A Profile of Today's SBML-Compatible Software
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A Profile of Today's SBML-Compatible Software

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Slides from presentation given at the Workshop on Interoperability in Scientific Computing during the 7th IEEE International Conference on e-Science Stockholm, Sweden, December 5, 2011.

Slides from presentation given at the Workshop on Interoperability in Scientific Computing during the 7th IEEE International Conference on e-Science Stockholm, Sweden, December 5, 2011.

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A Profile of Today's SBML-Compatible Software A Profile of Today's SBML-Compatible Software Presentation Transcript

  • A Profile of Todays SBML-Compatible Software Michael Hucka, Ph.D. Control and Dynamical Systems Dept. of Computing + Mathematical Sciences California Institute of Technology Pasadena, CA, USA 1
  • 1. BackgroundOutline 2. Survey results & discussion 3. Acknowledgments 2
  • 1. BackgroundOutline 2. Survey results & discussion 3. Acknowledgments 3
  • 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.A lingua franca for software (not humans) 4
  • Basic SBML concepts are fairly simpleThe reaction is central: a process occurring at a given rate f ([A],[B],[P ],...) na A + nb B ⇥ np P f (...) nc C ⇥ nd D + ne E + nf F . . . • Participants are pools of entities (species)Models can further include: • Other constants & variables • Unit definitions • Compartments • Annotations • Explicit math • Discontinuous events 5
  • Scope of SBML encompasses many types of models 6
  • 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 6
  • Today: spatially homogeneous models • Metabolic network models F i nd BioM exam ples i • Signaling pathway models http:/ odels Data n 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 6
  • Today: spatially homogeneous models • Metabolic network models F i nd BioM exam ples i • Signaling pathway models http:/ odels Data n base • Conductance-based models /biom odels .net/b • Neural models iomo dels • Pharmacokinetic/dynamics models • Infectious diseasesComing: SBML Level 3 package to support other types of models • Spatially inhomogeneous models • Qualitative/logical Scope of SBML encompasses many types of models 6
  • SBML Level 1 SBML Level 2 SBML Level 3predefined math functions user-defined functions user-defined functionstext-string math notation MathML subset MathML subsetreserved namespaces for no reserved namespaces no reserved namespaces annotations for annotations for annotationsno controlled annotation RDF-based controlled RDF-based controlled scheme annotation scheme annotation scheme no discrete events discrete events discrete events default values defined default values defined no default values monolithic monolithic modular 7
  • Where to learn more: SBML.org—the SBML portal 8
  • Where to learn more: SBML.org—the SBML portal Find SBML software 8
  • SBML Software Guide, with different views (same data) 9
  • Example: the software matrix10
  • Number of software systems supporting SBML300 229 in July 14 ↓200100 0 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 (counted in middle of each year) 11
  • 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)This year (2011): • Expanded survey - Basis of this talk 12
  • 1. BackgroundOutline 2. Survey results & discussion 3. Acknowledgments 13
  • New version of the SBML software survey 14
  • General features of the surveyOnline, implemented using commercial survey website28 questions • Mix of multiple choice, fill-in-the-blank, and hybrid questions85 responses by July 2011 • Removed incomplete responses • 81 software tools leftAvoided “corrections” to data 15
  • 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 14Framework 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 16
  • Mathematical frameworksQuestion: Regardless of whether your software provides simulation capabilities,what modeling frameworks does the package support when working with SBMLfiles? 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 17
  • General SBML-related characteristics Import Supports 28% SBML Level 3 Import & 36% Does not yet Export export support Level 3 11% 60% 64%Read SBML, write SBML, Percentage supporting or both? SBML Level 3 18
  • More 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 19
  • Other supported standardsMIRIAM 16 SBO 14 SBGN 13BioPAX 6CellML 3SED-ML 3MFAML 1 PNML 1 SBOL 1 0 5 10 15 20Total # software tools supporting other standards 20
  • Operating systems supported by the 81 tools 69 Microsoft Windows 8 64 Apple Mac OS 0 58 Linux 0 26 Web browser 7 0 20 40 60 80 Total Only this 21
  • 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? 22
  • License choices BSD 23 GPL 22 Custom license 13 LGPL 10Creative Commons 4 Apache License 1 Artistic License 1DARPA BioCOMP 1 MIT 1 None 5 0 20 40 60 80 Number of software tools 23
  • Final impressionsSome pleasing results • Large variety, including tools offering 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 - Many still missing, but not 150 • Only 1/3 of tools support SBML Level 3 • Low support for MIRIAM 24
  • 1. BackgroundOutline 2. Survey results & discussion 3. Acknowledgments 25
  • Agencies to thank for supporting SBMLNational Institute of General Medical Sciences (USA)European Molecular Biology Laboratory (EMBL)ELIXIR (UK)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 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) 26
  • Core SBML TeamFrank Bergmann Sarah Keating Lucian Smith 27
  • Attendees at SBML 10th Anniversary Symposium, Edinburgh, 2010A huge thank you to the community 28