This manual describes the Open Systems Pharmacology Suite. This includes technical descriptions of the different software elements together with examples and brief introductions to relevant scientific aspects including references for further reading. Naturally, the science described is selected based on our experience and judgment of relevance in the given context. Further, our “philosophy” is largely reflected in the software platform, and, vice versa, the software platform influences how we work and think.
The handbook is divided into the following parts:
"Mechanistic Modeling of Pharmacokinetics and Dynamics" provides a brief general introduction to the science of computational systems biology with a strong focus on mechanistic modeling of pharmacokinetics and –dynamics.
"Open Systems Pharmacology Suite" provides a brief overview of our software platform, its scope, and puts it into context with the science.
Thereafter, a technical description of the different software elements is presented starting with PK-Sim® focusing on physiologically-based pharmacokinetics in "Working with PK-Sim®".
MoBi® focusing on model customization and extension as well as on pharmacodynamics in "Working with MoBi®".
Tools shared between PK-Sim® and MoBi® and some workflow examples are presented in "Shared Tools and Example Workflows".
After that, the interfaces to the common computing environments Matlab® and R are described in "Working with Matlab® and R" and "R Toolbox for MoBi®", respectively.