Registry of Standard Biological Models: Difference between revisions
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|width="350px" class="green3" | '''Activities''' | |width="350px" class="green3" | '''Activities''' | ||
*Defining 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) | **Machine readable (XML, RDF) | ||
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**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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*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] | *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. | *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. | ||
Revision as of 07:26, 26 September 2007
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Talk to us at - BioSysBio 2007, iGEM Jamboree Workshop 2007 | |
Goals
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Activities
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- 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.