How to upload KEGG file to Simbiology so I can start analyzing.

How do I please upload KEGG file into my SimBiology workspace?

Answer 1

[Jeremy Huard]

Hi Juan Carlos,

KEGG files can't be imprted into SimBiology as is. You will need to convert them into SBML files first.

There are converters available to do this. for instance KEGG Translator. That being said, the resulting SBML file will contain the model structure but no kinetics because it's not contained in the original file. So you will need to define them to run your model.

May I suggest you to have a look at the Biomodels repository? It contains curated, runnable models which have been published and that you can download in SBML format and import in SimBiology.

Best,

Jérémy

[Juan Carlos Cao Yao]

Thank you, Jeremy, you have been my most important man of the day.

[Juan Carlos Cao Yao]

Hi Jeremy,

I am trying to simulate on SimBiology basic human cellular respiration, and see how changing the concetration of input species can yield different graphs. I tried BioModels and a lot of the files that were about respiration contained errors when imported and run. What can I do when those files which interest me are full of errors? I realised too a lot of them came from KEGG.

Within the curated files, I downloaded Chance_1960_Glycolysis_Respiration and it was runnable. But its specis had no units for concetration. I changed all the nonzero concentration species into mM units, and changed glucose to 5 mM. I am just trying to model cell respiration from a cell culture in a well, nothing to complex. It turns out the graph plotted nothing, it stayed constant at 0 and all the curves from the original file were gone. It doesn't seem to be simulating it right.

Among the curated models, I can't find many files of my interest, related to oxidative phosphorylation or extracellular matrix biosynthesis, as I find among the rest of the database, but which contain errors.

Could you help me, please? Thank you very much! This is very time-sensitive.

JC