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segrelab / comets

Computation of Microbial Ecosystems in Time and Space
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multitoxins basic implementation #44

Closed jeremymchacon closed 1 year ago

jeremymchacon commented 2 years ago

Basic implementation of multiple metabolites closing a bound with chained multiplicative hill functions. Use a model file block like so:

MET_REACTION_SIGNAL
multitoxin 2138 229,230 ub 0.05 1e-5,1e-6 7,8
//

Causes the upper bound of reaction 2138 to be influenced by the metabolite concentrations of exchange reactions 229, and 230, with this formula:

conc1,2 = met concentration of reaction 229, 230 (M)
bound = vmax * MULT_i [(k_i ^ h_i) / (k_i ^ h_i + conc_i ^ h_i) ] for mets i
bound = 0.05 * (1e-5^7) / (1e-5^7 + conc1^7) * (1e-6^8) / (1e-6^8 + conc2^8)
jeremymchacon commented 1 year ago

Hi Ilija, Would you please merge this when you get a moment?