  Many cytoskeletal systems are now sufficiently well known to permit their
precise quantitative modelling. Microtubule and actin filaments are well
characterized, and the associated proteins are often known, as well as their
abundance and the interactions between these elements. Thus, computer
simulations can be used to investigate the collective behavior of the system
precisely, in a way that is complementary to experiments. Cytosim is an Open
Source cytoskeleton simulation suite designed to handle large systems of
flexible filaments with associated proteins such as molecular motors. It also
offers the possibility to simulate passive crosslinkers, diffusible
crosslinkers, nucleators, cutters and discrete versions of the motors that only
step on unoccupied lattice sites on a filament. Other objects complement the
filaments by offering spherical or more complicated geometry that can be used
to represent chromosomes, nucleus or vesicles in the cell. Cytosim offers
simple 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 on
a new computer, ii) configure Cytosim to simulate the contraction of a 2D
actomyosin network, iii) produce a visual representation of the system. Next,
the system is probed by systematically varying a key parameter: the number of
crosslinkers. Finally, the visual representation of the system is complemented
by a numerical quantification of contractility to view, in a graph, how
contractility depends on the composition of the system. Overall, these
different steps constitute a typical workflow that can be applied with few
modifications, to tackle many other problems in the cytoskeletal field.
