Onboarded vector choice for synthesis products

[vinoo-igem]

As we expect to expand, we'll need to consider what (if any) other plasmids we may want to onboard at FreeGenes aside from pSB1C3/5 and in what cases do we want to build into them. So this is meant to openly discuss and provide some context.

[vinoo-igem]

And to provide some context, the primary reasons we chose to onboard pSB1C3/5 for this round of synthesis is

• consistency for past Interlab devices

• overall familiarity within the iGEM community

• used as L0 vector for Type IIS (Loop parts, note: it has a BsmBI site) before ...

• and high-copy chlor meshes well with what other standards tend to use for their L1s (Kan)

• FreeGenes has had issues with synthesizing into pOpen_v3, and last we chatted, prefer not to

• pOpen_v4 while much better for TWIST, is low-medium inducible copy and KanR, so not great for L0s as stated above

That's not to say there aren't better options we should adopt or improvements we should make to the pSB1CX! And to be clear, using pSB1C3/5 is an experiment as well, as we don't know if TWIST will also have issues with it like pOpen_v3.

[eyesmo]

IMO a lot of the design decisions we're thinking through here would benefit from more empirical data. In particular, an interlab study (or perhaps an iGEM mini-competition? Or perhaps a straightforward academic research project?) focused on determining the assembly capacity, fidelity, and reproducibility of a particular set of vector backbones, assembly overhangs, and standard parts would be invaluable. I could imagine such a study being planned and designed over the course of 2022, executed over the course of 2023 (during iGEM 2023?) and then the results guiding Registry and Distribution wetware design going forward.

[vignoni]

I like @eyesmo point of view. However, we need to think about two different things: One would be testing synthesis/assembly-related features that lie in the Twist FreeGenes area on the one hand, and the usage (assembly or direct use of a device from the distro) of those parts by the users (like iGEM teams or others). I see the first one guiding the core design decisions for the distro (like onboarded vector Backbone for synthesis), but I don't see how to perform such study other than what we are already doing/did already this past year. From the perspective of the second point, we are planning to run 3 interlabs this year, and we are open to design more interlabs for the future.