Registry of Standard Biological Models

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Revision as of 10:26, 26 September 2007 by Barry Canton (Talk | contribs)
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A collection of models of biological parts that can be reused and recombined to produce more complex models. A draft implementation of the registry is underway and collaborators are being sought.
Talk to us at - BioSysBio 2007, iGEM Jamboree Workshop 2007
Goals
  • To contribute to the Open Source Synthetic Biology effort.
  • To store, curate and support models related to physical DNA Biobricks.
  • To drive and guide the experimental characterization of BioBricks.
  • To enable the reuse of modular part models.
  • To provide a forum for modelers to contribute to the BioBricks effort.
Activities
  • Defining Standard Biological Models
  • Building a collection of standard biological models.
  • Define a modeling description language that is:
    • Machine readable (XML, RDF)
    • Capable of describing gene expression networks
    • Modular (standardized defined inputs/ouputs)
    • Hierarchical (models are composable)
    • Capable of describing models that can be related to experimental data.
Recent edits:



  • See this page for a draft implementation.
  • See this page for a draft on model implementations following CellML 1.1.
  • See this page to access current discussion on the implementation.


Interesting stuff to explore ...

  • SBML[1] and CellML[2] are already widely used standards. Are they what Synthetic Biology is looking for?
  • Petri Nets Markup language is already defining a modular/hierarchical approach. Could be interesting to investigate. [3]
  • Standardized outputs: how about using experimental data format to store computed results (like FCS from Flow cytometry), it could help also to define a validation schema when it comes to challenge predicted results with measured ones.
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