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Suppose I have all sequences of genes or proteins of certain species, are there any free tools I can use to generate a flux balance analysis model out of them?

What I was thinking is more like to annotate all the enzymes based on some annotation method. Then mapping these enzymes to known meta-metabolic networks that we know for instance the meta-metabolic network in KEGG database.

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To generate flux balance, one should now the stoichiometric numbers of all the reactions that are taking place, as well as the conditions (that could affect the reactions). I am not sure we have enough knowledge, time and computationally power to do this.

At the moment I'm only aware of a paper simulating the Mycoplasma genitalium cell. But I'm not sure it was worth the effort as I haven't seen replicated or redone with other species, perhaps the model was not accurate enough to be worth it.

The tools used are here. The licenses are not a standard, but at least they seem free.

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  • $\begingroup$ Thanks. What I was thinking is more like to annotate all the enzymes based on some annotation method. Then mapping these enzymes to known meta-metabolic networks that we know for instance the meta-metabolic network in KEGG database. $\endgroup$ – LifeWorks Jun 18 '18 at 23:09
  • $\begingroup$ Which would be your input? A list of genes? This is trivial to do, but you don't know how many active sites are in an enzyme nor if there is any inhibitor, and you would need to know the initial concentrations to see if you reach a steady state or not, and what is your end point is also a variable you should define $\endgroup$ – llrs Jun 19 '18 at 7:12

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