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Sunday, November 04, 2007

Cameron Neylon Drexel Talk

A Beginner’s Guide to Open Science(not for beginners but by beginners)
A talk by Cameron Neylon
STFC Rutherford Appleton Laboratory and School of Chemistry, University of Southampton

Audio (mp3)
Flash Screencast
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Update: transcript is now available

Presentation at 2:00 Friday November 2, 2007
Disque 109, Drexel University

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/



  • Thanks for this! Very interesting talk, look forward to hearing more in the future.

    By Blogger Unknown, at 8:16 PM  

  • Hello - Jay Bhatt, my professor at Drexel U, suggested I post my comments on this presentation. I attended the presentation last November on Jay's recommendation when I was taking his online library science course, Resources in Science and Technology. After attending the presentation, I shared some of my thoughts with the class from the perspective of a librarian-in-training. At the time, the class was discussing scholarly communication, which I personally think is changing in the face of new technology. I was interested to learn a bit about how laboratory scientists share information. Here are my comments from my class last November. I hope they are helpful and good luck!

    "I went to the talk at Drexel on Friday about Open Notebook Science and the use of blog technology to track and share what is happening in a laboratory. Working in a chemistry laboratory requires the creation of a lab journal - traditionally a paper based book where researchers (grad students and supervising scientists) record their experiments and share these experiments with their supervisors. The journals are meant to provide a record of the experiments with sufficient detail to be able to track where something might have gone wrong or what methods work. According to the speaker from the University of Southhampton, theses traditional notebooks have some limitations. Many researchers don't do a good job of keeping a written log of their work, the journals are difficult to share (especially if the researcher is off-site), and it is difficult to provide links between different experiments and their components and their results. So, they received a grant from a British agency to create an online version of the laboratory notebook.
    There are a couple of Web 2.0 ways of doing this. Researchers could use a wiki where the most recent version of the research is displayed, with changes and additions only visible in the wiki's version control record, or they might use a blog where the online version more closely resembles the original journal format. The University of Southampton is using the blog format while Drexel's researchers are experimenting with the wiki format. In some ways the online blog version has been difficult to implement. It was tough getting started and the some of their original goals (machine readable across systems) haven't been fully realized. They settled on a metadata system that provides a lot of flexibility (tagging) but little structure (no controlled vocabulary - frequent typos). This seems to work fine in terms of having only three people on a blog, but if they want to increase the number of users I think this metadata system will become a problem. In other ways it has been a success - it is easier to share information with colleagues who might not be located at the same place all the time. Overall, however, the researcher's assessment of the project was measured. It isn't necessarily easier to use this system than the paper system. It doesn't ensure good record keeping any better than the print version. And it doesn't sound like a lot of other researchers are picking up on it and starting to use it, but maybe it is still too new and untested.
    One of the potential issues with sharing lab data this way is the possibility of "being scooped" - that another researcher would take their research and publish with it first. In fact, the researchers at the University of Southampton hoped that their online blog/lab journal would provide a written record of their work and some kind of proof that they published first. I'm not sure that science is ready to accept a blog as proof of primacy, though, without the peer review element that seems to be so important to the creation of an official record.
    It is interesting to see how scientists are using the Web 2.0 tool, however. It is definitely a new way for scientists to share information that is outside the control of the traditional publishing channels."

    By Blogger Unknown, at 4:12 PM  

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