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Related Software

There are a variety of pharmacological modeling tools. Below is a (likely non-exhaustive) list of such tools categorized into free/open-source and commercial/proprietary tools, and grouped by programming language where applicable.

Free & Open-Source Tools

Python-Based Solutions

  • PharmPy – A Python-based toolkit for nonlinear mixed-effects modeling, focused on PK/PD applications. (GPL-3.0)
  • scipion-pkpd – A Python plugin for PK/PD modeling within the Scipion workflow engine. (GPL-3.0)
  • Chi – A Python-based pharmacometrics modeling tool. (BSD 3-Clause)

R-Based Solutions

  • PKPDsim – A package for PK/PD simulations supporting differential equations and stochastic models. (GPL-3.0)
  • mrgsolve – A model simulation tool designed for population PK/PD analysis. (MIT License)
  • nlme – A package for fitting nonlinear mixed-effects models, widely used in PK/PD analysis. (Part of R Base, freely available)
  • nlmixr – A flexible platform for nonlinear mixed-effects modeling, specifically designed for PK/PD applications. (GPL-2.0)
  • rxode2 – A powerful ODE-based solver for PK/PD and pharmacometrics simulations. (GPL-2.0)
  • Ubiquity – A modeling framework primarily based in R, designed for PK/PD and systems pharmacology applications. (BSD 3-Clause)

C++/GUI-Based Solutions

  • BioGears – A C++-based open-source human physiology simulation engine with a Java-based GUI. (Apache-2.0 License)

Command-Line Based

  • GNU MCSim – A Monte Carlo simulation tool written in C that supports differential equation modeling and Bayesian inference. (GPL-2.0)

GUI-Based Solutions

  • Open Systems Pharmacology – A comprehensive open-source suite for PBPK and PK/PD modeling, including:
    • PK-Sim – A tool for physiologically based pharmacokinetic (PBPK) modeling. (GPL-2.0)
    • MoBi – A tool for mechanistic modeling, allowing integration of molecular and cellular processes. (GPL-2.0)

Other Modeling Frameworks

  • Heta Project – A modeling framework for Quantitative Systems Pharmacology (QSP) and Systems Biology.

Commercial & Proprietary Applications

  • NONMEM – Industry-standard software for nonlinear mixed-effects modeling, widely used in population PK/PD studies.
  • Monolix – A powerful application for model-based PK/PD analysis with a user-friendly interface.
  • SimBiology (MATLAB) – A comprehensive system for mechanistic PK/PD and systems pharmacology modeling.
  • Phoenix WinNonlin – A suite for pharmacokinetic analysis and regulatory submissions.
  • PoPy – A Python-based tool designed for population PK/PD modeling. (Dual-licensed: Free for academic and educational use, commercial license required for industry applications and regulatory submissions)
  • Berkeley Madonna – A commercial mathematical modeling software for solving differential equations, widely used in pharmacometrics. (Proprietary License)
  • Pumas – A Julia-based platform for pharmaceutical modeling and simulation. (Proprietary: Free academic use, commercial license required for industry applications.)

Suggestions & Contributions

Notice something missing or an issue in the lists above? Feel free to reach out if you know of a missing pharmacological modeling tool or have a suggestion for an update. We welcome community contributions to enhance the accuracy and usefulness of this resource!