OpenWetWare:Nature Methods article

Title

OpenWetWare Protocols: an open-access online protocol resource for biological researchers.

Manuscript Type

Brief correspondence - 400 words maximum oops we are over this by around 20 words. Some help with shortening it perhaps...

Authors

Corresponding Author: James Hadfield, CRUK Cambridge Research Institute, Robinson Way, Cambridge CB2 0RE. Tel: +44 (0)1223 404250; Fax: +44 (0)1223 404208; email: james.hadfield@cancer.org.uk.
OpenWetWare steering committee: http://openwetware.org/wiki/OpenWetWare:Steering_committee_members

Note: This paper is being written and edited by any number of authors and the submission will be made after at least three OWW steering committee members agree it is ready. I am pretty sure this is not something that has been done before and we would like to be the first to use this method of writing and submission. It could prove a very useful way of creating methods and review articles.

• Jamesh008 04:59, 10 November 2006 (EST): I think this is ready to submit.
  • Jasonk 12:32, 10 November 2006 (EST) DNA Ligation should also be in really good shape before we submit, probably.
  • Sri Kosuri (talk) 14:44, 10 November 2006 (EST): I made changes to the structure of the text... I think it still needs work, but is a better place to start than the current text. Please see the talk page. If people like it, we should replace the current text. If not, we should continue talking.
• Reshma 12:55, 17 November 2006 (EST): Moved Sri's version here since there didn't seem to be significant opposition to it.
• Jamesh008 15:48, 20 November 2006 (EST): I do not have really significant opposition but read the talk page...
• Jamesh008 09:41, 8 December 2006 (EST): I have changed Sri's version after some discussion here and in the pub. I would like to see the term consensus in this article, I believe it has a meaning that all biologists will understand and see the innate problems with, but the important thing to me is it is simple to understand. An aggregate protocol probably means reading the what is an aggregate protocol page first. I also think that this article is more about encouraging new users and visitors, and that the definition and template pages will change over time anyway. I am going to be in the US until Christmas so i will not be able to comment or discuss this until the new year. Lets try and submit in january. Sorry for getting pulled in different directions and not pushing it along. I will be visiting Agencourt in boston on Monday 18th if anyone feels like saying hi before I leave for the airport. Let me know where you are and I can see if popping by to say hi will work with my horrible schedule.
• Reshma 15:21, 14 December 2006 (EST): See User talk:Jamesh008 ... also sent you an email.

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 [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.

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[2]. A protocol template encourages users to standardise the format making searching protocols much easier.

OpenWetWare contains two types of information sources for experimental protocols. First, users often store their own “specific 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. Second, users can gather information from many specific protocols to produce a “consensus protocol”. Individual protocols are linked with the consensus protocol and vice versa. A consensus protocol has a curator but anyone can edit, add notes and suggest alternative reagents or equipment. The DNA ligation protocol on OpenWetWare is one example of such a consensus protocol[3].

OpenWetWare differs from other protocol reference sources [4]. 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 [5]. This ease-of-use makes wikis an effective tool for collaborative authoring. Wikipedia, the online encyclopedia, is the most famous example. OpenWetWare 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.

References

1. OpenWetWare: http://openwetware.org/

2. Protocols: http://openwetware.org/wiki/Protocols

3. DNA ligation http://openwetware.org/wiki/DNA_Ligation.

4. ISBN:0-87969-577-3
5. ISBN:020171499X