Demo miniprep protocol?

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Timothy Fallon

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Apr 29, 2022, 4:03:22 PMApr 29
to biopro...@googlegroups.com
Hi PAML fans,

After grokking `PAML`, `PAMLED`, and the `container-ontology` a bit more from the HARMONY meeting & breakout sessions, I think an interesting avenue to demo would be a "Miniprep" protocol (small scale isolation of plasmid DNA, from a bacterial, typically E. coli, culture), including separate (or sub protocols?) for making the requisite buffers.

 

I think this would "stress test" the PAML concepts in the biology bench-lab protocol context (where generality & implicit protocols are the norm), vs PAML's current demos oriented more towards lab automation & microplate based experiment context (where specificity is more the norm).

 

Example of a commercially available Miniprep kit with protocol:

 

See the QIAprep Spin Miniprep Kit - (EN)] (https://www.qiagen.com/us/Resources/ResourceDetail?id=331740ca-077f-4ddd-9e5a-2083f98eebd5&lang=en)] for an abbreviated protocol for experts.

 

Some concerns I see here:

 

Unclear how to specify a solution (mixture of >1 liquid, solid, or gas substances), if they are not already present on a place like Pubchem. i.e. P1 buffer, P2 buffer, PB Buffer, etc., used in the protocols above.

 

Noting: the Buffer compositions are already known so the total solution can be specified from its sub-components:

 

I don't have the time to contribute to making such a protocol/demo "out of whole cloth", but if folks are interested in asynchronously working on this, I can apply my pragmatic bench biologist/chemist knowledge to give feedback and stress test it & maybe develop it a little with significant guidance. 
 
All the best,
-Tim
___________________________________
Timothy R. Fallon, PhD
NIH NRSA Postdoctoral Fellow - Moore Laboratory

Center for Marine Biotechnology and Biomedicine 
Scripps Institution of Oceanography 
University of California, San Diego 

tfa...@ucsd.edu
Google Scholar publications and citations
Website: http://photocyte.github.io
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Jake Beal

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Apr 30, 2022, 7:37:54 AMApr 30
to Timothy Fallon, bioprotocols
I'd say that if there are people who would commit to start using a PAML miniprep, then it could indeed be a good target.

The solution specification is simple from an representation perspective: we just need to create SBOL Component objects for each thing in the solution, the same way that we do when specifying media or experiment samples. I don't believe that can be done via PAMLED right now, but there are several different SBOL tools that will do it.

Bottom line: a good target, if there is somebody not already committed on our existing tests who wants to lead it.

Thanks,
-Jake


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