Section: New Software and Platforms

SiMuScale

We have developed within the team the SiMuScale platform, a software dedicated to exploring multi-scale population models (“SiMuScale” on researchgate, https://gforge.inria.fr/projects/simuscale). Coded in C++, SiMuScale is in active development since 2014. SiMuScale has been primarily developed to answer the need for an all-purpose, fast and flexible modeling tool for multiscale cell population dynamics. Biological agents (cells) are modeled by visco-elastic spheres, which are subject to mechanical constraints. Each cell possesses its own intracellular dynamics, coupled to other cells through bimolecular signals expressed at the surface of the cell. The internal state of the cell is also coupled to a behavioral state of the cell, which control the macroscopic fate: motility, growth, proliferation, death, etc. Mechanical interactions provide a 3D environment in which cells interact locally. SiMuScale is based on a core containing the simulator, and on plug-ins that contain the biological specifications of each cell. The core+plug-ins architecture makes it easier for the researcher to focus on the model and to capitalise on existing models, which all share the same framework and are compatible with each other. That way, SiMuScale makes the work of model writing and re-writing minimal and fits into reproducible research.