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iGEM-Engineering / iGEM-distribution

Repository for collective design of an iGEM DNA distribution
https://igem-distribution.readthedocs.io
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Defining plasmids #118

Open jakebeal opened 2 years ago

jakebeal commented 2 years ago

Related to #58, we need to distinguish between a pre-construction plasmid and a post-construction plasmid (e.g., with an insert replacing a dropout section)

GC-repeat commented 2 years ago

What if we consider that anything (insert, dropout section) between the cloning prefix and suffix is a part. In that case we may not have to distinguish pre and post-construction plasmid and we could just generalize the iGEM registry definition for a plasmid : plasmid = plasmid backone (including prefix and suffix) + part.

Current iGEM registry definiton : image

jakebeal commented 2 years ago

I think this would work for BioBricks, I don't believe it works for GoldenGate, which uses different backbones at different levels.

GC-repeat commented 2 years ago

I'm probably missing something here. Is having different backbones the issue ? Something more general may be : plasmid = backbone (without assembly context) + prefix + part + suffix.

jakebeal commented 2 years ago

That sounds reasonable to me for BioBricks and GoldenGate, though we definitely need to work the examples.

jakebeal commented 2 years ago

A proposal for this has been made in: https://github.com/SynBioDex/SEPs/blob/master/sep_055.md