SBML.jl — load systems biology models from SBML files
This package provides a straightforward way to load model- and simulation-relevant information from SBML files.
The representation does not follow the XML structure within SBML, but instead translates the contents into native Julia structs. This makes the models much easier to work with from Julia,
Quick-start
The "main" function of the library is readSBML, which does exactly what it says: loads a SBML model from disk into the SBML.Model:
julia> using SBML
julia> mdl = readSBML("Ec_core_flux1.xml")
SBML.Model(…)
julia> mdl.compartments
2-element Array{String,1}:
"Extra_organism"
"Cytosol"There are several functions that help you with using the data in the usual COBRA-style workflows, such as stoichiometry_matrix. Others are detailed in the relevant sections of the function reference.
julia> metabolites, reactions, S = stoichiometry_matrix(mdl)
julia> metabolites
77-element Array{String,1}:
"M_succoa_c"
"M_ac_c"
"M_etoh_c"
⋮
julia> S
77×77 SparseArrays.SparseMatrixCSC{Float64,Int64} with 308 stored entries:
[60, 1] = -1.0
[68, 1] = 1.0
[1 , 2] = 1.0
[6 , 2] = -1.0
⋮
[23, 76] = 1.0
[56, 76] = -1.0
[30, 77] = -1.0
[48, 77] = 1.0
julia> Matrix(S)
77×77 Array{Float64,2}:
0.0 1.0 0.0 0.0 0.0 0.0 0.0 … 0.0 0.0 0.0 0.0 0.0 0.0 0.0
0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
0.0 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
0.0 -1.0 0.0 0.0 0.0 0.0 0.0 … 0.0 0.0 0.0 0.0 0.0 0.0 0.0
0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 -1.0 0.0 0.0 0.0
0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 -1.0 0.0 0.0 0.0 0.0 0.0
⋮ ⋮ ⋱ ⋮ ⋮