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COBRA.jl
is a package written in Julia used to perform COBRA analyses such as Flux Balance Anlysis (FBA), Flux Variability Anlysis (FVA), or any of its associated variants such as distributedFBA
[1].
FBA and FVA rely on the solution of LP problems. The package can be used with ease when the LP problem is defined in a .mat
file according to the format outlined in the COBRA Toolbox [2].
If you are new to Julia, you may find the Beginner's Guide interesting. A working installation of Julia is required.
At the Julia prompt, add the COBRA
package:
julia> Pkg.add("COBRA")
Use the COBRA.jl
module by running:
julia> using COBRA
COBRA.jl
has been tested on Julia v0.5+
on Ubuntu Linux 14.04+, MacOS 10.7+, and Windows 7 (64-bit). All solvers supported by MathProgBase.jl
are supported by COBRA.jl
, but must be installed separately. A COBRA model saved as a .mat
file can be read in using MAT.jl
. MathProgBase.jl
and MAT.jl
are automatically installed during the installation of the COBRA.jl
package.
The comprehensive tutorials are based on interactive Jupyter notebooks.
The COBRA.jl
package is fully documented here. You may also display the documentation in the Julia REPL:
julia> ? distributedFBA
:bulb: Should you encounter any errors or unusual behavior, please refer first to the FAQ section or open an issue.
You can test the package using:
julia> Pkg.test("COBRA")
Shall no solvers be detected on your system, error messages may be thrown when testing the COBRA.jl
package.
The code has been benchmarked against the fastFVA
implementation [3]. A test model ecoli_core_model.mat
[4] can be used to pre-compile the code and can be downloaded using
julia> using HTTP, COBRA
julia> pkgDir = joinpath(dirname(pathof(COBRA)), "..")
julia> include(pkgDir*"/test/getTestModel.jl")
julia> getTestModel()
distributedFBA.jl
?The corresponding paper can be downloaded from here. You may cite distributedFBA.jl
as follows:
Laurent Heirendt, Ines Thiele, Ronan M. T. Fleming; DistributedFBA.jl: high-level, high-performance flux balance analysis in Julia. Bioinformatics 2017 btw838. doi: 10.1093/bioinformatics/btw838
.mat
format is loaded using the MAT.jl
package. A valid MATLAB license is not required.