CBM.jl

CBM.jl is a COBRA toolbox written in the Julia programming language.

CBM provides a broad range of functionality found in similar COBRA toolboxes, while being easy to use and providing top of the line performance.

Install the package by calling

Pkg.clone("https://github.com/isebarn/CBM")

within the Julia enviroment.

Full documentation is available here

Installation

Firsty, version 0.5 (or above) of Julia is required

In addition to Julia, you will also want to install a optimization solver. Free solvers are available and Cobra supports both GLPK and Clp, along with the proprietery solvers CPLEX and Gurobi

Getting Started

You can load the example model, e_coli_core which comes with the package by calling

using CBM
model = load_model(Pkg.dir() * "/CBM/Models/e_coli_core.json")

So your screen should read something like

               _
   _       _ _(_)_     |  A fresh approach to technical computing
  (_)     | (_) (_)    |  Documentation: http://docs.julialang.org
   _ _   _| |_  __ _   |  Type "?help" for help.
  | | | | | | |/ _  |  |
  | | |_| | | | (_| |  |  Version 0.5.0 (2016-09-19 18:14 UTC)
 _/ |\__ _|_|_|\__ _|  |  
|__/                   |  x86_64-linux-gnu

julia> using CBM
julia> model = load_model(Pkg.dir() * "/CBM/Models/e_coli_core.json")

           rxns :     95 Array{String,1}
           mets :     72 Array{String,1}
          genes :    137 Array{String,1}
              S :   6840 SparseMatrixCSC{Float64,Int64}
             lb :     95 Array{Float64,1}
             ub :     95 Array{Float64,1}
              c :     95 Array{Float64,1}
              b :     72 Array{Float64,1}
         csense :      3 Dict{String,Array{Any,1}}
   rxn_gene_mat :  13015 SparseMatrixCSC{Float64,Int64}
       rxn_name :     95 Array{String,1}
      rxn_rules :     95 Array{String,1}
  rxn_subsystem :     95 Array{String,1}
      rxn_extra :      3 Dict{String,Array{Any,1}}
    met_formula :     72 Array{String,1}
       met_name :     72 Array{String,1}
      met_extra :      2 Dict{String,Array{Any,1}}
      gene_name :    137 Array{String,1}
     gene_extra :      1 Dict{String,Array{Any,1}}
    description :     11     String

and to run flux balance analysis

julia> fba(model)
FBAsolution: 
       obj::  0.873922
         v::  95 element-array
     slack::  72 element-array
    rcosts::  95 element-array
   success::  Optimal
      info::  SolverInfo("glpk","GLP_OPT")

Benchmarks

Running benchmark tests on flux variability, single gene deletion and double gene deletion on the iJO1366 model demonstrates the performance capabilities of CBM.jl in comparison with COBRApy and the COBRA Toolbox

Simulation	CBM.jl	COBRApy	COBRA Toolbox	Fast FVA
flux variablity analysis	4.22	11.36	13.69	3.65
single gene deletion	2.14	4.33	87	N/A
double gene deletion	319	365	>3600	N/A

Note Note: The CBM.jl package is currently under development. Please report all problems to dia2@hi.is.

Licence

© Copyright 2016, Davíð Isebarn & Steinn Guðmundsson. Released under the MIT licence.