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Friday, October 05, 2007

Cameron Neylon ONS Talk at Drexel

I am very pleased to announce a talk by Cameron Neylon at Drexel next month:

A Beginner’s Guide to Open Science
(not for beginners but by beginners)

2:00 Friday November 2, 2007
Disque 109, Drexel University
32nd and Chestnut streets, Philadelphia, PA

Cameron Neylon, STFC Rutherford Appleton Laboratory and School of Chemistry, University of Southampton

The modern biochemistry or molecular biology laboratory generates large quantities of data that are generally stored across multiple computers attached to multiple instruments. Much of this data is never published and the majority languishes on old computers and is ultimately lost. At a local level this is a frustration for investigators who will often struggle to obtain specific pieces of data produced in their own laboratory. On a larger scale this is becoming a much more serious issue with the obligation of researchers to funding bodies to both preserve research data and make it available to other users increasingly becoming a formal a condition of publicly funded grants. Systems are required that can capture and preserve data along with sufficient information and metadata to make it possible for others to use this data.

In parallel with this a movement is growing within the research community that advocates greater openness in providing both the raw data from published studies as well as making available the large quantities of data that are never published. The logical extreme of this approach is Open Notebook Science [1], pioneered at Drexel University [2], where the researcher’s laboratory notebook is made available on the internet as it is recorded. Achieving the aims of Open Notebook Science also requires systems which can capture data and provide it in a useful format. In addition these systems must make the data visible to relevant online searches.

We are developing and using an electronic laboratory notebook based on a Blog format to capture experimental data in a biochemistry laboratory [3,4]. Within the system each sample is recorded in a single post. Analysis and manipulations of the sample are recorded in separate posts with links back to the input sample and forward to any products. All the information is made immediately available on the Web as it is recorded. The Blog engine has been specially built in house and has a number of features designed to enable and encourage the effective capture of data and metadata in the environment of a biochemistry laboratory. I will describe the Blog system and our evolving approach to capturing metadata as well as the process of integrating this with other web services to provide an open environment for recording work in the laboratory, laboratory materials, and validated procedures. The challenges and problems encountered in reconciling the twin aims of capturing data and making it available and readable will also be discussed along with the similarities and differences emerging between different approaches to Open Notebook Science [2,5,6].

[1] http://drexel-coas-elearning.blogspot.com/2006/09/open-notebook-science.html
[2] http://usefulchem.wikispaces.com/
[3] http://chemtools.chem.soton.ac.uk/projects/blog/blogs.php/blog_id/10
[4] http://chemtools.chem.soton.ac.uk/projects/blog/blogs.php/blog_id/13
[5] http://www.jeremiahfaith.com/open_notebook_science/
[6] http://www.michaelbarton.me.uk/

Tuesday, October 02, 2007

Periodic Table in Second Life

Further adding to the set of chemistry tools in Second Life, Hiro Sheridan has created a 3D periodic table with rotating atoms. Although not directly proportional, the relative sizes of the spheres are in the correct order. Clicking on them provides basic information about the corresponding element.

The 3D periodic table is available on the Chemistry Corner on Drexel Island (SLURL).

The Value of Dark Data

Tom Goetz wrote a thoughtful article "It's Time to Free the Dark Data of Failed Scientific Experiments" in Wired this week.

So what happens to all the research that doesn't yield a dramatic outcome —or, worse, the opposite of what researchers had hoped? It ends up stuffed in some lab drawer. The result is a vast body of squandered knowledge that represents a waste of resources and a drag on scientific progress. This information — call it dark data — must be set free.


There are some islands of innovation. Since 2002, the Journal of Negative Results in Biomedicine has offered a peer-reviewed home to results that go negative or against the grain. Earlier this year, the journal Nature started Nature Precedings, a Web-based forum for prepublication research and unpublished manuscripts in biomedicine, chemistry, and the earth sciences. At Drexel University, chemist Jean-Claude Bradley practices "open notebook" science — chronicling his lab's work and sharing data via blog and wiki. And PLoS is planning an open repository for research and data that is other wise abandoned.

The main focus of the article is on results that don't make it to an article because they are not interesting enough. "Failed Experiments" in this sense are those that do not uncover a hoped for correlation or, in synthetic organic chemistry, those where the desired product is not obtained.

However, there are many more shades of Dark Data. One large category often downplayed consists of experiments aborted because of mistakes and accidents. For example in EXP096, the product was spilled and lost. But all of the spectra and data collected up to that point are still perfectly usable for someone wanting to repeat this or a similar experiment. That is the reason researchers don't tear out pages from their lab notebooks when accidents happen. The same logic applies to Open Notebook Science, where the audience extends to the whole world.

Thanks to Attila for posting an early report.

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