Setconstraints¶
- individualizedLabReport(model, IndividualParameters, InputData, optionCardiacOutput)[source]¶
This function computes personalized physiolgical parameters based on the provided input data.
function [modelPersonalized,IndividualParametersNew] = individualizedLabReport(model,IndividualParameters, InputData,optionCardiacOutput)
INPUT model model structure, whole-body metabolic model IndividualParameters structure with Individual parameters to be
personalized or updated based on the input data. This structure, with default parameters, can be obtained using the script standardPhysiolDefaultParameters.m
InputData InputData: specify compartment by placing [bc], [u] or [csf] after the metabolite name optionCardiacOutput Different ways of calculatibg the cardiac
output based on physiological data have been implemented. - Based on heart rate and stroke volume: CardiacOutput = HeartRate * StrokeVolume. (optionCardiacOutput = 1, default) - Assume that cardiac output = blood volume.(optionCardiacOutput = 2) - Based on the polynomial suggested by Youndg et al [http://www.ams.sunysb.edu/~hahn/psfile/pap_obesity.pdf]: CardiacOutput = 9119-exp(9.164-2.91e-2*Wt+3.91e-4*Wt^2-1.91e-6*Wt^3); Wt = weight in kg (optionCardiacOutput = 0) - Based on Fick’s principle, which requires that the oxygen consumption rate is known: VO_2 = (CO* C_a) - (CO C_v); where CO = Cardiac Output, Ca = Oxygen concentration of arterial blood and Cv = Oxygen concentration of mixed venous blood. We assume that C_a is 200 ml O2/L and C_v is 150 ml O2/L. (optionCardiacOutput = 3) - Based on Fick’s principle, while estimating the VO_2 based on the body surface area (BSA): We use the Du Bois formula,[4][5]: BSA=0.007184 * Wt^0.425 Ht^0.725; Wt = weight in kg; Ht in cm; (optionCardiacOutput = 4)
OUTPUT modelPersonalized Updated model structure IndividualParametersNew Updated, personalized individual parameters
Ines Thiele, 2016-2018
- physiologicalConstraintsHMDBbased(model, IndividualParameters, ExclList, Type, InputData, Biofluid, setDefault, ExclMet, ExclMetAbbr)[source]¶
This function applies constraints to the whole-body metabolic model metabolite concentrations have to be given in uM organ weights have to be given in g Please note that reaction specific constraints are applied at the end of the function, which have been derived from the literature.
function modelConstraint = physiologicalConstraintsHMDBbased(model,IndividualParameters, ExclList, Type, InputData, Biofluid, setDefault,ExclMet,ExclMetAbbr)
INPUT model model structure IndividualParameters Structure containing physiological parameters,
as generated in standardPhysiolDefaultParameters
- ExclList List of reaction(s) to which no updated bound
should be assigned to
- Type Input type (either ‘xlsx’ (default) –> loads by default
‘Parsed_hmdbConc.xlsx’ or ‘direct’). If ‘direct’ InputData must be provided
- InputData first column corresponds to vmh id’s of
metabolites, 2nd to data points (will be set as lb and ub)
- Biofluid ‘all’ (default if type is xlsx). For direct:
‘bc’,’u’,’csf’
- setDefault If input data does not contain concentration information for a given metabolite
then a default concentration ranges will be used to calculate the constraints (default: 1) Note that the default metabolite concentration ranges are specified in IndividualParameters for the different biofluid compartments.
- ExclMet Specify if certain metabolites, and thus their associated reactions, should be
excluded from the constraint application (default: 0)
- ExclMetAbbr Provide list of metabolites that should be
excluded
OUTPUT modelConstraint model structure with updated constraints
Ines Thiele, 2015-2019
- physiologicalConstraintsHMDBbased_old(model, IndividualParameters, ExclList, Type, InputData, Biofluid, setDefault)[source]¶
apply constraints to Harvey metabolite concentrations have to be given in uM organ weights have to be given in g
INPUT model model structure IndividualParameters Structure containing physiological parameters,
as generated in standardPhysiolDefaultParameters
- Type Input type (either ‘xlsx’ (default) –> loads by default
‘Parsed_hmdbConc.xlsx’ or ‘direct’). If ‘direct’ InputData must be provided
- InputData first column corresponds to vmh id’s of
metabolites, 2nd to data points (will be set as lb and ub)
- Biofluid ‘all’ (default if type is xlsx). For direct:
‘bc’,’u’,’csf’
OUTPUT modelConstraint model structure with updated constraints
Ines Thiele, 2015/2016
- readInDietFromVMH(fileNameDiet)[source]¶
This function reads in the diet that has been created and downloaded from the https://www.vmh.life/#nutrition and converts it into the whole-body metabolic model consistent format.
[DietFormulation] = readInDietFromVMH(fileNameDiet)
INPUT fileNameDiet File name
OUTPUT DietFormulation Diet definition
Ines Thiele 2016-2019
- setDietConstraints(model, Diet, factor)[source]¶
This function sets diet constraints onto the bounds of the diet uptale reactions of a whole-body metabolic model. Units are given in mmol/day/person.
function model = setDietConstraints(model, Diet, factor)
INPUT model model structure Diet Diet option: ‘EUAverageDiet’ (default) factor value between 0 and 1; default is 1, i.e, 100% of the provided diet
OUTPUT model updated model strcution
Ines Thiele 2016-2019
- setFeedingFastingConstraints(model, feedingStatus, fastingValue, storageValue)[source]¶
This function sets constraints corresponding either to feeding (i.e., storage reactions are set to have a lower bound of 0 while the upper bounds are set to >0 (storage is enabled) or to fasting (i.e., storage reactions are set to have a lower bound of <0 (use of stored metabolites is enabled) while the upper bounds are set to 0 (storage is disabled).
function model = setFeedingFastingConstraints(model, feedingStatus,fastingValue,storageValue)
INPUT model model structure feedingStatus ‘feeding’ = default bounds for diet uptake fastingValue for all diet exchanges, use diet script to refine, organ storage is turned on;
‘fasting’ = all diet uptakes are closed, organ storage release is turned on
fastingValue default: fastingValue = -10; storageValue default: storageValue = 10;
OUTPUT model with updated constraints
Ines Thiele, 2015/2016