Recently we have provided new software to perform large-scale simulations of complex biological processes.
Timothy is a novel large scale parallel computational model allowing 3-D simulations of cell colonies growing and interacting with variable environment in previously unavailable tissue scale.
The cells are modeled as individuals located in the lattice-free 3-D space. The model incorporates cellular environment modelled in a continuous manner, mathematical description based on partial differential equations is formulated for selected important components of the environment. Discrete and continuous formulations are efficiently coupled in one model and allow considerations on different scales: sub-cellular, cellular and tissue scale.
High parallel scalability achieved allows simulation of up to 109 individual cells. This large scale computational approach allows for simulations to be carried out over realistic spatial scales up to 1cm in size i.e. the tissue scale.
See more: http://timothy.icm.edu.pl/
