sunnyxu / roadrunner.jl

Julia Bindings for libRoadRunner

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.

Note that RoadRunner.jl is only applicable on Windows and Linux, so users cannot run it on Mac until an update in the future.

Citing

If you use any of the software, please please cite the article (https://doi.org/10.1093/bioinformatics/btac770) and GitHub website (https://github.com/SunnyXu/RoadRunner.jl). Thanks.

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 Linux, and it is compliant for Julia version 1.1-1.9.

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*S1
    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 Y Zhu for his assisting and initiating this Julia package!