search

whole-cell-tutors / whole-cell-reduced

the reduced model developed in salt lake city
4 stars 2 forks source link

[ProteinDecay] reactions' names are wrong #7

Closed binfalse closed 9 years ago

binfalse commented 9 years ago

currently the reactions' names equal the reactions' ids. There are proper reaction names provided in Jonathan's excel sheets. We should use them.

binfalse commented 9 years ago

Actually, that's still a problem. I found https://github.com/whole-cell-tutors/whole-cell-reduced/blob/1371a2c17e3cd1a1abcb28f9a34a0e9ca805edff/ProteinDecay/protein-decay.py#L285

check(s1.setCompartment('c'), 'set species s1 compartment')

and expected that everything happens in c. turns out that some of them are actually in e.g. m, so we should be careful in naming the species, instead of just appending c. and we also need to add the missing compartments...

manikitos commented 9 years ago

I think that you reopened wrong issue, it should be #5