feat: curations and script for anaerobic metabolism#386
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…f anaerobic simulations and overall consistency with fermentative physiology. -Added data fluxomic data from 3 published works and extracellular product formation Nissen et al. 1996. Use anaerobic_flux_predictions.m to simulate. -A modification was added to growth.m and anaerobicModel.m such that the biomass composition of the anaerobic model does not override the one related with nitrogen limitation (see code more). -anaerobiosis.m runs all tests. -anaerobicModel. Summary of modifications in anaerobic model: -IDP2 blocked - Cofactor handling in biomass - Degree of reduction the biomass tweaked - FADH2 added to the biomass equation (succinate production through FRD1) -MAE1/NAPDH blocked
…rall consistency of the yeast genome-scale metabolic model with experimental data and fermentation physiology. - Checked all proton symport/antiport reactions and make sure that they only enter the cell. - Balance reactions and ensures that a correct molecular weight can be calculated for the biomass - Some modifications are media dependent (Carnitine shuttle and GLT1) and need to moved elsewhere. - Curated several reactions in terms of reversibility and cofactor specificity. - A couple of modifications added need to revised: -'r_0441', 'r_0442': LOT6 seems to use FMN/FMNH2 as a cofactor instead of sustrate/product. Consider removing reactions. - Blocked ammonium transport to the mitochondria (ammonia can difuse in position to ammonium).
Loads txt isntead of xlsx.
change txt to tsv extension in anaerobic flux predictions
updated the FADH2 coefficient.
Updates related with anaplerosis fixed the unusual flux through MAE1 and IDP1 (NADPH).
# Conflicts: # code/modelCuration/v9_0_2.m
# Conflicts: # code/otherChanges/anaerobicModel.m
# Conflicts: # code/otherChanges/anaerobicModel.m
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Main improvements in this PR:
anaerobicModel.mscript, so that the changes applied to the model for mimicing anaerobic growth are supported by literature data (Proposed changes to the anaerobic model #352).anaerobic_model.pyincode(Feat: A python function for anaerobic condition setup #310)I hereby confirm that I have:
developas a target branch (top left drop-down menu)