downloading P expansum model

[Rotembartuv]

Hi,

I'm trying to download the Pexpansum model and read it using cobrapy.
I'm getting an error on cobrapy that the sbml model is not valid.
do your models works with cobrapy?

[syprigen]

Hi,

Even though Cobraby is rising warnings on the SId not being valid and "discouraged" uses in the sbml format, it should still read the models correctly by translating the ids (mainly "-" being transformed to "42", "+" to "43" and "." to "46")
but for clarity, I will update the files within the week.

[Rotembartuv]

Ok
Waiting for your update! Thank you very much!!

[syprigen]

You should now be able to use the files in the "xml_cobraCompliantIds" folder without any warnings.

[Rotembartuv]

tnx

when Im trying to read the model in cobrapy I get only 8 reaction

Pexpansum.summary()
Objective

1.0 bmOUT = 0.8398830785672777

Uptake

               Metabolite                         Reaction      Flux  C-Number C-Flux

ALPHA-GLUCOSE_CCO-BOUNDARY EX_ALPHA-GLUCOSE_CCO-BOUNDARY 20 0 0.00%
AMMONIA_CCO-BOUNDARY EX_AMMONIA_CCO-BOUNDARY 25.63 0 0.00%
CPD-205_CCO-BOUNDARY EX_CPD-205_CCO-BOUNDARY 8.399E-05 0 0.00%
Elemental-Sulfur_CCO-BOUNDARY EX_Elemental-Sulfur_CCO-BOUNDARY 0.1084 0 0.00%
FE+2_CCO-BOUNDARY EX_FE+2_CCO-BOUNDARY 0.000168 0 0.00%
OXYGEN-MOLECULE_CCO-BOUNDARY EX_OXYGEN-MOLECULE_CCO-BOUNDARY 20 0 0.00%
PPI_CCO-BOUNDARY EX_PPI_CCO-BOUNDARY 4.385 0 0.00%
THIAMINE_CCO-BOUNDARY EX_THIAMINE_CCO-BOUNDARY 8.399E-05 0 0.00%

Secretion

Metabolite Reaction Flux C-Number C-Flux
BIOMASSb EX_BIOMASSb -0.8399 0 0.00%

[syprigen]

model = read_sbml_model("Pexpansum.xml")
print(len(model.reactions))
2614

There is 2614 reactions in this model. To know how to use cobrapy, please refer to https://cobrapy.readthedocs.io/en/latest/

[Rotembartuv]

The number of the reaction is correct, but the secrition in the summary showed nothing.

[zoey-rw]

I think the cobra-compliant SBML files appear to have lost their compartments within each metabolite ID. Then, when imported and re-saved by cobra, the compartments are considered "unused" and removed entirely by cobra.io.write_sbml_model.

I tried reading in the original SBMLs and re-saving with the argument "f_replace={}", but the compartments are still removed by cobra even when the metabolite IDs are left alone.