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="blue"| '''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="blue" | '''Goals'''
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|'''Goals'''
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*To contribute to the Open Source [[Synthetic Biology]] effort.
*To contribute to the Open Source [[Synthetic Biology]] effort.
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*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="blue" | '''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:
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**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.
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*See [[Registry of Standard Biological Models/General Architecture Discussion|this page]] to access current discussion on the implementation.
 

Current revision

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:



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