Microvessel Chaste: An Open Library for Spatial Modeling of Vascularized Tissues

Overview

Journal Biophys J

Publisher Cell Press

Specialty Biophysics

Date 2017 May 13

PMID 28494948

Citations 10

Authors

James A Grogan

Anthony J Connor

Bostjan Markelc

Ruth J Muschel

Philip K Maini

Helen M Byrne

Joe M Pitt-Francis

Affiliations

Soon will be listed here.

Abstract

Spatial models of vascularized tissues are widely used in computational physiology. We introduce a software library for composing multiscale, multiphysics models for applications including tumor growth, angiogenesis, osteogenesis, coronary perfusion, and oxygen delivery. Composition of such models is time consuming, with many researchers writing custom software. Recent advances in imaging have produced detailed three-dimensional (3D) datasets of vascularized tissues at the scale of individual cells. To fully exploit such data there is an increasing need for software that allows user-friendly composition of efficient, 3D models of vascularized tissues, and comparison of predictions with in vivo or in vitro experiments and alternative computational formulations. Microvessel Chaste can be used to build simulations of vessel growth and adaptation in response to mechanical and chemical stimuli; intra- and extravascular transport of nutrients, growth factors and drugs; and cell proliferation in complex 3D geometries. In addition, it can be used to develop custom software for integrating modeling with experimental data processing workflows, facilitated by a comprehensive Python interface to solvers implemented in C++. This article links to two reproducible example problems, showing how the library can be used to build simulations of tumor growth and angiogenesis with realistic vessel networks.

Citing Articles

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