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Software for SBML Today               Michael Hucka, Ph.D.   Department of Computing + Mathematical Sciences          Cali...
SBML = Systems Biology Markup LanguageFormat for representing computational models of biological processes •   Data struct...
afor                   nc )                fra ans              ua m           ing t hu      is al o  ML are (nSB tw  s of...
The process is central  •   Called a “reaction” in SBML  •   Participants are pools of entities (species)Models can furthe...
Some basics of SBML core model encodingWell-stirred compartments       c       n                                          ...
Species pools are located in compartments        c                   protein A                protein B        n          ...
Reactions can involve any species anywhere       c                   protein A                 protein B        n         ...
Reactions can cross compartment boundaries       c                  protein A                  protein B       n          ...
Reaction/process rates can be (almost) arbitrary formulas       c                   protein A          f1(x)           pro...
“Rules”: equations expressing relationships in addition to reaction sys.g1(x)    cg2(x)               protein A           ...
“Events”: discontinuous actions triggered by system conditionsg1(x)       cg2(x)                   protein A              ...
Annotations: machine-readable semantics and links to other resources   “This is identified                                 ...
Scope of SBML encompasses many types of models                                                 14
Today: spatially homogeneous models  •   Metabolic network models  •   Signaling pathway models  • Conductance-based model...
Today: spatially homogeneous models  •   Metabolic network models          F i nd                                       Bi...
Today: spatially homogeneous models  •   Metabolic network models             F i nd                                      ...
Where to learn more: SBML.org—the SBML portal                                                15
Where to learn more: SBML.org—the SBML portal                 Find SBML software                                          ...
SBML Software Guide, with different views (same data)                                                       16
How did we gather data on the software tools?Historically (until mid-2000’s): •   Word of mouth at workshops & conferences...
New version of the SBML software survey                                          18
General features of the surveyOnline, implemented using commercial survey website28 questions •   Mix of multiple choice a...
Purposes of the software systems   Question: Which of the following categories best describe your software?   (Check all t...
Purposes of the software systems   Question: Which of the following categories best describe your software?   (Check all t...
Purposes of the software systems   Question: Which of the following categories best describe your software?   (Check all t...
Purposes of the software systems   Question: Which of the following categories best describe your software?   (Check all t...
Purposes of the software systems   Question: Which of the following categories best describe your software?   (Check all t...
Purposes of the software systems   Question: Which of the following categories best describe your software?   (Check all t...
Mathematical frameworksQuestion: Regardless of whether your software provides simulationcapabilities, what modeling framew...
Mathematical frameworksQuestion: Regardless of whether your software provides simulationcapabilities, what modeling framew...
Specific SBML-specific characteristics Question: Which features of SBML can your software recognize and act on?Species, reac...
Other supported standardsQuestion: Which other standards does your software support?             MIRIAM                   ...
Operating systems supported by the 81 toolsMicrosoft Windows                                         69                   ...
Operating systems supported by the 81 tools                                 !Microsoft Windows                            ...
Availability of softwareFee-based                               Not                  Fee-based   2%                       ...
Final impressionsSome pleasing results •   Large variety, including tools with features SBML can’t yet represent     -   H...
National Institute of General Medical Sciences (USA)                          European Molecular Biology Laboratory (EMBL)...
Attendees at SBML 10th Anniversary Symposium, Edinburgh, 2010A huge thank you to the community                            ...
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Software for SBML Today

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Presentation given by Michael Hucka at HARMONY 2012, May 21-25, Department of Bioinformatics - BiGCaT, University of Maastricht, The Netherlands.

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Transcript of "Software for SBML Today"

  1. 1. Software for SBML Today Michael Hucka, Ph.D. Department of Computing + Mathematical Sciences California Institute of Technology Pasadena, CA, USAEmail: mhucka@caltech.edu Twitter: @mhucka HARMONY 2012, Maastricht, The Netherlands 2
  2. 2. SBML = Systems Biology Markup LanguageFormat for representing computational models of biological processes • Data structures + usage principles + serialization to XMLNeutral with respect to modeling framework • E.g., ODE, stochastic systems, etc. 3
  3. 3. afor nc ) fra ans ua m ing t hu is al o ML are (nSB tw s of 4
  4. 4. The process is central • Called a “reaction” in SBML • Participants are pools of entities (species)Models can further include: • Unit definitions • Other constants & variables • Annotations • Compartments • Explicit math • Discontinuous events Basic SBML concepts are fairly simple 5
  5. 5. Some basics of SBML core model encodingWell-stirred compartments c n 6
  6. 6. Species pools are located in compartments c protein A protein B n gene mRNAn mRNAc 7
  7. 7. Reactions can involve any species anywhere c protein A protein B n gene mRNAn mRNAc 8
  8. 8. Reactions can cross compartment boundaries c protein A protein B n gene mRNAn mRNAc 9
  9. 9. 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) mRNAc 10
  10. 10. “Rules”: equations expressing relationships in addition to reaction sys.g1(x) cg2(x) protein A f1(x) protein B . . . n f5(x) f2(x) gene f4(x) mRNAn f3(x) mRNAc 11
  11. 11. “Events”: discontinuous actions triggered by system conditionsg1(x) cg2(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...) 12
  12. 12. Annotations: machine-readable semantics and links to other resources “This is identified “This is an enzymatic cg1(x)by 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...) 13
  13. 13. Scope of SBML encompasses many types of models 14
  14. 14. Today: spatially homogeneous models • Metabolic network models • Signaling pathway models • Conductance-based models • Neural models • Pharmacokinetic/dynamics models • Infectious diseases Scope of SBML encompasses many types of models 14
  15. 15. Today: spatially homogeneous models • Metabolic network models F i nd BioM exam ples i • Signaling pathway models odels n Data http:/ base • Conductance-based models /biom odels .net/b • Neural models iomo dels • Pharmacokinetic/dynamics models • Infectious diseases Scope of SBML encompasses many types of models 14
  16. 16. Today: spatially homogeneous models • Metabolic network models F i nd BioM exam ples i • Signaling pathway models odels n Data http:/ base • Conductance-based models /biom odels .net/b • Neural models iomo dels • Pharmacokinetic/dynamics models • Infectious diseasesComing: SBML Level 3 packages to support other types • E.g.: Spatially inhomogeneous models, also qualitative/logical Scope of SBML encompasses many types of models 14
  17. 17. Where to learn more: SBML.org—the SBML portal 15
  18. 18. Where to learn more: SBML.org—the SBML portal Find SBML software 15
  19. 19. SBML Software Guide, with different views (same data) 16
  20. 20. How did we gather data on the software tools?Historically (until mid-2000’s): • Word of mouth at workshops & conferences • Direct contactMid/late-2000’s to ~2010: • Created electronic survey • Citation alerts (e.g., Web of Science)2011: • Expanded survey - Basis of this talk 17
  21. 21. New version of the SBML software survey 18
  22. 22. General features of the surveyOnline, implemented using commercial survey website28 questions • Mix of multiple choice and fill-in-the-blank85 responses by July 2011 • Removed incomplete responses • 81 software tools leftAvoided “corrections” to data 19
  23. 23. Purposes of the software systems Question: Which of the following categories best describe your software? (Check all that apply.) Simulation software 42Analysis s/w (in addition, or instead of, simulation) 40 Creation/model development software 31 Visualization/display/formatting software 31 Utility software (e.g., format conversion) 23 Data integration and management software 16 Repository or database 14 Framework or library (for use in developing s/w) 13 S/w for interactive env. (e.g., MATLAB, R, ...) 13 Annotation software 11 0 20 40 60 80 Total number of software tools 20
  24. 24. Purposes of the software systems Question: Which of the following categories best describe your software? (Check all that apply.) Simulation software 42Analysis s/w (in addition, or instead of, simulation) 40 Creation/model development software 31 Visualization/display/formatting software 31 Utility software (e.g., format conversion) 23 Data integration and management software 16 Repository or database 14 Framework or library (for use in developing s/w) 13 S/w for interactive env. (e.g., MATLAB, R, ...) 13 Annotation software 11 0 20 40 60 80 Total number of software tools 20
  25. 25. Purposes of the software systems Question: Which of the following categories best describe your software? (Check all that apply.) Simulation software 42Analysis s/w (in addition, or instead of, simulation) 40 Creation/model development software 31 Visualization/display/formatting software 31 Utility software (e.g., format conversion) 23 Data integration and management software 16 Repository or database 14 Framework or library (for use in developing s/w) 13 1/4 1/2 3/4 S/w for interactive env. (e.g., MATLAB, R, ...) 13 Annotation software 11 0 20 40 60 80 Total number of software tools 20
  26. 26. Purposes of the software systems Question: Which of the following categories best describe your software? (Check all that apply.) Simulation software 42Analysis s/w (in addition, or instead of, simulation) 40 Creation/model development software 31 Visualization/display/formatting software 31 Utility software (e.g., format conversion) 23 Data integration and management software 16 Repository or database 14 Framework or library (for use in developing s/w) 13 S/w for interactive env. (e.g., MATLAB, R, ...) 13 Annotation software 11 0 20 40 60 80 Total number of software tools 21
  27. 27. Purposes of the software systems Question: Which of the following categories best describe your software? (Check all that apply.) Simulation software 42Analysis s/w (in addition, or instead of, simulation) 40 Creation/model development software 31 Visualization/display/formatting software 31 Utility software (e.g., format conversion) 23 Data integration and management software 16 Repository or database 14 ? Framework or library (for use in developing s/w) 13 S/w for interactive env. (e.g., MATLAB, R, ...) 13 Annotation software 11 0 20 40 60 80 Total number of software tools 21
  28. 28. Purposes of the software systems Question: Which of the following categories best describe your software? (Check all that apply.) Simulation software 42Analysis s/w (in addition, or instead of, simulation) 40 Creation/model development software 31 Visualization/display/formatting software 31 Utility software (e.g., format conversion) 23 Data integration and management software 16 Repository or database 14 ? Framework or library (for use in developing s/w) 13 S/w for interactive env. (e.g., MATLAB, R, ...) 13 Annotation software 11 Low 0 20 40 60 80 Total number of software tools 21
  29. 29. Mathematical frameworksQuestion: Regardless of whether your software provides simulationcapabilities, what modeling frameworks does the package support whenworking with SBML files? Ordinary differential equations (ODE) 54 Discrete stochastic simulation 28 Discontinuous event handling 25 Differential-algebraic equations (DAE) 17 Logical/Boolean networks 11 Delay-differential equations (DDE) 9 Partial differential equations (PDE) 8None of the above, or other framework 20 0 20 40 60 80 Total number of software tools 22
  30. 30. Mathematical frameworksQuestion: Regardless of whether your software provides simulationcapabilities, what modeling frameworks does the package support whenworking with SBML files? Ordinary differential equations (ODE) 54 Discrete stochastic simulation 28 Discontinuous event handling 25 Differential-algebraic equations (DAE) 17 Logical/Boolean networks 11 Delay-differential equations (DDE) 9 Partial differential equations (PDE) 8None of the above, or other framework 20 E.g.: FBA 0 20 40 60 80 Total number of software tools 22
  31. 31. Specific SBML-specific characteristics Question: Which features of SBML can your software recognize and act on?Species, reactions, parameters, and/or compartments 65 Work with reaction kinetics 48 Work with stoichiometric relationships/maps 46 Work with other mathematical relationships 32 Work with conditional discontinuous events 27 Work with time delays 10 Other, or not applicable 14 0 20 40 60 80 Total number of software tools 23
  32. 32. Other supported standardsQuestion: Which other standards does your software support? MIRIAM 16 SBO 14 SBGN 13 BioPAX 6 CellML 3 SED-ML 3 MFAML 1 PNML 1 (Warning: SBOL 1 different scale) 0 5 10 15 20 Total # software tools supporting other standards 24
  33. 33. Operating systems supported by the 81 toolsMicrosoft Windows 69 8 Apple Mac OS 0 64 Linux 0 58 Web browser 26 7 0 20 40 60 80 Total Only this 25
  34. 34. Operating systems supported by the 81 tools !Microsoft Windows 69 8 Apple Mac OS 0 64 Linux 0 58 Web browser 26 7 0 20 40 60 80 Total Only this 25
  35. 35. Availability of softwareFee-based Not Fee-based 2% avail. 10% 21% Code Free Free available 98% 90% 79% Fees for Fees for non- Is source codeacademics academics available? 26
  36. 36. Final impressionsSome pleasing results • Large variety, including tools with features SBML can’t yet represent - Hopefully stands as testament to SBML’s utility • Nearly 80% are open sourceSome disappointing results • Low response turnout: 85 vs 230 tools in matrix • Low support for MIRIAM 27
  37. 37. National Institute of General Medical Sciences (USA) European Molecular Biology Laboratory (EMBL) ELIXIR (UK)Funding acknowledgments Beckman Institute, Caltech (USA) Keio University (Japan) JST ERATO Kitano Symbiotic Systems Project (Japan) (to 2003) JST ERATO-SORST Program (Japan) International Joint Research Program of NEDO (Japan) Japanese Ministry of Agriculture Japanese 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) 28
  38. 38. Attendees at SBML 10th Anniversary Symposium, Edinburgh, 2010A huge thank you to the community 29
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