Problem using SBML package

FH96 · November 17, 2022, 4:15am

Hi everyone!
I am trying to use SBML package. I read a xml model by readSBML. According to the docs, getS and getUBs should give the stoichiometric matrix and upper boundary of the reactions, respectively. However when I run them I face the error :
“VarError: getUBs/getS not defined”
It is weird to me …can anyone help?

ChrisRackauckas · November 17, 2022, 9:26am

Can you share a full example? This is probably best opened as an issue on the package.

MirekKratochvil · November 17, 2022, 10:09am

Hi,
can you please point me to where you read the docs with getS and getUBs functions? We have renamed these a long ago to stoichiometric_matrix, flux_objective and flux_bounds; these are now used e.g. as such:

github.com

LCSB-BioCore/COBREXA.jl/blob/master/src/base/types/SBMLModel.jl#L48


      
          Efficient counting of metabolites in [`SBMLModel`](@ref).
          """
          n_metabolites(model::SBMLModel)::Int = length(model.sbml.species)
          
          
"""
          $(TYPEDSIGNATURES)
          
          
Recreate the stoichiometry matrix from the [`SBMLModel`](@ref).
          """
          function stoichiometry(model::SBMLModel)::SparseMat
              _, _, S = SBML.stoichiometry_matrix(model.sbml)
              return S
          end
          
          
"""
          $(TYPEDSIGNATURES)
          
          
Get the lower and upper flux bounds of model [`SBMLModel`](@ref). Throws `DomainError` in
          case if the SBML contains mismatching units.
          """
          function bounds(model::SBMLModel)::Tuple{Vector{Float64},Vector{Float64}}

github.com

LCSB-BioCore/COBREXA.jl/blob/master/src/base/types/SBMLModel.jl#L59


      
              return S
          end
          
          
"""
          $(TYPEDSIGNATURES)
          
          
Get the lower and upper flux bounds of model [`SBMLModel`](@ref). Throws `DomainError` in
          case if the SBML contains mismatching units.
          """
          function bounds(model::SBMLModel)::Tuple{Vector{Float64},Vector{Float64}}
              lbu, ubu = SBML.flux_bounds(model.sbml)
          
          
    unit = lbu[1][2]
              getvalue = (val, _)::Tuple -> val
              getunit = (_, unit)::Tuple -> unit
          
          
    allunits = unique([getunit.(lbu) getunit.(ubu)])
              length(allunits) == 1 || throw(
                  DomainError(
                      allunits,
                      "The SBML file uses multiple units; loading needs conversion",

Using the proper function names should fix it. In case there’s old documentation hanging out somewhere, please send us a link (or open an issue) so that we can update it.
Thanks&best!
-mk
-mk

FH96 · November 19, 2022, 2:35am

Thanks Mirek for your attention

I have read docs from this link https://lcsb-biocore.github.io/SBML.jl/v0.2/

Are the functions you mentioned from SBML.jl or cobrexa.jl?

giordano · November 19, 2022, 5:46am

That’s a very old version of SBML.jl, latest one is v1.3.0. I guess the new question is: how did you get to the docs of v0.2 of SBML.jl? Is there any page pointing to that version specifically?

FH96 · November 19, 2022, 12:59pm

oh…Actually I was really careless about the version…It was a great lesson for me!

No, I googled for the docs and it was like the third result!