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Cellular Network Models SBML Standards Efforts

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Title: Cellular Network Models SBML Standards Efforts


1
Cellular Network Models SBML Standards Efforts
  • Herbert M Sauro
  • University of Washington

2
There many many modeling software tools
3
SBML in a Nutshell Systems Biology Markup
Language
  • A machine-readable format for representing
    computational models in systems biology
  • Domain systems of biochemical reactions
  • Specified using XML
  • Components in SBML reflect the natural conceptual
    constructs of the domain
  • Software tools write SBMLhumans dont!

4
SBML Describes a Model by Specifying the Cellular
Reactions Involved
OxPhos
Pi
Intermembrane Space
ADP
ATP
Cr
PCr
MiCK
MMCK
Cr
PCr
Cytosol
ATP
ADP
Pi
ATPase
Creatine kinase (CK)
Mitochondrial isoform (MiCK)
Phosphocreatine (PCr)
Myofibrillar isoform (MMCK)
5
Origins of SBML
1. In 1999 there was a grass roots effort to
develop an interchange format between SCAMP,
Gepasi and Metamod/MetaModel. 2. These efforts
coincided with the availability of substantial
funding from the Japanese Government (JST) and
Hiroaki Kitano as PI in 2000. The two efforts
were combined at Caltech to formulate the first
version of SBML.
6
Software and standards development
  • Factors contributing to the successful
    establishment of a standard
  • There should be a need at the grass root level.

7
Software and standards development
2. Funding helps to initiate a) Workshops,
Hackathons and software support for implementing
the standard and to help keep the community
focused and involved (DARPA, DOE, NIH). b)
Repositories. c) Compliance test suites
8
What are the benefits of SBML/CellML?
  • An unambiguous method for specifying models
  • Easily exchange models between research groups
  • The ability to compare different software tools
  • Encourages the building of resource repositories
  • Opens up the possibility of combining models
  • unambiguously

9
Model repositories
Nicolas Le Novere
BioModels.net 168 curated models as of April
2008. 76 uncurated models.
http//www.ebi.ac.uk/biomodels/
10
Ontologies ways to give meaning
  • SBO Systems Biology Ontology (Quantitative
    terms)
  • 2. MIASE The Minimum Information About a
  • Simulation Experiment
  • 3. TEDDY The Terminology for the Description of
  • Dynamics
  • 4. KiSAO Kinetic Algorithm Ontology
  • 5. SBML Level 3 Modularity

11
MIRIAM Minimum Information Requested in the
Annotation of biochemical Models
MIRIAM is not a file format but a minimum
specification on how a model should be made
available to the community Reference
correspondence encoding a model in a
recognized public standardized machine-readable
format. Attribution annotation - A model has to
provide the citation of the reference
description, lists its creators, and be attached
to some terms of distribution. External
resource annotation - each component of a model
must be annotated to allow its unambiguous
identification.
12
Application Simulator Compliance SBML Compliance
13
Standard Reusable Libraries Crossplatform, C/C
  • libSBML SBML Read/Write (Caltech)
  • SOSLib ODE based simulator (Vienna)
  • Antimony Interconvert SBML/CellML to and
    from human readable forms (Seattle)
  • libStructural Mass Conservation/Flux Analysis
    Library (Seattle)
  • ESS Advanced stochastic simulator (Virginia
    State)

All the libraries can be interlinked.
14
Acknowledgements
Current Funding
NIH/NIGMS
NSF
Previous Funding
(DOE)
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