Welcome to Pumas

Pumas (PharmaceUtical Modeling And Simulation) is a suite of tools used to perform quantitative analytics of various kinds across the horizon of pharmaceutical drug development. The purpose of this framework is to bring efficient implementations of all aspects of the analytics in this domain under one cohesive package. Pumas currently includes:

  • Non-compartmental Analysis
  • Specification of Nonlinear Mixed Effects (NLME) Models
  • Simulation of NLME models using differential equations or analytical solutions
  • Deep control over the differential equation solvers for high efficiency
  • Estimation of NLME parameters via Maximum Likelihood, Expectation Maximization and Bayesian methods
  • Automated covariate selection
  • Parallelization capabilities for both simulation and estimation
  • Mixed analytical and numerical problems
  • Simulation and estimation diagnostics for model post-processing
  • Interactive model exploration and diagnostics tools through webapps
  • Automated report generation for models and non-compartmental analysis
  • Global and local sensitivity analysis routines for multi-scale models
  • Bioequivalence analysis
  • Bioequivalence Power computation and sample size determination
  • Optimal design of experiments
  • Evaluation of model identifiability

Additional features are under development, with the central goal of providing a comprehensive parameter estimation tool, complete clinical trial simulation engine which combines efficiency with a standardized workflow, consistent nomenclature, and automated report generation. All of this takes place in the high level interactive Julia programming language and integrates with the other packages in the Julia ecosystem for a robust user experience.

Getting Started: Accessing Pumas

Pumas is available via JuliaHub, or as desktop or server application. The desktop and server applications are made available free of charge for academics, see Pumas for Academia. The onboarding video playlist on YouTube will guide you through the platform and help you get started.

Tip

For additional information and resources on using Pumas in the cloud, refer to JuliaHub's documentation. The documentation provides comprehensive tutorials and guides covering essential features. See, for example, the following guide on how to create batch jobs

One can start using Pumas by invoking it from the REPL (Read-Eval-Print Loop, the command line environment for Julia) as below.

using Pumas

Additional resources

The documentation covers the functionality of Pumas and establish the standardized nomenclature for the package. It serves as a single reference point for the various features of Pumas.

To find a general overview of resources visit Pumas Resources to find links to all our resources including educational videos, lists of publications using Pumas and more.

For resources oriented towards learning Pumas as a new users please find the tutorials at https://tutorials.pumas.ai/. There, you will find both an organized sequence of Learning Path tutorials written to guide you through the basics of Pumas as well as a large collection of individual tutorials covering specific topics in detail.

If you have questions about usage, please join the official Pumas Discourse and take part in the discussion there.

Pumas Development Team

Please visit https://pumas.ai/company to know more about our team and capabilities.

Citing Pumas

If you use Pumas within scientific reports, please cite Pumas via the following paper:

Rackauckas, Chris, et al. "Accelerated predictive healthcare analytics with pumas, a high performance pharmaceutical modeling and simulation platform." (2020).

or in Bibtex form:

@article{rackauckas2020accelerated,
  title={Accelerated predictive healthcare analytics with pumas, a high performance pharmaceutical modeling and simulation platform},
  author={Rackauckas, Chris and Ma, Yingbo and Noack, Andreas and Dixit, Vaibhav and Mogensen, Patrick Kofod and Byrne, Simon and Maddhashiya, Shubham and Santiago Calder{\'o}n, Jos{\'e} Bayo{\'a}n and Nyberg, Joakim and Gobburu, Jogarao VS and others},
  year={2020}
}

License

Pumas is covered by the JuliaHub EULA. Pumas is a proprietary product developed by Pumas-AI, Inc. It is available free of cost for educational and research institutes. For commercial use, please contact sales@pumas.ai or to know more visit Pumas for Enterprises.