Biomass¶

MATLAB functions in RAVEN/biomass of the RAVEN toolbox. Help text is collected from the source of the tracked branch.

Functions¶

Function	Summary
`fitParameters`	Fit parameters such as maintenance ATP by quadratic programming.
`getBiomassFractions`	Compute mass fraction per biomass component.
`scaleBiomassFraction`	Rescale a biomass component to a target value.
`scaleBiomassPseudoreaction`	Rescale a biomass component pseudoreaction.
`setGAM`	Set the growth-associated maintenance (GAM) coefficient.

Reference¶

fitParameters¶

Fit parameters such as maintenance ATP by quadratic programming.

Input arguments:

Name	Type	Description	Default
`model`	`struct`	a model structure.	required
`xRxns`	`cell`	cell array with the IDs of the reactions that will be fixed for each data point.	required
`xValues`	`double`	matrix with the corresponding values for each xRxns (columns are reactions).	required
`rxnsToFit`	`cell`	cell array with the IDs of reactions that will be fitted to.	required
`valuesToFit`	`double`	matrix with the corresponding values for each rxnsToFit (columns are reactions).	required
`parameterPositions`	`struct`	structure that determines where the parameters are in the stoichiometric matrix, with fields: position : cell array of vectors where each element contains the positions in the S-matrix for that parameter isNegative : cell array of vectors where the elements are true if that position should be the negative of the fitted value (to differentiate between production/consumption)	required

Name-value arguments:

Name	Type	Description
`fitToRatio`	`logical`	if the ratio of simulated to measured values should be fitted instead of the absolute value. Used to prevent large fluxes from having too large an impact (default true).
`initialGuess`	`double`	initial guess of the parameters (default ones).
`plotFitting`	`logical`	true if the resulting fitting should be plotted (default false).

Output arguments:

Name	Type	Description
`parameters`	`double`	fitted parameters in the same order as in parameterPositions.
`fitnessScore`	`double`	the corresponding residual sum of squares.
`exitFlag`	`double`	exit status returned by fminsearch.
`newModel`	`struct`	updated model structure with the fitted parameters.

Examples:

[parameters, fitnessScore, exitFlag, newModel]=fitParameters(model,...
    xRxns,xValues,rxnsToFit,valuesToFit,parameterPositions,fitToRatio,...
    initialGuess,plotFitting);

getBiomassFractions¶

Compute mass fraction per biomass component.

Compute the mass fraction (g/gDW) per biomass component plus the total. Mirrors raven_python.biomass.sum_biomass; the MATLAB counterpart of yeast-GEM's legacy sumBioMass.

The biomassConfig struct describes the per-organism biomass layout — see Parameters below. Components whose pseudoreaction is missing from the model contribute 0.

Input arguments:

Name	Type	Description	Default
`model`	`struct`	RAVEN model struct.	required
`biomassConfig`	`struct`	Struct describing the biomass layout, with fields: biomass_rxn : rxn id of the top-level biomass pseudoreaction. proton_met : met id of cytosolic H+ (used only by rescalePseudoreaction; may be unused here). components : cell array of component structs, each with fields: name : component name (e.g. 'protein'). pseudoreaction_name : model.rxnNames entry to identify the pseudoreaction. mass_strategy : 'mw' \| 'mw_minus_2h' \| 'mw_minus_water' \| 'grams' — see Notes below.	required

Output arguments:

Name	Type	Description
`fractions`	`struct`	Struct keyed by component name plus 'total': fractions.protein, fractions.RNA, ... etc. All values are in g/gDW.

Examples:

fractions = getBiomassFractions(model, biomassConfig);

Notes

mass_strategy values:

'mw'              MW from chemical formula
'mw_minus_2h'     MW − 2.016 g/mol (two protons released per charged
                  tRNA — protein-pseudoreaction substrates)
'mw_minus_water'  MW − 18.015 g/mol (water released per
                  polymerisation step — RNA / DNA)
'grams'           stoichiometry already in g/gDW (lipid backbone)

scaleBiomassFraction¶

Rescale a biomass component to a target value.

Rescale a biomass component to a target g/gDW value, optionally balancing a second component so the total biomass mass stays at 1 g/gDW. Mirrors raven_python.biomass.scale_biomass and yeast-GEM's legacy scaleBioMass.

Input arguments:

Name	Type	Description	Default
`model`	`struct`	RAVEN model struct.	required
`biomassConfig`	`struct`	Struct (see getBiomassFractions).	required
`componentName`	`char`	Component to rescale.	required
`newValue`	`double`	Target fraction in g/gDW.	required

Name-value arguments:

Name	Type	Description	Default
`balanceOut`	`char`	Second component name to adjust so the biomass total remains 1 g/gDW. Empty / omit to skip balancing.

Output arguments:

Name	Type	Description
`model`	`struct`	Modified model.

Examples:

model = scaleBiomassFraction(model, biomassConfig, 'protein', 0.5, 'carbohydrate');

scaleBiomassPseudoreaction¶

Rescale a biomass component pseudoreaction.

Multiply the substrate coefficients of one biomass component pseudoreaction by factor and rebalance H+ to preserve charge neutrality. Mirrors raven_python.biomass.rescale_pseudoreaction and yeast-GEM's legacy rescalePseudoReaction.

"Substrate" means every metabolite in the pseudoreaction whose metabolite name does NOT match the component name (the component's product is left untouched). After rescaling, the coefficient of biomassConfig.proton_met is recomputed so the pseudoreaction's total ionic charge sums to zero.

Input arguments:

Name	Type	Description	Default
`model`	`struct`	RAVEN model struct.	required
`biomassConfig`	`struct`	Struct (see getBiomassFractions).	required
`componentName`	`char`	Name of the component to rescale (must match biomassConfig.components{i}.name for some i, AND be the model.metNames of the produced metabolite in the matching pseudoreaction).	required
`factor`	`double`	Multiplicative factor.	required

Output arguments:

Name	Type	Description
`model`	`struct`	Modified model.

Examples:

model = scaleBiomassPseudoreaction(model, biomassConfig, 'protein', 0.9);

setGAM¶

Set the growth-associated maintenance (GAM) coefficient.

Set the growth-associated maintenance (GAM) coefficient in the biomass pseudoreaction, and optionally fix the non-growth maintenance (NGAM) reaction's bounds. Mirrors raven_python.biomass.set_gam and yeast-GEM's legacy changeGAM.

For every metabolite in the biomass pseudoreaction whose model.metNames entry is in cofactorMetNames, the stoichiometric coefficient is set to ±value preserving the sign of the current coefficient. Yeast-GEM scales ATP, ADP, H2O, H+ and phosphate (with ATP and H2O on the substrate side, ADP / H+ / phosphate on the product side).

Input arguments:

Name	Type	Description	Default
`model`	`struct`	RAVEN model struct.	required
`value`	`double`	New GAM value (mmol ATP / gDW per growth unit).	required
`biomassRxn`	`char`	Reaction id of the biomass pseudoreaction.	required
`cofactorMetNames`	`cell`	Cell array of metabolite NAMES (not IDs) to rescale, e.g. {'ATP','ADP','H2O','H+','phosphate'}.	required

Name-value arguments:

Name	Type	Description	Default
`ngamRxn`	`char`	NGAM reaction id. Required when ngamValue is supplied.
`ngamValue`	`double`	NGAM flux to fix. Sets the NGAM reaction's bounds to (ngamValue, ngamValue).

Output arguments:

Name	Type	Description
`model`	`struct`	Modified model.

Examples:

model = setGAM(model, 80, 'r_4041', {'ATP','ADP','H2O','H+','phosphate'});