75 errors arise from simulation of Biomodels model.

I need to run the model about alanine, asparte, glutamate metabolism in humans, from https://www.ebi.ac.uk/biomodels-main/BMID000000101165, but I get so many errors:

I really need to make this function. Unless amino acid metabolism models are available in any other database, I would like to troubleshoot these errors. For example, the very first error concerns cpdC00025*[Reaction cooperativity])-1)), which I read when I opened the block property editor for that reaction (reaction 117 of Model Browser). I have no idea what this error means. Is there something I could do to troubleshoot these incomprehensible errors? Thank you very much.

Answer 1

[Jeremy Huard]

The error message is pretty clear though. It says that some variables used in reaction rates are not defined. Actually the troubles are visible right after importing that file. There is a bunch red markers in the browser which already warns you about this issue even before simulating.

The reason for this is that this SBML file is not valid. You can test their validity here: http://sbml.org/Facilities/Validator

This SBML file does not seem curated and is actually not even available on the new Biomodels website.

So except if you are willing to debug this model, I suggest to have a look at other models. For instance those ones:

https://www.ebi.ac.uk/biomodels/search?query=human+metabolism

[Juan Carlos Cao Yao]

Thank you Jeremy. Does this mean this model cannot be easily debugged without considerable effort or expertise? Many of the files from BioModels are not valid. Would you suggest that there are other databases that have files that work or is BioModels pretty much the main one to go to. If it is my best option, then I will look for other models that are curated. Thank you!

[Juan Carlos Cao Yao]

My goal is simple. It is just modeling human cell metabolism cultured in a well. I would like to model carbohydrate metabolism, which I saw I could; amino acid metabolism; lipid metabolism (eg cholesterol), minerals metabolism, which I think are the main pathways for cell metabolism. Would you suggest any models that could be a good fit for my purpose? I don't mind where they come from, as long as they run and I can do things on them like changing concentrations and graphing their extracellular matrix production, which may require gene expression pathways. Thank you so much again if you could help me.