Difference between revisions of "Registry of Standard Biological Models"

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|bgcolor="#181860"|<font face="tahoma" size="2" color=#ffffff>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.</font>
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|bgcolor="#181860"|<font face="tahoma" size="2" color=#ffffff>A collection of models of biological parts that can be freely reused and composed with each other to produce more complex models.  A draft implementation of the registry is underway and collaborators are being sought.</font>
 
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|align="center"|'''Talk to us at''' - [[BioSysBio:abstracts/2007/Vincent_Rouilly | '''BioSysBio 2007''']], [http://www.syntheticbiology.ethz.ch/conf_2007 SB3.0], and [[Registry of Standard Biological Models/Presentation | '''iGEM Jamboree Workshop 2007''']]
 
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|colspan=2 width="700px" class="green2"| '''Talk to us at''' - [[BioSysBio:abstracts/2007/Vincent_Rouilly | '''BioSysBio 2007''']], [[Registry of Standard Biological Models/Presentation | '''iGEM Jamboree Workshop 2007''']]
 
 
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|width="350px" class="green3" | '''Goals'''
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|'''Goals'''
 
*To contribute to the Open Source [[Synthetic Biology]] effort.
 
*To contribute to the Open Source [[Synthetic Biology]] effort.
*To store, curate and support models related to physical DNA Biobricks.
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*To store, curate and support models related to [http://parts.mit.edu physical Biobricks].
 
*To drive and guide the experimental characterization of BioBricks.
 
*To drive and guide the experimental characterization of BioBricks.
 
*To enable the reuse of modular part models.
 
*To enable the reuse of modular part models.
 
*To provide a forum for modelers to contribute to the BioBricks effort.
 
*To provide a forum for modelers to contribute to the BioBricks effort.
 
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|width="350px" class="green3" | '''Activities'''
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*Defining Standard Biological Models
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|'''Activities'''
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*[[/Registry organization|Planning]] the architecture of a registry of standard biological models.
 
*Building a [[Registry of Standard Biological Models/Model Catalog|collection]] of standard biological models.
 
*Building a [[Registry of Standard Biological Models/Model Catalog|collection]] of standard biological models.
 
*Define a modeling description language that is:
 
*Define a modeling description language that is:
**Machine readable (XML, RDF)
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**Machine readable
 
**Capable of describing gene expression networks
 
**Capable of describing gene expression networks
 
**Modular (standardized defined inputs/ouputs)
 
**Modular (standardized defined inputs/ouputs)
 
**Hierarchical (models are composable)
 
**Hierarchical (models are composable)
 
**Capable of describing models that can be related to experimental data.
 
**Capable of describing models that can be related to experimental data.
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*See [[Registry of Standard Biological Models/CellML Practical|this page]] for a draft implementation.
 
*See [[Registry of Standard Biological Models/CellML Practical|this page]] for a draft implementation.
 
*See [[Registry_of_Standard_Biological_Models/Basic_Component_Models|this page]] for a draft on model implementations following CellML 1.1.
 
*See [[Registry_of_Standard_Biological_Models/Basic_Component_Models|this page]] for a draft on model implementations following CellML 1.1.
*See [[Registry of Standard Biological Models/General Architecture Discussion|this page]] to access current discussion on the implementation.
 
 
 
= Interesting stuff to explore ... =
 
 
*SBML[http://sbml.org/index.psp] and CellML[http://www.cellml.org/] 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. [http://www2.informatik.hu-berlin.de/top/pnml/pnml.html]
 
*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.
 

Latest revision as of 14:49, 4 October 2007

A collection of models of biological parts that can be freely reused and composed with each other to produce more complex models. A draft implementation of the registry is underway and collaborators are being sought.
Talk to us at - BioSysBio 2007, SB3.0, and iGEM Jamboree Workshop 2007
Goals
  • To contribute to the Open Source Synthetic Biology effort.
  • To store, curate and support models related to physical 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
  • Planning the architecture of a registry of standard biological models.
  • Building a collection of standard biological models.
  • Define a modeling description language that is:
    • Machine readable
    • 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:

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  • See this page for a draft implementation.
  • See this page for a draft on model implementations following CellML 1.1.