pwGetDefaultConfig


 config = pwGetDefaultConfig

 Returns the default configuration settings which are:

 

Configuration of PottersWheel analyses

 

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.



 

Distributed computing toolbox

  config.cluster.nNodes = 10;
    Number of cluster nodes, i.e. computers, to be used for the distributed calculation.
  config.cluster.command1 = 'jm = findResource(''scheduler'', ''type'', ''lsf'');';
    Commands that will be evaluated in order to create
    a job based on the distributed computing toolbox.
    Using multiple cores on the local machine:
    jm = findResource('scheduler', 'type', 'local');
    set(jm, 'DataLocation', pwd);
    job = createJob(jm, 'PathDependencies', {pwd});
  config.cluster.command2 = 'set(jm, ''ClusterMatlabRoot'', ''/opt/matlab'');';
    The path where Matlab is installed. For Harvard Medical School cluster:
    set(jm, 'ClusterMatlabRoot', '/opt/matlab');
  config.cluster.command3 = 'set(jm, ''SubmitArguments'', ''-q sysbio_1d'');';
    Setting for the one day slot sysbio_1d at the Harvard Medical School cluster:
    set(jm, 'SubmitArguments', '-q sysbio_1d');
  config.cluster.command4 = 'job = createJob(jm);';
    job = createJob(jm);
  config.cluster.command5 = '';
  config.cluster.command6 = '';
  config.cluster.command7 = '';
  config.cluster.command8 = '';
  config.cluster.command9 = '';
  config.cluster.command10 = '';


 

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



 

Default values

 
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;


 

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

pwSetConfig
pwGetConfig
pwSaveConfigToMatFile
pwSaveConfigToMFunction