pwGetDefaultConfig
config = pwGetDefaultConfig
Returns the default configuration settings which are:
Linear fit sequence analysis
config.analyses.linearFitSequenceAnalysis.showFitStartInHistograms = true;
Displays also the initial guess for each parameter in the fitted parameter histograms
config.analyses.linearFitSequenceAnalysis.useLogXInHistograms = false;
Displays the fitted parameter histograms with a logscale x-axis
PLE - Profile Likelihood Estimation
config.analyses.PLE.useGUI = true;
If true, the PLE user interface opens when the PLE method is initialized using pwPLEInit.
config.analyses.PLE.confLevelInUnitsOfStd = 1;
Confidence level in units of standard deviations,
i.e. a value of 1 corresponds to a one sigma interval (68%).
config.analyses.PLE.maxNumSteps = 100;
The maximum number of steps by which the
parameter of interest is increased or decreased to estimate the PL.
config.analyses.PLE.minStepSize = 0.01;
Minimum step size in % for the parameter value.
config.analyses.PLE.maxStepSize = 50;
Maximum step size in % for the parameter value.
config.analyses.PLE.relChi2StepIncrease = 0.1;
The step length is set to achieve a certain increase in the Chi2 value.
This parameter defines the relative amount compared to the Chi2 threshold.
A value of 0.1 corresponds to a 10% increase.
config.analyses.PLE.steppingMode = 1;
1 direct steps
2 progressive steps
config.analyses.PLE.alphaChi2Test = 0.05;
Significance level alpha for chi-square test based chi-square threshold (mode 3)
config.analyses.PLE.thresholdMode = 1;
1 Use relative chi-square threshold for simultaneous confidence level
2 Use relative chi-square threshold for separate confidence levels
3 Use absolute chi-square threshold based on chi-square test
config.analyses.PLE.breakOnParLimits = false;
If true, a parameter is not increased over its minimum
or maximum limit as defined in the model definition file.
config.analyses.PLE.showIterations = true;
If true, progress of the Profile Likelihood estimation is visualized.
Data import settings
config.data.yStdCalculation = 1;
1 error model of observation
2 std given in file
3 estimation with csaps spline (Matlab)
4 estimation with mgcv spline (R)
5 csvspl
6 estimation with the splinefit algorithm
config.data.yStd_smoothness = 0.2;
Smoothness of csaps splines. 0 = straight line, 1 = interpolating spline
config.data.yStd_h = 2;
2*h + 1 numbers will be used for yStd calculation
config.data.yStdMinRelative = 0;
config.data.yStdMinAbsolute = 0;
config.data.uCalculation = 2;
1 linear interpolation
2 smoothing spline interpolation (csaps, mgcv, or csvspl1)
3 smoothing spline (csaps)
4 smoothing spline (mgcv)
5 smoothing spline (csvspl1)
config.data.setNegSplineValuesToZero = true;
If true, negative spline interpolation values are set to zero.
Uncheck this if your input function may be negative by intention.
config.data.columnsToBeIgnored = {};
config.data.automaticColumnMapping = true;
If true, PottersWheel tries to automatically map column names
between external files and model observables
or to load a saved connection file.
config.data.arrangeFigures = true;
If true, figures will be arranged automatically after loading external data.
Graphical model designer
config.designer.warningWhenIncludingModel = true;
If true, a warning message appears when a second model
is to be included into a model within the model designer
config.designer.animationTime = 5;
Duration of the system animation in real time (seconds)
config.designer.nRotations = 1;
Number of rotations in the 3D animation.
config.designer.nIntegrations = 1;
Number of integrations per animation.
config.designer.nFramesInGif = 70;
Number of frames in an animated gif.
config.designer.showLabels = true;
If true, a label is displayed for each species.
config.designer.grid = 10;
Species snap to this grid when moved manually.
Special folders
config.folders.models
Folder for models: Model search path:
1 Current folder
2 '../Models'
3 Folder as specified in the configuration
config.folders.data
Folder for data: Data search path:
1 Current folder
2 '../Data'
3 Folder as specified in the configuration
config.folders.IDSO
Folder: IDSO search path:
1 Current folder
2 '../IDSO'
3 Folder as specified in the configuration
config.folders.repository
Folder for repositories
config.folders.configuration
Folder for configurations
config.folders.report
Folder for reports
config.folders.lccFolder
Folder where the C compiler lcc has been installed.
Macro folder
config.folders.addMacrosFolderToPath = true;
If true, the folder ../Macros will be added temporarilly
to the Matlab path when starting a new PottersWheel session.
General settings
config.general.doBackup = true;
backup of old model files if automatically saving new ones
config.general.verbosity = 3;
1 Only error messages
2 Warnings also
3 Short information also
4 Long information also
5 Debug information also
6 Long debug information also
config.general.pause = 3;
Time period to pause Matlab when calling pwPause.
If negative, a pressed key is required to continue.
config.general.resetConfigInSessionStart = true;
If false, the configuration is not reseted
when clearing the PottersWheel session, e.g. using pwClear.
config.general.resetRandInSessionStart = true;
See pwClear
config.general.warningWhenCleaningUp = true;
Prompts the user to confirm deleting temporary files when calling pwCleanUp.
config.general.extendedCoupleList = false;
If true, the currently used IDSO is displayed in upper list
of the main user interface.
Graphviz model visualization
config.graph.pageSize = '';
E.g. 8.5, 11
config.graph.maxSize = '8, 10';
config.graph.rotate = [];
E.g. 90
config.graph.withRules = false;
Integration settings
config.integration.integrator = 1;
1 radau5
2 radau
3 seulex
4 dop853
5 dopri5
6 odex
7 ode45
8 ode15s
9 ode23
10 ode23s
11 ode23t
12 ode23tb
13 ode113
14 cvodes (See help pwInstallSundialsTB)
config.integration.useFastIntegration = false;
Applicable for integrators 1, 2, and 5.
Fast integration requires a Fortran compiler.
Change this setting _before_ pressing the combine button.
config.integration.useMexODE = true;
Developer setting. Should be left to true.
config.integration.calcJacobian = false;
Requires the symbolic math toolbox.
config.integration.useJacobian = false;
Using the jacobian of the ODE system usually improves integration accuracy and robustness.
Requires the symbolic math toolbox.
config.integration.useBandedJacobian = false;
Applicable for integrators 1-6.
config.integration.useJPattern = false;
Applicable for integrators 7-13.
config.integration.calcSensitivities = false;
Applicable for integrator 14 (CVODES).
Calculates the sensitivities of x and y depending on time for each fitted parameter.
This setting is independent of optimization.useJacobian
and only used to display the sensitivities.
config.integration.useBreakpoints = true;
Developer setting. Should be left to true.
config.integration.opt.AbsTol = 1e-006;
config.integration.opt.BDF = [];
config.integration.opt.Events = [];
config.integration.opt.InitialStep = [];
config.integration.opt.Jacobian = [];
config.integration.opt.JConstant = [];
config.integration.opt.JPattern = [];
config.integration.opt.Mass = [];
config.integration.opt.MassConstant = [];
config.integration.opt.MassSingular = [];
config.integration.opt.MaxOrder = [];
config.integration.opt.MaxStep = [];
config.integration.opt.NonNegative = [];
config.integration.opt.NormControl = [];
config.integration.opt.OutputFcn = [];
config.integration.opt.OutputSel = [];
config.integration.opt.Refine = [];
config.integration.opt.RelTol = 0.001;
config.integration.opt.Stats = [];
config.integration.opt.Vectorized = [];
config.integration.opt.MStateDependence = [];
config.integration.opt.MvPattern = [];
config.integration.opt.InitialSlope = [];
config.integration.opt.MaxNumSteps = 1500;
(CVODES) Maximum number of steps to reach the next output time
pwAddX)">
X (Dynamic variables, pwAddX)
config.model.xStartValue = 0;
Value of x at integration start, usually at t=0.
config.model.xType = 'local';
Fitting type fix, local, or global. If the start value is 0, the default setting is fix.
config.model.xMinValue = 1e-005;
config.model.xMaxValue = 100000;
config.model.xTypeOfStartValue = 'concentration';
concentration or amount
pwAddK)">
K (Dynamic parameters, pwAddK)
config.model.kValue = 0.1;
config.model.kType = 'global';
fix, local, or global
config.model.kMinValue = 1e-005;
config.model.kMaxValue = 100000;
pwAddY)">
Y (Observables, pwAddY)
config.model.yErrorModel = '0.1 * y + 0.05 * max(y)';
0.1 * y corresponds to 10% relative error.
0.05 * max(y) corresponds to 5% error relative to the maximum.
config.model.yNoiseType = 'Gaussian';
Currently, only a Gaussian error model is supported
config.model.yPrefixScalingParameter = 'scale_';
pwAddS)">
S (Scaling parameters, pwAddS)
config.model.sValue = 1;
config.model.sType = 'local';
fix, local, or global
config.model.sMinValue = 1e-005;
config.model.sMaxValue = 100000;
pwAddC)">
C (Compartments, pwAddC)
config.model.cID = 'cell';
config.model.cSize = 1;
config.model.cName = 'cell';
config.model.cSpatialDimensions = 3;
config.model.cConstant = true;
Autocorrections
config.model.splitReversibleReactions = false;
If true, reversible reactions are automatically split into one forward and one back-reaction.
config.model.reconstructNetwork = false;
If true, the reaction network is determined automatically for ODE based models.
Please note that the original ODEs will be removed for successful network reconstruction.
(Still in BETA phase! Please compare original ODEs and ODEs generated by new network.)
Miscellaneous
config.model.negativeParsPossible = false;
If true, mantissa sliders in the equalizer are displayed from -1 to 1 instead of 0 to 1
config.model.compileAddedModels = true;
If true, several C MEX files are created and compiled for each added model.,
e.g. for the ODEs. Compare pwForcedCompilation.
config.model.autoSaveToMatFile = false;
If true, the model struct is saved to a *.mat file
after loading a model definition into PottersWheel. Compare pwAddModel.
Export to txt
config.model.export.includeComments = true;
config.model.export.includeHeaders = true;
config.model.export.includeNameLists = false;
config.model.export.removeBlanks = false;
If true, blanks in formulas are removed.
config.model.export.fileExtension = '.txt';
config.model.export.commentPrefix = '';
Prefix for lines containing PottersWheel comments like model name and date of export.
config.model.export.kHeader = 'Parameters:';
config.model.export.kFormat = '%-10s = %g';
E.g. %s = %g may lead to k1 = 0.3
config.model.export.x0Header = 'Initial values:';
config.model.export.x0Format = '%-5s(0) = %g';
E.g. %s(0) = %g may lead to X(0) = 13.2
config.model.export.oHeader = 'ODEs:';
config.model.export.oFormat = 'd(%-10s)/dt = %s';
E.g. d(%s)/dt = %s may lead to d(X)/dt = -k1*X + k2*Y
General optimization / fit settings
config.optimization.method = 2;
1 fminsearch
2 trustregion
3 genetic algorithm
4 simulated annealing
5 smarquardt
6 ssmlsqnonlin
7 ssmdn2fb
config.optimization.stopErrorLevel = 2;
config.optimization.levelOfHistoryStorage = 1;
1 Only fitted parameter values
2 Parameters and fit settings
3 Parameters, settings and trajectories
config.optimization.fitInLogParameterSpace = false;
Useful if the parameters span several orders of magnitude.
config.optimization.updateSliders = true;
If true, the sliders in the equalizer will be updated during optimization.
config.optimization.calcJacobian = false;
Requires the symbolic math toolbox.
config.optimization.useJacobian = false;
Requires integrator 14 (CVODES) and the symbolic math toolbox.
config.optimization.storeJacobian = false;
If true and if useJacobian == true,
the Jacobian of the optimization is stored
and can be retrieved with pwGetStoredOptimizationJacobian
config.optimization.derivativeCheck = false;
Compares the analytically determined Jacobian with the numerical approximation.
config.optimization.userFunction = '';
Function: User supplied function which will be minimized. See help pwSetOptimizationUserFunction.
config.optimization.useUserFunction = false;
If true, the user defined optimization function will be used (if available).
config.optimization.fitInitFunction = '';
Function: User supplied function which be will called before a fit (pwFit) is executed.
config.optimization.useFitInitFunction = false;
If true, the user defined fit init fuction is active (if available).
Fit sequence analysis
config.optimization.numberOfFitsInSequence = 10;
config.optimization.strengthOfDisturbance = 0.2;
Quasi random number generator
config.optimization.useQRNG = false;
config.optimization.useLogQRNG = false;
config.optimization.indexQRNG = 1;
config.optimization.autoResetQRNG = true;
ASAMIN simulated annealing
config.optimization.asamin.limitAcceptances = 1000;
ASA default 10000.
The maximum number of states accepted before quitting. If set to 0, then no limit is observed.
config.optimization.asamin.limitGenerated = 2000;
ASA default 99999.
The maximum number of states generated before quitting. If set to 0, then no limit is observed.
config.optimization.asamin.limitInvalid = 1000;
ASA default 1000.
Limit of repetitive invalid generated states.
config.optimization.asamin.acceptedToGeneratedRatio = 0.0001;
ASA default 1e-6.
The least ratio of accepted to generated states.
config.optimization.asamin.costPrecision = 1e-018;
ASA default 1e-18.
Precision required of the cost function if exiting because of reaching maximumCostRepeat.
config.optimization.asamin.maximumCostRepeat = 5;
ASA default 5.
Maximum number of times that the cost function repeats itself,
within limits set by Cost_Precision, before quitting.
config.optimization.asamin.numberCostSamples = 5;
ASA default 5.
When > 0, the initial cost temperature is calculated as the
average of the absolute values of numberCostSamples sampled cost functions.
config.optimization.asamin.temperatureRatioScale = 1e-005;
ASA default 1e-5.
Guide to the expected cost temperature of convergence
within a small range of the global minimum.
config.optimization.asamin.costParameterScale = 1;
ASA default 1.
Ratio of cost:parameter temperature annealing scales.
config.optimization.asamin.temperatureAnnealScale = 100;
ASA default 100.
Guide to achieve the expected cost temperature sought by temperatureRatioScale
within the limits expected by limitAcceptances.
config.optimization.asamin.userInitialParameters = true;
ASA default false.
If true, then the first user's guess is used to calculate this first state,
which is reasonable in PW.
config.optimization.asamin.sequentialParameters = -1;
ASA default -1.
If > 0, some parameters will be adapted during optimization sequentially
rather than simultaneously.
config.optimization.asamin.initialParameterTemperature = 1;
ASA default 1.
The initial temperature for all parameters.
config.optimization.asamin.acceptanceFrequencyModulus = 100;
ASA default 100.
Frequency of testing for periodic testing and reannealing,
dependent on the number of accepted states.
config.optimization.asamin.generatedFrequencyModulus = 10000;
ASA default 10000.
Frequency of testing for periodic testing and reannealing,
dependent on the number of generated states.
config.optimization.asamin.reannealCost = 1;
ASA default 1.
If 0, reannealing of the cost temperature is bypassed.
If 1, default reannealing.
Check ASA documentation for other values.
config.optimization.asamin.reannealParameters = true;
ASA default true.
Permits reannealing of the parameter temperatures to be part of the fitting process.
Set to false for systems with very large numbers of parameters
to decrease the number of function calls.
config.optimization.asamin.deltaX = 0.001;
ASA default 0.001.
Fractional increment of parameters used to take
numerical derivatives when calculating tangents for reannealing.
Ignored settings
config.optimization.asamin.asaOutFile = 'asa.log';
Currently ignored, i.e. always asa.log is used.
config.optimization.asamin.randSeed = [];
Currently ignored. Use asamin ('set', 'rand_seed', value) to reset the asamin seed manually.
config.optimization.asamin.testInCostFunc = false;
Currently ignored.
config.optimization.asamin.useRejectedCost = false;
Currently ignored.
config.optimization.asamin.includeIntegerParameters = false;
Currently ignored.
Genetic algorithm
config.optimization.ga.MutationFcn = 'mutationadaptfeasible';
config.optimization.ga.Generations = 200;
config.optimization.ga.PopInitRangeMin = 0;
config.optimization.ga.PopInitRangeMax = 0.1;
config.optimization.ga.Display = 'off';
off, iter, diagnose, final
config.optimization.ga.PopulationSize = 200;
config.optimization.ga.CrossoverFraction = 0.8;
config.optimization.ga.EliteCount = 2;
config.optimization.ga.FitnessScalingFcn = 'fitscalingrank';
config.optimization.ga.HybridFcn = [];
config.optimization.ga.StallGenLimit = 50;
config.optimization.ga.StallTimeLimit = 60;
config.optimization.ga.iterationsBetweenPlots = 5;
config.optimization.ga.TolFun = 1e-005;
Line search
config.optimization.linesearch.maxIter = 1000;
config.optimization.linesearch.TolFun = 1e-007;
config.optimization.linesearch.TolX = 1e-007;
config.optimization.linesearch.iterationsBetweenPlots = 40;
config.optimization.linesearch.Display = 'off';
config.optimization.linesearch.MaxFunEvals = 4000;
Trust region
config.optimization.trustregion.maxIter = 200;
config.optimization.trustregion.TolFun = 1e-005;
config.optimization.trustregion.TolX = 1e-005;
config.optimization.trustregion.iterationsBetweenPlots = 5;
Less iterations between updated plotting figures require more CPU time.
config.optimization.trustregion.Display = 'off';
off, iter, notify, final
Showing options
config.plotting.showA = false;
To show trajectories of algebraic equations
config.plotting.showU = false;
To show trajectories of the driving input in a separate figure
config.plotting.showX = false;
To show trajectories of the dynamic variables
config.plotting.showY = true;
To show trajectories and measurements of the observables
config.plotting.showZ = false;
To show trajectories of derived variables
config.plotting.showPhaseSpace = true;
If true, displays user grouped variables in a phase space view
config.plotting.showSensitivities = true;
If true, displays time dependent sensitivities dx/dp or dy/dp
of user defined pairs between variables X/Y and parameters K/x0/S if available.
config.plotting.singleFigure = false;
config.plotting.overwrite = true;
config.plotting.menuBar = false;
Show the menu bar
config.plotting.toolBar = false;
Show the tool bar
config.plotting.showFitting = true;
config.plotting.showFittingInfo = true;
config.plotting.showFit = true;
config.plotting.showSimulation = true;
config.plotting.showIterations = true;
config.plotting.showParNamesInIterationPlot = true;
config.plotting.showTitle = true;
config.plotting.showLegend = true;
config.plotting.showXYLabels = true;
config.plotting.showModelInfo = true;
config.plotting.showParInfo = true;
config.plotting.showChisqValue = true;
config.plotting.showXTickLabel = true;
config.plotting.showYTickLabel = true;
config.plotting.showInputLegend = false;
config.plotting.showT0InStimDepView = false;
config.plotting.forceTimeDependentView = false;
config.plotting.maxLegendEntries = 20;
Maximum number of legend entries
Saving options
config.plotting.saveFit = false;
To automatically save the figure after a fit
config.plotting.saveFrames = false;
To store e.g. a fit into memory for later use of pwSaveFrames
config.plotting.savePNG = true;
config.plotting.savePNGsmall = true;
config.plotting.saveEPS = false;
config.plotting.savePDF = false;
config.plotting.saveTIFFEPS = false;
config.plotting.saveJPG = false;
config.plotting.saveFIG = false;
config.plotting.saveEMF = false;
Line style
config.plotting.plotType = 3;
1 no data
2 lines data to model
3 error bars
4 only data points
config.plotting.lineWidthInIterationsPlot = 1.5;
config.plotting.lineWidthU = 1.5;
config.plotting.lineWidthUData = 1;
config.plotting.lineWidthX = 1.5;
config.plotting.lineWidthY = 1.5;
config.plotting.lineWidthYData = 1;
config.plotting.lineWidthZ = 1.5;
config.plotting.lineWidthA = 1.5;
config.plotting.lineColorU = [0 0.7 0];
r g b values
config.plotting.lineColorUData = [0 1 0];
r g b values
config.plotting.lineColorX = [0 0 1];
r g b values
config.plotting.lineColorY = [1 0 0];
r g b values
config.plotting.lineColorYData = [0 0 1];
r g b values
config.plotting.lineColorZ = [0 0 1];
r g b values
config.plotting.lineColorA = [0 0 1];
r g b values
config.plotting.lineMarkerU = 'none';
. o x + * s d v ^ < > p h none
config.plotting.lineMarkerUData = '.';
. o x + * s d v ^ < > p h none
config.plotting.lineMarkerX = 'none';
. o x + * s d v ^ < > p h none
config.plotting.lineMarkerY = 'none';
. o x + * s d v ^ < > p h none
config.plotting.lineMarkerYData = '.';
. o x + * s d v ^ < > p h none
config.plotting.lineMarkerZ = 'none';
. o x + * s d v ^ < > p h none
config.plotting.lineMarkerA = 'none';
. o x + * s d v ^ < > p h none
config.plotting.lineStyleU = '-';
: -. -- none
config.plotting.lineStyleUData = '-';
: -. -- none
config.plotting.lineStyleX = '-';
: -. -- none
config.plotting.lineStyleY = '-';
: -. -- none
config.plotting.lineStyleYData = 'none';
: -. -- none
config.plotting.lineStyleZ = '-';
: -. -- none
config.plotting.lineStyleA = '-';
: -. -- none
Font sizes
config.plotting.fsTitle = 11;
FontSize
config.plotting.fsLegend = 9;
FontSize
config.plotting.fsXYLabels = 9;
FontSize
config.plotting.fsModelInfo = 9;
FontSize
config.plotting.fsParInfo = 9;
FontSize
config.plotting.fsChisqValue = 12;
FontSize
config.plotting.fsXTickLabel = 9;
FontSize
config.plotting.fsYTickLabel = 9;
FontSize
Miscellaneous
config.plotting.figureColor = [0.83137254901961 0.8156862745098 0.7843137254902];
config.plotting.legendColor = [0.83137254901961 0.8156862745098 0.7843137254902];
config.plotting.axesColor = [1 1 1];
config.plotting.textColor = [0 0 0];
config.plotting.nFine = 200;
Number of plotted points for each trajectory.
Value change takes effect immediately - no re-combination of couples required.
config.plotting.useGrayColors = false;
If true, PottersWheel uses gray colors (not yet fully implemented).
config.plotting.multiTrajectoryColors = {};
config.plotting.multiTrajectoryColors{1} = [0 0 0];
config.plotting.multiTrajectoryColors{2} = [0 0 1];
config.plotting.multiTrajectoryColors{3} = [0 0.666666666666667 1];
config.plotting.multiTrajectoryColors{4} = [0.333333333333333 0.666666666666667 0];
config.plotting.multiTrajectoryColors{5} = [0 1 0];
config.plotting.multiTrajectoryColors{6} = [1 0.749019607843137 0];
config.plotting.multiTrajectoryColors{7} = [1 0.333333333333333 0];
config.plotting.multiTrajectoryColors{8} = [0.784313725490196 0.117647058823529 0];
config.plotting.multiTrajectoryColors{9} = [0.666666666666667 0 0.5];
config.plotting.multiTrajectoryColors{10} = [0.333333333333333 0 0.5];
config.plotting.stimuliColors = {};
config.plotting.opacity = 1;
To adjust the opacity of trajectories between 0 and 1.
An opacity of 1 corresponds to a normal plot with no transparency.
Attention: Semi-transparent lines are computationally more expensive.
config.plotting.lineSmoothing = false;
If true, all trajectories are displayed with anti-aliased, i.e. smoothed lines.
config.plotting.distanceToScreenBottom = 34;
config.plotting.distanceToScreenTop = 0;
config.plotting.distanceToScreenLeft = 0;
config.plotting.distanceToScreenRight = 0;
config.plotting.nSignificantDigits = 4;
config.plotting.spread = 0;
Used to spread stimulations within the same plot
so that lines which are plotted onto each other are visible.
config.plotting.colormapName = 'jet';
jet hsv hot cool spring summer autumn winter gray bone copper pink lines
config.plotting.parameterIDsMode = 1;
1 IDs
2 Names
3 IDsAndNames
config.plotting.variablesIDsMode = 1;
1 IDs
2 Names
3 IDsAndNames
config.plotting.userFunction = '';
Function: User supplied function which will be used for additional figures.
See pwSetPlottingUserFunction.
pwSim)">
Simulating data (pwSim)
config.simulation.setNegativeValuesToZero = true;
If true, negative simulated data is set to zero.
Latex settings
config.report.referenceFile = [];
A bibtex reference file, e.g. created with JabRef.
config.report.bibstyle = 'alpha';
alpha, plain, natbib
config.report.paperSize = 'a4paper';
a4paper, letter
See also