Other Simulations

MCell and CellBlender

MCell and CellBlender. MCell is an agent-based reaction-diffusion program that simulates the movement and interaction of molecules in 3D space (documentation). CellBlender is a Blender add-on that can be used as visual interface for MCell. With it you can create beautiful animations of your experiment - e.g. of a oscillating Min system as done in [1].

[1] Rex, Kerr., Herbert, Levine., Terrence, J., Sejnowski., Wouter-Jan, Rappel. (2006). Division accuracy in a stochastic model of Min oscillations in Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America, 103(2):347-352. doi: 10.1073/PNAS.0505825102

VCell

VCell is a comprehensive platform for modeling cell biological systems that is built on a central database and disseminated as a web application. It has many features. For example one can create a 3D cell based on microscopy images, then add reactions and pathways, and let VCell setup the simulation. [2] describes spatial modelling with VCell.

[2] Anne, E., Cowan., Ion, I., Moraru., James, C., Schaff., Boris, M., Slepchenko., Leslie, M., Loew. (2012). Spatial modeling of cell signaling networks.. Methods in Cell Biology, 110:195-221. doi: 10.1016/B978-0-12-388403-9.00008-4

CellSys/TiSim

CellSys/TiSim is a modular software tool for efficient off-lattice simulation of growth and organization processes in multicellular systems in two and three dimensions. It implements an agent-based model that approximates cells as isotropic, elastic and adhesive objects. Cell migration is modeled by an equation of motion for each cell. (from [3])

[3] Stefan, Hoehme., Dirk, Drasdo. (2010). A cell-based simulation software for multi-cellular systems. Bioinformatics, 26(20):2641-2642. doi: 10.1093/BIOINFORMATICS/BTQ437

Genie

Genie. Cool simulation to visualize genetic drift and gene flow in a population. It's browser-based, you can try it out on their website. The paper is [4].

[4] Castillo, A.I., Roos, B.H., Rosenberg, M.S. et al. Genie: an interactive real-time simulation for teaching genetic drift. Evo Edu Outreach 15, 3 (2022). doi.org: 10.1186/s12052-022-00161-7

MagicSoup

MagicSoup is an agent-based simulation with cells living, interacting, and replicating on a 2D grid. In this regard it is similar to Genie. In contrast to Genie however, it includes an algorithm which translates genomes into working metabolic and transduction pathways. In principle these pathways may seem similar to the ones in VCell. But VCell uses more sophisticated algorithms to model these pathways. Additionally, in VCell the cell itself can have a 2D or 3D shape. In MCell molecule movements within the 3D cell can even be simulated spatio-temporally. This doesn't exist in MagicSoup for now. Here, a cell is basically a homogenous bag of molecules. So, something like a Min system will not work in MagicSoup.