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Biology Articles » Bioinformatics » Chemistry of a cuppa: Helping to digitize the laboratories of tomorrow

Chemistry of a cuppa: Helping to digitize the laboratories of tomorrow

The brewing of tea formed a crucial component of a project which successfully took traditional paper laboratory books and moved them to digital formats. Now that knowledge and experience is being put to use in a subsequent project by University of Southampton computing researchers who are aiming to apply similar techniques to Bioinformatics.

The eScience project, which could revolutionize the way in which scientists share information, is appropriately called myTea. It has received funding of over £200,000 from the EPSRC (Engineering and Physical Sciences Research Council).

The researchers, from the School of Electronics and Computer Science at Southampton, and the University of Manchester, will draw on best practice design methods learned from other eScience projects, specifically, their own SmartTea project, which explored how paper-based information from a chemistry environment could be captured in digital forms. They will also refer to the University of Manchester's myGrid project in order to design an integrated experiment annotation capture system for bioinformaticians.

The initial exploration of the SmartTea project involved finding common ground which would enable the practices of the scientists, as recorded in their paper lab books, to be understood by the computer researchers.

'This was crucial for us,' said dr Monica Schraefel of the School of Electronics and Computer Science at Southampton. 'In order to help the scientists record their information digitally, we needed to be able to understand exactly how they described what they were doing in their paper lab books, and what aspects of it they recorded.'

After observing a team of chemists at work in the University labs, the researchers hit on the idea of watching the chemists make tea and record it as if it were an experiment, so that the researchers could understand exactly what was happening in the process on the bench as the scientists recorded it.

Because they knew what was happening during the tea-making, they could understand how the scientists chose to record and classify important aspects of the process, or to ignore things that were not important for the "experiment".'

'So now, instead of writing into a lab book, scientists will write into some other type of hardware, like a tablet PC,' said Monica Schraefel. 'That data is immediately written to a server so it is stored not only locally on the computer, but on the server, and therefore immediately accessible outside the lab and to other scientific communities. '

Armed with this experience, the researchers are now moving on to the field of Bioinformatics. Although the outcome of providing more effectively organized and accessible information is the same, the problems and processes are different.

'In the Chemistry lab we took the "book" out of the lab to capture lab processes into digital form,' said Monica Schraefel. 'The issue here is the reverse here: bioinformaticians are already all digital, and ironically, that's the problem: they create hundreds of files spread across their hard drive for an ongoing experiment, but have no easy way to associate files with an experiment. So, this time, we need to put some of the book back into the process, to help automatically generate a lab book-like view of their work to date, which they can annotate, plug into services like myGrid, or share with colleagues.

'This work addresses one of the central planks of the eScience project,' she added '-to get data from one scientific community out to another, right away, as soon as it happens.'

University of Southampton. February 2005.

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