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[cellml-discussion] Best Import/Encapsulation methods


Chronological Thread 
  • From: david.nickerson at nus.edu.sg (David Nickerson)
  • Subject: [cellml-discussion] Best Import/Encapsulation methods
  • Date: Mon, 13 Aug 2007 14:31:54 +0800
Hi,

From your brief description that seems like a reasonable way to
describe and assemble the model. Although looking at your code snippets
it might be worth mentioning that hyphens ('-') are illegal in CellML
names. If you want to send through your complete model hierarchy (or a
simplified version of it) I'd be happy to have a more thorough look at it.


David.

PS - its worth starting a new thread for a new topic so that messages
like this one don't get lost in other conversations.


----- ----- wrote:
> Hi everyone,
>
> Ive been creating a few models and Importing them and such to create more
> complex model.
>
> Example :
> I have 2 existing files (models) promoter-RBS_repressed and protein.
> These 2 respectively contain components promoter-RBS_repressed and Protein.
>
> promoter-RBS_repressed has an input of repressorConcentration and an output
> of synthesisRate.
> protein has an input of synthesisRate and an output of proteinConcentration.
>
> I want to create a single file with input: repressor concentration and
> output: protein concentration.
>
>
> What I have done is to create a 3rd file : repressed_protein-generator ,
> create a component : repressed_protein-generator,
> create connections and groups such that variables are recieved (from other
> models) by repressed protein generator and 'relayed' to
> promoter-RBS_repressed and any output variables from Protein are relayed to
> repressed_protein-generator which can output them.
>
> Segments of code from repressed_protein-generator:
>
> <group>
> <relationship_ref name="repressed_protein-generator"
> relationship="encapsulation"/>
> <component_ref component="repressed_protein-generator">
> <component_ref component="promoter-RBS_repressed"/>
> <component_ref component="Protein"/>
> </component_ref>
> </group>
> ......................................................
>
> <component name="repressed_protein-generator">
>
> <variable name="proteinConcentration" private_interface="in"
> public_interface="out" units="mole"/>
> <variable name="repressorConcentration" private_interface="out"
> public_interface="in" units="mole"/>
>
> </component>
> .....................................................
>
> <connection>
> <map_components component_1="repressed_protein-generator"
> component_2="promoter-RBS_repressed"/>
> <map_variables variable_1="repressorConcentration"
> variable_2="repressorConcentration"/>
> </connection>
>
> <connection>
> <map_components component_1="promoter-RBS_repressed"
> component_2="Protein"/>
> <map_variables variable_1="synthesisRate"
> variable_2="synthesisRate"/>
> </connection>
>
> <connection>
> <map_components component_1="Protein"
> component_2="repressed_protein-generator"/>
> <map_variables variable_1="proteinConcentration"
> variable_2="proteinConcentration"/>
> </connection>
>
>
>
>
> My question is : Is there a better way (more natural way..) to do this in
> CellML ?
>
>
> Thank you.
>
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--
David Nickerson, PhD
Research Fellow
Division of Bioengineering
Faculty of Engineering
National University of Singapore
Email: david.nickerson at nus.edu.sg


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