API Reference

jLM

jLM is an alternate interface to Lattice Microbes through the Jupyter notebook. For a quick introduction to jLM, please see the example notebook.

jLM	jLM top level.
jLM.CME	Well-stirred CME model
jLM.CMEPostProcessing	Post-processing for the Well-stirred CME model
jLM.RDME	Spatial model
jLM.RegionBuilder	Design lattice geometry
jLM.Solvers	Generic RDME solvers
jLM.Types	Simulation objects.
jLM.BaseTypes	Simulation object base class and collections
jLM.ColorGen	Defines ColorSeq, the color scheme generator
jLM.DisplayUtils	Auxiliary helper functions for presentation
jLM.JupyterDisplay	SpatialModel mixins for rich display in Jupyter
jLM.LmInteract	SpatialModel mixins for interaction with LM
jLM.Lattice	Cythonized lattice manipulation functions
jLM.LMLogger	Logger for Lattice Microbes
jLM.Analysis	Simulation analysis mixins for SpatialModel
jLM.Template	Templating engine tools
jLM.TexFmt	Dump simulation parameters as LaTeX

LM

Swig interface to Lattice Microbes

lm	Lattice Microbes Python Bindings