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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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Support SBOL Visual 2.0 icons #493

Open tramyn opened 6 years ago

tramyn commented 6 years ago

Currently, annotating iBioSim components with an SBOL component will replace iBioSim icon with a transcriptional unit icon. It would be nice if we support SBOL visual 2.0 icons instead. An example of this feature is annotating a species with a promoter retrieved from SynBioHub. After annotating the species, the shape representing the species is replaced with a transcriptional unit icon. What I would like to expect to see is a promoter icon instead since I am only annotating a promoter and not an entire transcriptional unit component.

cjmyers commented 6 years ago

There are a few reasons why this would be tricky.

1) This is included as a glyph icon, so we would need a glyph icon for every combination of components one might like to link. The only possibility would be to use the top-level glyph which would mean that in most cases this would be just a box (i.e., engineered region).

2) The "promoter" in iBioSim from a modeling perspective really only works in simulation for complete transcriptional units, so if the plan is to perform simulation, then it really should be a complete transcriptional unit.

However, my guess is you are using this to build interactions, which are not meant to be simulated individually. Rather this is a way to build interactions in SBOL. In that case, I can see the point to wanting to see the correct SBOL2 glyph. We could perhaps find a middle point that shows the top-level glyph then in the situation where it is an engineered region that happens to be a transcriptional unit, we could show the transcriptional unit rather than the box.