The software in this repo are Python Jupyter notebooks to perform simulations of chemotaxis with the simulation tool COMETS.
The pipeline for building a genome-scale model Pseudomonas simae from a sequenced genome, to simulation chemotaxis in colonies grown on agar plates is described in detail in:
Exploring chemotaxis in spatio-temporal stoichiometric models of metabolism: Pseudomonas simiae as a case study
Hui Shi, Ercole LiPuma, Haroon Qureshi, Phineas McMillan, Jing Zhang, Melisa Osborne, Ilija Dukovski, Daniel Segrè
Methods in Molecular Biology, Springer Nature (2026)
COMETS and its Python interface COMETSpy can be downloaded from: https://www.runcomets.org
The codes can be found at https://github.com/segrelab/comets and https://github.com/segrelab/cometspy