Bacteria-based networks are formed using native or engineered bacteria that communicate at nano-scale. This definition includes the micro-scale molecular transportation system which uses chemotactic bacteria for targeted cargo delivery, as well as genetic circuits for intercellular interactions like quorum sensing or light communication. To characterize the dynamics of bacterial networks accurately, we introduce BNSim, an open source, parallel, stochastic, and multiscale modeling platform which integrates various simulation algorithms, together with genetic circuits and chemotactic pathway models in a complex 3D environment.

Downloads and Links

Download source code: Release 2.5
Bacteria swarm formation video: Link
Supplementary document: Link