Software for SBML Today
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The document discusses the Systems Biology Markup Language (SBML), which is used for representing computational models of biological processes through a simple and flexible encoding system. It covers various aspects of SBML, including its modeling capabilities, software tools, features, and the types of models it supports, as well as the results of a survey on SBML software tools. Additionally, it highlights the diversity and utility of SBML and acknowledges the contributions of various funding organizations.
Software for SBML Today
- 1. Software for SBML Today Michael Hucka, Ph.D. Department of Computing + Mathematical Sciences California Institute of Technology Pasadena, CA, USA Email: mhucka@caltech.edu Twitter: @mhucka HARMONY 2012, Maastricht, The Netherlands 2
- 2. SBML = Systems Biology Markup Language Format for representing computational models of biological processes • Data structures + usage principles + serialization to XML Neutral with respect to modeling framework • E.g., ODE, stochastic systems, etc. 3
- 3. afor nc ) fra ans ua m ing t hu is al o ML are (n SB tw s of 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. Some basics of SBML core model encoding Well-stirred compartments c n 6
- 6. Species pools are located in compartments c protein A protein B n gene mRNAn mRNAc 7
- 7. Reactions can involve any species anywhere c protein A protein B n gene mRNAn mRNAc 8
- 8. Reactions can cross compartment boundaries c protein A protein B n gene mRNAn mRNAc 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. “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) mRNAc 11
- 11. “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...) 12
- 12. Annotations: machine-readable semantics and links to other resources “This is identified “This is an enzymatic c g1(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. Scope of SBML encompasses many types of models 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. 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. 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 Coming: 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. Where to learn more: SBML.org—the SBML portal 15
- 18. Where to learn more: SBML.org—the SBML portal Find SBML software 15
- 19. SBML Software Guide, with different views (same data) 16
- 20. How did we gather data on the software tools? Historically (until mid-2000’s): • Word of mouth at workshops & conferences • Direct contact Mid/late-2000’s to ~2010: • Created electronic survey • Citation alerts (e.g., Web of Science) 2011: • Expanded survey - Basis of this talk 17
- 21. New version of the SBML software survey 18
- 22. General features of the survey Online, implemented using commercial survey website 28 questions • Mix of multiple choice and fill-in-the-blank 85 responses by July 2011 • Removed incomplete responses • 81 software tools left Avoided “corrections” to data 19
- 23. Purposes of the software systems Question: Which of the following categories best describe your software? (Check all that apply.) Simulation software 42 Analysis 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. Purposes of the software systems Question: Which of the following categories best describe your software? (Check all that apply.) Simulation software 42 Analysis 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. Purposes of the software systems Question: Which of the following categories best describe your software? (Check all that apply.) Simulation software 42 Analysis 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. Purposes of the software systems Question: Which of the following categories best describe your software? (Check all that apply.) Simulation software 42 Analysis 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. Purposes of the software systems Question: Which of the following categories best describe your software? (Check all that apply.) Simulation software 42 Analysis 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. Purposes of the software systems Question: Which of the following categories best describe your software? (Check all that apply.) Simulation software 42 Analysis 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. Mathematical frameworks Question: Regardless of whether your software provides simulation capabilities, what modeling frameworks does the package support when working 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) 8 None of the above, or other framework 20 0 20 40 60 80 Total number of software tools 22
- 30. Mathematical frameworks Question: Regardless of whether your software provides simulation capabilities, what modeling frameworks does the package support when working 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) 8 None of the above, or other framework 20 E.g.: FBA 0 20 40 60 80 Total number of software tools 22
- 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. Other supported standards Question: 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. 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
- 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. Availability of software Fee-based Not Fee-based 2% avail. 10% 21% Code Free Free available 98% 90% 79% Fees for Fees for non- Is source code academics academics available? 26
- 36. Final impressions Some 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 source Some disappointing results • Low response turnout: 85 vs 230 tools in matrix • Low support for MIRIAM 27
- 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. Attendees at SBML 10th Anniversary Symposium, Edinburgh, 2010 A huge thank you to the community 29