BioMASS.jl

Julia interface to BioMASS, tailored to parameter estimation in systems biology models
Author himoto
Popularity
1 Star
Updated Last
1 Month Ago
Started In
October 2020

The BioMASS module for Julia

Actions Status version License: MIT ColPrac: Contributor's Guide on Collaborative Practices for Community Packages

Stable Dev

This module provides a Julia interface to the BioMASS parameter estimation.

Features

BioMASS.jl supports:

  • parameter estimation of ODE/DDE models
  • visualization of simulation results
  • bifurcation analysis

Usage

using BioMASS

model = load_model("./examples/fos_model");

# Estimate unknown model parameters against experimental observations.
optimize(model, 1, max_generation=20000, allowable_error=0.5)

# Save simulation results to figure/ in the model folder
visualize(model, viz_type="best", show_all=true)

Conversion of optimized parameters into BioMASS format

param2biomass("./examples/fos_model")

Installation

The package is a registered package, and can be installed with Pkg.add.

julia> using Pkg; Pkg.add("BioMASS")

or through the pkg REPL mode by typing

] add BioMASS

References