Daniel Machado

@liseklaks your case is more complicated, your models use mixed ids (from BiGG and KEGG) and have a few strange features... For example in `B_cenocepacia` metabolite `M_C0009` is in the...

Hi Iulia, Are you specifying a growth medium when you calculate MIP ? If you specify a growth medium it is only possible to calculate MIP if every species can...

Hi Nico, Your problems are related to these previously identified issues: https://github.com/cdanielmachado/smetana/issues/17 https://github.com/cdanielmachado/smetana/issues/10 To be honest, there is not much that can be done without trying to make the formulation...

Hi Nico, Yes, I would recommend always using `--molweight`. From my experience, minimizing the total mass of the consumed substrates, rather than simply the total number of substrates, results in...

Sorry for the very late reply guys, I struggle to keep up with issue requests... :) `gene_exp` is a dictionary where the keys are gene ids (same as in the...