A status update on COMBINE standardization       activities, with a focus on SBML                      Michael Hucka, Ph.D...
Introduction and motivation          COMBINEOutline          SBML          SED-ML          SBGN          Conclusion       ...
Introduction and motivation          COMBINEOutline          SBML          SED-ML          SBGN          Conclusion       ...
The many roles of computation in biological researchInstrument/device control, data management, data processing,database a...
Different tools   different interfaces & languages                                                   5
Communication is better with standard exchange formats                                                         6
Developing exchange standards is not easyDiverse set of knowledge needed •   Scientific needs •   Technical implementation ...
Introduction and motivation          COMBINEOutline          SBML          SED-ML          SBGN          Conclusion       ...
Motivations for the creation of COMBINERealizations about the state of affairs in late-2000’s •   Many efforts overlapped, b...
COMBINE StandardsBioPAX         Associated Standardization Efforts                                      Qualifiers          ...
Example common infrastructure provided by COMBINECommon URI scheme for specification documents •   E.g.: http://identifiers....
Some examples of goals for a common voiceCommunity standards are not standards branded by (e.g.) ISO •   Efforts are usuall...
Introduction and motivation          COMBINEOutline          SBML          SED-ML          SBGN          Conclusion       ...
SB       ML         :a     fo lin       rs g         of ua           tw fr             ar an               e ca14
SBML = Systems Biology Markup LanguageFormat for representing computational models of biological processes •   Data struct...
The process is central  •   Called a “reaction” in SBML  •   Participants are pools of entities (species)Models can furthe...
Traditional SBML models have been spatially homogeneous  •   Metabolic network models                                     ...
Level 3 package               What it enables                              StatusHierarchical model composition Models con...
Example: SBML Level 3 Hierarchical Model Composition    Core SBML         With hierarchical model compositionModel “A”    ...
The ‘comp’ package supports multiple arrangements                     Separate files (possibly in databases)Model “A” Compa...
Where to find package information & documents      http://sbml.org/Documents/Specifications                                 ...
Where to find package information & documents         http://sbml.org/Documents/SpecificationsTable for package information ...
Where to find software applications compatible with SBML                                                          22
Where to find software applications compatible with SBML                      Find SBML software                           ...
Where to find libraries for implementing SBML support                                                       23
Where to find libraries for implementing SBML support       Go to “Downloads”                                              ...
Where to find libraries for implementing SBML support          libSBML              JSBML                                  ...
Introduction and motivation          COMBINEOutline          SBML          SED-ML          SBGN          Conclusion       ...
Decroly & Goldbeter, PNAS, 1982                                        ?BIOMD0000000319 in BioModels Database          Nee...
SED-ML = Simulation Experiment Description MLApplication-independent format to capture procedures, algorithms,parameter va...
Waltemath et al., BMC Systems Biology, 2011Basic components of SED-ML Level 1 Version 1                                   ...
Software apps & libraries available for SED-ML Level 1 v.1Some SED-ML-compatible software today: •   libSedML •   jlibsedm...
Introduction and motivation          COMBINEOutline          SBML          SED-ML          SBGN          Conclusion       ...
Graphical representation of modelsToday: broad variation in graphical notation used in biological diagrams •   Between aut...
SBGN = Systems Biology Graphical NotationGoal: standardize the graphical notation in diagrams of biological processes3 sub...
SBGN support today                                        Being used in publications                                      ...
Introduction and motivation          COMBINEOutline          SBML          SED-ML          SBGN          Conclusion       ...
Attendees at SBML 10th Anniversary Symposium, Edinburgh, 2010Such standards are the work of a great community             ...
Get involved and make things better!COMBINE (Computational Modeling in Biology Network)                        http://co.m...
SBML was made possible thanks to funding from:National Institute of General Medical Sciences (USA)European Molecular Biolo...
I’d like your feedback!You can use this anonymous form: http://tinyurl.com/mhuckafeedback                                 ...
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A status update on COMBINE standardization activities, with a focus on SBML

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Presentation given to the NIH IMAG Model and Data Sharing workgroup on 24 January 2013.

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A status update on COMBINE standardization activities, with a focus on SBML

  1. 1. A status update on COMBINE standardization activities, with a focus on SBML Michael Hucka, Ph.D. Department of Computing + Mathematical Sciences California Institute of Technology Pasadena, CA, USA Email: mhucka@caltech.edu Twitter: @mhuckaNIH IMAG Model and Data Sharing Working Group webinar, 24 Jan. 2013 1
  2. 2. Introduction and motivation COMBINEOutline SBML SED-ML SBGN Conclusion 2
  3. 3. Introduction and motivation COMBINEOutline SBML SED-ML SBGN Conclusion 3
  4. 4. The many roles of computation in biological researchInstrument/device control, data management, data processing,database applications, statistical analysis, pattern matching, imageprocessing, text mining, chemical structure prediction, genomicsequence analysis, proteomics, other *omics, molecular modeling,molecular dynamics, kinetic simulation, simulated evolution,phylogenetics, ... (to name only a subset)!Focus here: modeling and simulation 4
  5. 5. Different tools different interfaces & languages 5
  6. 6. Communication is better with standard exchange formats 6
  7. 7. Developing exchange standards is not easyDiverse set of knowledge needed • Scientific needs • Technical implementation skills • Practical experienceThis has lead to different efforts for different facets of overall problem 7
  8. 8. Introduction and motivation COMBINEOutline SBML SED-ML SBGN Conclusion 8
  9. 9. Motivations for the creation of COMBINERealizations about the state of affairs in late-2000’s • Many efforts overlapped, but lacked coordination • Individual meetings meant more travel for many people • Limited and fragile funding didn’t support solid, coherent baseCOMBINE = Computational Modeling in Biology NetworkMain objectives: • Coordinate meetings • Coordinate standards development • Develop standard operating procedures and common tools • Provide a recognized voice 9
  10. 10. COMBINE StandardsBioPAX Associated Standardization Efforts Qualifiers Related Standardization Efforts GPMLStandardization efforts represented in COMBINE today 10
  11. 11. Example common infrastructure provided by COMBINECommon URI scheme for specification documents • E.g.: http://identifiers.org/combine.specifications/ sbgn.er.level-1.version-1 - Resolved and redirected to a page that lists where spec. is found - Actual documents can be stored anywhere 11
  12. 12. Some examples of goals for a common voiceCommunity standards are not standards branded by (e.g.) ISO • Efforts are usually too small to undertake the process required • However, lack of a standards body label is viewed negativelyCOMBINE can act as a standardization body for the communityAct as a common point of contact for: • Software developers • Publishers • Industry • Funding bodies • Legal entities 12
  13. 13. Introduction and motivation COMBINEOutline SBML SED-ML SBGN Conclusion 13
  14. 14. SB ML :a fo lin rs g of ua tw fr ar an e ca14
  15. 15. SBML = Systems Biology Markup LanguageFormat for representing computational models of biological processes • Data structures + usage principles + serialization to XML • (Mostly) Declarative, not procedural—not a scripting languageNeutral with respect to modeling framework • E.g., ODE, stochastic systems, etc.Development started in 2000, with first specification distributed in 2001 15
  16. 16. The process is central • Called a “reaction” in SBML • Participants are pools of entities (species)Models can further include: • Other constants & variables • Unit definitions • Compartments • Annotations • Explicit math • Discontinuous events Basic SBML concepts are fairly simple 16
  17. 17. Traditional SBML models have been spatially homogeneous • Metabolic network models Find exam • Signaling pathway models BioM odels ples in Data • Conductance-based models http: //bio base mod • Neural models els.ne t/bio mod els • Pharmacokinetic/dynamics models • Infectious diseasesDevelopment of SBML Level 3 packages is extending this scope • E.g.: Spatially inhomogeneous models, also qualitative/logical Scope of SBML encompasses many types of models 17
  18. 18. Level 3 package What it enables StatusHierarchical model composition Models containing submodels ✔Flux balance constraints Flux balance analysis models ✔Qualitative models Petri net models, Boolean models RCSpatial Nonhomogeneous spatial models draftMulticomponent species Entities w/ structure; also rule-based models draftGraph layout Diagrams of models draftGraph rendering Diagrams of models draftDistributions Numerical values as statistical distributions in devGroups Arbitrary grouping of components in devAnnotations Richer annotation syntaxDynamic structures Creation & destruction of componentsArrays & sets Arrays or sets of entities 18
  19. 19. Example: SBML Level 3 Hierarchical Model Composition Core SBML With hierarchical model compositionModel “A” Model “A” Compartments ... Compartments ... Species ... Species ... Parameters ... Parameters ... Reactions ... Reactions ... Model “B” Model “C” Compartments ... Compartments ... Species ... Species ... Parameters ... Parameters ... Reactions ... Reactions ... 19
  20. 20. The ‘comp’ package supports multiple arrangements Separate files (possibly in databases)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 of Species ... libraries of Parameters ... tested Reactions ... models.) 20
  21. 21. Where to find package information & documents http://sbml.org/Documents/Specifications 21
  22. 22. Where to find package information & documents http://sbml.org/Documents/SpecificationsTable for package information & links 21
  23. 23. Where to find software applications compatible with SBML 22
  24. 24. Where to find software applications compatible with SBML Find SBML software 22
  25. 25. Where to find libraries for implementing SBML support 23
  26. 26. Where to find libraries for implementing SBML support Go to “Downloads” 23
  27. 27. Where to find libraries for implementing SBML support libSBML JSBML 23
  28. 28. Introduction and motivation COMBINEOutline SBML SED-ML SBGN Conclusion 24
  29. 29. Decroly & Goldbeter, PNAS, 1982 ?BIOMD0000000319 in BioModels Database Need to capture the processes applied to models 25
  30. 30. SED-ML = Simulation Experiment Description MLApplication-independent format to capture procedures, algorithms,parameter values • Neutral format for encoding the steps to go from model to outputCan be used for • Simulation experiments encoding parametrizations & perturbations • Simulations using more than one model and/or method • Data manipulations to produce plot(s) 26
  31. 31. Waltemath et al., BMC Systems Biology, 2011Basic components of SED-ML Level 1 Version 1 27
  32. 32. Software apps & libraries available for SED-ML Level 1 v.1Some SED-ML-compatible software today: • libSedML • jlibsedml • SBW Simulation Tool • CellDesigner • Web tools • others http://sedml.org 28
  33. 33. Introduction and motivation COMBINEOutline SBML SED-ML SBGN Conclusion 29
  34. 34. Graphical representation of modelsToday: broad variation in graphical notation used in biological diagrams • Between authors, between journals, even people in same groupHowever, standard notations would offer benefits: • Consistency = easier to read diagrams with less ambiguity • Software support: verification of correctness, translation to math 30
  35. 35. SBGN = Systems Biology Graphical NotationGoal: standardize the graphical notation in diagrams of biological processes3 sublanguages to describe different facets of a model • Process Diagram: causal sequences of processes & their results - A node represents a given state of an entity • Entity Relationship: interactions bet. entities regardless of sequence - A node represents an entity regardless of state • Activity Flow: information flowing from one entity to another - Hybrid — shows flow of activity without state transitionsLanguages reuse same symbols, but their interpretations are different 31
  36. 36. SBGN support today Being used in publications Numerous software tools and databases • API libraries are under development See http://sbgn.org for moreMartin et al., Autophagy, Jan. 2013 Reactome Database — http://reactome.org 32
  37. 37. Introduction and motivation COMBINEOutline SBML SED-ML SBGN Conclusion 33
  38. 38. Attendees at SBML 10th Anniversary Symposium, Edinburgh, 2010Such standards are the work of a great community 34
  39. 39. Get involved and make things better!COMBINE (Computational Modeling in Biology Network) http://co.mbine.orgUpcoming: HARMONY at U. Connecticut Health Center, May 20–23 • HARMONY = Hackathon on Resources for Modeling in BiologyCOMBINE meeting planned for later this year 35
  40. 40. SBML was made possible thanks to funding from:National Institute of General Medical Sciences (USA)European Molecular Biology Laboratory (EMBL)JST ERATO Kitano Symbiotic Systems Project (Japan) (to 2003)JST ERATO-SORST Program (Japan)ELIXIR (UK)Beckman Institute, Caltech (USA)Keio University (Japan)International Joint Research Program of NEDO (Japan)Japanese Ministry of AgricultureJapanese Ministry of Educ., Culture, Sports, Science and Tech.BBSRC (UK)National Science Foundation (USA)DARPA IPTO Bio-SPICE Bio-Computation Program (USA)Air Force Office of Scientific Research (USA)STRI, University of Hertfordshire (UK)Molecular Sciences Institute (USA) 36
  41. 41. I’d like your feedback!You can use this anonymous form: http://tinyurl.com/mhuckafeedback 37

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