RoadRunner.jl

Author sys-bio
Popularity
2 Stars
Updated Last
1 Year Ago
Started In
May 2020

Julia Bindings for libRoadRunner

Build Status

Build Status

Introduction

This project represents a set of Julia (https://julialang.org/) bindings to libRoadRunner (http://libroadrunner.org/). libRoadrunner is a SBML compliant high performance and simulation engine for systems and synthetic biology. This RoadRunner.jl package supports SBML and Antimony (http://antimony.sourceforge.net/) files as input. If you use any of the software, please cite the GitHub website (https://github.com/SunnyXu/RoadRunner.jl).

Quick Start

julia> import Pkg
julia> Pkg.add("RoadRunner")
julia> using RoadRunner

Documentation

The documentation can be found at: https://SunnyXu.github.io/RoadRunner.jl/

The main code of this package is based on the existed software of libRoadRunner and libAntimony.

src/RoadRunner.jl and src/rrc_utilities_binding.jl refer to the documentation of libRoadRunner https://github.com/sys-bio/roadrunner.

src/antimony_binding.jl refers to the documentation of libAntimony C API-antimony_api.h (http://antimony.sourceforge.net/antimony__api_8h.html)

Requirements

This current version of Julia package is suitable for Window 64, and it is compliant for Julia version 1.1-1.5.

Examples

An example illustrating how to load an SBML file.

using RoadRunner
sbmlFile = "\\path\\to\\file.xml"
f = open(sbmlFile)
sbmlStr = read(f,String)
close(f)
rr = RoadRunner.createRRInstance()
RoadRunner.loadSBML(rr, sbmlStr)

An example showing how to load a model in Antimony format.

using RoadRunner
ant_str = """    
    const Xo, X1
    Xo -> S1; k1*Xo - k2*S1
    S1 -> S2; k3*S2
    S2 -> X1; k4*S2

    Xo = 1;   X1 = 0
    S1 = 0;   S2 = 0
    k1 = 0.1; k2 = 0.56
    k3 = 1.2; k4 = 0.9
"""
rr = RoadRunner.loada(ant_str)

We thank Luke Zhu (https://github.com/Lukez-pi/RoadRunner.jl) for his assisting and initiating this Julia package!

Used By Packages

No packages found.