PDEparams: parameter fitting toolbox for partial differential equations in python

Abstract

Motivation: Partial differential equations (PDEs) is a well-established and powerful tool to simulate multi-cellular biological systems. However, available free tools for validation against data are on development.

Results: The PDEparams module provides a flexible interface and readily accommodates different parameter analysis tools in PDE models such as computation of likelihood profiles, and parametric bootstrapping, along with direct visualization of the results. To our knowledge, it is the first open, freely available tool for parameter fitting of PDE models.

Availability and implementation: PDEparams is distributed under the MIT license. The source code, usage instructions and examples are freely available on GitHub at github.com/systemsmedicine/PDE_params.

Supplementary information: Supplementary data are available at Bioinformatics online.