Whats the best way to simulate gene transduction in a COBRA model? #1106
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I've seen how easy it is to simulate KO experiments with cobrapy, but I have not seen anything really about transduction/introduction of foreign genes to an existing model. Can someone point me in the right direction? Is it best to just create the metabolites/reactions and not worry about the genes themselves? Is the gpr (gene_reaction_rule) required to simulate metabolic flux? |
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Hello @mbutawan, Introducing new genes is a bit of manual work. If you know exactly what genes you want to introduce and the metabolic reaction catalyzed by the gene product, then I would just define a new reaction with the corresponding metabolites. You don't need to define the GPR in order to simulate flux but it can be nice as annotation/information and, of course, if you wanted to knock out the gene. If you only know that you want to produce a certain compound, then there are multiple tools available for pathway selection, for example, cameo. |
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Hello @Midnighter, Also thank you for the introduction to the new library! I'm sure I'll find a use for that in some project. |
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Hello @mbutawan,
Introducing new genes is a bit of manual work. If you know exactly what genes you want to introduce and the metabolic reaction catalyzed by the gene product, then I would just define a new reaction with the corresponding metabolites. You don't need to define the GPR in order to simulate flux but it can be nice as annotation/information and, of course, if you wanted to knock out the gene.
If you only know that you want to produce a certain compound, then there are multiple tools available for pathway selection, for example, cameo.