Tuesday, August 11, 2009

Physiome

Computer readable format for representing biological models.

  • SBML
  • SBO
  • CellML
  • SBGN
  • insilicoML
  • MML
  • VCML

SBML

  • Declarative not procedural
  • Level 3 will support composition of modules

CML
  • Explicit mathematical modeling.
  • Meta data provides context. Simulation and graphing meta data. Application specific annotations.

MIRIAM

  • Proposed guidelines for annotation and curation of quantitative models.
  • Tuples: {data item} {optional qualifier} {entity qualifier}

MIASE and SED-OM and SED-ML

  • Minimum information required to replicate a simulation.

SBGN

  • Three languages: Process diagram; Activity flow diagram; Entity relationship diagram.

Physiome model description

  • Software agnostic description of the model.
  • Encoding standards.
  • Annotation.
  • Describe simulation experiments.
  • Describe simulation experiments.
  • Post processing.

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