User's Reference (SBPOP)

Most up-to-date information
  • The user's reference for the SBPOP part of the SBPOP PACKAGE is limited to a brief overview of the available functions (I do have a real job and lack some time sometimes ...).
  • However, of course, in the MATLAB SBPOP package all functions are documented in every detail.
  • You find a detailed overview over the included functions when calling "help SBPOP" in MATLAB. Alternatively, you can call "doc SBPOP".
  • Help to each function can be obtained by "help functionname"

Functions - Overview

Simulates a given SBmodel with a given SBPOPdosing scheme.Simulates the application of a dosing schedule to a model that has been prepared for it (using the mergemoddosSBPOP function) and either plots or returns the simulation results
Installation of SBPD
 
installSBPOPInstallation script for the SBPOP package.
lookforSBPOPSearches SBPOP functions for strings and opens the documents in which these strings appear.
newscriptSBPOPFunction creating a template file for a new script.
newfunctionSBPOPFunction creating a template file for a new function.
setseedSBPOPSet the seed.
 
Dosing schedule related functions
 
SBPOPdosingCreates an SBPOPdosing object defining a dosing schedule.
SBPOPstructReturns the internal data structure of an object.
isSBPOPdosingChecks if input argument is an SBPOPdosing object.
SBPOPcreateDOSfileCreates a *.dos file with the dosing text description.
SBPOPcreateDOSINGCreating a desired SBPOPdosing scheme.
SBPOPdoseupdatevalueAllows to update the dosing amount for a given input, defined in an SBPOPdosing object.
SBPOPsimulate.
SBPOPmergemoddosBased on a model and dosing object, a new SBmodel is generated, that implements the defined dosings. Multiple dosing schedules are realized by updating the parameters of subsequent dosings using events.
mergemoddosSBPOPThis function takes an SBmodel and an SBPOPdosing scheme as inputs. It adds necessary elements to the model that are required to implement the different dosing inputs (bolus, infusion, absorption0, absorption1) for simulation purposes (e.g. by the SBPOPsimdosing function).
SBPOPsimdosing.
getmoddosinputinfoSBPOPChecks the availability of dosing input definitions used in the model in the dosing object and returns a structure similar to the "input" field structure of an SBmodel, augmented with the dosing information, defined in the SBPOPdosing object.
dosing2doseeventSBPOPThis function takes an SBPOP dosing object as input and returns a structure in which the dosing events, happening, are sorted according to the times at which they happen. Additionally, the output structure contains information about the dosing amount and the names of the parameters in a model to change in order to apply the dosing.
doseinputsSBPOPExtracts names and types of dosing inputs from a SBPOPdosing object.
 
General data file handling
 
SBPOPloadCSVdatasetLoads a CSV dataset as a MATLAB dataset.
SBPOPloadNONCSVdatasetLoads a non-CSV dataset as a MATLAB dataset. Example: NONMEM and Monolix output tables.
SBPOPexportCSVdatasetExports a MATLAB dataset as a CSV file.
SBPOPdataset2wideExpands a dataset from a row based format to a column based format.
SBPOPsas7bdat2csvConvert a sas7bdat file to a CSV file (Requires presence of SAS on your systems command line).
 
Plotting Tools
 
SBPOPplotCovarianceCatThis function plots the covariance relationship between a list of continuous variables and a list of categorical variabels.
SBPOPplotfacetgridThis function allows to generate facet-grid plot with many different settings.
SBPOPplotfillFunction allowing to plot shaded areas with transparency.
SBPOPplotHistogramThis function plots histograms of the data provided, allows grouping and plotting several histograms on top of each other.
SBPOPplotpairwiseCorrPlots pairwise correlations of data.
SBPOPplotQQQQ plot for provided input data.
SBPOPplottrellisNice function to do Trellis plots with many different settings.
SBPOPplotXYThis function plots Ydata vs. Xdata with many different settings.
 
Monolix related functions
 
SBPOPcreateMLXTRANfileCreate MLXTRAN structural model based on SBmodel and SBPOPdosing scheme.
SBPOPcreateMONOLIXprojectCreate Monolix project (includes structural model creation).
SBPOPrunMONOLIXprojectRuns specified Monolix project.
SBPOPsampleMONOLIXparamSamples population and individual parameters from a Monolix fitting result. The resulting population and individual parameters can be used for model simulations.
 
Figure export tools
 
printFigureSBPOPExports MATLAB figures as JPG, PNG, or PS files. For PS files it appends them in same file.
startNewPrintFigureSBPOPRemoves PS file (windows) or PDF file (unix) if it exists (so new figures are not appended).
convert2pdfSBPOPConverts PS to PDF files on unix/linux.
 
Other
 
getcolorsSBPOPFunction returns color settings and linestyles, etc. Useful for plots to be able to use better colors than the MATLAB default.
usernameSBPOPGet the name of the current user.
 
popPKPD Toolbox
Please note that the functions in the popPKPD Toolbox within SBPOP assume a standard dataset format. Nothing really exciting but some standard is needed in order to simplify things. This data format is documented in the help text of the function SBPOPcheckDataFormat and at every place where the user needs to see it.
Most available functions are general for both popPK and popPKPD. However, there are some which only deal with popPK. Please note that the functions assume that fits have been done with Monolix. NONMEM is out of scope (for now) - sorry!
 
popPK specific functions
 
SBPOPcreatePopPKprojectSet-up of a popPK workflow, automatically creating documented template scripts that can be used.
SBPOPexplorePopPKdataCreates a wide range of data exploration plots specific for popPK analyses.
SBPOPcleanPopPKdataSupports simple data cleaning specific for popPK analyses.
SBPOPconvert2popPKdatasetConvert dataset to popPK dataset. Removing placebo patients, keeping only certain columns, keeping only dose and PK in the dataset.
SBPOPbuildPopPKModelSpaceFunction allowing to generate a PK model subspace, running all the estimations, generating tables for comparison of models, and generating a wide range of fit analysis plots. For current limitations of possible models, please look at the help text to this function.
SBPOPfitanalysisPopPKFunction generating GOF plots for a range of PK models. No need to call it yourself. The function "SBPOPbuildPopPKModelSpace" does it already for you.
 
General popPK/popPKPD functions
 
SBPOPcheckDataFormatChecking the data format and reporting problems.
SBPOPexploreIndivDataThis function allows to plot individual data from a standardized PKPD dataset.
SBPOPexploreSummaryStatsThis function produces summary statistics for the provided dataset.
SBPOPexplorePopPDdataCreates a wide range of data exploration plots specific for popPD analyses.
SBPOPcleanPopPDdataSupports simple data cleaning specific for popPD analyses.
SBPOPconvert2popPDparametersDatasetConvert dataset to popPD dataset, including individual PK parameters for simulation of the PK.
SBPOPconvert2popPDconcentrationDatasetConvert dataset to popPD dataset, including individual concentrations to use as regression variable.
SBPOPconvert2popPKPDsimultaneousDatasetConvert dataset to popPKPD dataset, allowing simultaneous popPKPD fit.
SBPOPcleanImputeCovariatesCovariate imputation.
SBPOPcleanRemoveFewObsSubjectsRemoval of subjects with not more than Nobs observations.
SBPOPcleanRemovePlaceboSubjectsRemoval of placebo subjects.
SBPOPcleanRemoveRecordsIDsRemoval of user defined IDs and records.
SBPOPgetMonolixDataHeaderDetermination of Monolix header types.
SBPOPfitanalysisETAvsCOVPlots the individual variations over covariates and categorical covariates.
SBPOPfitanalysisGOFplotsProduces several plots that can be used for checking the goodness of fit.
SBPOPfitanalysisIndividualFitsPlots individual fits and population prediction against observed data over time.
SBPOPfitanalysisOutlierDetectionConsiders PWRES and searches for outliers and displays info about them.
SBPOPfitanalysisRandomEffectsPlots information about the random effects in different ways.
SBPOPcovariateChangeAssessmentAssesses the changes that a covariates introduces on the model parameters, based on the contents of the dataset (without uncertainty).
SBPOPcovariateAssessmentUncertaintyAssesses the changes that a covariates introduces on the model parameters, based on the contents of the dataset (with uncertainty).
SBPOPcompareModelsThis function allows to compare the same structural model for different estimation results from Monolix.
SBPOPcomparePopPKmodelsThis function allows to compare different popPK models created with the PKPD toolbox in SBPOP.
SBPOPassessInformationContentThis function allows to predict the information content in data of (a) future study/ies, given the planned dosing and observation schedule.
SBPOPcreateVPCGeneration and plotting of simple VPC.
SBPOPcreateStratifiedVPCAllows to generate a stratified VPC.
SBPOPcreatePopPKstratifiedVPCAllows to generate a stratified VPC with even less input arguments, but limited to popPK models built with the popPKPD toolbox in SBPOP.
SBPOPrunMONOLIXprojectFolderRuns all models in specified folder.
SBPOPfitanalysisProjectsFolderPlotsCreates fit analysis plots for all Monolix project folders in specified folder. The underlying models do not need to contain the same parameters.
SBPOPfitanalysisProjectsFolderInfoCreates model comparison tables for all Monolix project folders in specified folder. The underlying models do not need to contain the same parameters.
SBPOPfitanalysisGeneralPlotsPlots fit analysis plots for a single specified Monolix project folder.
 
EXPLORATORY functions - NOT yet included in public version of SBPOP
 
Early Biologics Modeling
 
standard_Drug_LigandTarget_model.txtbcThis is a TEXTBC format model, implementing a 3 compartment standard model to be used for antibody modeling when the target/targets are ligands. It is build in a modular way, can easily be simplified and extended if needed. The advantage of a standardized model are standard parameter, state, and variable names, that can be assumed and used in associated functions.
SBPOPcreateDRUGligandTargetModelThis function just copies the standard model (drug vs. ligand as target) to the current folder under the given name and makes it available to the user to edit, modify, and customize.
SBPOPtissuedataThis function is simply a collection of literature data from two references, that stores the volumes of different tissues and the corresponding volumes of the interstitial spaces (human values only).
SBPOPplotDoseEffectCurveThis function plots a dose/effect curve for given input arguments.
SBPOPplotDoseParamCurveThis function plots a dose/parameter curve for given input arguments. Different effect levels are used as parameters for the different curves.
SBPOPoptimizeDRUGkineticsThis function will estimate parameters of the standard model to adjust the kinetics of a drug molecule (mAb, nanobody, etc.) to desired properties (alpha and beta halflife and percentage of steady-state distribution between disease tissue and plasma).
SBPOPoptimizeLigandTARGETkineticsThis function will estimate parameters of the standard model to adjust the kinetics of a target (ligand) to desired properties (alpha and beta halflife).
SBPOPoptimizeLigandTARGETsynthesisThis function will estimate parameters of the standard model to adjust the steady-state concentrations of a target (ligand) to desired properties (plasma/disease tissue/peripheral tissue concentrations).
 
PBPK model simulation and parameter fit
Not all PBPK model functions in SBPOP are documented here below. Functions for building complete PBPK models are available but some work is needed on them.
 
SBPOPsimpbpkThis function simulates a PBPK model and plots the results. If the results are not plotted (when an output argument is given) then the results are returned to the MATLAB workspace.
SBPOPfitpbpkThis function estimates defined parameters in the given PBPK model in order to fit the model simulation to the provided measurements. It returns the fitted model.
 

SBPOP PUBLICATIONS

Publications, discussing results obtained with the help of the SBPOP PACKAGE, are asked to reference the most relevant of the following papers and additionally the link to this webpage:

  • Systems Biology Toolbox for MATLAB: A computational platform for research in Systems Biology, Bioinformatics, 22(4), 514-515, 2006, doi:10.1093/bioinformatics/bti799
  • SBaddon: high performance simulation for the Systems Biology Toolbox for MATLAB, Bioinformatics, 23(5), 646-647, 2007, doi:10.1093/bioinformatics/btl668
  • SBPOP Package: Efficient support for model based drug development from mechanistic models to complex trial simulation, PAGE meeting, Glasgow, UK [abstract]
  • Enhancing population pharmacokinetic modeling efficiency and quality using an integrated workflow, Journal of Pharmacokinetics and Pharmacodynamics, doi:10.1007/s10928-014-9370-4, 2014.
SBPOP NEWS
  • 16th March 2015: Many small improvements ... also SBML export now fully working again
  • 20th January 2015: Many improvements ... Windows 64bit support and compatibility with MATLAB versions >=R2014B
  • 28th July 2014: Happy to announce that our paper about efficient conduct of popPK anlalyses has been published (doi:10.1007/s10928-014-9370-4)
  • 3rd July 2014: Update to Revision 1361 (due to packaging bug in Rev 1352)
  • 18th June 2014: Update to Revision 1352 (popPK modeling workflow MONOLIX and NONMEM, "median" modeling support)
  • 25th March 2014: Update to Revision 1278
  • 7th May 2013: Revision 1172 had a minor bug due to packaging of the public version - main impact on running SBPDgui. Fixed now in Revision 1176
  • 2nd May 2013: SBTOOLBOX2 and SBPD are now integrated into the same package, called "SBPOP PACKAGE". The new combined package additionally includes "SBPOP", focusing on PK/PKPD/PBPK models, population modeling, nonlinear mixed effect parameter estimation, clinical trial simulation