Welcome

Welcome to the wiki of the invitro_neuro project.

Overview

This is a C++ project that implements the agent-based modelling method to simulate biological problems relevant to cell-scale mechanics, and cell/extracellular matrix interactions, and so on. More specifically, it can simulate:

• cell mechanics: growth, division (symmetric or asymmetric mitosis), apoptosis and necrosis, polarisation, migration, differentiation/transformation, generation of cell protrusions
• cell--cell interactions
• cell--extracellular matrix interactions
• impact of biomechanical and biochemical cues in cells behaviour
• vascularisation and angiogenesis

Installation

Compilation of the source code is straightforward, while no special installation is required to run your simulations. In principle, one should follow the most relevant rules listed in the makefile that comes with the project. The important rules one needs to execute are setup_biodynamo and install_biodynamo - it is self evident what they do ;) More importantly, this project is heavily dependent on the BioDynaMo platform, a C++ suite for agent-based modelling simulations. Currently the project has been tested and operates in Linux (Ubutu and CentOS7) and macOS (Catalina, Big Sur) machines.

Testing

We are doing our best to keep up testing and maintaining the project up-to-date :) However, a series of examples can be found in the examples folder of the project, while the user could run all example simulations by executing the following command on the terminal make tests.

How do I get it?

If you'd like to test or/and use this project, please contact the repository owner, Dr Vasileios Vavourakis, with a brief description of who you are, what you're going to use it for, and we'll send you a copy asap. This helps us understand your needs while it could guide future development of this project.

Acknowledgements

We are thankful to the support and help of several people: Dr Roman Bauer, Dr Jean de Montigny, Mr Ahmad Hesam and Mr Lukas Breitwieser.