OpenWetWare talk:Nature Methods article


 * 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:consensus protocol --> Help:Consensus protocol
 * Jamesh008:consensus protocol template --> Protocols/Consensus template
 * 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.
 * Jamesh008 17:21, 10 November 2006 (EST): Thanks to everyone that has started editing this. I was a little worried that as a very new member of OWW it was perhaps only putting across my particular point of view. Here's hoping we have a consensus by the end of next week!
 * Jamesh008 09:41, 8 December 2006 (EST): Made some more changes let me know what you think?

major edits
Jamesh008 09:41, 20 November 2006 (EST): I am happy with the flow of the article and what it is trying to get across, however I still have a strong feeling to keeping consensus as part ot the description for aggregated or standarised protocols. Perhaps it is worth a paragraph to try and get across some of your points. Explain what we mean by consensus, although I think this will be easily understood by most readers, and explain some of the limitations.
 * 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 several pros of OWW protocols
 * Jamesh008 17:21, 10 November 2006 (EST): I especially like the part about video and data sets. This really sets us apart from anything in print. However there seems to be no mention of consensus protocols as something unique anymore. The reason I wanted to get this article written in the first place was to highlight what a community can gain from working on a consensus for the building blocks of scientfic investigation, lab protocols. We all have a generally held consensus about most biological processes that have grown from small experimental steps. I was mostly interested in the consensus protocol idea as my background is expression arrays where small deviations in experimental procedure can mask the true biological differences. I will think about this over the weekend and try a re-edit of my own.
 * Sri Kosuri (talk) 17:54, 10 November 2006 (EST): I like the idea of a "consensus" protocol a lot. But we should be careful with our language and intent.  For the sake of clarity, I want to split "consensus" into optimal and standardized for clarity.  An optimal protocol actually has data to support why (or under what conditions) a certain protocol is better than another.  A standardized protocol is saying, this is how everyone does it, but we are not quite sure why. A standardized protocol may be "optimal", but more likely than not historical accident.  I think "optimal" protocols are clearly superior to "standardized" protocols.  I also think "standardized" protocols have a lot of value, especially if they are proven to work fairly well.  That way people can scientifically test deviations from the standard, to work towards optimal protocols.
 * Anyways, point being, if we are saying that we should standardize or optimize protocols, then the letter is completely wrong (both versions). While OWW can be a useful tool towards getting towards standardized/optimized protocols, the thesis that we should work towards them is intellectually quite deep and would require its own arguments (e.g., your microarry example). I know for sure that many scientists think standardizing protocols is really bad for science.  A letter for "concensus" protocols (standardized or optimal) would require one to explain why concensus is a good thing (at least a paragraph)... what would be the process of reaching concensus (at least a paragraph), and perhaps, why OWW is a good place to start.
 * As for aggregation... I personally think that aggregation will serve a purpose of moving more people towards at least standardized and maybe optimized protocols. I think that until a major push for this happens, scientists are going to be very skeptical about pronouncements of consensus.. unless someone wants to spend a lot of time making lucid arguments (with experimental data) as to what the particular variations are and why they are suboptimal.  I think declaring it by fiat (whether by us, or someone else) is going to be very difficult.  I would rather start modestly, hope for lots of aggregation of knowledge, and hopefully build something better.  Even right now, the tips and troubleshooting from disparate users on the DNA Ligation page is useful.
 * Those are my thoughts... at least for now... hope it helps
 * The reason for getting the article done in the first place is really to increase OWW user base. OWW is only as good as it users and the more we have the greater the breadth and depth of our knowledge.
 * Sorry for taking so long to get back to you all. A very bust week or two recently.

Torsten Waldminghaus 13:50, 3 March 2008 (EST): The article sounds very good to me but what happened to it? I guess the note "8 days till submission" is not valid anymore?

Reshma 13:05, 10 March 2008 (EDT): Yeah we never got around to finishing and submitting it.

Torsten Waldminghaus 03:50, 11 March 2008 (CDT): My feeling when reading the comments and discussion is that people want to make it a bit to perfect. I guess that is a good way of doing things and certainly the article should be as good as possible. On the other hand I would prefer a medium quality article being published than no article being published. It is just a short note to get a hand full of new users and not an attempt to change the world. If we are honest a not so perfect article would fit well to OWW which is on a good way but far from being perfect. This is probably implied by the way OWW works and actually science in general and life and ... . My suggestion would be to make some final polishing and submit it with all compromises that such a joint adventure needs rather than letting it lay around any longer. As a fresh user I'm always irritated when I find pages that seem to be interesting and but than I find out that the last change was made years ago. If nobody wants to proceed with the article I would delete the link from the Protocol page to not confuse more people.

Article
OpenWetWare (http://openwetware.org) is a wiki (see box 1) promoting the sharing of information, know-how, and experience in biological science and engineering OpenWetWare. 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 (http://openwetware.org/wiki/Protocols) 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 MolecularCloning. 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 Cunningham-2001. 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.