minimal media question

[amarsh26]

Hello,

When I manually enter the media from minimal_medium(model, max_growth), I receive a different biomass (0.8571429) then using tool to obtain minimal medium for FBA (0.876997). The max_growth used to obtain the minimal was the default. Is this expected behavior?

In addition, if I slightly increase the value for mobd in the manually entered minimal media from (0.000006 to 0.000007) and change no other values, the biomass increase to 0.8761609907. I was also wondering if this is expected.

The data was obtained using the iML1515 model of E. coli.

Thanks!

[cdiener]

Sorry for the delayed response. By hand do you mean just typing the first x digits? Than this would be expected because this is not the exact value returned and you would be truncating it...

[amarsh26]

Hi,

Sorry for the late reply; I got pulled away from looking into this. Yes, I am taking the output produced from
model_default_growth = iml1515_model.slim_optimize()
minimal_medium(iml1515_model, model_default_growth)
which is
EX_pi_e 0.845957 EX_mn2_e 0.000606 EX_fe2_e 0.014085 EX_glc__D_e 10.000000 EX_zn2_e 0.000299 EX_mg2_e 0.007608 EX_ca2_e 0.004565 EX_ni2_e 0.000283 EX_cu2_e 0.000622 EX_cobalt2_e 0.000022 EX_mobd_e 0.000006 EX_so4_e 0.220845 EX_nh4_e 9.471495 EX_k_e 0.171184 EX_cl_e 0.004565 EX_o2_e 22.131763
and manually entering this data (including entering zero for compounds not in this output, but are occurring in the default media).

Thank you so much for your help!

[cdiener]

Yeah, if you manually enter the data that will introduce small errors what will change the output slightly. The default output will not show all digits of a float, so something like 0.10000023344 will become 0.1 there. If you just copy that you something that is somewhat but not exactly the same. If you assign directly without truncating it should be much closer, e. g.

# ...
model_default_growth = iml1515_model.slim_optimize() 
med = minimal_medium(iml1515_model, model_default_growth) 
with iml1515_model as mod:
    mod.medium = med
    model_minimal_growth = mod.slim_optimize()
print(model_default_growth, model_minimal_growth)

Those values should be within the solver tolerance.

[amarsh26]

Thanks so much for your help!