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Slides from presentation given at the Computational Cell Biology Summer School, 2011, at Cold Spring Harbor Laboratory in New York, USA, July 2011.
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SBML (the Systems Biology Markup Language), BioModels Database, and related resources
Michael Hucka, Ph.D.(On behalf of many people)
California Institute of TechnologyPasadena, California, USA
2Friday, July 15, 2011
Background and context
Overview of SBML
Survey of some software resources for SBML
Related efforts
Acknowledgements
Roa
dmap
3Friday, July 15, 2011
Background and context
Overview of SBML
Survey of some software resources for SBML
Related efforts
Acknowledgements
Roa
dmap
4Friday, July 15, 2011
Must weave solutions using different methods & tools
5Friday, July 15, 2011
Need effective sharing of models
Not enough simply to publish lists of equations!
Need a software-independent format
• No single package answers all needs
• New techniques (⇒ new tools) are developed continuously
• Different packages have different niche strengths
- Strengths are often complementary
Need to capture both
• Mathematical content of a model
• Semantic content of a model
6Friday, July 15, 2011
Goal: reproducible and reusable models and simulations7Friday, July 15, 2011
Background and context
Overview of SBML
Survey of some software resources for SBML
Related efforts
Acknowledgements
Roa
dmap
8Friday, July 15, 2011
Format for representing quantitative models
• Defines object model + rules for its use
- Serialized to XML
Neutral with respect to modeling framework
• ODE vs. stochastic vs. ...
A lingua franca for software
• Not procedural
SBML = Systems Biology Markup Language
9Friday, July 15, 2011
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 simple
naA + nbBf([A],[B],[P ],...)−−−−−−−−−−−−→npP
ncCf(...)−−−→ ndD + neE + nfF
...
• Unit definitions
• Annotations
10Friday, July 15, 2011
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 simple
naA + nbBf([A],[B],[P ],...)−−−−−−−−−−−−→npP
ncCf(...)−−−→ ndD + neE + nfF
...
Can be anything conceptually compatible
• Unit definitions
• Annotations
10Friday, July 15, 2011
Some basics of SBML core model encoding
c
n
๏ Well-stirred compartments
11Friday, July 15, 2011
Some basics of SBML core model encoding
c
n
protein A protein B
gene mRNAn mRNAc
12Friday, July 15, 2011
Some basics of SBML core model encoding
c
n
protein A protein B
gene mRNAn mRNAc
๏ Reactions can involve any species anywhere
13Friday, July 15, 2011
Some basics of SBML core model encoding
c
n
protein A protein B
gene mRNAn mRNAc
๏ Reactions can cross compartment boundaries
14Friday, July 15, 2011
๏ Reaction/process rates can be (almost) arbitrary formulas
Some basics of SBML core model encoding
c
n
protein A protein B
gene mRNAn mRNAc
f1(x)
f2(x)
f3(x)f4(x)
f5(x)
15Friday, July 15, 2011
๏ “Rules”: equations expressing relationships in addition to reaction sys.
Some basics of SBML core model encoding
c
n
protein A protein B
gene mRNAn mRNAc
f1(x)
f2(x)
f3(x)
g1(x)g2(x)
.
.
.
f4(x)
f5(x)
16Friday, July 15, 2011
๏ “Events”: discontinuous actions triggered by system conditions
Some basics of SBML core model encoding
c
n
protein A protein B
gene mRNAn mRNAc
f1(x)
f2(x)
f3(x)
g1(x)g2(x)
.
.
.
Event1: when (...condition...), do (...assignments...)
Event2: when (...condition...), do (...assignments...)
...
f4(x)
f5(x)
17Friday, July 15, 2011
Event1: when (...condition...), do (...assignments...)
Event2: when (...condition...), do (...assignments...)
...
Some basics of SBML core model encoding
c
n
protein A protein B
gene mRNAn mRNAc
f1(x)
f2(x)
f3(x)
g1(x)g2(x)
.
.
.
f4(x)
f5(x)
“This event represents ...”
“This is identified by GO id # ...”
“This is an enzymatic reaction with EC # ...”
“This is a transport into the nucleus ...” “This compartment
represents the nucleus ...”
18Friday, July 15, 2011
Scope of SBML is not limited to one kind of model
Signaling pathway models Fernandez et al. (2006)
DARPP-32 Is a Robust Integrator of Dopamine and Glutamate Signals
PLoS Computational Biology
BioModels Database model#BIOMD0000000153
19Friday, July 15, 2011
Scope of SBML is not limited to one kind of model
Signaling pathway models
Conductance-based models
• “Rate rules” for temporal evolution of quantitative parameters
Hodgkin & Huxley (1952)
A quantitative description of membrane current and its application to conduction and excitation in nerve
J. Physiology 117:500–544
BioModels Database model#BIOMD0000000020
20Friday, July 15, 2011
Scope of SBML is not limited to one kind of model
Signaling pathway models
Conductance-based models
• “Rate rules” for temporal evolution of quantitative parameters
Neural models
• “Events” for discontinuous changesin quantitative parameters
Izhikevich EM. (2003)
Simple model of spiking neurons.
IEEE Trans Neural Net.
BioModels Database model#BIOMD0000000127
21Friday, July 15, 2011
Scope of SBML is not limited to one kind of model
Signaling pathway models
Conductance-based models
• “Rate rules” for temporal evolution of quantitative parameters
Neural models
• “Events” for discontinuous changesin quantitative parameters
Pharmacokinetic/dynamics models
• “Species” is not required to be abiochemical entity
Tham et al. (2008)
A pharmacodynamic model for the time course of tumor shrinkage by gemcitabine + carboplatin in non-small cell lung cancer patients
Clin. Cancer Res. 14
BioModels Database model#BIOMD0000000234
22Friday, July 15, 2011
Scope of SBML is not limited to one kind of model
Signaling pathway models
Conductance-based models
• “Rate rules” for temporal evolution of quantitative parameters
Neural models
• “Events” for discontinuous changesin quantitative parameters
Pharmacokinetic/dynamics models
• “Species” is not required to be abiochemical entity
Infectious diseases
Munz et al. (2009 )
When zombies attack!: Mathematical modelling of an outbreak of zombie infection
Infectious Disease Modelling Research Progress, eds. Tchuenche et al., p. 133–150
BioModels Database model#MODEL1008060001
23Friday, July 15, 2011
0
100
200
300
2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011
(counted in middle of each year)
229 as of July 14 ↓
Number of software systems supporting SBML
24Friday, July 15, 2011
What are SBML “Levels”?
Specification document available from http://sbml.org/Documents
Newest: Level 3 Version 1 Core
• Oct. 2010
About SBML “Levels”:
• Levels help manage significant restructuring of SBML architecture
• Levels coexist
- E.g., Level 2 models will remain valid and exist for a long time
• A Level is not solely a vertical change (i.e., more features)—there is horizontal change too (i.e., changes to existing elements)
25Friday, July 15, 2011
SBML continues to evolve
26Friday, July 15, 2011
SBML Level 3—A modular SBML
SBML Level 3 Core
Package X Package Y
Package Z
A package adds constructs & capabilities
Models declare which packages they use
• Applications tell users which packages they support
Package development can be decoupled
27Friday, July 15, 2011
Package Specification status
Graph layout Level 3 version defined; in review
Multicomponent species Level 3 version defined; in review
Hierarchical composition Level 3 specification under discussion
Groups Level 3 specification under discussion
Qualitative models Level 3 specification under discussion
Spatial geometry Level 3 specification under discussion
Arrays & sets Specification proposed
Distribution & ranges Specification proposed
Steady-state models Specification proposed
Graph rendering Specification proposed
Spatial diffusion Specification needed
Dynamic structures Specification needed
28Friday, July 15, 2011
Package Specification status
Graph layout Level 3 version defined; in review
Multicomponent species Level 3 version defined; in review
Hierarchical composition Level 3 specification under discussion
Groups Level 3 specification under discussion
Qualitative models Level 3 specification under discussion
Spatial geometry Level 3 specification under discussion
Arrays & sets Specification proposed
Distribution & ranges Specification proposed
Steady-state models Specification proposed
Graph rendering Specification proposed
Spatial diffusion Specification needed
Dynamic structures Specification needed
Extends SBML species to represent:• Entities that can exist under
different states affecting their behaviors
• Entities that are complexes of other entities
28Friday, July 15, 2011
Package Specification status
Graph layout Level 3 version defined; in review
Multicomponent species Level 3 version defined; in review
Hierarchical composition Level 3 specification under discussion
Groups Level 3 specification under discussion
Qualitative models Level 3 specification under discussion
Spatial geometry Level 3 specification under discussion
Arrays & sets Specification proposed
Distribution & ranges Specification proposed
Steady-state models Specification proposed
Graph rendering Specification proposed
Spatial diffusion Specification needed
Dynamic structures Specification needed
Models composed of submodels
28Friday, July 15, 2011
Package Specification status
Graph layout Level 3 version defined; in review
Multicomponent species Level 3 version defined; in review
Hierarchical composition Level 3 specification under discussion
Groups Level 3 specification under discussion
Qualitative models Level 3 specification under discussion
Spatial geometry Level 3 specification under discussion
Arrays & sets Specification proposed
Distribution & ranges Specification proposed
Steady-state models Specification proposed
Graph rendering Specification proposed
Spatial diffusion Specification needed
Dynamic structures Specification needed
Grouping model entities together, for conceptual and annotation purposes
28Friday, July 15, 2011
Package Specification status
Graph layout Level 3 version defined; in review
Multicomponent species Level 3 version defined; in review
Hierarchical composition Level 3 specification under discussion
Groups Level 3 specification under discussion
Qualitative models Level 3 specification under discussion
Spatial geometry Level 3 specification under discussion
Arrays & sets Specification proposed
Distribution & ranges Specification proposed
Steady-state models Specification proposed
Graph rendering Specification proposed
Spatial diffusion Specification needed
Dynamic structures Specification needed
Models in which entity variables are not quantities; e.g., boolean models
28Friday, July 15, 2011
Package Specification status
Graph layout Level 3 version defined; in review
Multicomponent species Level 3 version defined; in review
Hierarchical composition Level 3 specification under discussion
Groups Level 3 specification under discussion
Qualitative models Level 3 specification under discussion
Spatial geometry Level 3 specification under discussion
Arrays & sets Specification proposed
Distribution & ranges Specification proposed
Steady-state models Specification proposed
Graph rendering Specification proposed
Spatial diffusion Specification needed
Dynamic structures Specification needed
2-D and 3-D geometry of physical objects (compartments & species)
28Friday, July 15, 2011
Example: Hierarchical Model Composition
Species ...Compartments ...
Parameters ...Reactions ...
Model “A”
Current SBML
29Friday, July 15, 2011
Example: Hierarchical Model Composition
Species ...Compartments ...
Parameters ...Reactions ...
Model “A”
Current SBML
Species ...Compartments ...
Parameters ...Reactions ...
Model “A”
With model composition
Species ...Compartments ...
Parameters ...Reactions ...
Model “B”
Species ...Compartments ...
Parameters ...Reactions ...
Model “C”
29Friday, July 15, 2011
More scenarios
Species ...Compartments ...
Parameters ...Reactions ...
Model “A”
Species ...Compartments ...
Parameters ...Reactions ...
Model “B”
Species ...Compartments ...
Parameters ...Reactions ...
Model “B”
Species ...Compartments ...
Parameters ...Reactions ...
Model “B”
...
30Friday, July 15, 2011
More scenarios
Species ...Compartments ...
Parameters ...Reactions ...
Model “A”
Species ...Compartments ...
Parameters ...Reactions ...
Model “B”
Species ...Compartments ...
Parameters ...Reactions ...
Model “C”
Model “D”
Species ...Compartments ...
Parameters ...Reactions ...
31Friday, July 15, 2011
More scenarios
Species ...Compartments ...
Parameters ...Reactions ...
Model “A”
Species ...Compartments ...
Parameters ...Reactions ...
Model “B”
Separate files/resources
Species ...Compartments ...
Parameters ...Reactions ...
Model “C”
Model “C”
Model “D”
Species ...Compartments ...
Parameters ...Reactions ...
Model “D”
Model “B”
Think: libraries of well-tested
models
32Friday, July 15, 2011
Links/references/replacements
Model “outer”
S1 S2
Compartment “c”
Compartment “q”
Model “inner”
X1 X2
33Friday, July 15, 2011
Links/references/replacements
Model “outer”
S1 S2
Compartment “c”
Compartment “q”
Model “inner”
X1 X2
Model “outer”
Compartment “c”
S1 S2 inner/X2
Implied model
33Friday, July 15, 2011
Background and context
Overview of SBML
Survey of some software resources for SBML
Related efforts
Acknowledgements
Roa
dmap
34Friday, July 15, 2011
SBML.org
35Friday, July 15, 2011
SBM
L So
ftw
are
Gui
de
36Friday, July 15, 2011
SBM
L So
ftw
are
Gui
de
Find SBML software
36Friday, July 15, 2011
SBML Software Guide37Friday, July 15, 2011
Some particularly full-featured, general simulation tools
COPASI: ODE & stochastic simulation, parameter scanning, powerful plotting capabilities, much more
CellDesigner: graphical editing interface, SBGN support, SABIO-RK integration, much more
iBioSim: special features for genetic circuit models for synthetic biology
Virtual Cell: web-based interface
roadRunner & SBW: .NET support, many tools in toolkit
38Friday, July 15, 2011
Onl
ine
SBM
L Va
lidat
or
39Friday, July 15, 2011
Onl
ine
SBM
L Va
lidat
or
39Friday, July 15, 2011
Onl
ine
SBM
L Va
lidat
or
40Friday, July 15, 2011
Onl
ine
SBM
L Va
lidat
or
Validate SBML files
40Friday, July 15, 2011
(Demo)(demo)
41Friday, July 15, 2011
How
to
keep
in t
ouch
42Friday, July 15, 2011
How
to
keep
in t
ouch
Front-page news
42Friday, July 15, 2011
How
to
keep
in t
ouch
Twitter & RSS feeds
42Friday, July 15, 2011
How
to
keep
in t
ouch
Mailing lists/forums
42Friday, July 15, 2011
SBML mailing lists & online forum interface
Suggest subscribing to sbml-announce (it’s very low volume)
43Friday, July 15, 2011
Software API libraries: libSBML & JSBML
44Friday, July 15, 2011
libSBML
๏ Reads, writes, validates SBML
• Hundreds of rules for helping to ensure correct SBML
๏ Unit checking & conversion
๏ Well-tested
๏ Written in portable C++
• Linux, Mac, Windows, FreeBSD
๏ APIs for C, C++, C#, Java, Octave, Perl, Python, Ruby, MATLAB (some via SWIG)
๏ Can use Expat, libxml2, or Xerces
๏ Open-source under LGPL
๏ Developed by Sarah Keating, Frank Bergman, Ben Bornstein, Akiya Jouraku, & Mike Hucka, with substantial contributions from many other people
Latest stable version: 5.0.0http://sbml.org/Software/libSBML
45Friday, July 15, 2011
JSBML
Pure Java implementation
API is highly compatible with libSBML
• Functionality is subset of libSBML functionality
Under active development
• Already in use in apps
• Help welcome!
Main developers: Andreas Dräger & Nicolas Rodriguez
46Friday, July 15, 2011
BioModels Database
47Friday, July 15, 2011
http://biomodels.net/biomodels
48Friday, July 15, 2011
Features of BioModels Database
Stores & serves quantitative models of biological interest
• Free, public resource
• Models must be described in peer-reviewed publication(s)
All models are curated by hand to reproduce published results
Imports & exports models in several formats
• SBML, CellML, SciLab, XPP, BioPAX
Developed by Nicolas Le Novère’s group (EBI), funded by EBI & NIH
Today: 600+ models
49Friday, July 15, 2011
(demo)
50Friday, July 15, 2011
Background and context
Overview of SBML
Survey of some software resources for SBML
Related efforts
Acknowledgements
Roa
dmap
51Friday, July 15, 2011
Growing community, greater challenges52Friday, July 15, 2011
Representationformat
Model Procedures Results
Minimal inforequirements
Semantics—
Mathematical
Other
SBRML
?
annotations annotations annotations
53Friday, July 15, 2011
Representationformat
Model Procedures Results
Minimal inforequirements
Semantics—
Mathematical
Other
SBRML
?
annotations annotations annotations
53Friday, July 15, 2011
Annotations can answer questions:
• “What exactly is this entity you call X?”
• “What other identities does this entity have?”
• “What exactly is the process represented by equation ‘e17’?”
• “What role does constant ‘k3’ play in equation ‘e17’?”
• “What mathematical framework is being assumed?”
• “What organism is this in?”
• ... etc. ...
Multiple annotations on same entity are common
Annotations add semantics and connections
54Friday, July 15, 2011
For semantics of a model’s math
Human- & program-accessible
• Browser interface
• Web services
Math formulas in MathML
Systems Biology Ontology (SBO)
55Friday, July 15, 2011
For semantics of a model’s math
Human- & program-accessible
• Browser interface
• Web services
Math formulas in MathML
Systems Biology Ontology (SBO)
55Friday, July 15, 2011
For semantics of a model’s math
Human- & program-accessible
• Browser interface
• Web services
Math formulas in MathML
Systems Biology Ontology (SBO)
55Friday, July 15, 2011
<sbml ...> ... <listOfCompartments> <compartment id="cell" size="1e-15" /> </listOfCompartments> <listOfSpecies> <species compartment="cell" id="S1" initialAmount="1000" /> <species compartment="cell" id="S2" initialAmount="0" /> <listOfSpecies> <listOfParameters> <parameter id="k" value="0.005" sboTerm="SBO:0000339" /> <listOfParameters> <listOfReactions> <reaction id="r1" reversible="false"> <listOfReactants> <speciesReference species="S1" stoichiometry="2" sboTerm="SBO:0000010" /> </listOfReactants> <listOfProducts> <speciesReference species="S1" stoichiometry="2" sboTerm="SBO:0000011" /> </listOfProducts> <kineticLaw sboTerm="SBO:0000052"> <math> ... <math> ...</sbml>
56Friday, July 15, 2011
<sbml ...> ... <listOfCompartments> <compartment id="cell" size="1e-15" /> </listOfCompartments> <listOfSpecies> <species compartment="cell" id="S1" initialAmount="1000" /> <species compartment="cell" id="S2" initialAmount="0" /> <listOfSpecies> <listOfParameters> <parameter id="k" value="0.005" sboTerm="SBO:0000339" /> <listOfParameters> <listOfReactions> <reaction id="r1" reversible="false"> <listOfReactants> <speciesReference species="S1" stoichiometry="2" sboTerm="SBO:0000010" /> </listOfReactants> <listOfProducts> <speciesReference species="S1" stoichiometry="2" sboTerm="SBO:0000011" /> </listOfProducts> <kineticLaw sboTerm="SBO:0000052"> <math> ... <math> ...</sbml>
SBO:0000339
56Friday, July 15, 2011
<sbml ...> ... <listOfCompartments> <compartment id="cell" size="1e-15" /> </listOfCompartments> <listOfSpecies> <species compartment="cell" id="S1" initialAmount="1000" /> <species compartment="cell" id="S2" initialAmount="0" /> <listOfSpecies> <listOfParameters> <parameter id="k" value="0.005" sboTerm="SBO:0000339" /> <listOfParameters> <listOfReactions> <reaction id="r1" reversible="false"> <listOfReactants> <speciesReference species="S1" stoichiometry="2" sboTerm="SBO:0000010" /> </listOfReactants> <listOfProducts> <speciesReference species="S1" stoichiometry="2" sboTerm="SBO:0000011" /> </listOfProducts> <kineticLaw sboTerm="SBO:0000052"> <math> ... <math> ...</sbml>
SBO:0000339
“forward bimolecular rate constant, continuous case”
56Friday, July 15, 2011
MIRIAM = “Minimum Information Requested In the Annotation of Models”
Addresses 2 general areas
MIRIAM is not specific to SBML
What is MIRIAM?
Requirements for reference correspondence
Scheme for encoding annotations
Annotations for attributing model
creators & sources
Annotations for referring to external
data resources
57Friday, July 15, 2011
MIRIAM = “Minimum Information Requested In the Annotation of Models”
Addresses 2 general areas
MIRIAM is not specific to SBML
What is MIRIAM?
Requirements for reference correspondence
Scheme for encoding annotations
Annotations for attributing model
creators & sources
Annotations for referring to external
data resources
Scheme for encoding annotations
57Friday, July 15, 2011
MIRIAM cross-references are simple triples
Data type identifier
Data item identifier
Annotation qualifier
Model element
Entity referenced
relationship qualifier(optional)
{ }(Required) (Required) (Optional)
URI chosen from agreed-upon list
Syntax & value space depends on data type
Format:
Controlled vocabulary term
58Friday, July 15, 2011
Why worry about standard ways of writing annotations?
Structured, machine-readable annotations increase your model’s utility
• Allow more precise identification of model components
- Understand model structure
- Compare models
- Integrate models
- Search models
• Adds a semantic layer—integrates knowledge into the model
- Understand the underlying biology
- Reuse models
- Convert models to other forms
59Friday, July 15, 2011
Annotations permit inter-database linking
60Friday, July 15, 2011
Annotations permit inter-database linking
60Friday, July 15, 2011
<species metaid="metaid_0000009" id="species_3" compartment="c_1"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" > <rdf:Description rdf:about="#metaid_0000009"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:obo.chebi:CHEBI%3A15996"/> <rdf:li rdf:resource="urn:miriam:kegg.compound:C00044"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> </species>
SBML defines a syntax for annotations
61Friday, July 15, 2011
<species metaid="metaid_0000009" id="species_3" compartment="c_1"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" > <rdf:Description rdf:about="#metaid_0000009"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:obo.chebi:CHEBI%3A15996"/> <rdf:li rdf:resource="urn:miriam:kegg.compound:C00044"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> </species>
SBML defines a syntax for annotations
<rdf:Bag> <rdf:li rdf:resource="urn:miriam:obo.chebi:CHEBI%3A15996"/> <rdf:li rdf:resource="urn:miriam:kegg.compound:C00044"/> </rdf:Bag>
Data references
61Friday, July 15, 2011
<species metaid="metaid_0000009" id="species_3" compartment="c_1"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" > <rdf:Description rdf:about="#metaid_0000009"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:obo.chebi:CHEBI%3A15996"/> <rdf:li rdf:resource="urn:miriam:kegg.compound:C00044"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> </species>
SBML defines a syntax for annotations
<bqbiol:is>
</bqbiol:is>
Relationship qualifier
61Friday, July 15, 2011
“Term #1.1.1.1 (alcohol dehydrogenase) in the Enzyme Commission’s Enzyme Nomenclature database”
⇒ urn:miriam:ec-code:1.1.1.1{URN scheme established
by the MIRIAM project
{Chosen by the creator of theentry in MIRIAM Resources
62Friday, July 15, 2011
http://www.ebi.ac.uk/miriam
MIRIAM Resources provides URI dictionary & resolver
Community-maintained
63Friday, July 15, 2011
http://www.ebi.ac.uk/miriam
MIRIAM Resources provides URI dictionary & resolver
Community-maintained
63Friday, July 15, 2011
MIRIAM identifiers now in use by many other projects
Data resources• BioModels Database (kinetic models)• PSI Consortium (protein interaction)• Reactome (pathways)• Pathway Commons (pathways)• SABIO-RK (reaction kinetics)• Yeast consensus model database• E-MeP (structural genomics)
Application software• ARCADIA• BioUML• COPASI• libAnnotationSBML• libSBML• Saint• SBML2BioPAX• SBML2LaTeX• SBMLeditor• semanticSBML• Snazer• SBW• The Virtual Cell
64Friday, July 15, 2011
Annotations enable many interesting possibilities
http://www.semanticsbml.org
65Friday, July 15, 2011
Representationformat
Model Procedures Results
Minimal inforequirements
Semantics—
Mathematical
Other
SBRML
?
annotations annotations annotations
66Friday, July 15, 2011
Representationformat
Model Procedures Results
Minimal inforequirements
Semantics—
Mathematical
Other
SBRML
?
annotations annotations annotations
66Friday, July 15, 2011
SED-ML = Simulation Experiment Description ML
Application-independent format
Captures procedures, algorithms, parameter values
• Steps to go from model to output
libSedML project developing API library
<sbml ...> ... <listOfCompartments> <compartment id="cell" size="1e-15" /> </listOfCompartments> <listOfSpecies> <species compartment="cell" id="S1" initialAmount="1000" /> <species compartment="cell" id="S2" initialAmount="0" /> <listOfSpecies> <listOfParameters> <parameter id="k" value="0.005" sboTerm="SBO:0000339" /> <listOfParameters> <listOfReactions> <reaction id="r1" reversible="false"> <listOfReactants> <speciesReference species="S1" stoichiometry="2" sboTerm="SBO:0000010" /> ...
?
67Friday, July 15, 2011
Background and context
Overview of SBML
Survey of some software resources for SBML
Related efforts
Acknowledgements
Roa
dmap
68Friday, July 15, 2011
People on SBML Team & BioModels Team
SBML Team BioModels.net TeamMichael Hucka Nicolas Le NovèreSarah Keating Camille Laibe
Frank Bergmann Nicolas RodriguezLucian Smith Nick Juty
Nicolas Rodriguez Vijayalakshmi ChelliahLinda Taddeo Michael SchubertAkiya Joukarou Lukas EndlerAkira Funahashi Chen Li
Kimberley Begley Harish DharuriBruce Shapiro Lu LiAndrew Finney Enuo HeBen Bornstein Mélanie Courtot
Ben Kovitz Alexander BroicherHamid Bolouri Arnaud HenryHerbert Sauro Marco DonizelliJo Matthews
Maria Schilstra
VisionariesHiroaki Kitano
John Doyle
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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)
National Science Foundation (USA)
International Joint Research Program of NEDO (Japan)
JST ERATO-SORST Program (Japan)
Japanese Ministry of Agriculture
Japanese Ministry of Educ., Culture, Sports, Science and Tech.
BBSRC (UK)
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 & BioModels.net70Friday, July 15, 2011
Where to find out more
Thank you for listening!
SBML http://sbml.org
libSBML & JSBML http://sbml.org/Software
BioModels Database http://biomodels.net/biomodels
MIRIAM http://biomodels.net/miriam
SED-ML http://biomodels.net/sed-ml
SBO http://biomodels.net/sbo
KiSAO http://www.ebi.ac.uk/compneur-srv/kisao/
TEDDY http://www.ebi.ac.uk/compneur-srv/teddy/
71Friday, July 15, 2011