Community-driven efforts at collaborative knowledge production have recently taken off (Olson, Zimmerman and Bos 2008). The success of Wikipedia is only the most widely known example. More recently still, biologists have taken up Wiki-type tools. One reason is that there is a data deluge (Borgman 2007), especially in the life sciences. The paper will examine a number of case studies drawn from a range of different efforts, such as myExperiment, GeneWiki, BioModels.net, and OpenWetware. The main focus of this research is community dynamics: who contributes? Are there small cores of contributors and large peripheries of occasional contributors (as has been found for Wikipedia)? What are the trade-offs between centralized control versus self-curation in community-driven efforts? Are there disagreements about the quality, formats, and means of classifying and representing the data? These issues have become critical, as Leonelli (2007) has shown in her study of the TAIR database.The paper will review the variety of current collaborative online efforts under way in order to identify the various factors that influence their different trajectories, focusing particularly on the role of gatekeepers and the patterns of contributions over time. The paper will also make comparisons with community-driven discovery and databases in other fields, for example literature (PynchonWiki) and volunteer computing efforts as in climate change (Climateprediction.net). The conclusion will discuss the outlook for this way of doing science. To what extent do these tools represent a paradigm shift in biology, or is this ‘old wine in new bottles’?

This presentation explores concepts from the General Theory of Scientific/Intellectual Movements (Frickel & Gross, 2005) in relation to extension of scientific communication by use of online research tools in the life sciences. It supplements Frickel and Gross’s work by claiming that online methods of communication open up the possibility of faster and more extensive agreement and support for new ideas and techniques.This may also result in a reduced need for rebellion against established gatekeepers such as senior scientists, grant-awarding bodies and journal editors by providing a new, efficient and widespread method of dissemination of an “individual’s or group’s thoughts and research findings” (Frickel & Gross, 2005, p. 214).Scientists do not consider informal dissemination and discussion on the Internet a substitute for the circulation of formal journal articles. However, online dialogue does in fact modify the ensuing formal print products by facilitating refinement of research results in advance of publication through open consultation with peers. Data from interviews with working scientists and observations of laboratory and Web 2.0 sites supports the argument.

Frickel, S. & Gross, N. (2005). A general theory of scientific/intellectual movements. American Sociological Review, 70, (204-232)

In this presentation, Meyer & Power will discuss the various impacts Web 2.0 research tools are having on users. This theme will be developed using data from several projects: a survey of users that indicates the importance of bottom-up innovation in research, a project looking at topics science bloggers address, an analysis of the JOVE online journal for visually sharing and commenting on laboratory methods, and a project to develop a toolkit for measuring the impacts of web-based resources. These projects each illustrate an aspect of how we can understand uses of these new technologies as they move from the innovation space of tool developers into the everyday use space of normal researchers.

Slides are available.

Cameron has summarised the discussion and findings, and there’s also a good summary of the first day written by Duncan Hull who works with myexperiment in Manchester.

Lots of discussion was generated on the first day with Cameron’s survey about lab books and their usage. I found it interesting that there was variation and a lack of common standards about how to record experiments, how to keep and archive lab books, and even whether entries should be dated or not, even amongst our small group. One of the workshop’s aims was to discover whether the ChemTools system, originally built by Jeremy Frey’s lab in Southampton, could work with experimental procedures in other labs.

The ChemTools system was designed to be open and flexible, it’s based on a blog style system with a lot of custom PHP scripting. The basic concept is that each ‘thing’ in the lab – every input and output of a procedure – has its own post. Metadata used in tagging is particularly important as that connects particular items in a procedural workflow. This can be linked via hypertext in the lab blog, and via barcodes in the physical world (see above for an example).

For a non-production system built by a couple of PhD students, it’s impressive that the workshoppers were able to generate some posts in one afternoon. The group also discovered quite a few usability issues, most of which would be fairly easy to fix. The biggest issue seems to be the time-suck of the current UI – it’s just not suited to writing tabular data, which is the most useful output style for many experiments. To some extent this issue can be alleviated by the existing templating system, and perhaps some Ajax javascripting could be incorporated to make table creation a bit more WYSIWYG. Automation of some of these post-creation processes is being posited for the not-too-distant future.

Further upcoming developments include links to environmental data in the lab (fridge temperatures and other mechanical interactions). Looking forward – keep an eye on Cameron’s blog. His post about rich RSS feeds and tools to make information connections to do things like potentially automatically manage lab stocks predicts much exciting stuff to come!

Conclusions – it’s not [yet] particularly easy to ‘blog the lab’, and requires a fair amount of thinking about one’s experimental protocols and work practices in terms of figuring out what is good metadata to record. However, the richness and connectedness of the data produced using this system does enable the scientist to quickly locate essential data when it comes to writing papers.

What about privacy, trust and levels of access to this lab data? That’s a discussion for a later post.

[Note: this post was originally published on my OII blog, which is about to be subsumed into this one, hence the double-post. Original comments on this post have been reproduced below]

Dear Ben

Just having one in the Elephant Hotel. Raining
cats & dogs. Coming home as soon as we have had our dinner.

What a day.

Love from Mum & Dad

xxx

To Doris

With love from

Horace