API reference

getinitialconditions(model)

Create array of initial conditions from a libsbml Model.

Example

julia> u0 = getinitialconditions(model)
2-element Array{Pair{Num,Float64},1}:
 A(t) => 1.0
 B(t) => 0.0

getmodel(sbmlfile::String)

Given an sbmlfile return a PyObject (libsbml.Model).

Example

julia> model = getmodel(SBML_FILE)
PyObject <Model conversion_reaction_0 "Conversion Reaction 0">

getparameters(model)

Create array of parameters from a libsbml Model.

Example

julia> pars = getparameters(model)
3-element Array{Pair{Num,Float64},1}:
          k1 => 0.8
          k2 => 0.6
 compartment => 1.0

getreactions(model)::Array

Create array of Reactions from a libsbml model.

Example

julia> rxs = getreactions(model)
2-element Array{ModelingToolkit.Reaction,1}:
 ModelingToolkit.Reaction{Any,Float64}(compartment*k1*A(t), SymbolicUtils.Term{Real}[A(t)],
                                       SymbolicUtils.Term{Real}[B(t)], [1.0], [1.0],
                                       Pair{Any,Float64}[B(t) => 1.0, A(t) => -1.0], true)
 ModelingToolkit.Reaction{Any,Float64}(compartment*k2*B(t), SymbolicUtils.Term{Real}[B(t)],
                                       SymbolicUtils.Term{Real}[A(t)], [1.0], [1.0],
                                       Pair{Any,Float64}[B(t) => -1.0, A(t) => 1.0], true)

sbml2odeproblem(sbmlfile::String,tspan;jac::Bool=true)

Convert model from SBML file to an ODEProblem and return it.

Arguments

• sbmlfile::String: path to SBML file.
• tspan: The solution u(t) will be computed for tspan[1] ≤ t ≤ tspan[2].
• jac::Bool=true: Jacobian matrix.

Example

julia> prob = sbml2odeproblem(SBML_FILE,(0.0,10.0))
ODEProblem with uType Array{Float64,1} and tType Float64. In-place: true
timespan: (0.0, 10.0)
u0: [0.0, 1.0]

sbml2odesystem(sbmlfile::String)

Given an sbmlfile return an ODESystem with default_u0 and default_p set.

Example

julia> sys = sbml2odesystem(SBML_FILE)
Model ##ODESystem#270 with 2 equations
States (2):
  B(t) [defaults to 0.0]
  A(t) [defaults to 1.0]
Parameters (3):
  k2 [defaults to 0.6]
  compartment [defaults to 1.0]
  k1 [defaults to 0.8]

simulatesbml(sbmlfile::String,tspan;saveat::Real=1.,jac::Bool=true,
             solver=OrdinaryDiffEq.Tsit5())

Simulate model from SBML file and return an ODESolution.

Arguments

• sbmlfile::String: path to SBML file.
• tspan: The solution u(t) will be computed for tspan[1] ≤ t ≤ tspan[2].
• saveat::Real=1.: time intervals of u(t) output.
• jac::Bool=true: Jacobian matrix.
• solver=OrdinaryDiffEq.Tsit5(): Integration algorithm.

Example

julia> sol = simulatesbml("mymodel.sbml",(0.0,1.0))
retcode: Success
Interpolation: 1st order linear
t: 2-element Array{Float64,1}:
 0.0
 1.0
u: 2-element Array{Array{Float64,1},1}:
 [0.0, 1.0]
 [0.4, 0.6]