Ingeneue: the first general purpose program designed to construct and analyze models of genetic networks (von Dassow, Meir, Munro, Odell, Sunderland, Kim)
[Links to website]
Skeledyne: is a 3D, force based simulation code for cytoskeletal dynamics in arbitrarily shaped
cells. It keeps track of diffusion, convection, and biochemical reaction of soluble factors as described here (Odell)
ParMSpindle: a 3D, force-based simulation of the ParM mediated segregation of bacterial plasmids, tracking the biochemical state of each monomer with experimentally determined filament dynamics (Alberts)
RocketBugs: a simulation of the actin-based motility of Listeria monocytogenes. From Alberts and Odell (2004), Rafelski, Alberts, and Odell (2009), and beyond hopefully (Alberts)
RocketBugsRender: a special rendering and graphing program for the simulation output of "RocketBugs", the actin-based Listeria motility simulations (Alberts)
ActinScope: a force-less dendritic actin simulation in Java. Play with arena size, biochemical rates, etc and gather statistics (Alberts)
Morphogenie: this code allows the user to vary initial shape and cortical elasticity parameters to investigate force-mediated changes in cell shape during embryogenesis (Munro, Sherrard, Hechter and Dawes)
LatCon: a 3D, force-based simulation of the lateral contraction model for node coalescence in S. pombe (Alberts)
Oligomer: simulated "diffusion" of multiarmed bodies that can
oligomerize (with varying affinities) to one another. Motivated by the seemingly contiguous, but diffusionally distinct cytoplasmic zones in the syncytial blastoderm of D. melanogaster (Gile and Munro)
Meshwork: a 3D, force-based simulation of dendritic and cross-linked actin networks, as on the cortex of C. elegans, with the aim to simulate that contractile network and its rheology (Gile and Munro)