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MyersResearchGroup / iBioSim

iBioSim is a computer-aided design (CAD) tool aimed for the modeling, analysis, and design of genetic circuits. It is capable of importing and exporting models specified using the Systems Biology Markup Language (SBML). iBioSim also supports the Synthetic Biology Open Language (SBOL), an emerging standard for information exchange in synthetic biology.
http://www.async.ece.utah.edu/ibiosim
Apache License 2.0
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Cannot connect genetic production to CDS #502

Open jakebeal opened 6 years ago

jakebeal commented 6 years ago

I want to be able to make an interaction in which genetic production actually comes from a particular CDS, rather than a whole transcriptional unit. Otherwise, multi-product TUs are in the strange state where you can't tell what coding sequence is responsible for which products.

cjmyers commented 6 years ago

This one is a bit tricky, and it would be great to discuss this with you a bit further. Right now it is a bit cumbersome to express this in SBOL. It can be done, but it requires the use of MapsTo. Since iBioSim is built for modeling and from a modeling perspective knowing which CDS produced a protein is not important, we took the simpler approach of just connecting interactions to transcriptional units. However, I do understand from a genetic design perspective, this information is important. Also, this is one of the main stumbling blocks to the extension of SBOLDesigner to interactions as well.

What I think it will come down to is figuring out both the best way to represent this in SBOL as well as the best way to infer a more human consumable representation. To make this work though we will need to restrict the patterns that we can map to this more human readable form. Anyway, this is another thing I hope we can discuss when we meet up.

On Feb 7, 2018, at 1:22 PM, Jacob Beal notifications@github.com wrote:

I want to be able to make an interaction in which genetic production actually comes from a particular CDS, rather than a whole transcriptional unit. Otherwise, multi-product TUs are in the strange state where you can't tell what coding sequence is responsible for which products.

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