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.
Highlights
Spatial models of vascularized tissue are used to study the growth and response to treatment of tumors (1), angiogenesis (2), osteogenesis (3), coronary perfusion (4), and tissue oxygenation (5)
We introduce Microvessel Chaste, an opensource Python/Cþþ library for composing spatial models of vascularized tissues
We present examples showing how these components can be combined to generate numerical solutions of biophysical models of interest, focusing on tumor growth and angiogenesis
Summary
Spatial models of vascularized tissue are used to study the growth and response to treatment of tumors (1), angiogenesis (2), osteogenesis (3), coronary perfusion (4), and tissue oxygenation (5). Composition of spatial models of vascularized tissues is a time-consuming process, with most researchers writing custom software. Examples of such multiscale/hybrid models include those developed by Anderson and Chaplain (6), Alarcon et al (7), Frieboes et al (8), Shirinifard et al. Several groups, including Liu et al (16), Secomb et al (2), and Beard et al (17), have produced more general software that focuses on modeling and integration with imaging data.
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