MuMoT is a software tool developed at the University of Sheffield as part of the DiODe project. It is open source and can be accessed on the MuMoT GitHub page, including full documentation and installation instructions.
MuMoT aims at life scientists/biologists with little mathematical background and engineers designing collective behaviours. It runs inside Jupyter notebooks. MuMoT will be available as Python package that is easy to install on a personal computer and can also be run as server: launch example-filled User Manual now in your web-browser on MyBinder. MuMoT is designed in an object-oriented and modular fashion to make it easy to maintain and to extend functionality.
Core developers: James A. R. Marshall, Andreagiovanni Reina, Thomas Bose (all at University of Sheffield)
Packaging, documentation, deployment: Will Furnass (University of Sheffield)
Windows compatibility: Renato P. Vasquez (Princeton University)
Schematic of a typical workflow in MuMoT.
MuMoT’s core features:
- requires simple input: all functionality is based on providing information about the system as chemical reaction
- allows model exploration with simple commands, including model visualisation (see stream plot below as an example)
- automatically generates mathematical equations, including ODEs, Master equation, system size expansion, Fokker-Planck equation (integrates with $\mathsf{\LaTeX}$ to display & export equations)
- allows studying effects of noise both analytically and graphically
- allows interactive analysis controlled by simple sliders using IPython widgets
- allows network analysis of agent-based simulations
- features stochastic simulations of the system
- automated figure formatting in publication-ready quality
Example input and output in MuMoT: stream plot of honey bee nest-site selection model with two alternatives, A and B (Seeley et al. (2012) and Pais et al. (2013), cf. our PRE article Reina et al. (2017) ). Fixed points are shown (blue hollow circle: saddle point, green full circle: stable fixed point).
Try it out! The User Manual can be accessed (and worked with straight away) via this link (it may take a few seconds, or a bit longer, until the server is ready) or you can get started by having a look at these tutorials.
