SBML L3 Packages - brief overview and current status

Sarah Keating

SBML Level 3 Packages

Status – July 2014

spatial

qual

Submodel 1 Submodel 2

comp

layout

core

SBML Level 3 Packages Modular approach



sbml.org/Documents/Specifications

#SBML_Level_3_Packages




Status

Status

Released

Specification document complete

Specification document approved

Two implementations

Status

Status

SUBJECT TO CHANGE

Implementations being worked on

Specification document being worked on

Draft available

Status

Status

Currently no activity

Package has been proposed

Stalled

Status

Status

Discussion


model submodel1 submodel2

enzyme

simple

Hierarchical Model Composition (comp)

<comp:listOfModelDefinitions> <comp:modelDefinition comp:id="enzyme"> <listOfCompartments> ... <comp:modelDefinition comp:id=“simple"> <listOfCompartments> ...

<model> ... <comp:listOfSubmodels> <comp:submodel comp:id="A" comp:modelRef="enzyme"/> <comp:submodel comp:id="B" comp:modelRef="simple“/> </comp:listOfSubmodels> </model>


model submodel1 submodel2

enzyme

simple


<comp:listOfExternalModelDefinitions> <comp:externalModelDefinition comp:id="ExtMod1“ comp:source="enzyme_model.xml" comp:modelRef="enzyme"/>



<listOfExternalModelDefinitions> <comp:externalModelDefinition comp:id="ExtMod1“ comp:source="enzyme_model.xml" comp:modelRef="enzyme"/>



Any URI

<comp:submodel comp:id="B" comp:modelRef="simple"> <comp:listOfDeletions> <comp:deletion comp:portRef="J0_port" comp:id="oldrxn"/> </comp:listOfDeletions>

<species id="S" compartment="compartment" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"> <comp:replacedBy comp:portRef="S_port" comp:submodelRef="B"/>

<compartment id="compartment" spatialDimensions="3" size="1" constant="true"> <comp:listOfReplacedElements> <comp:replacedElement comp:idRef="compartment" comp:submodelRef="A"/>




Library Support

libSBML Version 1 Release 2

JSBML Version 1 Release 2

Software Support

Antimony Reads/creates/writes

iBioSim Reads/creates/writes/simulates

COPASI Reads/simulates

Flux Balance Constraints (fbc)

<fbc:listOfFluxBounds> <fbc:fluxBound fbc:reaction="R1" fbc:operation="lessEqual" fbc:value="1"/> <fbc:fluxBound fbc:reaction="R1" fbc:operation=“greaterEqual" fbc:value=“0"/>

<reaction id="R1" reversible="false" fast="false"> <listOfReactants> <speciesReference species="IN" stoichiometry="1" constant="true"/> </listOfReactants> <listOfProducts> <speciesReference species="A" stoichiometry="1" constant="true"/> </listOfProducts> </reaction>

FluxBound 0 <= R1 <= 1


<fbc:listOfObjectives fbc:activeObjective="objective1"> <fbc:objective fbc:id="objective1" fbc:type="maximize"> <fbc:listOfFluxes> <fbc:fluxObjective fbc:reaction="R1" fbc:coefficient="1"/> <fbc:fluxObjective fbc:reaction="R2" fbc:coefficient=“2"/> </fbc:listOfFluxes> </fbc:objective>

Objective: maximize 1 R1 + 2 R2









Library Support

libSBML Version 1

JSBML Version 1

Software Support

SBW Flux Balance Reads/creates/writes/simulates

PySCeS-CBM Reads/creates/writes/simulates

COBRA libSBML converts to/from COBRA format

Qualitative Models (qual)

<qual:listOfQualitativeSpecies> <qual:qualitativeSpecies qual:compartment="cytosol" qual:constant="false" qual:id="A" qual:maxLevel="2" qual:name="sds" qual:initialLevel="0"/> <qual:transition qual:id="tr_A"> <qual:listOfInputs> <qual:input qual:qualitativeSpecies="A" qual:thresholdLevel="1" qual:transitionEffect="none“ /> </qual:listOfInputs> <qual:listOfOutputs> <qual:output qual:qualitativeSpecies=“B" qual:transitionEffect="assignmentLevel"/> </qual:listOfOutputs>


<qual:listOfFunctionTerms> <qual:functionTerm qual:resultLevel="2"> <math xmlns="http://www.w3.org/1998/Math/MathML">  <apply><or/><apply><and/> <apply><geq/><ci>A</ci><cn>1</cn> ... </qual:functionTerm> <qual:functionTerm qual:resultLevel="1"> <math xmlns="http://www.w3.org/1998/Math/MathML">  <qual:defaultTerm qual:resultLevel="0"/>



Library Support

libSBML Version 1

JSBML Version 1

Software Support

GinSim Reads/creates/writes/simulates

CellNetOpt Reads/creates/writes/simulates

CellCollective Reads/creates/writes/simulates

Layout (layout)

Layout (layout)

<listOfSpecies> <species id=“Glucose" compartment="compartment" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false“/>

<layout:listOfSpeciesGlyphs> <layout:speciesGlyph layout:id="sGlyph_0" layout:species=“Glucose" > <layout:boundingBox> <layout:position layout:x="16" layout:y="18"/> <layout:dimensions layout:width="62" layout:height="40"/> </layout:boundingBox> </layout:speciesGlyph>

Library Support

libSBML Version 1

JSBML Version 1

Software Support

COPASI Reads/creates/writes/displays

Online Viewer Reads/displays

SBW Reads/displays

Layout (layout)

Rendering (render)

text

text

<listOfSpecies> <species id=“Glucose" compartment="compartment" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false“/>

<layout:listOfSpeciesGlyphs> <layout:speciesGlyph layout:id="sGlyph_0" layout:species=“Glucose" >

Rendering (render)

<render:listOfStyles> <render:style render:idList=" sGlyph_0 "> <render:g render:stroke="black" render:stroke-width="1" render:fill-rule="nonzero" render:font-size="0" render:font-family="sans-serif" render:font-style="normal" render:font-weight="normal"> <render:curve render:transform="1,0,0,1,0,30“>

Library Support

libSBML Latest specification

JSBML Latest specification

Software Support

COPASI Reads/creates/writes/displays

Online Viewer Reads/displays

SBW Reads/displays

Rendering (render)

Multistate and Multicomponent species (multi)

Multistate and Multicomponent sp (multi)

stA

c1

B1

f1

c1

B2

f1


<multi:speciesType multi:id=“st_c" /> <multi:speciesType multi:id=“st_f" /> <multi:speciesType multi:id="st_B"> <multi:listOfSpeciesTypeInstances> <multi:speciesTypeInstance multi:id=“c1” multi:speciesType="st_c" multi:occur="1" /> <multi:speciesTypeInstance multi:id=“f1” multi:speciesType="st_f" multi:occur="1"/> </multi:listOfSpeciesTypeInstances> </multi:speciesType>

c1

B1

f1


<multi:speciesType multi:id="stA"> <multi:listOfSpeciesTypeInstances> <multi:speciesTypeInstance multi:id="B1“ multi:speciesType="st_B" multi:occur="1" /> <multi:speciesTypeInstance multi:id="B2“ multi:speciesType="st_B" multi:occur="1" /> </multi:listOfSpeciesTypeInstances> </multi:speciesType>

stA

c1

B1

f1

c1

B2

f1

Library Support


JSBML Older specification

Software Support

Simmune Reads/creates/writes/

Virginia Tech


Spatial processes (spatial)

<spatial:geometry spatial:coordinateSystem=“cartesian"> <spatial:listOfCoordinateComponents> <spatial:coordinateComponent spatial:id="x" spatial:type="cartesianX“ spatial:unit="um”> <spatial:boundaryMin spatial:id="Xmin" spatial:value="0"/> <spatial:boundaryMax spatial:id="Xmax" spatial:value="100"/> </spatial:coordinateComponent> <spatial:coordinateComponent spatial:id="y" spatial:type="cartesianY“ spatial:unit="um”> <spatial:boundaryMin spatial:id="Ymin" spatial:value="0"/> <spatial:boundaryMax spatial:id="Ymax" spatial:value="100"/> </spatial:coordinateComponent> </spatial:listOfCoordinateComponents> </spatial:geometry>



<parameter id="u_diff_X" value="0.02" constant="true”> <spatial:diffusionCoefficient spatial:variable="u" spatial:type=“isotropic"/> </parameter>

<species id="X" compartment="fish" initialConcentration="0“ substanceUnits="molecules" hasOnlySubstanceUnits="false“ boundaryCondition="false" constant="false" spatial:isSpatial="true“>

<reaction id="re2" name="re2" reversible="false" fast="false" spatial:isLocal="true"> <listOfReactants> <speciesReference species="X" stoichiometry="1" constant="true"/> </listOfReactants> . . .

Library Support



Software Support

VCell Reads/creates/writes/simulates


Arrays (arrays)

<species id=“A" compartment=“C" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false“> <arrays:listOfDimensions> <arrays:dimension arrays:size="n" arrays:arrayDimension="0"/> <arrays:dimension arrays:size="n" arrays:arrayDimension=1/> </arrays:listOfDimensions> </species>

Arrays (arrays)

<parameter id=“n“ value=“4” constant=“true”/>

<initialAssignment symbol=“A"> <arrays:listOfDimensions> <arrays:dimension arrays:id="i" arrays:size="n" arrays:arrayDimension="0"/> <arrays:dimension arrays:id=“j" arrays:size="n" arrays:arrayDimension="0"/> </arrays:listOfDimensions> <arrays:listOfIndices> <arrays:index arrays:referencedAttribute=“symbol" arrays:arrayDimension="0"> <math/></index> <arrays:index arrays:referencedAttribute=“symbol" arrays:arrayDimension=“1"> <math/></index> </arrays:listOfIndices> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <selector/> <ci> B </ci><ci> i </ci><ci> j </ci> </apply> </math>

Arrays (arrays)

A[i][j] = B[i][j]

Library Support



Software Support

iBioSim In development

Arrays (arrays)

Distributions (distrib)


<functionDefinition id="normal"> <math xmlns="http://www.w3.org/1998/Math/MathML">  <distrib:drawFromDistribution> <distrib:listOfDistribInputs> <distrib:distribInput distrib:id="arg1" distrib:index="0"/> <distrib:distribInput distrib:id="arg2" distrib:index="1"/> </distrib:listOfDistribInputs> <UncertML xmlns="http://www.uncertml.org/3.0"> <NormalDistribution definition="http://www.uncertml.org/distributions/normal"> <mean> <var varId="arg1"/> </mean> <variance> <var varId="arg2"/> </variance> </NormalDistribution> </UncertML> </distrib:drawFromDistribution> </functionDefinition>


<functionDefinition id="normal"> </functionDefinition>

<initialAssignment symbol="V"> <math xmlns="http://www.w3.org/1998/Math/MathML” <apply> <ci>normal</ci> <ci>V_pop</ci> <ci>V_omega</ci> </apply> </math> </initialAssignment>


<parameter id="V" constant="true"> <distrib:uncertainty distrib:id="un1"> <UncertML xmlns="http://www.uncertml.org/3.0"> <NormalDistribution definition="http://www.uncertml.org/distributions/normal"> <mean> <var varId="V_pop"/> </mean> <variance> <var varId="V_omega"/> </variance> </NormalDistribution> </UncertML> </distrib:uncertainty> </parameter>


Library Support


JSBML

Software Support

Groups (groups)

<species id="ATPc" compartment="cytosol" substanceUnits="mole" constant="false" hasOnlySubstanceUnits="false" boundaryCondition="true" /> <species id="ATPm" compartment="mitochon" substanceUnits="mole" constant="false" hasOnlySubstanceUnits="false" boundaryCondition="true" />

<groups:group groups:id="ATP" groups:kind="classification"> <groups:listOfMembers sboTerm="SBO:0000248"> <groups:member groups:idRef="ATPc" /> <groups:member groups:idRef="ATPm" /> </groups:listOfMembers>

Groups (groups)

<groups:listOfMemberConstraints groups:membersShareType="true"> <groups:memberConstraint groups:distinctAttribute="compartment" /> <groups:memberConstraint groups:identicalAttribute="constant" /> </groups:listOfMemberConstraints> </groups:group>

Library Support



Software Support

Groups (groups)

Required Elements (req)


<functionDefinition id="normal"> <math xmlns="http://www.w3.org/1998/Math/MathML">  <distrib:drawFromDistribution> <!– information about distribution --> <req:listOfChangedMaths> <req:changedMath req:changedBy=http://www.sbml.org/sbml/level3/version1/distrib/version1 req:viableWithoutChange="true" /> </req:listOfChangedMaths>

http://www.sbml.org/sbml/level3/version1/distrib/version1


<functionDefinition id="normal"> <math xmlns="http://www.w3.org/1998/Math/MathML">  <distrib:drawFromDistribution> <!– information about distribution --> <req:listOfChangedMaths> <req:changedMath req:changedBy=http://www.sbml.org/sbml/level3/version1/distrib/version1 req:viableWithoutChange="true" /> </req:listOfChangedMaths>

http://www.sbml.org/sbml/level3/version1/distrib/version1

Library Support



Software Support

SBML L3 Packages - brief overview and current status

Education