Options
PK-Sim® can be customized using several options. To do this, click on the Options Button 
within the Utilities Ribbon Tab.
General Tab
Numerical Properties
Allows scientific notation: You can specify if parameter values and results are displayed in scientific notation and if they are very small or large.
Decimal place: You can specify the number of decimal places displayed for parameter values and results.
Absolute tolerance and Relative tolerance: You can specify the absolute and relative tolerance to control the error of the ODE solver. Changes will only affect simulations that are created after changing values.
Maximum number of processors to use for tasks that can be executed in parallel (population simulations, parameter identification, parallel execution of simulations).
Number of bins: number of bins to display in histograms of populations/population simulations for parameter distribution.
Setting tolerances higher than the default values (absolute tolerance: 1.0E-10; relative tolerance: 1.0E-5) may reduce simulation time but cause convergence errors.
Look and Feel
Active skin: The program's graphical appearance can be changed by changing the skin in the Skins group next to the Options icon.
Number of recent file items shown: Changes the number of recent documents displayed within the File Tab. The program needs to be restarted for the changes to take effect.
Preferred view layout: Choose from either tabbed or accordion view, e.g., the Compound window.
Restore opened view when loading project: Open tabs (e.g., particular simulations, individuals, or compounds) are saved upon saving and restored when re-opening the project. Warning—this may significantly impact a project's loading time!
Show software update notification if available: When enabled and connected to the internet, a check for new versions of PK-Sim® is done automatically.
Defaults
Species and Population: Changes the default species and default population used for the creation of a new individual or population.
Parameter layout: Changes the default parameter layout used for parameters shown within the Anatomy & Physiology tab of an individual and the Parameters tab of a simulation.
Lipophilicity, Fraction unbound, and Solubility: You can specify the defaults for the description used for the Experiment input box when a new compound is created.
Population analysis: After the first simulation run, an analysis window opens automatically. This option sets the default type of this first analysis ('Time Profile', 'Box Whisker', ...).
Chart y scale: Default scaling (lin or log) of the y axis in new time-profile charts.
Icon Sizes
You can change the size of the icons displayed within the Tree view, the Tabs, and the Context menu
Template Database
Template database path: The path to the template database. You can create a new template database by clicking on
Load metabolites when loading compound: Choose whether or not to load the metabolites of a compound when loading a (parent) compound.
Colors
Formula parameter: Changes the background color for parameters that are calculated by a formula.
Parameter changed: Changes the background color for formula-calculated parameters that have been changed by the user.
Chart background and Chart diagram background: Changes the chart colors. For simulation charts, this is the default if no other color is specified in the Chart Editor of the Results Tab.
Color group observed data from same folder when dropping to chart: If enabled, when adding observed data sets to a chart via drag-and-drop from a folder (or multiple folders) within the "Observed Data" group, all data sets within one folder will get the same color.
Application Tab
MoBi Executable Path: Path to the location of the MoBi.exe file
Specify the path to a species-specific Expression Database you would like to use by clicking on the three dots in the Expression Database column in the row of the species you require.
The available expression databases can be downloaded from the gene expression databases repository.
Last updated