Nutritionalgorithm

addElementTracker(model, Element, rxnTags)

addElementTracker creates artificial metabolites and reactions that track the flux of a particular element through reactions with specified string tags.

USAGE

• [model] = addElementTracker (model,Element,rxnTags,trackString)

• INPUTS –

  model: COBRA model structure with minimal fields:

  • .S

  • .c

  • .ub

  • .lb

  • .mets

  • .rxns

  Element: element you are interested in (e.g., ‘N’) rxnTags: string or cell array containing the strings that mark

  reactions of interest to keep track of

Outputs

model: Returns the input model with added tracking reactions and the key “Track” reaction

Authors: Bronson R. Weston 2022

convert_EX_to_diet(model)

convert_EX_to_diet takes a model with typical exchange reactions (i.e., ‘EX_’) and translates them to uptake (diet) and secretion (exit) reactions.

USAGE:

[model] = convert_EX_to_diet(model)

INPUTS:

model: COBRA model structure with minimal fields:

• .S

• .c

• .ub

• .lb

• .mets

• .rxns

Outputs

model: Returns the input model with new uptake (’Diet_’) and secretion

(’Exit_’) reactions

Authors: Bronson R. Weston 2022

getMolFormula(model, metabolite)

getMolFormula takes a metabolite in a specified model and returns the molecular formula.

integrate_cVector_into_model(model)

sintegrate_cVector_into_model incorporates the c vector directly into the model as the reaction ‘obj_fun_rxn’.

nutritionAlgorithm(model, rois, roisMinMax, options)

This algorithm identifies the minimal changes to a diet necessary to get a desired change in one or more reactions of interest (rois). If a metabolite is entered instead of a reaction, the algorithm will optimize the diet with a sink or demand reaction for the corresponding metabolite of interest. For a walkthrough of the algorithm, see NutritionAlgorithmWalkthrough.mlx To cite the algorithm, please cite Weston and Thiele, 2022 and the COBRA Toolbox as specified on opencobra.github.io/cobratoolbox/stable/cite.html :USAGE: [newDietModel,pointsModel,roiFlux,pointsModelSln,menuChanges,detailedAnalysis] = nutritionAlgorithm (model,rois,roisMinMax,options)

INPUTS

model – COBRA model structure with minimal fields:

• .S

• .c

• .ub

• .lb

• .mets

• .rxns

rois: cell array of all reactions of interest roisMinMax: cell array of ‘min’/’max’ entries for rois

OPTIONAL INPUTS

options – Structure containing the optional specifications:

• .display: display results “off” or “on”?

• .roiWeights: a vector of weights for each reaction of interest

default is equal to 1

• .targetedDietRxns: A nx2 cell array that specifies any dietary

items to target and the corresponding weight for adding the item.

• .foodRemovalWeighting: Determines the relationship of food

removal weight with the weights specified by targetedDietRxns. The following are valid inputs for foodRemovalWeighting.

• ‘ones’ -> all dietary reactions from targetedDietRxns have a removal weight of one

• ‘inverse’ -> all dietary reactions from targetedDietRxns have a removal weight of one

• ‘ditto’ -> weights are equal to that of targetedDietRxns

added weights - nx2 cell array -> a customized cell array that functions like targedDietRxns but instead allows costomized weights for removing a food item rather than adding it. - {} empty cell array -> (default) An empty array assumes all dietary reactions are available from removal with a weight of one

• .slnType: Specify if solution should be ‘Detailed’ or ‘Quick’.

  Default setting is ‘Detailed’

• .roiBound: ‘Unbounded’ or ‘Bounded’. Default is ‘Bounded’.

• .foodAddedLimit: Specify a limit to the points produced by

  adding food to the diet

• .foodRemovedLimit: Specify a limit to the points produced by

  removing food from the diet

• .OFS: the Objective Flux Scalar initiates a limiting threshold

for the solution’s objective function performance. A OFS of 1 means that the nutrition algorithm solution will produce a result that is atleast equal to, or greater than the maximum flux of the objective reaction on the original diet

OUTPUT

newDietModel – An copy of the input model with updated diet

reaction bounds to reflect recomended dietary changes

pointsModel: The resulting model that is used to identify

recomended dietary changes. It includes points reactions and food added/removed reactions.

roiFlux: Returns the flux values for each roi in the points sln

pointsModelSln: Returns the entire points solution to pointsModel

menuChanges: Summarizes the recommended dietary changes

detailedAnalysis: Provides solutions for each simulation conducted in

the detailed analysis