A database of protocols?

When we were doing a workshop recently about a huge range of bioinformatics/genomics database resources a young researcher came up and asked about one of the types of resources we didn’t yet include in our list–and I thought it was an excellent question.

Is there a database of protocols?

That’s such a good question–and I can see why it would be so useful to bench scientists. Yeah, I can show you all the software we cover. But there are still other needs, and searchable protocols would be very handy.

Off the top of my head I pointed her to the Current Protocols publications. I relied on those in grad school–but at that time they were in the red binder on the second shelf, and Hiram would always pull out the old chapters and put in the new ones–on actual paper!!

I also mentioned JOVE–the Journal of Visualized Experiments.  Jennifer talked about this before as a tip of the week. Since then they had to move to subscription, but it’s possible this young scholar’s institution does subscribe to that.

Trey remembered Open Wetware.

UPDATES: Great stuff from readers–thanks:

APD offers: NAR Methods http://nar.oxfordjournals.org/collections/index.dtl

Natalie offers: Protocol-Online http://www.protocol-online.org/ and her collected list: http://www.bib.umontreal.ca/sa/laboratoire-indispensables.htm

Jennifer suggests BioTechniques http://biotechniques.com/ and for  protein structure notes this resource: http://kb.psi-structuralgenomics.org/


Do you know of others? I’ll edit the post as people bring them along. Thanks!

6 thoughts on “A database of protocols?

  1. Jennifer

    Thanks for adding this to Mary’s post, APD.

    I think some of the SciVee movies might also qualify as methods, but it is not devoted to presenting methods as many of the other mentions are.

  2. Mary Post author

    Thanks folks!

    I was considering also adding the different sites where communities keep their protocols–like WormBase, or Zfin, but I generally assume the community has pointed young researchers to those.

  3. Natalie

    Check out what is available at your academic library. I maintain a Web section devoted to protocols and methods, and point to resources we suscribe to: Methods in Enzymology, Nature Protocols, Springer Protocols, as well as to a number of specific journals.

    A free resource you may want to add to the list is Protocols Online.

  4. Jennifer

    it isn’t a database, but I think BioTechniques deserves mention here. People in the yeast labs where I worked as a post-doc saved articles in a notebook similar to the big red notebooks you describe for current protocols.

    Plus many focused databases do provide methods – a great example of one is the structural biology techniques provided by The Protein Structure Initiative Structural Genomics Knowledgebase (PSI-SGKB, http://kb.psi-structuralgenomics.org), even down to the level of each step of the cloning, crystallization, what worked what didn’t for specific structures, what might work for your proteins via similarity matches and computational predictions.

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