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Related Concept Videos

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Cancer therapies are various modes of treatment, such as surgery, radiation therapy, and chemotherapy that are administered to cancer patients.
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Genes usually encode proteins necessary for the proper functioning of a healthy cell. Mutations can often cause changes to the gene expression pattern, thereby altering the phenotype.
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Chaste: Cancer, Heart and Soft Tissue Environment.

Fergus R Cooper1, Ruth E Baker1, Miguel O Bernabeu2

  • 1Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford, UK.

Journal of Open Source Software
|May 16, 2023
PubMed
Summary
This summary is machine-generated.

Chaste is an open-source simulation package for physiology and biology, offering modules for cardiac electrophysiology, cell-based tissue modeling, and lung ventilation. This software provides a reliable, extensible framework for scientific research.

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Area of Science:

  • Computational Biology
  • Physiological Modeling
  • Scientific Software Engineering

Background:

  • Physiological and biological systems require sophisticated computational models for understanding complex processes.
  • Existing simulation tools often lack the flexibility, verification, or accessibility needed for diverse research applications.
  • The Cancer, Heart And Soft Tissue Environment (Chaste) project emerged to address these limitations.

Purpose of the Study:

  • To present Chaste as a versatile, open-source simulation package for physiological and biological modeling.
  • To highlight the modular design and specific application modules (Cardiac Chaste, Cell-based Chaste, Lung Chaste).
  • To emphasize the software engineering principles ensuring code quality, reusability, and reliability for the scientific community.

Main Methods:

  • Development of a modular and extensible software architecture.
  • Implementation of specialized libraries for continuum mechanics, cardiac electrophysiology, and cell-based tissue simulations.
  • Integration of common scientific computing infrastructure, including linear algebra, mesh handling, and differential equation solvers.
  • Rigorous testing and verification processes for all developed modules.

Main Results:

  • Chaste provides high-performance, verified simulation frameworks for cardiac electrophysiology (Cardiac Chaste).
  • It offers efficient and extensible tools for cell-based modeling of biological tissues (Cell-based Chaste), supporting various modeling approaches.
  • A novel, efficient, and verified package for lung ventilation modeling (Lung Chaste) is available, coupling airway mechanics with organ-scale ventilation.

Conclusions:

  • Chaste is a robust, open-source simulation package supporting diverse physiological and biological research areas.
  • Its modular design and rigorous engineering facilitate code quality, reusability, and reliability.
  • The package empowers researchers in cardiac and respiratory physiology, cancer, and developmental biology with advanced computational tools.