OpenWetWare talk:Nature Methods article

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Revision as of 14:31, 10 November 2006 by Reshma P. Shetty (talk | contribs) (major edits)
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  • User:Jamesh008 30/10/06 11.52GMT: Let me know what you think.
  • Jasonk 08:24, 30 October 2006 (EST): Looks good, thanks for taking the intiative on this. I would suggest that we have a strong example of a consensus protocol that we could show to new members (as an example of good practice), and probably as a reference in the article itself (to give readers a working example as a proof of principle). As mentioned in previous discussions DNA ligation is perhaps not in the best shape to serve this role, any suggestions for protocols that could be cleaned up and have an editor recruited?
    • Jasonk 08:24, 30 October 2006 (EST):re: The "official editor" of the protocol -- this is going to be a little tricky I think. I don't think its a good idea to provide a person with "edit approval" at the software level (in fact its not realy easily technically feasible anyway), but you could imagine editors having a socially-mandated final say over the article (sort of like I consider myself to have the final say over my userpage even though anyone can edit it). Should a dispute arise (e.g. a "revert war" as it would be called on wikipedia), the SC could mediate. other thoughts on this, the general idea of someone having "editor status" over a general page is something we haven't done previously. Do people think it would hurt contributions? My guess is it would be a net positive, since the editor at least would have incentive to do the work of aggregating accross lab-specific protocols, something were not seeing too much of at the moment.
  • Reshma 09:05, 30 October 2006 (EST): Awesome idea. We've been talking about how we should publish something regarding OpenWetWare. One thing that I think will be important to emphasize in the article is that OWW goes one step further than most other online protocol sites like Nature Methods, CSHL protocols and protocols online. Namely, that it is easily editable and that everyone can edit the same space. We should discuss the pros and cons of this approach as well as try to dispel some of the common concerns. I'll think about this a bit and try to write something up.
  • Sri Kosuri (talk) 09:10, 30 October 2006 (EST): Awesome idea! Thanks for taking the initiative. I'll have more to say over the next couple of days... but this is a great start.
  • User:Jamesh008 16.15GMT 30/10/06: Glad you like the idea, please start editing what I have already done. Spread the word and ask users to look at Talk:Jamesh008:consensus protocol, Talk:Protocols/Template, User talk:Jamesh008, Jamesh008:consensus protocol and Jamesh008:consensus protocol template for some discussion on the subject.
  • Reshma 16:48, 9 November 2006 (EST): Made a few moves ...
  • Jamesh008 04:58, 10 November 2006 (EST): I think this is about ready to submit.
  • Sri Kosuri (talk) 11:15, 10 November 2006 (EST): I think there are substantial changes left to be made... i'll try to make changes that i would like seen by the end of the day.

major edits

  • Sri Kosuri (talk) 14:40, 10 November 2006 (EST): I've made some significant changes to the structure of the text.... You can pretty much see how things are organized. It's not perfect, but I think it's a better place to continue editing than the current text. I wanted to make one major comment. I think we should change the name to aggregate protocol, instead of consensus. Consensus seems really offputting to me... who's consensus? e.g., the dna ligation page's procedure is exactly that of the endy lab procedure. is that really consensus... wouldn't maniatas, or neb be a better consensus? i think aggregate implies that this is aggregating knowledge from the individual protocols, which is i think what we are trying to do here.
    • Jasonk 15:07, 10 November 2006 (EST):Agree with Sri about the consensus comment - a consensus protocol might be something to shoot for down the road, but it's not what we're doing at the moment.
  • Reshma 16:31, 10 November 2006 (EST): I like the new version below ... specifically that it enumerates


OpenWetWare ( is a wiki (see box 1) promoting the sharing of information, know-how, and experience in biological science and engineering [1]. Individuals and groups use OpenWetWare to easily organize information and collaborate with one another. In the process, information about research topics, laboratories, ordering, equipment maintenance and operation, strains, safety, chemicals, protocols and more become available to the larger research community.

OpenWetWare contains two types of information sources for experimental protocols. First, users often store their own protocols, which are not necessarily written to be easily followed by others. In practice, however, most protocols are written to be shared within at least a laboratory, and so are often clear enough to provide a useful starting point. The protocols section of OpenWetWare ( is an attempt to collect and generalize the existing protocols on the site, and provide general background, tips, and references for the procedure. The DNA ligation protocol on OpenWetWare is one example of such an aggregate protocol.

OpenWetWare differs from other protocol reference sources [2]. First, there are growing numbers of individual's protocols, allowing people to compare and contrast variations. Second, the wiki allows quick and easy editing, allowing individuals to keep their information current, as well as access other's current information. Third, efforts to aggregrate protocols provide background, general and specific protocols, tips, and references not commonly found elsewhere. Fourth, the ability to add new features such as video, data sets, data processing algorithms and more is already built in. Finally, OpenWetWare also has information on equipment, chemicals, lab notebooks etc. that are often part and parcel of any particular laboratory protocol.

OpenWetWare is a growing community and we encourage researchers to join and contribute to the dissemination of biological knowledge.

Box 1

What is a wiki? A wiki is a type of website that allows users to easily add or edit content [3]. This ease-of-use makes wikis an effective tool for collaborative authoring. Wikipedia, the online encyclopedia, is the most famous example. OpenWetWare, like Wikipedia, is open for anyone to view but requires registration to edit. Registration ensures that all edits on OpenWetWare are attributable to a known individual. The open style of wikis which allows any user to edit most pages is a cause for concern for some. However, for the scientific community, we see this as enabling the free flow of ideas and information. Furthermore, all wikis maintain a revision history for every page to allow reversion of edits, track page development and deal with any mistaken or malicious edits. This historical log is especially important for the sciences where new, possibly incorrect, information is continuously discovered.