Micodymora is a python package allowing the simulation of Ordinary Differential Equations (ODE) models of microbial population dynamics, as presented in Delattre et al, J. R. Soc. Interface, 2020. For further details and to access the package, please visit the GitHub page.
MI-Sim is a MATLAB graphical user-interface whose main function is the numerical analysis of dynamical systems describing ecological interactions (motifs) as presented in "Wade M, et al, PLoS ONE, 2017". Software available at GitHub and Mathworks.
EvoFBA - This is a MATLAB implementation of the evolutionary and ecological dynamics simulations of growing E.coli populations as presented in "Grosskopf T, et al, BMC Evol Bio, 2016". These simulations involve mimicking growth dynamics of E.coli cells using dynamical constraint-based modeling of cellular metabolism and mimicking ecological dynamics through differential equations describing concentrations of media components. See the associated paper for further details. ZIP files
We made a video describing how we culture anaerobes in the lab:
We also made a short video describing our research on microbial communities.