a profile of today's sbml-compatible software
DESCRIPTION
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.TRANSCRIPT
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
1
Out
line 1. Background
2. Survey results & discussion
3. Acknowledgments
2
Out
line 1. Background
2. Survey results & discussion
3. Acknowledgments
3
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
4
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
5
Scope of SBML encompasses many types of models6
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
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
6
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
6
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
7
Where to learn more: SBML.org—the SBML portal
8
Find SBML software
Where to learn more: SBML.org—the SBML portal
8
SBML Software Guide, with different views (same data)9
Exam
ple:
the
sof
twar
e m
atri
x
10
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
11
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
12
Out
line 1. Background
2. Survey results & discussion
3. Acknowledgments
13
New version of the SBML software survey
14
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
15
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
16
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?
17
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?
18
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
19
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
20
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
21
Availability of software
Fee-based2%
Free98%
Fees for academics
Fee-based10%
Free90%
Fees for non-academics
Notavail.21%
Codeavailable
79%
Is source code available?
22
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
23
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
24
Out
line 1. Background
2. Survey results & discussion
3. Acknowledgments
25
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
26
Core SBML Team
Frank Bergmann Sarah Keating Lucian Smith
27
A huge thank you to the community
Attendees at SBML 10th Anniversary Symposium, Edinburgh, 2010
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