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chaste codegen: automatic CellML to C++ code generation with fixes for singularities and automatically generated Jacobians

Hendrix, Maurice; Clerx, Michael; Tamuri, Asif U; Keating, Sarah M; Johnstone, Ross H; Cooper, Jonathan; Mirams, Gary R

chaste codegen: automatic CellML to C++ code generation with fixes for singularities and automatically generated Jacobians Thumbnail


Authors

Maurice Hendrix

Asif U Tamuri

Sarah M Keating

Ross H Johnstone

Jonathan Cooper



Abstract

Hundreds of different mathematical models have been proposed for describing electrophysiology of various cell types. These models are quite complex (nonlinear systems of typically tens of ODEs and sometimes hundreds of parameters) and software packages such as the Cancer, Heart and Soft Tissue Environment (Chaste) C++ library have been designed to run simulations with these models in isolation or coupled to form a tissue simulation. The complexity of many of these models makes sharing and translating them to new simulation environments difficult. CellML is an XML format that offers a solution to this problem and has been widely-adopted. This paper specifically describes the capabilities of chaste_codegen, a Python-based CellML to C++ converter based on the new cellmlmanip Python library for reading and manipulating CellML models. While chaste_codegen is a Python 3 redevelopment of a previous Python 2 tool (called PyCML) it has some additional new features that this paper describes. Most notably, chaste_codegen has the ability to generate analytic Jacobians without the use of proprietary software, and also to find singularities occurring in equations and automatically generate and apply linear approximations to prevent numerical problems at these points.

Citation

Hendrix, M., Clerx, M., Tamuri, A. U., Keating, S. M., Johnstone, R. H., Cooper, J., & Mirams, G. R. (2022). chaste codegen: automatic CellML to C++ code generation with fixes for singularities and automatically generated Jacobians. Wellcome Open Research, 6, Article 261. https://doi.org/10.12688/wellcomeopenres.17206.1

Journal Article Type Article
Acceptance Date Mar 7, 2022
Online Publication Date Mar 7, 2022
Publication Date Mar 7, 2022
Deposit Date Mar 8, 2022
Publicly Available Date Mar 9, 2022
Journal Wellcome Open Research
Electronic ISSN 2398-502X
Publisher F1000Research
Peer Reviewed Peer Reviewed
Volume 6
Article Number 261
DOI https://doi.org/10.12688/wellcomeopenres.17206.1
Keywords General Biochemistry, Genetics and Molecular Biology; Medicine (miscellaneous)
Public URL https://nottingham-repository.worktribe.com/output/7356912
Publisher URL https://wellcomeopenresearch.org/articles/6-261/v1

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