MIRIAM and MIASE

329 views

Published on

  • Be the first to comment

  • Be the first to like this

MIRIAM and MIASE

  1. 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. 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. 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. 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. 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

×