Demo miniprep protocol?

[photocyte]

Via scrum discussions, established it might be nice to have a Github issue for this idea originally raised on the mailing list (https://groups.google.com/g/bioprotocols/c/8P7fhCUlYXo), and that it be marked as a good beginner issue.

I'm open to help on this!

"
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
"

[vignoni]

I think this is interesting enough and will try to start working on this as soon as I get a student which is planned to come in September.

[photocyte]

I think Minipreps are an example of a strictly linear protocol without feedback that would be well suited to representation and editing in LabOP-docx . See this issue:
#195

I think the Zymo Zyppy protocol would be a good one to implement. It has fewer steps:
Kit link: https://www.zymoresearch.com/products/zyppy-plasmid-miniprep-kit
Protocol link: https://files.zymoresearch.com/protocols/_d4019_d4020_d4036_d4037_zyppy_plasmid_miniprep_kit.pdf

However, the Zyppy miniprep buffers are proprietary (albeit likely highly similar to the Qiagen buffers), unlike the Qiagen buffers which are undisclosed but still known anyway.

[saisam17]

Did this manufacturer kit protocol ever get made into a LabOp representation? If so, could you please share it. I am working on identifying how to represent manufacturer kits in general and this would be helpful.

[danbryce]

I don’t think so. I believe this issue was never taken up by anyone. A kit could be represented by a protocol that has several output parameters. Each parameter would be a container with a reagent. Then, this kit protocol would be included as a subprotocol of another protocol using it.

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On Jun 6, 2024, at 5:23 AM, saisam17 ***@***.***> wrote: Did this manufacturer kit protocol ever get made into a LabOp representation? If so, could you please share it. I am working on identifying how to represent manufacturer kits in general and this would be helpful. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>