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.