Important functions


General commands
Start PottersWheel or bring main window to front pw
Open equalizer pe, pwEqualizer
Open configuration pwConfiguration
Get and set configuration struct pwGetConfig, pwSetConfig
Load and save configuration pwSaveConfigToMatFile, pwLoadConfigFromMatFile
Load and save repository (complete working state) pwSaveRepository, pwLoadRepository
Arrange figures pwArrange
Start a new session pwClear
Open model designer pwDesigner
Open model creation wizard pwNewModel
Open input designer pwInputDesigner
Open a model in the Matlab text editor pwEdit


Adding elements within a model definition file
Dynamic variable pwAddX
Dynamic parameter pwAddK
Reaction pwAddR
Driving input function pwAddU
Observable pwAddY
Scaling paramter pwAddS
Compartment pwAddC
Algebraic equation (assignment rule) pwAddA
Soft constraint pwAddConstraint
User defined function pwAddFunction
Differential equation pwAddODE
Derived variable pwAddZ
Event pwAddE
Derived parameter pwAddP


Adding model and data to PottersWheel
Add model pwAddModel
Add data pwAddData
Select a certain model-data couple pwSelect, pwGetNumberOfCouples
Combine model-data couples into an assembly pwCombine
Add model from library pwAddModelFromLibrary
Add data from library pwAddDataFromLibrary
Saving a model

pwSaveModel, pwSaveModelKeepingCustomStructure, pwSaveSelectedModelsWithFittedParValues

Simulate synthetic data pwSim
Split stimuli pwSplitStimuli
Force MEX compilation of a model pwForcedCompilation
Reload a modified model pwReload
Duplicate a model pwDuplicate


Model integration and trajectory plotting
Integrate and draw the model trajectories pwDraw
Select which figures to show (a, u, x, y, z) pwShowFigure
Set the used integrator pwSetIntegrator (or via config)
Activate fast integration pwFastIntegration (or via config)
Get or set parameter value pwGetFitParameterValuesByID, pwSetFitParamterValuesByID
Get plotting data pwGetPlottingData, pwGetPlottingData2


Start a fit pwFit
Start a fit sequence pwF2, pwF3
Apply a boosted fit, i.e. combine trust region and simulated annealing pwFitBoost
Turn log fitting on or off pwSetLogFitting (or via config)
Set optimizer pwSetOptimizer (or via config)
Turn plotting during fitting on or off pwShowFitting
Get the current chi-square value, number of data points, and statistical measures pwGetChisqAndN, pwGoodnessOfFit
Get specific or best fit of sequence pwGetBestFit, pwUseFitOfLastFitSequence
Disturb parameter values pwDisturb
Fit only k, s, or x0 pwFitDynamicParameters, pwFitScalingParameters, pwFitStartValues
Reset parameter values pwReset, pwSetResetValues


Fit analysis
Linear fit sequence analysis pwFitSequenceAnalysis
Plot a subset of best fits pwTrajectoriesOfManyParameterSettings
Analyse residuals pwAnalysisOfResiduals
Start PLE (Profile Likelihood Exploit) pwPLEInit
Start MOTA (Mean optimal transformation approach) pwMota
Remove fits pwClearFitHistory, pwFitHistoryDeleteFits
Merge fit sequences pwFitHistoryMergeFitSequences


Start a new report pwReportNew
Append last analysis step to report pwReportAppendLastStep
Generate a report pwReportGenerate
Save figures of last step (report independent) pwSaveFiguresOfLastStep


Model import and export
Import custom model format (including BNG etc.) pwConvertCustomFormatToPW
Export to Matlab pwExportCouplesToMatlab
Export to SBML pwExportCouplesToSBML, pwExportModelToSBML


Check installation and available toolboxes pwCheckSystem
Delete temporary files pwCleanUp
Close all figures except for the user interfaces pwCloseFigures
Installing the CVODES integrators of Sundials pwInstallSundialsTB