recent developments in sbml

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Short summary of recent SBML developments given at the COMBINE (COmputational Modeling in BIology NEtwork) 2014 meeting held at the University of Southern California in August, 2014. The meeting page is available at http://co.mbine.org/events/COMBINE_2014

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  • 1. Recent Developmentsin SBMLMichael Hucka, Ph.D.Department of Computing and Mathematical SciencesCalifornia Institute of TechnologyPasadena, CA, USAEmail: mhucka@caltech.edu Twitter: @mhuckaCOMBINE 2014, Los Angeles,August 2014

2. What is SBML for, and why would anyone care? 3. ABC-SysBio CellNetAnalyzer Karyote* PaVESy SBW: Auto LayoutacslXtreme CellNOpt KEGGconverter PAYAO sbw: javasimALC Cellware KEGGtranslator PET sbw: stochastic simulatorAMIGO CLEML Kineticon PhysioLab Modeler SCIpathAntimony CL-SBML Kinsolver PINT SED-ML Web ToolsAPMonitor COBRA libAnnotationSBML PK-Sim / MoBi semanticSBMLArcadia CompuCell3D libRoadRunner PNK SensSBAsmparts ConsensusPathDB libSBML PottersWheel SGMPAthena COPASI libSBMLSim PRISM Sigmoid*AutoSBW CRdata libStruct ProcessDB SIGNALIGNAVIS CycSim MASS Toolbox ProMoT SignaLinkBALSA CySBML MatCont PROTON SigPathBASIS Cytoscape MathSBML pybrn SigTranBetaWB Cyto-Sim Medicel PyDSTool SIMBABifurcation Discovery Tool DBSolve MEMOSys PySB SimBiologyBiGG DEDiscover MesoRD PySCeS SimpathicaBiNoM Dizzy Meta-All RANGE SimPheny*BiNoM Cytoscape Plugin DOTcvpSB Metaboflux RAVEN Simulate3DBio Sketch Pad E-CELL MetaCrop Reactome Simulation Core LibraryBioBayes ecellJ MetaFluxNet ReMatch Simulation ToolBIOCHAM EPE Metannogen RMBNToolbox SimWizBioCharon ESS Metatool roadRunner SloppyCellBioCyc Facile MetExplore RSBML SmartCellBioGRID FAME MetNetMaker SABIO-RK SnoopyBiological Networks FASIMU MIRIAM Resources Saint SOSlibBioMet Toolbox FBASBW MMT2 SBFC SPDBSBioModels Database FERN modelMaGe SBML Harvester SRSBioModels Importer FluxBalance ModeRator SBML Layout STEPSBioNessie Fluxor Modesto SBML Reaction Finder StochKitBioNetGen Genetdes Moleculizer SBML Translators StochPyBioPARKIN Genetic Network Analyzer MonaLisa SBML2APM StochSimBioPathwise Gepasi Monod SBML2BioPax STOCKSBioPAX2SBML Gillespie2 MOOSE SBML2LaTeX SurreyFBABioRica GINsim MuVal (Multi-valued logic) SBML2NEURON SyBiLBioSens GNAT Narrator SBML2Octave SYCAMOREBioSPICE Dashboard GNU MCSim nemo SBML2SMW SynBioSSBioSpreadsheet GRENDEL NetBuilder' SBML2TikZ SystripBioSyS HSMB NetPath SBML2XPP TERANODE SuiteBioTapestry HybridSBML NetPro SBMLEditor The Cell CollectiveBioUML iBioSim Odefy SBML-PET-MPI TideBoolNet IBRENA Omix SBMLR TinkerCellbraincirc Insilico Discovery ONDEX SBML-SAT TrelisBRENDA insilicoIDE optflux SBML-shorthand UTKornToolsBSTLab iPathways Oscill8 SBMLSim VANTEDByoDyn JACOBIAN PANTHER Pathway SBMLsqueezer VcellCADLIVE Jacobian Viewer PathArt sbmltidy WebCellCain Jarnac Pathway Access SBMLToolbox WinSCAMPCARMEN JarnacLite Pathway Analyser SBMM assistant Wolfram SystemModelerCell Illustrator JDesigner Pathway Builder SBO xCelleratorCellDesigner JigCell Pathway Solver SBSI XholonCellerator JSBML Pathway Tools SBToolbox2 XPPAUTCellMC JSim PathwayLab sbtranslateCellML2SBML JWS Online PATIKAweb SBWMany software tools for !modeling available today 4. https://www.behance.net/gallery/d/7465033Modeling often entails the !use of more than one tool 5. Often need flexible,!intermediate connections 6. Why not simply distribute a model in the original format? 7. Why not simply distribute a model in the original format?Yes, do that vital for good science Others can try to run model, understand it, verify it, reuse it, etc. Opinion: should always do this 8. Why not simply distribute a model in the original format?Yes, do that vital for good science Others can try to run model, understand it, verify it, reuse it, etc. Opinion: should always do thisBut its still not ideal for communication of scientific results Biological semantics usually not encoded Not everyone can run the same software Not everyone wants to use the same software What if they want to use a different conceptual framework? How will people relate the model to other work? 9. What is SBML? 10. The raw SBML (as XML) 11. The raw SBML (as XML)Dont work with it directly! Let software do it. 12. SBML = Systems Biology Markup LanguageFormat for representing models of biological processes Data structures + principles + serialization to XML (Mostly) Declarative, not proceduralnot a scripting language(Mostly) neutral with respect to modeling framework E.g., ODE, stochastic systems, etc.For software to read/write, not humans 13. The process is central Literally called reaction (not necessarily biochemical) Participants are pools of entities of the same kind (species)na1 A + nb1 B f1(...) nc1 Cna2 A + nd2 D f2(...) ne1 Enc3 C f3(...) nf3 F + ng3 G... Species are located in containers (compartments)Models can further include: Other constants & variables Discontinuous events Unit definitions Annotations Other, explicit mathCore SBML concepts are fairly simple 14. Example of model type Example modelTypical ODE models (e.g., cell differentiation)BioModels Database model#BIOMD0000000451Conductance-based models (e.g., Hodgin-Huxley)BioModels Database model#BIOMD0000000020Typically do not use SBML reaction construct,!but instead use rate rules constructNeural models (e.g., spiking neurons)BioModels Database model#BIOMD0000000127Typically use events for discontinuous changesPharmacokinetic/dynamics modelsBioModels Database model#BIOMD0000000234Species are not required to be biochemical entitiesInfectious diseases BioModels Database model#MODEL1008060001List originally by Nicolas Le NovreCore SBML constructs support many types of models 15. Accepted by dozens of journals *100s of software tools available today Libraries: libSBML, JSBML 260+ listed in SBML Software Guide 1000s of models available ... in public databases, e.g., !BioModels Database, Reactome ... as supplementary data to papers ... in private repositorieshttp://sbml.org* http://sbml.org/Documents/Publications_known_to_accept_submissions_in_SBML_format http://sbml.org/SBML_Software_GuideMany examples of SBML and software resources are available 16. What resources are available for software developers? 17. SBML specification documents 18. API libraries 19. API librariesGo to Downloads 20. API librarieslibSBML JSBML 21. SBML Test Suite http://sbml.org/Facilities/SBML_Test_SuiteSuite of test cases (1200) + test runners (both standalone app & online)Database of test results on sbml.org 22. Online SBML Validator http://sbml.org/Facilities/Validator 23. Online SBML Validator http://sbml.org/Facilities/ValidatorFind it! here 24. Online SBML Validator http://sbml.org/Facilities/Validator 25. SBML Software Guide http://sbml.org/SBML_Software_GuideInformation about knownSBML compatible softwareNew questionnaire pleasefill it out if youre a developer!New version of the guide iscoming! 26. SBML Software Guide http://sbml.org/SBML_Software_GuideInformation about knownSBML compatible softwareNew questionnaire pleasefill it out if youre a developer!New version of the guide iscoming!ll 27. SBML Software Guide http://sbml.org/SBML_Software_GuideInformation about knownSBML compatible softwareNew questionnaire pleasefill it out if youre a developer!New version of the guide iscoming! 28. SBML Software Guide http://sbml.org/SBML_Software_GuideInformation about knownSBML compatible softwareNew questionnaire pleasefill it out if youre a developer!New version of the guide isClick!coming! here 29. What has been happening with SBML lately? 30. Level 3 packages add constructs !on top of SBML Level 3 Core 31. StatusLevel 3 package What it enablesHierarchical model composition Models containing submodels !Flux balance constraints Constraint-based models !Qualitative models Petri net models, Boolean models !Graph layout Diagrams of models !Multicomponent/state species Entities w/ structure; also rule-based models draftSpatial Nonhomogeneous spatial models draftGraph rendering Diagrams of models draftGroups Arbitrary grouping of components draftArrays & sets Arrays or sets of entities draftDynamic structures Creation & destruction of components draftDistributions Numerical values as statistical distributions in devAnnotations Richer annotation syntax 32. StatusLevel 3 package What it enablesHierarchical model composition Models containing submodels !Flux balance constraints Constraint-based models !Qualitative models Petri net models, Boolean models !Graph layout Diagrams of models !Multicomponent/state species Entities w/ structure; also rule-based UpdatedmodelsdraftSpatial Nonhomogeneous spatial modUelpsdatedmodels UpdateddraftGraph rendering Diagrams of models draftGroups Arbitrary grouping of components draftArrays & sets Arrays or sets of entities UpdateddraftDynamic structures Creation & destruction of componentsNewdraftDistributions Numerical values as statistical distributions in devAnnotations Richer annotation syntax 33. Community-based development processDefines process for Proposing changes andadditions to SBML andSBML packages Developing specifications Voting The roles of editorsSmall changes forthcomingin package requirements andprocedures 34. Frank BergmannMichael HuckaNicolas Le NovreBrett OlivierSven SahleDagmar WaltemathSBML EditorsStefan HoopsSarah KeatingChris MyersJames SchaffLucian SmithDarren WilkinsonCurrent Past(chair) 35. Google Summer of Code 2014Open Bioinformatics Foundation (OBF) as mentoring organizationVictor KofiaIbrahim VazirabadLeandro WatanabeRedesign the implementation of theJSBML math class ASTNodeCreate a CellDesigner plugin for JSBML thatwill convert between the layout format usedby CellDesigner and SBML Level 3 layoutImplement support in JSBML for theSBML Level 3 Arrays package 36. Acknowledgments 37. Mike Hucka, Sarah Keating, Frank Bergmann, Lucian Smith,Andrew Finney, Herbert Sauro, Hamid Bolouri, Ben Bornstein, MariaSchilstra, Jo Matthews, Bruce Shapiro, Linda Taddeo, Akira Funahashi,Akiya Juraku, Ben Kovitz, Nicolas Rodriguez, Andreas Drger, Alex ThomasSBML &JSBML Team:SBML Editors:Mike Hucka, Frank Bergmann, Sarah Keating, Nicolas Le Novre, Chris Myers,Lucian Smith, Stefan Hoops, Sven Sahle, James Schaff, Dagmar Walte

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