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ewallace / ewallace.github.io

Wallace Lab website
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Agree where lab stuff belongs and strains #50

Open ewallace opened 3 years ago

ewallace commented 3 years ago

We have multiple people working on how to make glycerol stocks and the strain database. @LauraT89 added info on making glycerol stocks in pull request #48. I've created a branch lab-stuff-strains with that draft so that we can work on that without it accidentally reaching the staging branch.

Do we need one page for all reagents and strains (including the strain database organisation), or a separate page describing strains and the strains database?

Direct links to :

LauraT89 commented 3 years ago

We discussed this between us and agreed that there’s a lot of overlap with what could go where. Glycerol stocks went into this section because it’s to do with physically making and storing strains, which seemed to come under the wet lab category, rather than about the data storage itself. Jamie was going to put a link to this section in the data storage section so it would be easy to navigate between the two.

ewallace commented 3 years ago

We have a good page on this from November, still in the lab-stuff-strains branch. I'm going to add some info there on strain description and plasmid maps, then ask for more review.

ewallace commented 3 years ago

Protocols.io for making glycerol stocks was not accessible to me.

Whose is it? @RoseyBayne? @j-aux? We should share it with the lab page.

j-aux commented 3 years ago

It's mine. it's shared on the lab protocols now.

ewallace commented 3 years ago

I've (after only 2 months) done a round of edits on these.

The key edit was about listing the columns for yeast strains, including strain nomenclature. I put a link in to Getting Started With Yeast, section on Genetic Nomenclature. Maybe we should also include the relevant table on the page. Some journals have sections on nomenclature, e.g. Molecular and Cellular Biology.

We still need to do something similar for plasmids, including a link to snapgene/dna files and a convention on naming the files.

Note that it should be possible to search RSpace lab notebook for a yeast strain id (or plasmid id) and find all the experiments by everyone that use that strain.

I also fixed some links so they worked, thanks @j-aux for the protocols.io link.

ewallace commented 3 years ago

Also we should add suggestions on oligo naming and organization for individuals, (e.g. oEW199, sequence, notes) and a reminder that tables of oligos and plasmids need to go in publications. Although we're not going to have a single oligo database as a lab because that would be crazy.

ewallace commented 3 years ago

This issue is largely addressed by #78.

BUT we didn't add the oligo organization suggestions.