title: On-lattice agent-based simulation of populations of cells within the open-source Chaste framework.
abstract: Over the years, agent-based models have been developed that combine cell division and reinforced random walks of cells on a regular lattice, reaction-diffusion equations for nutrients and growth factors; and ordinary differential equations for the subcellular networks regulating the cell cycle. When linked to a vascular layer, this multiple scale model framework has been applied to tumour growth and therapy. Here, we report on the creation of an agent-based multi-scale environment amalgamating the characteristics of these models within a Virtual Physiological Human (VPH) Exemplar Project. This project enables reuse, integration, expansion and sharing of the model and relevant data. The agent-based and reaction-diffusion parts of the multi-scale model have been implemented and are available for download as part of the latest public release of Chaste (Cancer, Heart and Soft Tissue Environment; http://www.cs.ox.ac.uk/chaste/), part of the VPH Toolkit (http://toolkit.vph-noe.eu/). The environment functionalities are verified against the original models, in addition to extra validation of all aspects of the code. In this work, we present the details of the implementation of the agent-based environment, including the system description, the conceptual model, the development of the simulation model and the processes of verification and validation of the simulation results. We explore the potential use of the environment by presenting exemplar applications of the 'what if' scenarios that can easily be studied in the environment. These examples relate to tumour growth, cellular competition for resources and tumour responses to hypoxia (low oxygen levels). We conclude our work by summarizing the future steps for the expansion of the current system.
authors.affiliation: Centre for Mathematical Medicine and Biology, School of Mathematical Sciences, University of Nottingham, Nottingham NG7 2RD, UK.
authors.forename: Grazziela P
authors.initials: GP
authors.lastname: Figueredo
authors.affiliation: Centre for Mathematical Medicine and Biology, School of Mathematical Sciences, University of Nottingham, Nottingham NG7 2RD, UK.
authors.forename: Tanvi V
authors.initials: TV
authors.lastname: Joshi
authors.affiliation: Oxford University Computing Laboratory, Department of Computer Science, University of Oxford, Wolfson Building, Oxford OX1 3QD, UK.
authors.forename: James M
authors.initials: JM
authors.lastname: Osborne
authors.affiliation: Oxford University Computing Laboratory, Department of Computer Science, University of Oxford, Wolfson Building, Oxford OX1 3QD, UK ; Oxford Centre for Collaborative Applied Mathematics, Oxford OX1 3LB, UK.
authors.forename: Helen M
authors.initials: HM
authors.lastname: Byrne
authors.affiliation: Centre for Mathematical Medicine and Biology, School of Mathematical Sciences, University of Nottingham, Nottingham NG7 2RD, UK.
authors.forename: Markus R
authors.initials: MR
authors.lastname: Owen
keywords: agent-based simulation; cancer; cell cycle; lattice models; multi-scale model; tumour hypoxia