1 Introduction

2 User Interface

2.1 Tabs

2.1.1 Simulations Tab

2.1.2 Parameters Tab

2.1.3 Import / Export Tab

2.1.4 Settings Tab

2.1.5 References Tab

3 Parameter Sets

The app maintains a database of parameter sets. A parameter set contains all parameters required by the PK model to simulate the PK of a specific drug in a specific species.

A parameter set consists of

Some of the model parameters are not part of a parameter set but will be derived from those on demand.

Species-specific parameters are shared across all drugs available for that species. Therefore, changing a species-specific parameter would impact the other drugs defined for that species as well.

After initialization, the app includes a list of predefined drugs (parameter sets).

These drugs are read-only in a sense that their parameters cannot be changed. However, custom species and drugs can be added to the app, either by using the New button from the Species or Drug menu or by importing parameter files in the Parameters tab. Custom parameter sets are editable within the app.

Note that a custom drug added to an existing species will only allow editing the drug-specific but not the species-specific parameters. Only if also a custom species was created, these parameters can be edited as well. Derived parameters can never be edited (directly) but their values would change by editing the respective input parameters.

A list of all available parameter sets can be found in the Parameters tab (upper box). The lower box in this tab shows the individual parameters of the currently active drug and species.

3.1 Editing Individual Parameters

3.2 Creating New Drugs and Species

3.3 Importing and Exporting New Drugs amd Species

3.3.1 Exporting Parameter Sets

Parameter sets can be exported from the Parameters tab (upper box). This functionality allows you to save a local copy of one or more app internal parameter sets as a csv file on your computer. Saved parameter sets might serve as templates to be modified and uploaded again as new parameter sets (see Section Importing Parameter Sets).

Select (highlight) the drugs which should get exported and click the Export Parameters button. A “Save as…” dialog will open to allow you choosing a location and file name.

3.3.2 Importing Parameter Sets

3.3.2.1 Charge Class

The only non-numeric parameter required is the charge class. This has to be encoded numerically as 1 = “acid”, 2 = “neutral”, 3 = “base”, or 4 = “zwitterion.” This parameter has the pseudo unit “acid,neutral,base,zwitterion” to indicate the allowed options.

3.3.2.2 Unit Conversion

The app uses fixed units internally, however the import tool allows the user to use different units and aims to convert those during the import. Generally, allowed units in input files are:

  • mass: kg, g, mg, ug, ng
  • molar: mol, mmol, umol, nmol
  • time: min, h
  • volume: L, mL, uL, nL
  • area: cm2 (written as cm2), mm2 (written as mm2)

Combined units for flows (area/time) and molecular weights (mass/molar) can also be converted.

The (pseudo) unit for parameter charge class (see Section Charge Class) must not be altered in the input parameter set.

An error is raised in case the unit conversion failed.