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Many cytoskeletal systems are now sufficiently well known to permit theirprecise quantitative modelling. Microtubule and actin filaments are wellcharacterized, and the associated proteins are often known, as well as theirabundance and the interactions between these elements. Thus, computersimulations can be used to investigate the collective behavior of the systemprecisely, in a way that is complementary to experiments. Cytosim is an OpenSource cytoskeleton simulation suite designed to handle large systems offlexible filaments with associated proteins such as molecular motors. It alsooffers the possibility to simulate passive crosslinkers, diffusiblecrosslinkers, nucleators, cutters and discrete versions of the motors that onlystep on unoccupied lattice sites on a filament. Other objects complement thefilaments by offering spherical or more complicated geometry that can be usedto represent chromosomes, nucleus or vesicles in the cell. Cytosim offerssimple command-line tools for running a simulation and displaying its results,that are versatile and do not require programming skills. In this workflow,step-by-step instructions are given to: i) install the necessary environment ona new computer, ii) configure Cytosim to simulate the contraction of a 2Dactomyosin network, iii) produce a visual representation of the system. Next,the system is probed by systematically varying a key parameter: the number ofcrosslinkers. Finally, the visual representation of the system is complementedby a numerical quantification of contractility to view, in a graph, howcontractility depends on the composition of the system. Overall, thesedifferent steps constitute a typical workflow that can be applied with fewmodifications, to tackle many other problems in the cytoskeletal field.

A typical workflow to simulate cytoskeletal systems with Cytosim