TiFoSi: an Efficient Tool for Mechanobiology Simulations of Epithelia

AboutThis document is an extended version of the main text where some details and results are fleshed out. Further details can be also found in the manual of the code and at TiFoSis website: http://tifosi.thesimbiosys.com. MotivationEmerging phenomena in developmental biology and tissue engineering are the result of feedbacks between gene expression and cell biomechanics. In that context, in silico experiments are a powerful tool to understand fundamental mechanisms and to formulate and test hypotheses. ResultsHere we present TiFoSi, a computational tool to simulate the cellular dynamics of planar epithelia. TiFoSi allows to model feedbacks between cellular mechanics and gene expression (either in a deterministic or a stochastic way), the interaction between different cell populations, the custom design of the cell cycle and cleavage properties, the protein number partitioning upon cell division, and the modeling of cell communication (juxtacrine and paracrine signalling). TiFoSi fills a niche in the field of software solutions to simulate the mechanobiology of epithelia because of its functionalities, computational efficiency, and its user-friendly approach to design in silico experiments using XML configuration files. Availabilityhttp://tifosi.thesimbiosys.com Contactjbuceta@lehigh.edu