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README.md

This open source Systems Pharmacology project makes formerly commercial software tools PK-Sim® and MoBi® available as freeware under the GPLv2 License. All source code is public.

Latest suite release can be found here: http://setup.open-systems-pharmacology.org

We invite everyone in the field of Systems Pharmacology, be it in academia, industry or regulatory bodies, to use the platform. Active participation of computer and modeling & simulation scientists in the further development of the modeling & simulation platform, the incorporated systems models, processes for their qualifaction and application etc. is encouraged and highly welcome! Please follow the community’s activities in this GitHub project.

Discussion forum for the Open Systems Pharmacology Project

Visit and subscribe to the Open Systems Pharmacology Project Forum to stay up-to-date with the community and receive updates on new software releases, models as well as discussions.

Open Systems Pharmacology Suite with PK-Sim® and MoBi® for Quantitative Systems Pharmacology

Unmatched Flexibility - Unlimited Transparency

platform concept

The Open Systems Pharmacology Suite contains different software tools and has been designed using a modular concept to allow efficient multi-scale modeling and simulation. The overall platform with its various software tools is implemented in a modular way as will be explained in more detail below. The central software tools PK-Sim® and MoBi® make use of building blocks as introduced here. While PK-Sim® is based on a whole-body concept, the focus of its counterpart, MoBi®, is at the molecular level. However, both tools extend to additional physiological scales as illustrated.

PK-Sim

PK-Sim® is a comprehensive software tool for whole-body physiologically based pharmacokinetic modeling. It enables rapid access to all relevant anatomical and physiological parameters for humans and the most common laboratory animals (mouse, rat, minipig, dog, monkey, beagle and rabbit) that are contained in the integrated database. Moreover, access to different PBPK calculation methods to allow for fast and efficient model building and parameterization is provided. Relevant generic passive processes, such as distribution through blood flow as well as specific active processes such as metabolization by a certain enzyme are automatically taken into account by PK-Sim®. Like most PBPK modeling tools, PK-Sim® is designed for use by non-modeling experts and only allows for minor structural model modifications. Unlike most PBPK modeling tools though, PK-Sim® offers different model structures to choose from, e.g. to account for important differences between small and large molecules. More importantly, PK-Sim® is fully compatible with the expert modeling software tool MoBi®, thereby allowing full access to all model details including the option for extensive model modifications and extensions. This way customized systems pharmacology models may be set up to deal with the challenges of modern drug research and development.

PK-Sim® uses building blocks that are grouped into Individuals, Populations, Compounds, Formulations, Administration Protocols, Events, Observers and Observed Data. Building blocks from these groups are combined to produce a model. The advantage of building blocks is that they can be reused. For example, after having established a model for a drug after single dose intravenous administration to an animal species, just substitute the individual by a suitably parameterized virtual human population and obtain a first in man simulation model. Further substitute the formulation, to obtain a controlled-release per oral simulation model, substitute the protocol to obtain a multiple dose simulation model, or substitute the compound to obtain a simulation model for another drug.

MoBi

MoBi® is a systems biology software tool for multiscale physiological modeling and simulation. Within the restrictions of ordinary differential equations, almost any kind of (biological) model can be imported or set up from scratch. Examples include biochemical reaction networks, compartmental disease progression models, or PBPK models. However, de novo development of a PBPK model, for example, is very cumbersome such that the preferred procedure is to import them from PK-Sim®. Importantly, MoBi® also allows for the combination of the described examples and thereby is a very powerful tool for modeling and simulation of multi-scale physiological systems covering molecular details on the one hand and whole-body architecture on the other hand.

De novo model establishment and simulation is supported by graphical tools and building blocks to support expert users. MoBi® uses building blocks that are grouped into Molecules, Reactions, Spatial Structures, Passive Transports, Observers, Events, Molecule Start Values, Parameter Start Values and Observed Data. Building blocks out of the above-mentioned groups can be combined to generate models. The advantage of building blocks is that they can be reused. For example, a different set of starting values may define a new scenario, situation, or individual. Refine a Reaction(s) network and update it in all tissues where it should be considered.

Toolboxes for Matlab and R

The MoBi® toolboxes for R and Matlab® are interfaces to the common statistical and technical computing environments, respectively. Basically, the toolboxes can be used to access and modify model parameters as well as to execute simulations and retrieve results. That way, the toolboxes can be used to script or code batch simulations, analysis tasks, or customized workflows to any complexity. Results can be visualized using the options available in the respective environment. Apart from the communication and exchange via Matlab®, PK-Sim® and MoBi® have import and export functions that allow for the import of experimental data via MS Excel® and models based on SBML or the export of simulation results via MS Excel®, for example.

Code Status

Setup status PK-Sim status MoBi status R status Installation Validator status

Software installation

How to install setups for the Open Systems Pharmacology Suite with PK-Sim® and MoBi®

  1. Download the Software Setup and install it on your computer. Make sure you are provided with administrator rights; these are required!
  2. Download PK-Sim Gene Expression Database(s) and copy to a folder accessible for all users.
  3. Configure PK-Sim Gene Expression Database(s) (for details view the Open Systems Pharmacology Suite manual)

System Requirements

Operating Systems (64 bit only)

OSP Suite

Windows 7®, Windows 8®, Windows 10®, Windows Server 2008 R2®, Windows Server 2012 R2®, Windows Server 2016®, Windows Server 2019®

R-Toolbox

All Windows operating systems listed above and Linux (precompiled packages available for Ubuntu 18.04 and CentOS 7)

Processor

Minimum: 1 GHz (the faster the better!)

Memory

Minimum: 2 GB RAM (3+ GB recommended)

Disk Space

Minimum: 2 GB

Optional Software

  • Matlab® (version 2017b or later)
  • R® (versions 3.5 / 3.6 - 64bit)

Code of conduct

Everyone interacting in the Open Systems Pharmacology community (codebases, issue trackers, chat rooms, mailing lists etc...) is expected to follow the Open Systems Pharmacology code of conduct.

Contribution

We encourage contribution to the Open Systems Pharmacology community. Before getting started please read the contribution guidelines. If you are contributing code, please be familiar with the coding standards.

All trademarks within this document belong to their legitimate owners.