Integration with Tellurium

Tellurium is a Python package built on top of

libRoadRunner, a C++ package for simulation and analysis of models in systems biology. Antimony is a model definition language for SBML models that was written by the authors of Tellurium and libRoadRunner.

Since PyCoTools has adopted Antimony, the same model can be simulated and analysed with both COPASI and tellurium.

Here’s a short example of how using the tellurium back end.

import tellurium as te

antimony_string = """
model simple_parameter_estimation()
    compartment Cell = 1;

    A in Cell;
    B in Cell;
    C in Cell;

    // reactions
    R1: A => B ; Cell * k1 * A;
    R2: B => A ; Cell * k2 * B * C;
    R3: B => C ; Cell * k3 * B;
    R4: C => B ; Cell * k4 * C;

    // initial concentrations
    A = 100;
    B = 1;
    C = 1;

    // reaction parameters
    k1 = 0.1;
    k2 = 0.1;
    k3 = 0.1;
    k4 = 0.1;
end
"""

mod = te.loada(antimony_string)

# simulate a time series with 11 time points between 0 and 10
timeseries_data = mod.simulate(0, 10, 11)

# compute the steady state
mod.conservedMoietyAnalysis = True
mod.setSteadyStateSolver('nleq')
mod.steadyState()
mod.steadyStateSelections = ['A', 'B', 'C']
print(dict(zip(*mod.steadyStateSelections,
                mod.getSteadyStateValues()))