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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 Level 3 Packages
SBML Level 3 Packages
sbml.org/Documents/Specifications
#SBML_Level_3_Packages
SBML Level 3 Packages
SBML Level 3 Packages
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
SBML Level 3 Packages
model
submodel1
submodel2
enzyme
simple
Hierarchical Model Composition
(comp)
<comp:listOfModelDefinitions>
<comp:modelDefinition comp:id="enzyme">
<listOfCompartments> ...
<comp:modelDefinition comp:...
model
submodel1
submodel2
enzyme
simple
Hierarchical Model Composition
(comp)
<comp:listOfExternalModelDefinitions>
<comp:externalModelDefinition comp:id="ExtMod1“
comp:source="enzyme_model.xml"
comp:...
<listOfExternalModelDefinitions>
<comp:externalModelDefinition comp:id="ExtMod1“
comp:source="enzyme_model.xml"
comp:model...
<comp:submodel comp:id="B" comp:modelRef="simple">
<comp:listOfDeletions>
<comp:deletion comp:portRef="J0_port" comp:id="o...
Hierarchical Model Composition
(comp)
Hierarchical Model Composition
(comp)
Library Support
libSBML Version 1 Release 2
JSBML Version 1 Release 2
Software Suppo...
Flux Balance Constraints
(fbc)
<fbc:listOfFluxBounds>
<fbc:fluxBound fbc:reaction="R1" fbc:operation="lessEqual" fbc:value="1"/>
<fbc:fluxBound fbc:react...
<fbc:listOfObjectives fbc:activeObjective="objective1">
<fbc:objective fbc:id="objective1" fbc:type="maximize">
<fbc:listO...
<fbc:listOfObjectives fbc:activeObjective="objective1">
<fbc:objective fbc:id="objective1" fbc:type="maximize">
<fbc:listO...
<fbc:listOfObjectives fbc:activeObjective="objective1">
<fbc:objective fbc:id="objective1" fbc:type="maximize">
<fbc:listO...
Flux Balance Constraints
(fbc)
Library Support
libSBML Version 1
JSBML Version 1
Software Support
SBW Flux Balance Reads/c...
Qualitative Models
(qual)
<qual:listOfQualitativeSpecies>
<qual:qualitativeSpecies qual:compartment="cytosol" qual:constant="false"
qual:id="A" qual...
<qual:listOfFunctionTerms>
<qual:functionTerm qual:resultLevel="2">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<!--...
Qualitative Models
(qual)
Library Support
libSBML Version 1
JSBML Version 1
Software Support
GinSim Reads/creates/writes/s...
Layout
(layout)
Layout
(layout)
<listOfSpecies>
<species id=“Glucose" compartment="compartment" initialConcentration="0"
hasOnlySubstanceU...
Library Support
libSBML Version 1
JSBML Version 1
Software Support
COPASI Reads/creates/writes/displays
Online Viewer Read...
Rendering
(render)
text
text
<listOfSpecies>
<species id=“Glucose" compartment="compartment" initialConcentration="0"
hasOnlySubstanceUnits="false" bou...
Library Support
libSBML Latest specification
JSBML Latest specification
Software Support
COPASI Reads/creates/writes/displ...
Multistate and Multicomponent
species
(multi)
Multistate and Multicomponent sp
(multi)
stA
c1
B1
f1
c1
B2
f1
Multistate and Multicomponent sp
(multi)
<multi:speciesType multi:id=“st_c" />
<multi:speciesType multi:id=“st_f" />
<mult...
Multistate and Multicomponent sp
(multi)
<multi:speciesType multi:id="stA">
<multi:listOfSpeciesTypeInstances>
<multi:spec...
Library Support
libSBML Latest specification
JSBML Older specification
Software Support
Simmune Reads/creates/writes/
Virg...
Spatial processes
(spatial)
<spatial:geometry spatial:coordinateSystem=“cartesian">
<spatial:listOfCoordinateComponents>
<spatial:coordinateComponent ...
Spatial processes
(spatial)
<parameter id="u_diff_X" value="0.02" constant="true”>
<spatial:diffusionCoefficient spatial:v...
Library Support
libSBML Latest specification
JSBML Latest specification
Software Support
VCell Reads/creates/writes/simula...
Arrays
(arrays)
<species id=“A" compartment=“C" initialConcentration="0"
hasOnlySubstanceUnits="false" boundaryCondition="false" constant=...
<initialAssignment symbol=“A">
<arrays:listOfDimensions>
<arrays:dimension arrays:id="i" arrays:size="n" arrays:arrayDimen...
Library Support
libSBML Latest specification
JSBML Latest specification
Software Support
iBioSim In development
Arrays
(ar...
Distributions
(distrib)
Distributions
(distrib)
<functionDefinition id="normal">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<!-- math for u...
Distributions
(distrib)
<functionDefinition id="normal">
</functionDefinition>
<initialAssignment symbol="V">
<math xmlns=...
Distributions
(distrib)
<parameter id="V" constant="true">
<distrib:uncertainty distrib:id="un1">
<UncertML xmlns="http://...
Distributions
(distrib)
Library Support
libSBML Latest specification
JSBML
Software Support
Groups
(groups)
<species id="ATPc" compartment="cytosol" substanceUnits="mole" constant="false"
hasOnlySubstanceUnits="false" boundaryCond...
Library Support
libSBML Latest specification
JSBML Latest specification
Software Support
Groups
(groups)
Required Elements
(req)
Required Elements
(req)
<functionDefinition id="normal">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<!-- math for u...
Required Elements
(req)
<functionDefinition id="normal">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<!-- math for u...
Library Support
libSBML Latest specification
JSBML Latest specification
Software Support
Required Elements
(req)
SBML Level 3 Packages
SBML L3 Packages - brief overview and current status
SBML L3 Packages - brief overview and current status
SBML L3 Packages - brief overview and current status
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SBML L3 Packages - brief overview and current status

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An overview of the SBML L3 packages under development and their current status

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SBML L3 Packages - brief overview and current status

  1. 1. Sarah Keating SBML Level 3 Packages Status – July 2014
  2. 2. spatial qual Submodel 1 Submodel 2 comp layout core SBML Level 3 Packages Modular approach
  3. 3. SBML Level 3 Packages
  4. 4. SBML Level 3 Packages sbml.org/Documents/Specifications #SBML_Level_3_Packages
  5. 5. SBML Level 3 Packages
  6. 6. SBML Level 3 Packages
  7. 7. SBML Level 3 Packages
  8. 8. Status
  9. 9. Status Released  Specification document complete  Specification document approved  Two implementations
  10. 10. Status
  11. 11. Status SUBJECT TO CHANGE  Implementations being worked on  Specification document being worked on Draft available
  12. 12. Status
  13. 13. Status  Currently no activity  Package has been proposed Stalled
  14. 14. Status
  15. 15. Status Discussion
  16. 16. SBML Level 3 Packages
  17. 17. model submodel1 submodel2 enzyme simple Hierarchical Model Composition (comp)
  18. 18. <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> Hierarchical Model Composition (comp)
  19. 19. model submodel1 submodel2 enzyme simple Hierarchical Model Composition (comp)
  20. 20. <comp:listOfExternalModelDefinitions> <comp:externalModelDefinition comp:id="ExtMod1“ comp:source="enzyme_model.xml" comp:modelRef="enzyme"/> <model> ... <comp:listOfSubmodels> <comp:submodel comp:id="A" comp:modelRef="enzyme"/> <comp:submodel comp:id="B" comp:modelRef="simple“/> </comp:listOfSubmodels> </model> Hierarchical Model Composition (comp)
  21. 21. <listOfExternalModelDefinitions> <comp:externalModelDefinition comp:id="ExtMod1“ comp:source="enzyme_model.xml" comp:modelRef="enzyme"/> <model> ... <comp:listOfSubmodels> <comp:submodel comp:id="A" comp:modelRef="enzyme"/> <comp:submodel comp:id="B" comp:modelRef="simple“/> </comp:listOfSubmodels> </model> Hierarchical Model Composition (comp) Any URI
  22. 22. <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"/> Hierarchical Model Composition (comp)
  23. 23. Hierarchical Model Composition (comp)
  24. 24. Hierarchical Model Composition (comp) 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
  25. 25. Flux Balance Constraints (fbc)
  26. 26. <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 Flux Balance Constraints (fbc)
  27. 27. <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 Flux Balance Constraints (fbc)
  28. 28. <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 Flux Balance Constraints (fbc)
  29. 29. <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 Flux Balance Constraints (fbc)
  30. 30. Flux Balance Constraints (fbc) 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
  31. 31. Qualitative Models (qual)
  32. 32. <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> Qualitative Models (qual)
  33. 33. <qual:listOfFunctionTerms> <qual:functionTerm qual:resultLevel="2"> <math xmlns="http://www.w3.org/1998/Math/MathML"> <!-- (A >= 1 and A < 2) or C < 1 --> <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"> <!-- (A < 1) and C >= 1 --> <qual:defaultTerm qual:resultLevel="0"/> Qualitative Models (qual)
  34. 34. Qualitative Models (qual) 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
  35. 35. Layout (layout)
  36. 36. 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>
  37. 37. Library Support libSBML Version 1 JSBML Version 1 Software Support COPASI Reads/creates/writes/displays Online Viewer Reads/displays SBW Reads/displays Layout (layout)
  38. 38. Rendering (render) text text
  39. 39. <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“>
  40. 40. Library Support libSBML Latest specification JSBML Latest specification Software Support COPASI Reads/creates/writes/displays Online Viewer Reads/displays SBW Reads/displays Rendering (render)
  41. 41. Multistate and Multicomponent species (multi)
  42. 42. Multistate and Multicomponent sp (multi) stA c1 B1 f1 c1 B2 f1
  43. 43. Multistate and Multicomponent sp (multi) <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
  44. 44. Multistate and Multicomponent sp (multi) <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
  45. 45. Library Support libSBML Latest specification JSBML Older specification Software Support Simmune Reads/creates/writes/ Virginia Tech Multistate and Multicomponent sp (multi)
  46. 46. Spatial processes (spatial)
  47. 47. <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> Spatial processes (spatial)
  48. 48. Spatial processes (spatial) <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> . . .
  49. 49. Library Support libSBML Latest specification JSBML Latest specification Software Support VCell Reads/creates/writes/simulates Spatial processes (spatial)
  50. 50. Arrays (arrays)
  51. 51. <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”/>
  52. 52. <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]
  53. 53. Library Support libSBML Latest specification JSBML Latest specification Software Support iBioSim In development Arrays (arrays)
  54. 54. Distributions (distrib)
  55. 55. Distributions (distrib) <functionDefinition id="normal"> <math xmlns="http://www.w3.org/1998/Math/MathML"> <!-- math for use if distrib is ignored --> <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>
  56. 56. Distributions (distrib) <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>
  57. 57. Distributions (distrib) <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>
  58. 58. Distributions (distrib) Library Support libSBML Latest specification JSBML Software Support
  59. 59. Groups (groups)
  60. 60. <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>
  61. 61. Library Support libSBML Latest specification JSBML Latest specification Software Support Groups (groups)
  62. 62. Required Elements (req)
  63. 63. Required Elements (req) <functionDefinition id="normal"> <math xmlns="http://www.w3.org/1998/Math/MathML"> <!-- math for use if distrib is ignored --> <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>
  64. 64. Required Elements (req) <functionDefinition id="normal"> <math xmlns="http://www.w3.org/1998/Math/MathML"> <!-- math for use if distrib is ignored --> <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>
  65. 65. Library Support libSBML Latest specification JSBML Latest specification Software Support Required Elements (req)
  66. 66. SBML Level 3 Packages

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