How to represent a generalized metabolic model using SBML and SBGN?
A Profile of Today's SBML-Compatible Software
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Transcript of A Profile of Today's SBML-Compatible Software
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A Profile of Today's SBML-Compatible Software
Michael Hucka, Ph.D.
Control and Dynamical SystemsDept. of Computing + Mathematical Sciences
California Institute of TechnologyPasadena, CA, USA
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Out
line 1. Background
2. Survey results & discussion
3. Acknowledgments
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Out
line 1. Background
2. Survey results & discussion
3. Acknowledgments
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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.
A lingua franca for software (not humans)
SBML = Systems Biology Markup Language
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The reaction is central: a process occurring at a given rate
• Participants are pools of entities (species)
Models can further include:
• Other constants & variables
• Compartments
• Explicit math
• Discontinuous events
Basic SBML concepts are fairly simple
naA + nbBf([A],[B],[P ],...)������������⇥npP
ncCf(...)���⇥ ndD + neE + nfF
...
• Unit definitions
• Annotations
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Scope of SBML encompasses many types of models6
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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 models6
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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
Find examples inBioModels Databasehttp://biomodels.net/biomodels
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Today: spatially homogeneous models
• Metabolic network models
• Signaling pathway models
• Conductance-based models
• Neural models
• Pharmacokinetic/dynamics models
• Infectious diseases
Coming: SBML Level 3 package to support other types of models
• Spatially inhomogeneous models
• Qualitative/logical
Scope of SBML encompasses many types of models
Find examples inBioModels Databasehttp://biomodels.net/biomodels
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SBML Level 1 SBML Level 2 SBML Level 3
predefined math functions user-defined functions user-defined functions
text-string math notation MathML subset MathML subset
reserved namespaces for annotations
no reserved namespaces for annotations
no reserved namespaces for annotations
no controlled annotation scheme
RDF-based controlled annotation scheme
RDF-based controlled annotation scheme
no discrete events discrete events discrete events
default values defined default values defined no default values
monolithic monolithic modular
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Where to learn more: SBML.org—the SBML portal
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Find SBML software
Where to learn more: SBML.org—the SBML portal
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SBML Software Guide, with different views (same data)9
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Exam
ple:
the
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twar
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atri
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0
100
200
300
2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011
(counted in middle of each year)
229 in July 14 ↓
Number of software systems supporting SBML
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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)
This year (2011):
• Expanded survey
- Basis of this talk
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Out
line 1. Background
2. Survey results & discussion
3. Acknowledgments
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New version of the SBML software survey
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General features of the survey
Online, implemented using commercial survey website
28 questions
• Mix of multiple choice, fill-in-the-blank, and hybrid questions
85 responses by July 2011
• Removed incomplete responses
• 81 software tools left
Avoided “corrections” to data
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Question: Which of the following categories best describe your software? (Check all that apply.)
Purposes of the software systems
Total number of software tools
Simulation software
Analysis s/w (in addition, or instead of, simulation)
Creation/model development software
Visualization/display/formatting software
Utility software (e.g., format conversion)
Data integration and management software
Repository or database
Framework or library (for use in developing s/w)
S/w for interactive env. (e.g., MATLAB, R, ...)
Annotation software
0 20 40 60 80
11
13
13
14
16
23
31
31
40
42
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Mathematical frameworks
Ordinary differential equations (ODE)
Discrete stochastic simulation
Discontinuous event handling
Differential-algebraic equations (DAE)
Logical/Boolean networks
Delay-differential equations (DDE)
Partial differential equations (PDE)
None of the above, or other framework
0 20 40 60 80
20
8
9
11
17
25
28
54
Total number of software tools
Question: Regardless of whether your software provides simulation capabilities, what modeling frameworks does the package support when working with SBML files?
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General SBML-related characteristics
SupportsSBML Level 3
36% Does not yet support Level 3
64%
Percentage supporting SBML Level 3
Import28%
Export11%
Import & export60%
Read SBML, write SBML,or both?
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Question: Which features of SBML can your software recognize and act on?
More specific SBML-specific characteristics
Species, reactions, parameters, and/or compartments
Work with reaction kinetics
Work with stoichiometric relationships/maps
Work with other mathematical relationships
Work with conditional discontinuous events
Work with time delays
Other, or not applicable
0 20 40 60 80
14
10
27
32
46
48
65
Total number of software tools
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Other supported standards
MIRIAM
SBO
SBGN
BioPAX
CellML
SED-ML
MFAML
PNML
SBOL
0 5 10 15 20
1
1
1
3
3
6
13
14
16
Total # software tools supporting other standards
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Operating systems supported by the 81 tools
Microsoft Windows
Apple Mac OS
Linux
Web browser
0 20 40 60 80
7
0
0
8
26
58
64
69
Total Only this
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Availability of software
Fee-based2%
Free98%
Fees for academics
Fee-based10%
Free90%
Fees for non-academics
Notavail.21%
Codeavailable
79%
Is source code available?
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License choices
BSD
GPL
Custom license
LGPL
Creative Commons
Apache License
Artistic License
DARPA BioCOMP
MIT
None
0 20 40 60 80
5
1
1
1
1
4
10
13
22
23
Number of software tools
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Final impressions
Some 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 source
Some 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
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Out
line 1. Background
2. Survey results & discussion
3. Acknowledgments
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National 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)
Agencies to thank for supporting SBML
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Core SBML Team
Frank Bergmann Sarah Keating Lucian Smith
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A huge thank you to the community
Attendees at SBML 10th Anniversary Symposium, Edinburgh, 2010
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