Standardize pseudoreaction names #39
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Two points
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- Standardized names for biomass, sink, exchange, atpm, and demand reactions - Uses the prefixes EX_, DM_, SK_, BIOMASS_, and ATPM - If pseudoreactions have gpr's, then log a warning - If DM_, SK_, or EX_ have coefficients not 1 or -1, then log a warning - Closes SBRG/bigg_models#84, SBRG/bigg_models#149, SBRG/bigg_models#175
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For instance, rename EX_glc__D_c to DM_glc__D_c. Previously, this was just a warning. Also added subsystems "Extracellular exchange", "Intracellular demand", "Intracellular source/sink", and "Biomass and maintenance functions".
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Also added subsystems for pseudoreactions: "Extracellular exchange", "Intracellular demand", "Intracellular source/sink", and "Biomass and maintenance functions". |
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See also SBRG/bigg_models#177 |
zakandrewking
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Standardize pseudoreaction names
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I'm still testing this.