Demo miniprep protocol?

[Timothy Fallon]

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:

https://www.qiagen.com/us/products/discovery-and-translational-research/dna-rna-purification/dna-purification/plasmid-dna/qiaprep-spin-miniprep-kit/

 

See the QIAprep Miniprep Handbook: (https://www.qiagen.com/us/Resources/ResourceDetail?id=22df6325-9579-4aa0-819c-788f73d81a09&lang=en)] for the full 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:

https://openwetware.org/wiki/Qiagen_Buffers

 

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

Pronouns: (he/him/his)

[Jake Beal]

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

--
You received this message because you are subscribed to the Google Groups "bioprotocols" group.
To unsubscribe from this group and stop receiving emails from it, send an email to bioprotocols...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/bioprotocols/B7F9034E-B493-4795-ADFB-95A5E48DB605%40ucsd.edu.
For more options, visit https://groups.google.com/d/optout.