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* fix: label axes of growth plot * fix: scaleBioMass balance_out to 1 g/gDCW * fix: anaerobicModel no overwrite of biomass comp. * chore: regenerate growth predictions
* feat: initial model curations as defined in May * feat: separate general curations and test script * feat: separate glycine and nitrogen functions * A number of model mofications are suggested to improve the accuracy of 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 * A number of modification are proposed to improve the accuracy and overall 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). * Updated code for flux predictions in anaerobic conditions. Loads txt isntead of xlsx. * FADH=0.06 mmol/gDW change txt to tsv extension in anaerobic flux predictions * Add files via upload * Update v9_0_2.m * Update anaerobicModel.m updated the FADH2 coefficient. * Update anaerobicModel.m Updates related with anaplerosis fixed the unusual flux through MAE1 and IDP1 (NADPH). * Update v9_0_2.m * Update anaerobicModel.m * Update anaerobicModel.m * refactor: anaerobicModel * fix: label axes of growth plot * fix: scaleBioMass balance_out to 1 g/gDCW * fix: anaerobicModel no overwrite of biomass comp. * chore: regenerate growth predictions * fix: anaerobicModel no rescale of biomass * fix: anaerobic_flux_predictions readtable * Update v9_1_0.m * feat: functions run from matlab path * feat: scaleBioMass reports final output * refactor: run functions from path + other refactor * feat: sumBioMass uses metFormulas not data files * feat: 9.1.0 curate r_0013 and biomass * WIP * fix: rxn balance curations and script refactor * WIP * feat: test reducing methionine content * feat: adapt amino acid content in biomass * feat: disable GCV except N-lim and Gly N-source * feat: make 9.1.0 model * refactor: update model loading to use earlier version 9.0.2 * feat: include anaerobic curation figures * feat: correct H+ in protein biomass pseudorxn * fix: v910_anaerobic_fluxes * fix: report CoD as R2 and not Pearson's r * feat: python anaerobic_model script * fix: recover some functions --------- Co-authored-by: davidhcsic <davidhenriques@Davids-MacBook-Pro.local> Co-authored-by: davidhcsic <32391339+davidhcsic@users.noreply.github.com>
# Conflicts: # README.md # data/testResults/growth.png # model/yeast-GEM.xml # model/yeast-GEM.yml
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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:
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