API Reference¶

Delay differential equations¶

Integrate a system of delay differential equations defined by

`rd_solve`	Solve a system of reaction-diffusion equations in space and time.
`constant_diff_coeffs`	Function for use with rd_solve() for constant diffusion coefficients.

Uses the Gillespie stochastic simulation algorithm to sample from probability distribution of particle counts over time.

`phase_portrait`	Plots the phase portrait for a 2D dynamical system in the u-v plane.
`streamplot`	Draws streamlines of a vector field.
`xyt_plot`	Create an interactive plot some the output of rd_solve().
`interactive_xy_plot`	Create an interactive x-y plot in Bokeh.

`act_hill`	Dimensionless production rate for a gene activated by x.
`rep_hill`	Dimensionless production rate for a gene repressed by x.
`aa_and`	Dimensionless production rate for a gene regulated by two activators with AND logic in the absence of leakage.
`aa_or`	Dimensionless production rate for a gene regulated by two activators with OR logic in the absence of leakage.
`aa_or_single`	Dimensionless production rate for a gene regulated by two activators with OR logic in the absence of leakage with single occupancy.
`rr_and`	Dimensionless production rate for a gene regulated by two repressors with AND logic in the absence of leakage.
`rr_or`	Dimensionless production rate for a gene regulated by two repressors with OR logic in the absence of leakage.
`rr_and_single`	Dimensionless production rate for a gene regulated by two repressors with AND logic in the absence of leakage with single occupancy.
`ar_and`	Dimensionless production rate for a gene regulated by one activator and one repressor with AND logic in the absence of leakage.
`ar_or`	Dimensionless production rate for a gene regulated by one activator and one repressor with OR logic in the absence of leakage.
`ar_and_single`	Dimensionless production rate for a gene regulated by one activator and one repressor with AND logic in the absence of leakage with single occupancy.
`ar_or_single`	Dimensionless production rate for a gene regulated by one activator and one repressor with OR logic in the absence of leakage with single occupancy.

`ffl_app`	Create a Bokeh app for exploring the dynamics of feed-forward loops in response to a step input.
`promiscuous_222_app`	Create a Bokeh app for exploring promiscuous ligand-receptor binding for a system with two types of receptor A, two types of receptor B, and two ligands.