative to the location of the `prepHumanModelForftINIT` function. Since the location of the files relative to the...

No, I'm not really aware of any automatic functionality that could be used to update this, unfortunately.

@mihai-sysbio I'm hesitant about using an E.C.-based approach, since the E.C. number does not necessarily specify the reaction substrates. So in many cases you can have an E.C. that represents...

They do not need to be unique, but they also should not be super general (to the point where hundreds of reactions have the same name - I'm thinking this...

@cherkaos > For example, heme biosynthesis is in both lists but it was reported in the Human1 manuscript that it doesn't pass in blood. How could that be if it...

Hi @CadavidJoseL, I think I partially answered this question in the Gitter chat, but let me know if not. It's true that the checkTasks and tINIT algorithms modify the pseudo...