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Fails to simulate an SBML model (Species does not have a compartment attribute!) #592

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TorkelE opened this issue Mar 12, 2024 · 0 comments
Open

Fails to simulate an SBML model (Species does not have a compartment attribute!) #592

TorkelE opened this issue Mar 12, 2024 · 0 comments

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@TorkelE
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TorkelE commented Mar 12, 2024

I have a model stored in a sbml file. I want to simulate it using NFSim:

import pysb
import numpy as np
from pysb.importers.sbml import model_from_sbml
from pysb.examples import robertson
from pysb.simulator.bng import BngSimulator

# Perform simulation.
model = model_from_sbml("../Data/multistate.xml")
sim = BngSimulator(model, tspan=np.linspace(0, 1))
x = sim.run(n_runs=1, method='nf')

Here, the last line gives an error:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/user/anaconda3/lib/python3.11/site-packages/pysb/simulator/bng.py", line 211, in run
    bngfile.execute()
  File "/home/user/anaconda3/lib/python3.11/site-packages/pysb/bng.py", line 474, in execute
    raise BngInterfaceError('\n'.join(captured_error_lines) + "\n" +
pysb.bng.BngInterfaceError: 
ABORT: Species does not have a compartment attribute! at line 3 of file ./pysb0.species
  at line 100

I am unsure how to deal with this. I have pasted the sbml file below, if that is useful. I have been able to load and simualte this file using E.g. RoadRunner and SBMLToolkit, so I think the file should be fine.

<?xml version="1.0" encoding="UTF-8"?>
<!-- Created by BioNetGen 2.7.0  -->
<sbml xmlns="http://www.sbml.org/sbml/level2/version3" level="2" version="3">
  <model id="multistate">
    <listOfUnitDefinitions>
      <unitDefinition id="substance" name="substance">
        <listOfUnits>
          <unit kind="item" exponent="1" multiplier="1"/>
        </listOfUnits>
      </unitDefinition>
    </listOfUnitDefinitions>
    <listOfCompartments>
      <compartment id="cell" size="1"/>
    </listOfCompartments>
    <listOfSpecies>
      <species id="S1" compartment="cell" initialAmount="5360" name="R(a,l)"/>
      <species id="S2" compartment="cell" initialAmount="1160" name="L(r)"/>
      <species id="S3" compartment="cell" initialAmount="5360" name="A(Y~U,r)"/>
      <species id="S4" compartment="cell" initialAmount="0" name="L(r!1).R(a,l!1)"/>
      <species id="S5" compartment="cell" initialAmount="0" name="A(Y~U,r!1).R(a!1,l)"/>
      <species id="S6" compartment="cell" initialAmount="0" name="A(Y~U,r!1).L(r!2).R(a!1,l!2)"/>
      <species id="S7" compartment="cell" initialAmount="0" name="A(Y~P,r!1).L(r!2).R(a!1,l!2)"/>
      <species id="S8" compartment="cell" initialAmount="0" name="A(Y~P,r!1).R(a!1,l)"/>
      <species id="S9" compartment="cell" initialAmount="0" name="A(Y~P,r)"/>
    </listOfSpecies>
    <listOfParameters>
      <!-- Independent variables -->
      <parameter id="R0" value="5360"/>
      <parameter id="L0" value="1160"/>
      <parameter id="A0" value="5360"/>
      <parameter id="kon" value="0.01"/>
      <parameter id="koff" value="0.1"/>
      <parameter id="kAon" value="0.01"/>
      <parameter id="kAoff" value="0.1"/>
      <parameter id="kAp" value="0.01"/>
      <parameter id="kAdp" value="0.1"/>
      <!-- Observables -->
      <parameter id="A_P" constant="false"/>
      <parameter id="A_unbound_P" constant="false"/>
      <parameter id="A_bound_P" constant="false"/>
      <parameter id="RLA_P" constant="false"/>
    </listOfParameters>
    <listOfRules>
      <!-- Observables -->
      <assignmentRule variable="A_P">
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <plus/>
              <ci> S7 </ci>
              <ci> S8 </ci>
              <ci> S9 </ci>
            </apply>
          </math>
      </assignmentRule>
      <assignmentRule variable="A_unbound_P">
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <plus/>
              <cn> 0 </cn>
              <ci> S9 </ci>
            </apply>
          </math>
      </assignmentRule>
      <assignmentRule variable="A_bound_P">
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <plus/>
              <ci> S7 </ci>
              <ci> S8 </ci>
            </apply>
          </math>
      </assignmentRule>
      <assignmentRule variable="RLA_P">
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <plus/>
              <cn> 0 </cn>
              <ci> S7 </ci>
            </apply>
          </math>
      </assignmentRule>
    </listOfRules>
    <listOfReactions>
      <reaction id="R1" reversible="false">
        <listOfReactants>
          <speciesReference species="S1"/>
          <speciesReference species="S2"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="S4"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> kon </ci>
              <ci> S1 </ci>
              <ci> S2 </ci>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
      <reaction id="R2" reversible="false">
        <listOfReactants>
          <speciesReference species="S1"/>
          <speciesReference species="S3"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="S5"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> kAon </ci>
              <ci> S1 </ci>
              <ci> S3 </ci>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
      <reaction id="R3" reversible="false">
        <listOfReactants>
          <speciesReference species="S2"/>
          <speciesReference species="S5"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="S6"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> kon </ci>
              <ci> S2 </ci>
              <ci> S5 </ci>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
      <reaction id="R4" reversible="false">
        <listOfReactants>
          <speciesReference species="S4"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="S1"/>
          <speciesReference species="S2"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> koff </ci>
              <ci> S4 </ci>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
      <reaction id="R5" reversible="false">
        <listOfReactants>
          <speciesReference species="S3"/>
          <speciesReference species="S4"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="S6"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> kAon </ci>
              <ci> S3 </ci>
              <ci> S4 </ci>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
      <reaction id="R6" reversible="false">
        <listOfReactants>
          <speciesReference species="S5"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="S1"/>
          <speciesReference species="S3"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> kAoff </ci>
              <ci> S5 </ci>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
      <reaction id="R7" reversible="false">
        <listOfReactants>
          <speciesReference species="S6"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="S2"/>
          <speciesReference species="S5"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> koff </ci>
              <ci> S6 </ci>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
      <reaction id="R8" reversible="false">
        <listOfReactants>
          <speciesReference species="S6"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="S3"/>
          <speciesReference species="S4"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> kAoff </ci>
              <ci> S6 </ci>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
      <reaction id="R9" reversible="false">
        <listOfReactants>
          <speciesReference species="S6"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="S7"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> kAp </ci>
              <ci> S6 </ci>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
      <reaction id="R10" reversible="false">
        <listOfReactants>
          <speciesReference species="S7"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="S2"/>
          <speciesReference species="S8"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> koff </ci>
              <ci> S7 </ci>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
      <reaction id="R11" reversible="false">
        <listOfReactants>
          <speciesReference species="S7"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="S4"/>
          <speciesReference species="S9"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> kAoff </ci>
              <ci> S7 </ci>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
      <reaction id="R12" reversible="false">
        <listOfReactants>
          <speciesReference species="S7"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="S6"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> kAdp </ci>
              <ci> S7 </ci>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
      <reaction id="R13" reversible="false">
        <listOfReactants>
          <speciesReference species="S2"/>
          <speciesReference species="S8"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="S7"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> kon </ci>
              <ci> S2 </ci>
              <ci> S8 </ci>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
      <reaction id="R14" reversible="false">
        <listOfReactants>
          <speciesReference species="S1"/>
          <speciesReference species="S9"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="S8"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> kAon </ci>
              <ci> S1 </ci>
              <ci> S9 </ci>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
      <reaction id="R15" reversible="false">
        <listOfReactants>
          <speciesReference species="S4"/>
          <speciesReference species="S9"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="S7"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> kAon </ci>
              <ci> S4 </ci>
              <ci> S9 </ci>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
      <reaction id="R16" reversible="false">
        <listOfReactants>
          <speciesReference species="S8"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="S1"/>
          <speciesReference species="S9"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> kAoff </ci>
              <ci> S8 </ci>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
      <reaction id="R17" reversible="false">
        <listOfReactants>
          <speciesReference species="S8"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="S5"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> kAdp </ci>
              <ci> S8 </ci>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
      <reaction id="R18" reversible="false">
        <listOfReactants>
          <speciesReference species="S9"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="S3"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> kAdp </ci>
              <ci> S9 </ci>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
    </listOfReactions>
  </model>
</sbml>
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@TorkelE