SBML to Chaste mapping

[kwabenantim]

Compartments

SBML	Chaste
Compartment	Parameter in OdeSystem set to compartment size

Example

SBML

<listOfCompartments>
  <compartment id="cell" metaid="metaid_0000040" name="cell" size="1">
  </compartment>
</listOfCompartments>

Chaste

class FooOdeSystem : public AbstractOdeSystem
{
  mParameters.push_back(1.0); // cell
}

template <>
void CellwiseOdeSystemInformation<FooOdeSystem>::Initialise()
{
  this->mParameterNames.push_back("cell");
}

[kwabenantim]

Species

SBML	Chaste
Species defined by Reactions	State variable in OdeSystem
Species defined by Assignment Rule	DerivedQuantity in OdeSystem
Species defined by Rate Rule	State variable in OdeSystem
Species defined by Algebraic Rule	Not supported
Species defined as a boundary condition	DerivedQuantity in OdeSystem

Example 01

Species defined by Reactions

SBML

<listOfSpecies>
  <species compartment="cell" hasOnlySubstanceUnits="true" id="CycBt" initialAmount="0.001"
    metaid="metaid_0000041" name="CycBt">
  </species>
</listOfSpecies>

<listOfReactions>
  <reaction id="CycBt_synthesis" metaid="metaid_0000059" name="CycBt synthesis"
    reversible="false">
    <listOfProducts>
      <speciesReference metaid="_240586" species="CycBt" />
    </listOfProducts>
    <kineticLaw metaid="_240598" sboTerm="SBO:0000047">
      <math xmlns="http://www.w3.org/1998/Math/MathML">
        <ci> k1 </ci>
      </math>
    </kineticLaw>
  </reaction>
  
  <reaction id="CycBdegradation" metaid="metaid_0000060" name="CycBt degradation"
    reversible="false">
    <listOfReactants>
      <speciesReference metaid="_240610" species="CycBt" />
    </listOfReactants>
    <kineticLaw metaid="_240622" sboTerm="SBO:0000049">
      <math xmlns="http://www.w3.org/1998/Math/MathML">
        <apply>
          <times />
          <ci> k2p </ci>
          <ci> CycBt </ci>
        </apply>
      </math>
    </kineticLaw>
  </reaction>
  
</listOfReactions>

Chaste

FooOdeSystem::FooOdeSystem()
{
  double CycBt = 0.001;
  mStateVariables.push_back(CycBt);
}

template <>
void CellwiseOdeSystemInformation<FooOdeSystem>::Initialise()
{
    this->mVariableNames.push_back("CycBt");
    this->mInitialConditions.push_back(0.001);
}

void FooOdeSystem::EvaluateYDerivatives(... time, ... &rY, ... &rDY)
{
    double CycBt = rY[0];
    
    double CycBt_synthesis = k1;
    double CycBdegradation = k2p * CycBt;

    rY[0] = CycBt_synthesis - CycBdegradation;
}

Example 02

Species defined by Assignment Rule

SBML

<listOfSpecies>
  <species compartment="cell" hasOnlySubstanceUnits="true" id="Trimer" metaid="metaid_0000044"
    name="Trimer">
  </species>
</listOfSpecies>

<listOfRules>
  <assignmentRule metaid="metaid_0000056" variable="Trimer">
    <math xmlns="http://www.w3.org/1998/Math/MathML">
      <apply>
        <times />
        <cn> 2 </cn>
        <ci> CycBt </ci>
      </apply>
    </math>
  </assignmentRule>
</listOfRules>

Chaste

template <>
void CellwiseOdeSystemInformation<FooOdeSystem>::Initialise()
{
    this->mDerivedQuantityNames.push_back("Trimer");
}

void FooOdeSystem::EvaluateYDerivatives(... time, ... &rY, ... &rDY)
{
    ...
    double Trimer = 2 * CycBt;
    ...
}

Example 03

Species defined as boundary condition with an assignment rule becomes a derived quantity

SBML

<listOfSpecies>
  <species boundaryCondition="true" compartment="cell" hasOnlySubstanceUnits="true" id="CDC15i"
    metaid="metaid_0000182" name="CDC15i">
  </species>
</listOfSpecies>

<listOfRules>
  <assignmentRule metaid="metaid_0000227" variable="CDC15i">
    <math xmlns="http://www.w3.org/1998/Math/MathML">        
      <apply>
        <minus/>
        <ci> CDC15T </ci>
        <ci> CDC15 </ci>
      </apply>
    </math>
</assignmentRule>
</listOfRules>

Chaste

template <>
void CellwiseOdeSystemInformation<FooOdeSystem>::Initialise()
{
    this->mDerivedQuantityNames.push_back("CDC15i");
}

void FooOdeSystem::EvaluateYDerivatives(... time, ... &rY, ... &rDY)
{
    ...
    double  CDC15i = CDC15T - CDC15;
    ...
}

Example 04

Species defined as boundary condition without an assignment rule becomes a derived quantity with an extra assignment rule
SBML

<listOfSpecies>
  <species boundaryCondition="true" compartment="cell" hasOnlySubstanceUnits="true" id="CDC15i" name="CDC15i" initialAmount="0.015">
  </species>
</listOfSpecies>

Chaste

template <>
void CellwiseOdeSystemInformation<FooOdeSystem>::Initialise()
{
    this->mDerivedQuantityNames.push_back("CDC15i");
}

void FooOdeSystem::EvaluateYDerivatives(... time, ... &rY, ... &rDY)
{
    ...
    double  CDC15i = 0.015; // extra assignment rule
    ...
}

[kwabenantim]

Parameters

SBML	Chaste
Parameter (constant=true or not specified)	OdeSystem const double member set to parameter value
Parameter (constant=false)	Parameter in OdeSystem
Parameter defined by assignment rule	OdeSystem double member used as intermediary variable
Parameter defined by rate rule	State variable in OdeSystem

Example 01

Constant parameter.

SBML

<listOfParameters>
  <parameter id="k1" metaid="metaid_0000004" name="k1" value="0.04"/>
</listOfParameters>

Chaste

class FooOdeSystem : public AbstractOdeSystem
{
  const double k1 = 0.04;
}

Example 02

Variable parameter.

SBML

<listOfParameters>
   <parameter name="wnt_level" constant="false" id="wnt_level" value="0" />
</listOfParameters>

Chaste

FooOdeSystem::FooOdeSystem()
{
  mParameters.push_back(0.0); // wnt_level
}

template <>
void CellwiseOdeSystemInformation<FooOdeSystem>::Initialise()
{
  this->mParameterNames.push_back("wnt_level");
}

Example 03

Parameter defined by assignment rule.

SBML

<listOfParameters>
  <parameter constant="false" id="TF" metaid="metaid_0000052" name="TF"/>
</listOfParameters>

<listOfRules>
  <assignmentRule metaid="metaid_0000057" variable="TF">
    <math xmlns="http://www.w3.org/1998/Math/MathML">
      <apply>
        <plus />
        <ci> A1 </ci>
        <ci> A2 </ci>
        </apply>
      </apply>
    </math>
  </assignmentRule>
</listOfRules>

Chaste

class FooOdeSystem : public AbstractOdeSystem
{
 double TF;
}

FooOdeSystem::ProcessRules()
{
  TF = A1 + A2;
}

Example 04

Parameter defined by rate rule becomes a state variable.

SBML

<listOfParameters>
  <parameter metaid="_963734" id="Cln2" name="Cln2" value="0.0078" constant="false" />
 </listOfParameters>

<listOfRules>
  <rateRule metaid="_963701" variable="Cln2">
    <math xmlns="http://www.w3.org/1998/Math/MathML">
      <apply>
        <minus />
        <apply>
          <times />
          <ci> mass </ci>
          <apply>
            <plus />
            <ci> ks_n2 </ci>
            <apply>
              <times />
              <ci> ks_n2_ </ci>
              <ci> SBF </ci>
            </apply>
          </apply>
        </apply>
        <apply>
          <times />
          <ci> kd_n2 </ci>
          <ci> Cln2 </ci>
        </apply>
      </apply>
    </math>
  </rateRule>
</listOfRules>

Chaste

FooOdeSystem::FooOdeSystem()
{
  double Cln2 = 0.0078;
  mStateVariables.push_back(Cln2);
}

template <>
void CellwiseOdeSystemInformation<FooOdeSystem>::Initialise()
{
    this->mVariableNames.push_back("Cln2");
    this->mInitialConditions.push_back(0.0078);
}

void FooOdeSystem::EvaluateYDerivatives(... time, ... &rY, ... &rDY)
{
    double Cln2 = rY[0];
    
    ...

    rY[0] = mass * (ks_n2 + ks_n2_ * SBF) - kd_n2 * Cln2;
}

[kwabenantim]

Rules

SBML	Chaste
Rate Rule	rDY[i] = rate_equation;
Assignment Rule	intermediate_var = assignment_equation;
Algebraic Rule	Not implemented

[kwabenantim]

Events

SBML	Chaste
Trigger	if (trigger condition) calculate trigger distance...
Assignment to Species (Chaste state variable)	SetStateVariable(expr); SetDefaultInitialCondition(expr);
Assignment to Species (Chaste DerivedQuantity)	Not allowed
Assignment to Parameter	SetParameter(expr);

[kwabenantim]

Function Definitions

SBML	Chaste
<functionDefinition id="foo" ...>	double foo(...){...}

Example

SBML

<listOfFunctionDefinitions>
  <functionDefinition id="BAR_123" metaid="metaid_0000003" name="BAR">
    <math xmlns="http://www.w3.org/1998/Math/MathML">
      <lambda>
        <bvar>
          <ci> A1 </ci>
        </bvar>
        <bvar>
          <ci> A2 </ci>
        </bvar>
        <apply>
          <plus />
          <ci> A1 </ci>
          <ci> A2 </ci>
          </apply>
        </apply>
      </lambda>
    </math>
  </functionDefinition>
</listOfFunctionDefinitions>

Chaste

inline double FooOdeSystem::BAR_123(double A1, double A2)
{
    return A1 + A2;
}

[kwabenantim]

Reactions

SBML	Chaste
<reaction id="foo"...>	foo = reaction_kinetic_law_equation;

[kwabenantim]

Note: This mapping is currently outdated. An updated version will be produced and added to documentation.