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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,120 @@ | ||
| { | ||
| "state": { | ||
| "global_time": "0.0", | ||
| "dfba": { | ||
| "_type": "process", | ||
| "address": "local:DynamicFBA", | ||
| "config": { | ||
| "model_file": "/Users/helenscott/Documents/PhD/Segre-lab/GEM-repos/ecoli/iJO1366.xml", | ||
| "model": "None", | ||
| "kinetic_params": { | ||
| "Glucose": [ | ||
| "0.5", | ||
| "1.0" | ||
| ], | ||
| "Acetate": [ | ||
| "0.5", | ||
| "2.0" | ||
| ], | ||
| "CO2": [ | ||
| "0.5", | ||
| "1.0" | ||
| ] | ||
| }, | ||
| "biomass_reaction": "BIOMASS_Ec_iJO1366_WT_53p95M", | ||
| "substrate_update_reactions": { | ||
| "Glucose": "EX_glc__D_e", | ||
| "Acetate": "EX_ac_e", | ||
| "CO2": "EX_co2_e" | ||
| }, | ||
| "biomass_identifier": "Biomass", | ||
| "bounds": { | ||
| "EX_o2_e": {}, | ||
| "ATPM": {} | ||
| } | ||
| }, | ||
| "inputs": { | ||
| "substrates": { | ||
| "Glucose": [ | ||
| "fields", | ||
| "Glucose" | ||
| ], | ||
| "Acetate": [ | ||
| "fields", | ||
| "Acetate" | ||
| ], | ||
| "CO2": [ | ||
| "fields", | ||
| "CO2" | ||
| ], | ||
| "Biomass": [ | ||
| "fields", | ||
| "Biomass" | ||
| ] | ||
| } | ||
| }, | ||
| "outputs": { | ||
| "substrates": { | ||
| "Glucose": [ | ||
| "fields", | ||
| "Glucose" | ||
| ], | ||
| "Acetate": [ | ||
| "fields", | ||
| "Acetate" | ||
| ], | ||
| "CO2": [ | ||
| "fields", | ||
| "CO2" | ||
| ], | ||
| "Biomass": [ | ||
| "fields", | ||
| "Biomass" | ||
| ] | ||
| } | ||
| }, | ||
| "interval": 1.0, | ||
| "_inputs": { | ||
| "substrates": "map[positive_float]" | ||
| }, | ||
| "_outputs": { | ||
| "substrates": "map[positive_float]" | ||
| } | ||
| }, | ||
| "fields": { | ||
| "Glucose": "10.0", | ||
| "Acetate": "0.0", | ||
| "CO2": "0.0", | ||
| "Biomass": "0.1" | ||
| }, | ||
| "emitter": { | ||
| "_type": "step", | ||
| "address": "local:ram-emitter", | ||
| "config": { | ||
| "emit": { | ||
| "dfba": "any", | ||
| "fields": "any", | ||
| "global_time": "any" | ||
| } | ||
| }, | ||
| "inputs": { | ||
| "dfba": [ | ||
| "dfba" | ||
| ], | ||
| "fields": [ | ||
| "fields" | ||
| ], | ||
| "global_time": [ | ||
| "global_time" | ||
| ] | ||
| }, | ||
| "_inputs": { | ||
| "dfba": "any", | ||
| "fields": "any", | ||
| "global_time": "any" | ||
| }, | ||
| "_outputs": {}, | ||
| "outputs": {} | ||
| } | ||
| } | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,106 @@ | ||
| { | ||
| "state": { | ||
| "global_time": "0.0", | ||
| "dfba": { | ||
| "_type": "process", | ||
| "address": "local:DynamicFBA", | ||
| "config": { | ||
| "model_file": "textbook", | ||
| "model": "None", | ||
| "kinetic_params": { | ||
| "glucose": [ | ||
| "0.5", | ||
| "1.0" | ||
| ], | ||
| "acetate": [ | ||
| "0.5", | ||
| "2.0" | ||
| ] | ||
| }, | ||
| "biomass_reaction": "Biomass_Ecoli_core", | ||
| "substrate_update_reactions": { | ||
| "glucose": "EX_glc__D_e", | ||
| "acetate": "EX_ac_e" | ||
| }, | ||
| "biomass_identifier": "biomass", | ||
| "bounds": { | ||
| "EX_o2_e": {}, | ||
| "ATPM": {} | ||
| } | ||
| }, | ||
| "inputs": { | ||
| "substrates": { | ||
| "glucose": [ | ||
| "fields", | ||
| "glucose" | ||
| ], | ||
| "acetate": [ | ||
| "fields", | ||
| "acetate" | ||
| ], | ||
| "biomass": [ | ||
| "fields", | ||
| "biomass" | ||
| ] | ||
| } | ||
| }, | ||
| "outputs": { | ||
| "substrates": { | ||
| "glucose": [ | ||
| "fields", | ||
| "glucose" | ||
| ], | ||
| "acetate": [ | ||
| "fields", | ||
| "acetate" | ||
| ], | ||
| "biomass": [ | ||
| "fields", | ||
| "biomass" | ||
| ] | ||
| } | ||
| }, | ||
| "interval": 1.0, | ||
| "_inputs": { | ||
| "substrates": "map[positive_float]" | ||
| }, | ||
| "_outputs": { | ||
| "substrates": "map[positive_float]" | ||
| } | ||
| }, | ||
| "fields": { | ||
| "glucose": "10.0", | ||
| "acetate": "0.0", | ||
| "biomass": "0.1" | ||
| }, | ||
| "emitter": { | ||
| "_type": "step", | ||
| "address": "local:ram-emitter", | ||
| "config": { | ||
| "emit": { | ||
| "dfba": "any", | ||
| "fields": "any", | ||
| "global_time": "any" | ||
| } | ||
| }, | ||
| "inputs": { | ||
| "dfba": [ | ||
| "dfba" | ||
| ], | ||
| "fields": [ | ||
| "fields" | ||
| ], | ||
| "global_time": [ | ||
| "global_time" | ||
| ] | ||
| }, | ||
| "_inputs": { | ||
| "dfba": "any", | ||
| "fields": "any", | ||
| "global_time": "any" | ||
| }, | ||
| "_outputs": {}, | ||
| "outputs": {} | ||
| } | ||
| } | ||
| } |
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