SBML¶

import¶

In [1]:

import matplotlib.pyplot as plt

from modelbase.ode import Model, Simulator
from modelbase.sbml.parser import Parser

from pathlib import Path

import matplotlib.pyplot as plt from modelbase.ode import Model, Simulator from modelbase.sbml.parser import Parser from pathlib import Path

UserWarning: Assimulo not found, disabling sundials support.

In [2]:

file = Path("assets") / "00001-sbml-l3v2.xml"
parser = Parser(file=file)
m, y0 = parser.build_model_from_sbml()

file = Path("assets") / "00001-sbml-l3v2.xml" parser = Parser(file=file) m, y0 = parser.build_model_from_sbml()

In [3]:

s = Simulator(m)
s.initialise(y0)
t, y = s.simulate(10)

s = Simulator(m) s.initialise(y0) t, y = s.simulate(10)

In [4]:

fig, ax = s.plot(xlabel="Time", ylabel="Concentration")
plt.show()

fig, ax = s.plot(xlabel="Time", ylabel="Concentration") plt.show()

export¶

In [5]:

import matplotlib.pyplot as plt

from modelbase.ode import Model, Simulator
from modelbase.ode import ratelaws as rl
from modelbase.ode import ratefunctions as rf

import matplotlib.pyplot as plt from modelbase.ode import Model, Simulator from modelbase.ode import ratelaws as rl from modelbase.ode import ratefunctions as rf

In [6]:

m = Model()
m.add_parameters({"v0": 1, "k1p": 0.5, "k1m": 1, "k2": 0.1})
m.add_compounds(["X", "Y"])
m.add_reaction_from_ratelaw(rate_name="v0", ratelaw=rl.Constant(product="X", k="v0"))
m.add_reaction_from_ratelaw(
    rate_name="v1",
    ratelaw=rl.ReversibleMassAction(
        substrates=["X"], products=["Y"], k_fwd="k1p", k_bwd="k1m"
    ),
)
m.add_reaction_from_ratelaw(
    rate_name="v2", ratelaw=rl.MassAction(substrates=["Y"], products=[], k_fwd="k2")
)

s = Simulator(m)
s.initialise({"X": 0, "Y": 0})
t, y = s.simulate(100)
fig, ax = s.plot(xlabel="Time [au]", ylabel="Concentration [au]")
plt.show()

m = Model() m.add_parameters({"v0": 1, "k1p": 0.5, "k1m": 1, "k2": 0.1}) m.add_compounds(["X", "Y"]) m.add_reaction_from_ratelaw(rate_name="v0", ratelaw=rl.Constant(product="X", k="v0")) m.add_reaction_from_ratelaw( rate_name="v1", ratelaw=rl.ReversibleMassAction( substrates=["X"], products=["Y"], k_fwd="k1p", k_bwd="k1m" ), ) m.add_reaction_from_ratelaw( rate_name="v2", ratelaw=rl.MassAction(substrates=["Y"], products=[], k_fwd="k2") ) s = Simulator(m) s.initialise({"X": 0, "Y": 0}) t, y = s.simulate(100) fig, ax = s.plot(xlabel="Time [au]", ylabel="Concentration [au]") plt.show()

In [7]:

print(m.write_sbml_model())

print(m.write_sbml_model())

<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" sboTerm="SBO:0000062" level="3" version="2" fbc:required="false">
  <model id="modelbase__45__model__45__2026__45__06__45__07" name="modelbase__45__model" substanceUnits="mole" timeUnits="second" extentUnits="mole" fbc:strict="true">
    <listOfUnitDefinitions>
      <unitDefinition id="per_second">
        <listOfUnits>
          <unit kind="second" exponent="-1" scale="0" multiplier="1"/>
        </listOfUnits>
      </unitDefinition>
    </listOfUnitDefinitions>
    <listOfCompartments>
      <compartment id="c" name="cytosol" spatialDimensions="3" size="1" units="litre" constant="true"/>
    </listOfCompartments>
    <listOfSpecies>
      <species id="X" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
      <species id="Y" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
    </listOfSpecies>
    <listOfReactions>
      <reaction id="v0" reversible="false">
        <listOfProducts>
          <speciesReference species="X" stoichiometry="1" constant="false"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <ci> v0 </ci>
          </math>
        </kineticLaw>
      </reaction>
      <reaction id="v1" reversible="true">
        <listOfReactants>
          <speciesReference species="X" stoichiometry="1" constant="false"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="Y" stoichiometry="1" constant="false"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <minus/>
              <apply>
                <times/>
                <ci> k1p </ci>
                <ci> X </ci>
              </apply>
              <apply>
                <times/>
                <ci> k1m </ci>
                <ci> Y </ci>
              </apply>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
      <reaction id="v2" reversible="false">
        <listOfReactants>
          <speciesReference species="Y" stoichiometry="1" constant="false"/>
        </listOfReactants>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> k2 </ci>
              <ci> Y </ci>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
    </listOfReactions>
  </model>
</sbml>