From OpenWetWare
Jump to navigationJump to search
  • RS 14:48, 30 May 2006 (EDT)': Thought I would get the ball rolling on a protocols template. Feel free to revise further.


Discussion on Adopt-a-protocol from OpenWetWare:Ideas:

  • Jasonk 15:49, 23 September 2006 (EDT): Long term, it might be cool to have people sign on as the "official" aggregator of information about a particular protocol/material/whatever. They wouldn't have any more edit right over anyone else or anything, but would be in charge of curating the entry. In the long term would be cool if this was something that was resume'-able. Similar to how someone might be listed as one of (many) authors in a large review book (e.g. Neidhardt et al E.coli and Salmonella volumes). Might serve as a mechanism to encourage people to do this job...
  • Jamesh008 09:08, 15 October 2006 (GMT): Not sure if this is the correct way to contribute to a discussion but here goes. How do people think protocols will be amalgamated? I see some issues with individual personal, lab, group, institute or country protocols needing to be different due to local procurement, laws, equipment all sorts of things. Might it be a good idea to have a consensus protocol with an official aggregator? This would be the protocol that brought all info together. This would then allow individuals as above to keep info pertinent to them in their protocol. Each consensus protocol could list all individual protocols in the references and each individual could link to the consensus at the top of their page. If it is resume'-able then there may be pressures to decide who gets elected?
  • Reshma 10:52, 13 October 2006 (EDT): Hey James, so what you're suggesting is totally along the lines of what other's have been thinking. As you said, we should probably have one consensus page like DNA ligation on a given technique which describes general background on the protocol and then links to a bunch of lab or individual specific protocols like Silver:Ligation and others. I think right now we still need more folks to work on and update these consensus pages but it would be great if in the future there were several people interested in each aggregation page. Any ideas on how to make this process easier so that people are more likely to build these consensus pages?
  • JH 16:08, 17 October 2006 (GMT): Check out the way I am thinking about consensus protocols here.


  • JH 17 Oct 06: I would like to discuss protocol template(s) and naming both specifically and generally but one problem I have is that there seem to be too many places to discuss things! Where should discussions be directed???
    • Template
      • I would like to see the procedure broken down with subsections used for different steps in teh procedure.
      • I also like the idea of a central protocol,a consensus as I called it OpenWetWare:Ideas, and this seems to be an idea others agree with but there does not appear to be a consensus about how to implement this. If DNA Ligation is the current best practice it leaves a lot to be desired as it is not actually a protocol in it's own right but just links to other lab specific protocols.
      • I am a little confused about naming pages. I created several protocols with the express intention of getting them out into the community. It looks like I may have jumped the gun a little and perhaps I should have made two protocols at the same time; a general one linking from the protocols page with my lab specific one referenced as a specific protocol. However these would, for now, be almost exactly the same.
      • The reason I want to get this right is I have a lot of other protocols to add and where I am setting up I am trying to get a WIKI installed as our intranet. Lots of people are afraid of the fact that anybody can edit your pages, lots of convincing is needed. Being able to lock lab specific pages might well be the thing that brings lots more labs into OWW.
  • JH 17 Oct 06:
    • Consensus protocols: For now I will make a consensus protocol page/template on my user page and show you what i am thinking. I did not want to jump in and add tot he protocols template and it is locked anyway.
  • Reshma 12:06, 17 October 2006 (EDT): Hey James. First off, all your protocol contributions are awesome and it sounds like you have a lot more planned, that's great. With regards to some of the issues you've raised...
  1. The only reason the protocol template page is protected is cause we had a couple instances of people accidentally modifying the template page rather than copying it. (i.e. they overwrote or moved the page to their own protocol). So we just locked it to make it obvious to people that they should copy it. I'll unlock it now so that you can edit it. Or we can get you sysop status so that you can edit it despite the fact that it is protected.
  2. Totally agree that discussions are fragmented and it is confusing about where to put them. So sorry about that. We're still trying to figure out the best way for people to conduct discussions. In general, the best place is on the relevant talk page (if there is one). That's why I am responding to you here. We created the OpenWetWare:Ideas page for those random ideas that you just don't know where to put. For discussions between just two people, they often occur on a user talk page (like yours and Sri's).
  3. I think you are totally right that it would be great to have a consensus protocol on the main protocol page, as you have done at Jamesh008:consensus DNA ligation protocol. We just need more folks willing to put together and maintain these consensus protocols. (A lot of folks are more interested, understandably, in posting and editing their own lab specific protocols, rather than general OWW consensus protocols. As our community grows, I expect consensus protocols to emerge more and more.
  4. I also agree that the procedure section of a protocol should/can be broken into steps. Really, the protocol template is just a guide that people can customize to their own needs. I think it is totally reasonable to update Protocols/Template to include subsections within the Procedure section.
  5. In terms of protocol naming, in general the convention has been that generic terms like DNA ligation are consensus pages and then labs and individuals use prefixes like Knight:DNA ligation. Sometimes, if the person is the first to contribute a protocol of that kind, then they'll just name their page generically. If someone else comes along and wants to add a new version of that same protocol, then they can move the existing page to a lab/individual specific name, create a consensus page, and then link their new version off the consensus page. Given that it sounds like you will be adding a lot of protocols, you might want to go ahead and create a consensus page and a lab specific page linked from there at the same time. But that is pretty much up to you. Basically, the OpenWetWare:Etiquette is that people can edit generically named pages mercilessly but should use more caution with lab specific pages.
  6. Totally agree that DNA ligation leaves a lot to be desired as the "ideal" protocol. Please feel free to improve it according to your Jamesh008:consensus DNA ligation protocol.
  7. From everything you've said, it sounds like we might want to have two templates. Protocols/Template is a template for an individual protocol instance and perhaps Protocols/Consensus template could be a template for consensus protocols (it would essentially be copied from your Jamesh008:consensus protocol template).
  8. Regarding your suggestion of locking lab specific pages ... it is definitely an issue that has come up a lot. Check out the debate at OpenWetWare:Software/Private Pages. I think it is safe to say that everyone still has mixed feelings about it. But given that we don't have the resources to implement permissions/access control, it ends up being kind of a moot point for the time being (until we get more resources).
  • Austin Che 12:37, 17 October 2006 (EDT): With the imminent move to the new server, I've been doing some rearranging of things and I've set up a really trivial way for us to host subwikis that can have arbitrary permissions (e.g. pages that are completely private to the world, pages that only particular people can edit, etc.). I'll put my current ideas on to OpenWetWare:Software/Private Pages soon.
  • JH 15.47 18 Oct 06: Responses to Reshma:
  1. Protected protocol template - sensible to keep stuff like this protected so new users don't make a mistake. I will see if I can help out with the new user documentation to help prevent mistakes when adding protocols. I an not sure about unlocking it though and am not sure sysop status is needed for me; what does that mean?
  2. Fragmented discussions - I have replied to several discussions today and referred to other discussion in my replies, it does seems difficult to keep track of discussion but now I am using the watch function more, it helps a lot.
  3. Consensus protocol on the main protocol page - I will be willing to act as an editor for a couple of the protocols I have submitted where I have lots of experience and where a consensus is required. If people adopt only one or two protocols this should not be too onerous.
  4. Procedure section of a protocol - these were my suggestions. I do not expect there to be a perfect consensus on the layout of different protocols. Sometimes they will need to be different. I started using OWW as I could not get a template from nature Methods due to copyright, I want to have everyone in my lab using the same layout so it is easy to find things and update things. OWW lets me do this and share at the same time.
  5. Naming still confuses me.
  6. DNA ligation leaves a lot to be desired as the "ideal" protocol - I do not want to appear as having savaged someones work; this is an example of things I think could be done better generally. I would not be a good DNA ligation editor.
  7. -
  8. Two templates - yes exactly and I would hope over time that the front protocols page would be almost exclusivley consensus protocols. After all how many years have we all been referring to Maniatis!