# README

This manual describes the [Open Systems Pharmacology Suite](https://www.open-systems-pharmacology.org). It includes a technical description of each software element with examples and references for further reading. The aim of the manual is to assist users in effectively developing PBPK models.

Documentation for the developers of the Open Systems Pharmacology Suite and more technical details are provided [here](https://dev.open-systems-pharmacology.org/).

The handbook is divided into the following parts:

## Mechanistic Modeling of Pharmacokinetics and Dynamics

"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.

[Go to: Mechanistic Modeling of Pharmacokinetics and Dynamics](https://docs.open-systems-pharmacology.org/mechanistic-modeling-of-pharmacokinetics-and-dynamics/modeling-concepts/modeling-concepts-pbpk-modeling-systems-biology)

## Open Systems Pharmacology Suite

"Open Systems Pharmacology Suite" provides a brief overview of our software platform, its scope, and puts it into context with the science.

[Go to: Open Systems Pharmacology Suite](https://docs.open-systems-pharmacology.org/open-systems-pharmacology-suite/modules-philsophy-building-blocks)

## Working with PK-Sim®

A technical description of the different software elements is presented starting with PK-Sim® focusing on physiologically-based pharmacokinetics in "Working with PK-Sim®".

[Go to: Working with PK-Sim®](https://docs.open-systems-pharmacology.org/working-with-pk-sim/pk-sim-documentation/pk-sim-quick-guide)

## Working with MoBi®

MoBi® focusing on modular model customization and extension as well as on pharmacodynamics in "Working with MoBi®".

[Go to: Working with MoBi®](https://docs.open-systems-pharmacology.org/working-with-mobi/mobi-documentation/first-steps)

## Shared Tools and Example Workflows

Tools shared between PK-Sim® and MoBi® and some workflow examples are presented in "Shared Tools and Example Workflows".

[Go to: Shared Tools and Example Workflows](https://docs.open-systems-pharmacology.org/shared-tools-and-example-workflows/features-of-tables)

## Working with R

The interfaces to the common computing environment R is described in "Working with R".

[Go to: Working with R](https://docs.open-systems-pharmacology.org/working-with-r/introduction-ospsuite-r)


---

# Agent Instructions: Querying This Documentation

If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.

Perform an HTTP GET request on the current page URL with the `ask` query parameter:

```
GET https://docs.open-systems-pharmacology.org/readme.md?ask=<question>
```

The question should be specific, self-contained, and written in natural language.
The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.