SBML (the Systems Biology Markup Language), BioModels Database, and related resources

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Slides from presentation given at the Computational Cell Biology Summer School, 2011, at Cold Spring Harbor Laboratory in New York, USA, July 2011.

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SBML (the Systems Biology Markup Language), BioModels Database, and related resources

  1. 1. SBML (the Systems Biology Markup Language), BioModels Database, and related resources Michael Hucka, Ph.D. (On behalf of many people) California Institute of Technology Pasadena, California, USAFriday, July 15, 2011 2
  2. 2. Background and context Overview of SBML Survey of some software resources for SBML Related efforts Acknowledgements RoadmapFriday, July 15, 2011 3
  3. 3. Background and context Overview of SBML Survey of some software resources for SBML Related efforts Acknowledgements RoadmapFriday, July 15, 2011 4
  4. 4. Must weave solutions using different methods & toolsFriday, July 15, 2011 5
  5. 5. Need effective sharing of models Not enough simply to publish lists of equations! Need a software-independent format • No single package answers all needs • New techniques ( new tools) are developed continuously • Different packages have different niche strengths - Strengths are often complementary Need to capture both • Mathematical content of a model • Semantic content of a modelFriday, July 15, 2011 6
  6. 6. Goal: reproducible and reusable models and simulationsFriday, July 15, 2011 7
  7. 7. Background and context Overview of SBML Survey of some software resources for SBML Related efforts Acknowledgements RoadmapFriday, July 15, 2011 8
  8. 8. SBML = Systems Biology Markup Language Format for representing quantitative models • Defines object model + rules for its use - Serialized to XML Neutral with respect to modeling framework • ODE vs. stochastic vs. ... A lingua franca for software • Not proceduralFriday, July 15, 2011 9
  9. 9. Basic SBML concepts are simple The reaction is central: a process occurring at a given rate • Participants are pools of entities (species) f ([A],[B],[P ],...) na A + nb B − − − − − − → np P −−−−−− f (...) nc C −− −→ nd D + ne E + nf F . . . Models can further include: • Other constants & variables • Unit definitions • Compartments • Annotations • Explicit math • Discontinuous eventsFriday, July 15, 2011 10
  10. 10. Basic SBML concepts are simple The reaction is central: a process occurring at a given rate • Participants are pools of entities (species) Can be anything conceptually f ([A],[B],[P ],...) na A + nb B − − − − − − → np P −−−−−− compatible f (...) nc C −− −→ nd D + ne E + nf F . . . Models can further include: • Other constants & variables • Unit definitions • Compartments • Annotations • Explicit math • Discontinuous eventsFriday, July 15, 2011 10
  11. 11. Some basics of SBML core model encoding ๏ Well-stirred compartments c nFriday, July 15, 2011 11
  12. 12. Some basics of SBML core model encoding c protein A protein B n gene mRNAn mRNAcFriday, July 15, 2011 12
  13. 13. Some basics of SBML core model encoding ๏ Reactions can involve any species anywhere c protein A protein B n gene mRNAn mRNAcFriday, July 15, 2011 13
  14. 14. Some basics of SBML core model encoding ๏ Reactions can cross compartment boundaries c protein A protein B n gene mRNAn mRNAcFriday, July 15, 2011 14
  15. 15. Some basics of SBML core model encoding ๏ Reaction/process rates can be (almost) arbitrary formulas c protein A f1(x) protein B n f5(x) f2(x) gene f4(x) mRNAn f3(x) mRNAcFriday, July 15, 2011 15
  16. 16. Some basics of SBML core model encoding ๏ “Rules”: equations expressing relationships in addition to reaction sys. g1(x) c g2(x) protein A f1(x) protein B . . . n f5(x) f2(x) gene f4(x) mRNAn f3(x) mRNAcFriday, July 15, 2011 16
  17. 17. Some basics of SBML core model encoding ๏ “Events”: discontinuous actions triggered by system conditions g1(x) c g2(x) protein A f1(x) protein B . . . n f5(x) f2(x) gene f4(x) mRNAn f3(x) mRNAc Event1: when (...condition...), Event2: when (...condition...), ... do (...assignments...) do (...assignments...)Friday, July 15, 2011 17
  18. 18. Some basics of SBML core model encoding “This is identified by “This is an enzymatic c g1(x) GO id # ...” reaction with EC # ...” g2(x) . protein A f1(x) protein B . “This is a transport . n into the nucleus ...” “This compartment represents the nucleus ...” f5(x) f2(x) gene f4(x) mRNAn f3(x) mRNAc “This event represents ...” Event1: when (...condition...), Event2: when (...condition...), ... do (...assignments...) do (...assignments...)Friday, July 15, 2011 18
  19. 19. Signaling pathway models Fernandez et al. (2006) DARPP-32 Is a Robust Integrator of Dopamine and Glutamate Signals PLoS Computational Biology BioModels Database model #BIOMD0000000153 Scope of SBML is not limited to one kind of modelFriday, July 15, 2011 19
  20. 20. Signaling pathway models Hodgkin & Huxley (1952) A quantitative description of Conductance-based models membrane current and its • application to conduction and “Rate rules” for temporal evolution excitation in nerve of quantitative parameters J. Physiology 117:500–544 BioModels Database model #BIOMD0000000020 Scope of SBML is not limited to one kind of modelFriday, July 15, 2011 20
  21. 21. Signaling pathway models Izhikevich EM. (2003) Simple model of spiking neurons. Conductance-based models IEEE Trans Neural Net. • “Rate rules” for temporal evolution of quantitative parameters BioModels Database model #BIOMD0000000127 Neural models • “Events” for discontinuous changes in quantitative parameters Scope of SBML is not limited to one kind of modelFriday, July 15, 2011 21
  22. 22. Signaling pathway models Tham et al. (2008) A pharmacodynamic model for Conductance-based models the time course of tumor shrinkage by gemcitabine + • “Rate rules” for temporal evolution of quantitative parameters carboplatin in non-small cell lung cancer patients Clin. Cancer Res. 14 Neural models BioModels Database model • “Events” for discontinuous changes in quantitative parameters #BIOMD0000000234 Pharmacokinetic/dynamics models • “Species” is not required to be a biochemical entity Scope of SBML is not limited to one kind of modelFriday, July 15, 2011 22
  23. 23. Signaling pathway models Munz et al. (2009 ) Conductance-based models When zombies attack!: Mathematical modelling of an • “Rate rules” for temporal evolution of quantitative parameters outbreak of zombie infection Infectious Disease Modelling Research Progress, eds. Tchuenche et al., p. 133–150 Neural models • “Events” for discontinuous changes in quantitative parameters BioModels Database model #MODEL1008060001 Pharmacokinetic/dynamics models • “Species” is not required to be a biochemical entity Infectious diseases Scope of SBML is not limited to one kind of modelFriday, July 15, 2011 23
  24. 24. Number of software systems supporting SBML 300 229 as of July 14 ↓ 200 100 0 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 (counted in middle of each year)Friday, July 15, 2011 24
  25. 25. What are SBML “Levels”? Specification document available from http://sbml.org/Documents Newest: Level 3 Version 1 Core • Oct. 2010 About SBML “Levels”: • Levels help manage significant restructuring of SBML architecture • Levels coexist - E.g., Level 2 models will remain valid and exist for a long time • A Level is not solely a vertical change (i.e., more features)—there is horizontal change too (i.e., changes to existing elements)Friday, July 15, 2011 25
  26. 26. SBML continues to evolveFriday, July 15, 2011 26
  27. 27. SBML Level 3—A modular SBML Package Z Package X Package Y SBML Level 3 Core A package adds constructs & capabilities Models declare which packages they use • Applications tell users which packages they support Package development can be decoupledFriday, July 15, 2011 27
  28. 28. Package Specification status Graph layout Level 3 version defined; in review Multicomponent species Level 3 version defined; in review Hierarchical composition Level 3 specification under discussion Groups Level 3 specification under discussion Qualitative models Level 3 specification under discussion Spatial geometry Level 3 specification under discussion Arrays & sets Specification proposed Distribution & ranges Specification proposed Steady-state models Specification proposed Graph rendering Specification proposed Spatial diffusion Specification needed Dynamic structures Specification neededFriday, July 15, 2011 28
  29. 29. Package Specification status Graph layout Level 3 version defined; in review Multicomponent species Level 3 version species to represent: Extends SBML defined; in review • Entities that can exist under Hierarchical composition Level 3 specification under discussion different states affecting their Groups behaviors Level 3 specification under discussion • Entities that are complexes of Qualitative models Level 3 specification under discussion other entities Spatial geometry Level 3 specification under discussion Arrays & sets Specification proposed Distribution & ranges Specification proposed Steady-state models Specification proposed Graph rendering Specification proposed Spatial diffusion Specification needed Dynamic structures Specification neededFriday, July 15, 2011 28
  30. 30. Package Specification status Graph layout Level 3 version defined; in review Multicomponent species Level 3 version defined; in review Hierarchical composition Models composed of submodels Level 3 specification under discussion Groups Level 3 specification under discussion Qualitative models Level 3 specification under discussion Spatial geometry Level 3 specification under discussion Arrays & sets Specification proposed Distribution & ranges Specification proposed Steady-state models Specification proposed Graph rendering Specification proposed Spatial diffusion Specification needed Dynamic structures Specification neededFriday, July 15, 2011 28
  31. 31. Package Specification status Graph layout Level 3 version defined; in review Multicomponent species Level 3 version defined; in review Hierarchical composition Level 3 specification under discussion Grouping model entities together, Groups Level 3 specification under discussion for conceptual and annotation Qualitative models Level 3 specification under discussion purposes Spatial geometry Level 3 specification under discussion Arrays & sets Specification proposed Distribution & ranges Specification proposed Steady-state models Specification proposed Graph rendering Specification proposed Spatial diffusion Specification needed Dynamic structures Specification neededFriday, July 15, 2011 28
  32. 32. Package Specification status Graph layout Level 3 version defined; in review Multicomponent species Level 3 version defined; in review Hierarchical composition Level 3 specification under discussion Groups Level 3 specification under discussion Models in which entity variables are Qualitative models Levelquantities; e.g., boolean models not 3 specification under discussion Spatial geometry Level 3 specification under discussion Arrays & sets Specification proposed Distribution & ranges Specification proposed Steady-state models Specification proposed Graph rendering Specification proposed Spatial diffusion Specification needed Dynamic structures Specification neededFriday, July 15, 2011 28
  33. 33. Package Specification status Graph layout Level 3 version defined; in review Multicomponent species Level 3 version defined; in review Hierarchical composition Level 3 specification under discussion Groups Level 3 specification under discussion Qualitative models Level 3 specification under discussion 2-D and 3-D geometry of physical Spatial geometry Level 3 specification under discussion objects (compartments & species) Arrays & sets Specification proposed Distribution & ranges Specification proposed Steady-state models Specification proposed Graph rendering Specification proposed Spatial diffusion Specification needed Dynamic structures Specification neededFriday, July 15, 2011 28
  34. 34. Example: Hierarchical Model Composition Current SBML Model “A” Compartments ... Species ... Parameters ... Reactions ...Friday, July 15, 2011 29
  35. 35. Example: Hierarchical Model Composition Current SBML With model composition Model “A” Model “A” Compartments ... Compartments ... Species ... Species ... Parameters ... Parameters ... Reactions ... Reactions ... Model “B” Model “C” Compartments ... Compartments ... Species ... Species ... Parameters ... Parameters ... Reactions ... Reactions ...Friday, July 15, 2011 29
  36. 36. More scenarios Model “A” Compartments ... Species ... Parameters ... Reactions ... Model “B” Model “B” Model “B” Compartments ... Compartments ... Compartments ... Species ... Species ... Species ... Parameters ... Parameters ... Parameters ... ... Reactions ... Reactions ... Reactions ...Friday, July 15, 2011 30
  37. 37. More scenarios Model “A” Compartments ... Species ... Parameters ... Reactions ... Model “B” Model “C” Compartments ... Compartments ... Model “D” Species ... Species ... Compartments ... Parameters ... Parameters ... Species ... Reactions ... Reactions ... Parameters ... Reactions ...Friday, July 15, 2011 31
  38. 38. More scenarios Separate files/resources Model “A” Compartments ... Model “B” Species ... Compartments ... Parameters ... Species ... Model “C” Reactions ... Parameters ... Compartments ... Reactions ... Species ... Model “B” Parameters ... Model “C” Reactions ... Model “D” Model “D” Compartments ... Think: Species ... libraries of Parameters ... well-tested Reactions ... modelsFriday, July 15, 2011 32
  39. 39. Links/references/replacements Model “outer” Model “inner” S1 S2 Compartment “c” X1 X2 Compartment “q”Friday, July 15, 2011 33
  40. 40. Links/references/replacements Model “outer” Model “inner” S1 S2 Compartment “c” X1 X2 Compartment “q” Implied model Model “outer” S1 S2 inner/X2 Compartment “c”Friday, July 15, 2011 33
  41. 41. Background and context Overview of SBML Survey of some software resources for SBML Related efforts Acknowledgements RoadmapFriday, July 15, 2011 34
  42. 42. SBML.orgFriday, July 15, 2011 35
  43. 43. SBML Software GuideFriday, July 15, 2011 36
  44. 44. SBML Software Guide Find SBML softwareFriday, July 15, 2011 36
  45. 45. SBML Software GuideFriday, July 15, 2011 37
  46. 46. Some particularly full-featured, general simulation tools COPASI: ODE & stochastic simulation, parameter scanning, powerful plotting capabilities, much more CellDesigner: graphical editing interface, SBGN support, SABIO-RK integration, much more iBioSim: special features for genetic circuit models for synthetic biology Virtual Cell: web-based interface roadRunner & SBW: .NET support, many tools in toolkitFriday, July 15, 2011 38
  47. 47. Online SBML ValidatorFriday, July 15, 2011 39
  48. 48. Online SBML ValidatorFriday, July 15, 2011 39
  49. 49. Online SBML ValidatorFriday, July 15, 2011 40
  50. 50. Online SBML Validator Validate SBML filesFriday, July 15, 2011 40
  51. 51. (demo) (Demo)Friday, July 15, 2011 41
  52. 52. How to keep in touchFriday, July 15, 2011 42
  53. 53. How to keep in touch Front-page newsFriday, July 15, 2011 42
  54. 54. Twitter & RSS feeds How to keep in touchFriday, July 15, 2011 42
  55. 55. How to keep in touch Mailing lists/forumsFriday, July 15, 2011 42
  56. 56. Suggest subscribing to sbml-announce (it’s very low volume) SBML mailing lists & online forum interfaceFriday, July 15, 2011 43
  57. 57. Software API libraries: libSBML & JSBMLFriday, July 15, 2011 44
  58. 58. libSBML ๏ Reads, writes, validates SBML Latest stable version: 5.0.0 • Hundreds of rules for helping http://sbml.org/Software/libSBML to ensure correct SBML ๏ Unit checking & conversion ๏ Well-tested ๏ Written in portable C++ • Linux, Mac, Windows, FreeBSD ๏ APIs for C, C++, C#, Java, Octave, Perl, Python, Ruby, MATLAB (some via SWIG) ๏ Developed by Sarah Keating, ๏ Can use Expat, libxml2, or Frank Bergman, Ben Bornstein, Xerces Akiya Jouraku, & Mike Hucka, with substantial contributions ๏ Open-source under LGPL from many other peopleFriday, July 15, 2011 45
  59. 59. JSBML Pure Java implementation API is highly compatible with libSBML • Functionality is subset of libSBML functionality Under active development • Already in use in apps • Help welcome! Main developers: Andreas Dräger & Nicolas RodriguezFriday, July 15, 2011 46
  60. 60. BioModels DatabaseFriday, July 15, 2011 47
  61. 61. http://biomodels.net/biomodelsFriday, July 15, 2011 48
  62. 62. Features of BioModels Database Stores & serves quantitative models of biological interest • Free, public resource • Models must be described in peer-reviewed publication(s) All models are curated by hand to reproduce published results Imports & exports models in several formats • SBML, CellML, SciLab, XPP, BioPAX Developed by Nicolas Le Novère’s group (EBI), funded by EBI & NIH Today: 600+ modelsFriday, July 15, 2011 49
  63. 63. (demo)Friday, July 15, 2011 50
  64. 64. Background and context Overview of SBML Survey of some software resources for SBML Related efforts Acknowledgements RoadmapFriday, July 15, 2011 51
  65. 65. Growing community, greater challengesFriday, July 15, 2011 52
  66. 66. Model Procedures Results Representation format SBRML Minimal info ? requirements Semantics— Mathematical Other annotations annotations annotationsFriday, July 15, 2011 53
  67. 67. Model Procedures Results Representation format SBRML Minimal info ? requirements Semantics— Mathematical Other annotations annotations annotationsFriday, July 15, 2011 53
  68. 68. Annotations add semantics and connections Annotations can answer questions: • “What exactly is this entity you call X?” • “What other identities does this entity have?” • “What exactly is the process represented by equation ‘e17’?” • “What role does constant ‘k3’ play in equation ‘e17’?” • “What mathematical framework is being assumed?” • “What organism is this in?” • ... etc. ... Multiple annotations on same entity are commonFriday, July 15, 2011 54
  69. 69. Systems Biology Ontology (SBO) For semantics of a model’s math Human- & program-accessible • Browser interface • Web services Math formulas in MathMLFriday, July 15, 2011 55
  70. 70. Systems Biology Ontology (SBO) For semantics of a model’s math Human- & program-accessible • Browser interface • Web services Math formulas in MathMLFriday, July 15, 2011 55
  71. 71. Systems Biology Ontology (SBO) For semantics of a model’s math Human- & program-accessible • Browser interface • Web services Math formulas in MathMLFriday, July 15, 2011 55
  72. 72. <sbml ...> ... <listOfCompartments> <compartment id="cell" size="1e-15" /> </listOfCompartments> <listOfSpecies> <species compartment="cell" id="S1" initialAmount="1000" /> <species compartment="cell" id="S2" initialAmount="0" /> <listOfSpecies> <listOfParameters> <parameter id="k" value="0.005" sboTerm="SBO:0000339" /> <listOfParameters> <listOfReactions> <reaction id="r1" reversible="false"> <listOfReactants> <speciesReference species="S1" stoichiometry="2" sboTerm="SBO:0000010" /> </listOfReactants> <listOfProducts> <speciesReference species="S1" stoichiometry="2" sboTerm="SBO:0000011" /> </listOfProducts> <kineticLaw sboTerm="SBO:0000052"> <math> ... <math> ... </sbml>Friday, July 15, 2011 56
  73. 73. <sbml ...> ... <listOfCompartments> <compartment id="cell" size="1e-15" /> </listOfCompartments> <listOfSpecies> <species compartment="cell" id="S1" initialAmount="1000" /> <species compartment="cell" id="S2" initialAmount="0" /> <listOfSpecies> <listOfParameters> <parameter id="k" value="0.005" sboTerm="SBO:0000339" /> SBO:0000339 <listOfParameters> <listOfReactions> <reaction id="r1" reversible="false"> <listOfReactants> <speciesReference species="S1" stoichiometry="2" sboTerm="SBO:0000010" /> </listOfReactants> <listOfProducts> <speciesReference species="S1" stoichiometry="2" sboTerm="SBO:0000011" /> </listOfProducts> <kineticLaw sboTerm="SBO:0000052"> <math> ... <math> ... </sbml>Friday, July 15, 2011 56
  74. 74. <sbml ...> ... <listOfCompartments> <compartment id="cell" size="1e-15" /> </listOfCompartments> <listOfSpecies> <species compartment="cell" id="S1" initialAmount="1000" /> <species compartment="cell" id="S2" initialAmount="0" /> <listOfSpecies> <listOfParameters> <parameter id="k" value="0.005" sboTerm="SBO:0000339" /> SBO:0000339 <listOfParameters> <listOfReactions> <reaction id="r1" reversible="false"> <listOfReactants> <speciesReference species="S1" stoichiometry="2" sboTerm="SBO:0000010" /> </listOfReactants> <listOfProducts> <speciesReference species="S1" stoichiometry="2" sboTerm="SBO:0000011" /> </listOfProducts> <kineticLaw sboTerm="SBO:0000052"> <math> ... <math> ... </sbml> “forward bimolecular rate constant, continuous case”Friday, July 15, 2011 56
  75. 75. What is MIRIAM? MIRIAM = “Minimum Information Requested In the Annotation of Models” Addresses 2 general areas Requirements for reference Scheme for encoding correspondence annotations Annotations for Annotations for attributing model referring to external creators & sources data resources MIRIAM is not specific to SBMLFriday, July 15, 2011 57
  76. 76. What is MIRIAM? MIRIAM = “Minimum Information Requested In the Annotation of Models” Addresses 2 general areas Requirements for reference Scheme for encoding correspondence annotations Annotations for Annotations for attributing model referring to external creators & sources data resources MIRIAM is not specific to SBMLFriday, July 15, 2011 57
  77. 77. Model Entity element referenced relationship qualifier (optional) MIRIAM cross-references are simple triples { Data type identifier Data item identifier Annotation qualifier } (Required) (Required) (Optional) Format: URI chosen from Syntax & value space Controlled agreed-upon list depends on data type vocabulary termFriday, July 15, 2011 58
  78. 78. Why worry about standard ways of writing annotations? Structured, machine-readable annotations increase your model’s utility • Allow more precise identification of model components - Understand model structure - Compare models - Integrate models - Search models • Adds a semantic layer—integrates knowledge into the model - Understand the underlying biology - Reuse models - Convert models to other formsFriday, July 15, 2011 59
  79. 79. Annotations permit inter-database linkingFriday, July 15, 2011 60
  80. 80. Annotations permit inter-database linkingFriday, July 15, 2011 60
  81. 81. SBML defines a syntax for annotations <species metaid="metaid_0000009" id="species_3" compartment="c_1"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" > <rdf:Description rdf:about="#metaid_0000009"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:obo.chebi:CHEBI%3A15996"/> <rdf:li rdf:resource="urn:miriam:kegg.compound:C00044"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> </species>Friday, July 15, 2011 61
  82. 82. SBML defines a syntax for annotations <species metaid="metaid_0000009" id="species_3" compartment="c_1"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" > <rdf:Description rdf:about="#metaid_0000009"> <bqbiol:is> Data references <rdf:Bag> <rdf:li rdf:resource="urn:miriam:obo.chebi:CHEBI%3A15996"/> <rdf:li rdf:resource="urn:miriam:kegg.compound:C00044"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> </species>Friday, July 15, 2011 61
  83. 83. SBML defines a syntax for annotations <species metaid="metaid_0000009" id="species_3" compartment="c_1"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" > <rdf:Description rdf:about="#metaid_0000009"> <bqbiol:is> Relationship qualifier <rdf:Bag> <rdf:li rdf:resource="urn:miriam:obo.chebi:CHEBI%3A15996"/> <rdf:li rdf:resource="urn:miriam:kegg.compound:C00044"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> </species>Friday, July 15, 2011 61
  84. 84. “Term #1.1.1.1 (alcohol dehydrogenase) in the Enzyme Commission’s Enzyme Nomenclature database” urn:miriam:ec-code:1.1.1.1 { { URN scheme established Chosen by the creator of the by the MIRIAM project entry in MIRIAM ResourcesFriday, July 15, 2011 62
  85. 85. MIRIAM Resources provides URI dictionary & resolver http://www.ebi.ac.uk/miriam Community-maintainedFriday, July 15, 2011 63
  86. 86. MIRIAM Resources provides URI dictionary & resolver http://www.ebi.ac.uk/miriam Community-maintainedFriday, July 15, 2011 63
  87. 87. MIRIAM identifiers now in use by many other projects Data resources Application software • BioModels Database (kinetic models) • ARCADIA • PSI Consortium (protein interaction) • BioUML • Reactome (pathways) • COPASI • Pathway Commons (pathways) • libAnnotationSBML • libSBML • SABIO-RK (reaction kinetics) • Saint • Yeast consensus model database • SBML2BioPAX • E-MeP (structural genomics) • SBML2LaTeX • SBMLeditor • semanticSBML • Snazer • SBW • The Virtual CellFriday, July 15, 2011 64
  88. 88. Annotations enable many interesting possibilities http://www.semanticsbml.orgFriday, July 15, 2011 65
  89. 89. Model Procedures Results Representation format SBRML Minimal info ? requirements Semantics— Mathematical Other annotations annotations annotationsFriday, July 15, 2011 66
  90. 90. Model Procedures Results Representation format SBRML Minimal info ? requirements Semantics— Mathematical Other annotations annotations annotationsFriday, July 15, 2011 66
  91. 91. <sbml ...> ... <listOfCompartments> <compartment id="cell" size="1e-15" /> </listOfCompartments> <listOfSpecies> ? <species compartment="cell" id="S1" initialAmount="1000" /> <species compartment="cell" id="S2" initialAmount="0" /> <listOfSpecies> <listOfParameters> <parameter id="k" value="0.005" sboTerm="SBO:0000339" /> <listOfParameters> <listOfReactions> <reaction id="r1" reversible="false"> <listOfReactants> <speciesReference species="S1" stoichiometry="2" sboTerm="SBO:0000010" /> ... SED-ML = Simulation Experiment Description ML Application-independent format Captures procedures, algorithms, parameter values • Steps to go from model to output libSedML project developing API libraryFriday, July 15, 2011 67
  92. 92. Background and context Overview of SBML Survey of some software resources for SBML Related efforts Acknowledgements RoadmapFriday, July 15, 2011 68
  93. 93. People on SBML Team & BioModels Team SBML Team BioModels.net Team Michael Hucka Nicolas Le Novère Sarah Keating Camille Laibe Frank Bergmann Nicolas Rodriguez Lucian Smith Nick Juty Nicolas Rodriguez Vijayalakshmi Chelliah Linda Taddeo Michael Schubert Akiya Joukarou Lukas Endler Akira Funahashi Chen Li Kimberley Begley Harish Dharuri Bruce Shapiro Lu Li Andrew Finney Enuo He Ben Bornstein Mélanie Courtot Ben Kovitz Alexander Broicher Hamid Bolouri Arnaud Henry Herbert Sauro Visionaries Marco Donizelli Jo Matthews Hiroaki Kitano Maria Schilstra John DoyleFriday, July 15, 2011 69
  94. 94. National Institute of General Medical Sciences (USA) European Molecular Biology Laboratory (EMBL) ELIXIR (UK) Beckman Institute, Caltech (USA) Keio University (Japan) JST ERATO Kitano Symbiotic Systems Project (Japan) (to 2003) National Science Foundation (USA) International Joint Research Program of NEDO (Japan) JST ERATO-SORST Program (Japan) Japanese Ministry of Agriculture Japanese Ministry of Educ., Culture, Sports, Science and Tech. BBSRC (UK) DARPA IPTO Bio-SPICE Bio-Computation Program (USA) Air Force Office of Scientific Research (USA) STRI, University of Hertfordshire (UK) Molecular Sciences Institute (USA)Agencies to thank for supporting SBML & BioModels.netFriday, July 15, 2011 70
  95. 95. Where to find out more SBML http://sbml.org libSBML & JSBML http://sbml.org/Software BioModels Database http://biomodels.net/biomodels MIRIAM http://biomodels.net/miriam SED-ML http://biomodels.net/sed-ml SBO http://biomodels.net/sbo KiSAO http://www.ebi.ac.uk/compneur-srv/kisao/ TEDDY http://www.ebi.ac.uk/compneur-srv/teddy/ Thank you for listening!Friday, July 15, 2011 71

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