-
Notifications
You must be signed in to change notification settings - Fork 43
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #100 from SysBioChalmers/devel
GECKO 2.0.0
- Loading branch information
Showing
48 changed files
with
151,303 additions
and
729 deletions.
There are no files selected for viewing
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
Large diffs are not rendered by default.
Oops, something went wrong.
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 +1,2 @@ | ||
| Condition Ptot D Glucose [mmol/gDw h] CO2 production [mmol/gDwh] Oxygen uptake [mmol/gDwh] Pyruvate succinate Glycerol Acetate Ethanol | ||
| Std 0.4228 0.1 1.1 2.7 2.5 8.06E-05 1.00E-05 0.001893379 0.089483471 1.00E-05 |
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
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
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
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
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
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 +1,68 @@ | ||
| function parameters = getModelParameters | ||
| % getModelParameters | ||
| % | ||
| % Set model and organism specific parameters that are used by the | ||
| % ecModel generation pipeline. | ||
| % | ||
| % Ivan Domenzain. Last edited: 2020-01-20 | ||
| % | ||
|
|
||
| %Average enzyme saturation factor | ||
| parameters.sigma = 0.5; | ||
|
|
||
| %Total protein content in the cell [g protein/gDw] | ||
| parameters.Ptot = 0.5; %Assumed constant | ||
|
|
||
| %Minimum growth rate the model should grow at [1/h] | ||
| parameters.gR_exp = 0.41; %[g/gDw h] | ||
|
|
||
| %Provide your organism scientific name | ||
| parameters.org_name = 'saccharomyces cerevisiae'; | ||
|
|
||
| %Provide your organism KEGG ID | ||
| parameters.keggID = 'sce'; | ||
|
|
||
| %The name of the exchange reaction that supplies the model with carbon (rxnNames) | ||
| parameters.c_source = 'D-glucose exchange (reversible)'; | ||
|
|
||
| %Rxn Id for biomass pseudoreaction | ||
| parameters.bioRxn = 'r_4041'; | ||
|
|
||
| %Rxn Id for non-growth associated maitenance pseudoreaction | ||
| parameters.NGAM = 'r_4046'; | ||
|
|
||
| %Compartment name in which the added enzymes should be located | ||
| parameters.enzyme_comp = 'cytoplasm'; | ||
|
|
||
| %Rxn names for the most common experimentally measured "exchange" fluxes | ||
| %For glucose and o2 uptakes add the substring: " (reversible)" at the end | ||
| %of the corresponding rxn name. This is due to the irreversible model | ||
| %nature of ecModels. NOTE: This parameter is only used by fitGAM.m, so if | ||
| %you do not use said function you don not need to define it. | ||
| parameters.exch_names{1} = 'growth'; | ||
| parameters.exch_names{2} = 'D-glucose exchange (reversible)'; | ||
| parameters.exch_names{3} = 'oxygen exchange (reversible)'; | ||
| parameters.exch_names{4} = 'carbon dioxide exchange'; | ||
|
|
||
| %Biomass components pseudoreactions (proteins, carbs and lipids lumped | ||
| %pools). NOTE: This parameter is only used by scaleBioMass.m, so if you do | ||
| %not use said function you don not need to define it. (optional) | ||
| parameters.bio_comp{1} = 'protein'; | ||
| parameters.bio_comp{2} = 'carbohydrate'; | ||
| parameters.bio_comp{3} = 'lipid backbone'; | ||
| parameters.bio_comp{4} = 'lipid chain'; | ||
|
|
||
| %Polymerization costs from Forster et al 2003 - table S8. NOTE: This | ||
| %parameter is only used by scaleBioMass.m, so if you do not use said | ||
| %function you don not need to define it. (optional) | ||
| parameters.pol_cost(1) = 37.7; %Ptot | ||
| parameters.pol_cost(2) = 12.8; %Ctot | ||
| parameters.pol_cost(3) = 26.0; %RNA | ||
| parameters.pol_cost(4) = 26.0; %DNA | ||
|
|
||
| %Rxn IDs for reactions in the oxidative phosphorylation pathway (optional) | ||
| parameters.oxPhos{1} = 'r_1021'; | ||
| parameters.oxPhos{2} = 'r_0439'; | ||
| parameters.oxPhos{3} = 'r_0438'; | ||
| parameters.oxPhos{4} = 'r_0226'; | ||
| end |
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
Oops, something went wrong.