Simulation Code

These code packages are released as free software under the terms of GNU General Public License. The image and text typically link to source file (.java) archives --the proper choice for those who wish to study or modify simulation code. For all others, the Apple, Windows, and Java JAR icons (if presented) link to a self-contained OS X application, Windows EXE, and executable JAR file, respectively

Links to Ingeneue

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]

Links to Furrowspec

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)

Links to ParMSpindle

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)

Mac Application Windows Application Executable Jar
Links to RocketBug source code

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)

Executable Jar

Links to RocketBugRender source code

RocketBugsRender: a special rendering and graphing program for the simulation output of "RocketBugs", the actin-based Listeria motility simulations (Alberts)

Mac Application Executable Jar

Links to ActinScope

ActinScope: a force-less dendritic actin simulation in Java. Play with arena size, biochemical rates, etc and gather statistics (Alberts)

Mac Application Windows Application Jar File

Release of the software packages below is pending publication of their related research papers. Links connect to a description of each package's capabilities and show sample simulations...

Links to Morphogenesis code

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)

Links to LatCon Source Code

LatCon: a 3D, force-based simulation of the lateral contraction model for node coalescence in S. pombe (Alberts)

Links to Oligomer

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)

Links to Meshwork

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)