Open Systems Pharmacology
ForumSetup
v11
v11
  • README
  • Open Systems Pharmacology Suite Manual & Copyright
  • How to Contribute
  • Mechanistic Modeling of Pharmacokinetics and Dynamics
    • Modeling Concepts
      • PBPK Modeling - Systems Biology
      • PK and PD Modeling
      • Principles of PBPK Modeling
      • Expression Data for PBPK Modeling
      • Modeling of Proteins
      • PD and Reaction Network Modeling
  • Open Systems Pharmacology Suite
    • Modules, Philosophy, and Building Blocks
    • Getting Started
  • Working with PK-Sim
    • PK-Sim Documentation
      • Quick Guide‌
      • Options
      • Projects
      • Creating Individuals
      • Creating Populations
      • Expression Profile
      • Compounds: Definition and Work Flows
      • Compounds: Defining Inhibition/Induction Processes
      • Administration Protocols
      • Events
      • Formulations
      • Simulations
      • Importing and Exporting Project Data and Models
      • Conversion of Projects from Previous Version
      • Command Line Interface - CLI
  • Working with MoBi
    • MoBi‌ Documentation
      • First Steps
      • The Building Block Concept
      • Model Building and Model Components
      • Setting up a Simulation
      • Simulation Results
      • Diagrams Overview
      • Tools
      • Reuse of Project Information from Previous Versions
  • Shared Tools and Example Workflows
    • Features of Tables
    • Chart Component
    • Comparison of Building Blocks
    • Parameter Identification
    • Sensitivity Analysis
    • Import and Edit of Observed Data
    • Default, Display and Base Units
    • Working Journal
    • History Manager and History Reporting‌
    • Setting up a Reaction Network‌
    • Setting up a Drug-Drug Interaction in PK-Sim‌
    • Qualification‌
  • Working with R‌
    • ospsuite-R Documentation
  • Appendix
    • Appendix
    • OSP Suite Fact Sheet
  • References
    • References
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  1. Working with PK-Sim
  2. PK-Sim Documentation

Projects

The organization of simulations is supported by PK-Sim® with a building block concept. Each project contains a Building Block window that comprises one or several building blocks for individuals, populations, compounds, formulations, protocols, events and observed data. Simulations that are created with the building blocks and comparisons of simulations are organized in a separate window. The user can create subfolders for organization of observed data, simulations and comparison.

Only one project can be opened at a time in one PK-Sim® instance. If you wish to work on more than one project in parallel you may start separate instances of PK-Sim® for each individual project. If the identical project is already being accessed by yourself or by another user, PK-Sim® will warn you and open the project as read-only. You will still be able to use the project but won't be able to save your changes.

The following table gives an overview on how to manage projects using the File tab:

Function, Icon
Shortcut
Description

Ctrl+N

A new project is generated. The current project is closed. If you have not saved the current project yet, you will be asked if you want to do so. If you answer Yes, all data belonging to the current project are saved using the current file-name. If the project/file name is undefined, a dialog window will open for you to specify the project name.

Ctrl+O

Select the *.pksim5 file you want to open. • Only one project can be opened at a time. If a project is already open, you are asked if the currently open project should be saved before closing. • If you wish to work on more than one project in parallel, you may start separate instances of PK-Sim® for each individual project.

The project is closed. If you have not yet saved the current project, you are asked if you want to do so. If you answer Yes, all data belonging to the project are saved using the current file-name. If the project/ file name is undefined, a will open for you to specify the project name. A new project can then be created, subsequently.

Ctrl+S

You can save your project by either selecting Save or Save as.

Ctrl+D

You can enter, show or change a description for the project.

An overview of the PK-Sim® version information is given.

Alt+F4

PK-Sim® is closed. If you have not yet saved the current project, you are asked if you want to do so. If you answer Yes, all data belonging to the project are saved using the current file-name. If the project name is undefined, a dialog window will open for you to specify the project name.

The visualization of a project is organized in different panels. Each panel can be hidden or be made visible by clicking on the respective icon in the View Tab. The panels have the following meaning:

Panel, Icon
Description
PreviousOptionsNextCreating Individuals

Last updated 2 years ago

Create a new project

Open an existing project

Close the project

Save the project

Show or edit project description

Export project to snapshot

Export current project to snapshot. S. for details.

Load project from snapshot

Create a new project from snapshot. S. for details.

Select Journal

Assign a working journal to the current project. S. for details.

About this application

Exit the application

Building Blocks

Within this panel the building blocks Individuals, Populations, Compounds, Formulations, Administration Protocols, Events and Observed Data are organized and can be accessed. Detailed information for each building block can be found in: ● ● ● ● ● ● ● .

Simulations

In this panel all simulations of a project are managed. A detailed description on how simulations are set up and managed can be found in . Besides simulations, this panel contains the following objects: ● Simulation comparisons (s. for details) ● Parameter Identifications (s. for details) ● Sensitivity Analyses (s. for details)

History Manager

Every user action performed within a given project work is documented within this panel. Features of the History Manager are described in .

Comparison

Shows comparison results of 2 building blocks or 2 simulations. S. for details.

Working Journal

Shows the working journal of the current project. S. for details.

Working Journal Diagram

Shows the working journal of the current project. S. for details.

Shared Tools - Working Journal
PK-Sim® - Creating Individuals
PK-Sim® - Creating Populations
PK-Sim®- Compounds: Definition and Work Flows
PK-Sim® - Formulations
PK-Sim® - Administration Protocols
PK-Sim® - Events
Shared Tools - Import and Edit of Observed Data
Shared Tools - History manager and history reporting
Shared Tools - Comparison of Building Blocks
Shared Tools - Working Journal
PK-Sim® - Simulations
Shared Tools - Parameter Identification
Shared Tools - Sensitivity Analysis
PK-Sim® - Simulations: Comparison charts
Shared Tools - Working Journal
Exporting Project to Snapshot / Loading Project from Snapshot
Exporting Project to Snapshot / Loading Project from Snapshot