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sbpax SW 4 HCLS Aug 28 2012

SBPAX : Turning Bio Knowledge into Math Models, Automated. Oliver Ruebenacker (PanGenX) SW 4 HCLS, Tue, Aug 28, 2012 www.sbpax.org. www.sbpax.org SW 4 HCLS Aug 28 2012. Biological Pathway Exchange (BioPAX, www.biopax.org). Molecular Pathways in OWL :

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sbpax SW 4 HCLS Aug 28 2012

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  1. SBPAX: Turning Bio Knowledge into Math Models, Automated Oliver Ruebenacker (PanGenX)SW 4 HCLS, Tue, Aug 28, 2012www.sbpax.org www.sbpax.org SW 4 HCLS Aug 28 2012

  2. Biological Pathway Exchange (BioPAX, www.biopax.org) • Molecular Pathways in OWL: • Physical Entities (Protein, DNA, RNA, Complex, Small Molecule), Interactions (Conversion, Control, etc.), States (Phosphorylations, etc.) • Cross-references to DBs (molecules, functions, publications, etc) • Genes, provenance, evidence, etc. • Versions: Level 3 (2010), Level 4 in progress • Governance: community, elected editors • Tools: PaxTools, Online Validator, Cytoscape Plugin • Interoperability: Combine Core Standard www.sbpax.org SW 4 HCLS Aug 28 2012

  3. Qualitative Bio Knowledge on Web • Pathway Commons(BioPAX Level 2): • BioGRID, MSKCC Cancer Cell Map, HPRD, HumanCyc, SBCNY, IntAct, MINT, NCI/Nature PID, Reactome • 1,623 pathways, 585,000 interactions, 106,000 physical entities, 564 organisms • BioPAX Level 3 being tested • UniProt: 531,473 SwissProt, 16,504,022 TrEMBL • ChEBI: 26,091 entries • NCBI Taxonomy: 814,119 taxons • Foundational Model of Anatomy: 120,000+ terms www.sbpax.org SW 4 HCLS Aug 28 2012

  4. Systems Biology Pathway Exchange (SBPAX, www.sbpax.org) • Integrated with BioPAX classes • Extension to BioPAX L3 as SBPAX3 • Proposal for BioPAX L4 • Arranges Systems Biology terms (e.g. Systems Biology Ontology), numbers and units into hierarchies • Units based on Units of Measurement Expressions (UOME) www.sbpax.org SW 4 HCLS Aug 28 2012

  5. Systems Biology Ontology (SBO) • Project by BioModels.net, curator Nick Juty • Comprehensive collection of SB-relevant terms, hierarchical • Includes terms for many rate laws, parameters and quantities • For rate laws, includes math expression and references to SBO terms of the parameters (e.g. term for Michaelis-Menten rate law refers to term for Michaelis constant) www.sbpax.org SW 4 HCLS Aug 28 2012

  6. Units of Measurement Expressions (UOME) • UOME core: ontology to define units: • By scaling, exponentiation, offset, product or quotient of other units • By reference to controlled vocabulary (e.g. UO) • UOME list: long list of predefined units (e.g. micro mole per milligram per minute) • Can convert to SBML/VCell units www.sbpax.org SW 4 HCLS Aug 28 2012

  7. Quantitative Bio Knowledge on Web • SABIO-RK: SBML export, rich on SBO; implemented BioPAX L3, SBPAX3 export; • Signaling Gateway Molecule Pages: 672 curated pages (interactions), large diversity of quantitative values, BioPAX L3 and SBPAX3 export • MetaCyc, EcoCyc: collecting enzymatic rate constants; SBML, BioPAX L3 export; SBPAX3 interest; www.sbpax.org SW 4 HCLS Aug 28 2012

  8. Virtual Cell • Time-course simulations: • Deterministic or stochastic • Spatial or compartmental • Physiological Model: • Compartments (e.g. anatomical structures) • Abundancies (e.g. concentrations / molecule numbers) • Processes (e.g. chemical reactions) • Can be converted to math model • Math Model: • General differential equations • Openness: • Open source, MIT- licensed www.sbpax.org SW 4 HCLS Aug 28 2012

  9. Virtual Cell Architecture Client: Java app + native libs (Win, Linux, Mac) Start from Web (JNLP) Some standalone capacity Talks to Server Server: Java, spawns solver processes, talks to database Database: Oracle (any SQL would do) Solvers: Processes run on cluster Mostly C++ www.sbpax.org SW 4 HCLS Aug 28 2012

  10. Bob's Theory • Question: How do FUD, BBL, OMG interact? • Bob the Biologisthas a theory • Now he needs to test it (simulation!) FUD FUD FUD LOL IMHO ? ? ? OMG OMG BBL BBL Bob the Biologist The Question Bob's Theory www.sbpax.org SW 4 HCLS Aug 28 2012

  11. A realistic Model for Bob's Theory • For realistic simulation, need some context Bob's Theory (new exciting research) The Context (stuff everyone knows already) www.sbpax.org SW 4 HCLS Aug 28 2012

  12. Trends • Biological Details → Complete Knowledge • Knowledge → Computer-processable • Knowledge → Public • Computers → Much faster • Bio Models → Complete Biochem Details • Model Building → Automatic • Model Builder → Knowledgebase Frontend www.sbpax.org SW 4 HCLS Aug 28 2012

  13. Bio Knowledge from Web into VCell • Systems Biology Linker (SyBiL) at VCell: Grab Bio Knowledge from Web to build and annotate models • Qualitative: Queries Pathway Commons, UniProt, ChEBI; imports BioPAX (since years) • Quantitiative: SBPAX3 from SGMP, SABIO-RK www.sbpax.org SW 4 HCLS Aug 28 2012

  14. Same Reality  Many Models Model = Biology + Method • Biology: biological reality; qualitative + quantitative; general + specific (  BioPAX, SBPAX) • Method: cropping, filtering, merging, requirements, assumptions, simplifications, omissions, artifacts (  SED-ML) • Model: Math ( SBML, VCML, CellML) www.sbpax.org SW 4 HCLS Aug 28 2012

  15. Demo • Demo of latest VCell features www.sbpax.org SW 4 HCLS Aug 28 2012

  16. Acknowledgements • VCell: Jim Schaff, Michael Blinov, Ion Moraru, Dan Vasiliescu, Xintao Wei, Fei Gao, Anu Lakshminarayana • BioPAX: Emek Demir, Gary Bader, Igor Rodchenkov, Andria Splendiani, Peter D'Eustachio, Huaiyu Mi • Signaling Gateway Molecule Pages: Ashok Dinasarapu • SBO: Nick Juty • SABIO-RK: Wolgang Mueller, Martin Golebiewski, Ulrike Wittig, Renate Kania, Lenneke Jong, Enkhjargal Algaa "Stagnation and the search for truth are always opposites." - Nadezhda Tolokonnikova www.sbpax.org SW 4 HCLS Aug 28 2012

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