1. MIBBI Workshop 2010, Ruedesheim, Germany, 1st
- 2nd
December
Project Briefings:
Minimum Information Required in
the Annotation of Models
MIRIAM
Minimum Information About a
Simulation Experiment
MIASE
Nick Juty, EMBL-EBI
MIBBI project briefing

2. MIBBI Workshop 2010, Ruedesheim, Germany, 1st
- 2nd
December
Tyson et al (1991)
PNAS 88(1):7328-32
Scope of MIRIAM and MIASE
biochemical model mathematical model
computational modelsimulation

3. MIRIAM compliance
Models must:
Be clearly linked to a single reference description and
accompanied by full attribution and details of creation/modification
Be encoded in a public machine-readable format and reflect the structure of the
biological processes described in the reference paper (list of reactions etc.)
Be instantiable in a simulation (possess initial conditions etc.)
Be Annotated to unambiguously identify each model constituent (MIRIAM URNs)
Minimal Information Required In the Annotation of Models
Support:
MIRIAM compliance supported by model encoding formats: SBML, CellML,
NeuroML. Implementation of MIRIAM URNs facilitated by MIRIAM Resources
MIRIAM URNs supported by
Data resources: BioModels Databases, PSI consortium, Pathway commons,
SABIO-RK, Consensus metabolic model databases, E-MeP database, etc.
Application software: ARCADIA, BIOUML, COPASI, libAnnotationSBML,
LibSBML, SAINT, SBML2BioPAX, SBML2LaTeX, SBMLeditor, SemanticSBML,
Snazer, Systems Biology Workbench, The Virtual Cell, etc.
Status:
Published: Le Novère et al. (2005) Nat Biotechnol 23: 1509-1515
http://biomodels.net/miriam/

4. MIRIAM compliance
MIASE-compliance rules:
All models used in the experiment must be identified, accessible,
and fully described.
A precise description of the simulations and other procedures must be provided.
All information necessary to obtain the desired numerical results must be
provided.
Minimal Information About a Simulation Experiment
Support:
MIASE compliance is supported for instance via the Simulation Experiment
Description Markup Language (SED-ML), and CellML metadata
MIASE Archive
Status:
Under Revision: Waltemath et al. (2011) PLoS Comput Biol
http://biomodels.net/miase/

5. MIBBI Workshop 2010, Ruedesheim, Germany, 1st
- 2nd
December
Acknowledgments
Richard Adams
Daniel A Beard
Frank T Bergmann
Upinder S Bhalla
Randall Britten
Vijayalakshmi Chelliah
Michael T Cooling
Jonathan Cooper
Edmund Crampin
Alan Garny
Stefan Hoops
Michael Hucka
Peter Hunter
Edda Klipp
Andrew Finney
Upinder S Bhalla
Fabien Campagne
Julio Collado-Vides
Mélanie Courtot
Edmund Crampin
Matt Halstead
Stefan Hoops
Michael Hucka
Nick Juty
Edda Klipp
Camille Laibe
Nicolas Le Novère
Andrew Miller
Ion Moraru
David Nickerson
Poul Nielsen
Macha Nikolski
Sven Sahle
Herbert Sauro
Henning Schmidt
Jacky Snoep
Dominic Tolle
Dagmar Waltemath
Olaf Wolkenhauer
Camille Laibe
Nicolas Le Novère
Allyson Lister
Pedro Mendes
Poul Nielsen
Herbert M Sauro
Bruce Shapiro
Jacky L Snoep
Hugh Spence
Neil Swainston