a profile of today's sbml-compatible software

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


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

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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

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





• Neural models



Scope of SBML encompasses many types of models

Find examples inBioModels Databasehttp://biomodels.net/biomodels

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• Neural models



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

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

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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

12

Out

line 1. Background


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

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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

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


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?

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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


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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

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

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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

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

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Out

line 1. Background


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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