the myTea project
Improving capture of experiments for bioinformatics practitioners.
Traditionally, scientists have used paper lab books to capture the process and results of their experiments; these results have then been written up and published in journals, months (or years) later.
The Semantic Web and Semantic Grid, however, are motivating a possible sea change in the way scientists make their work available. With the Semantic Grid, a Web-based technology for sharing data and computation, scientists can share information in richer forms than traditional lab books and publishing has allowed. They will be able to make rafts of data generated in experiments available to other scientists, and to the public for compariosn exploration and study; they can share analyses of information and collaborate in new ways.
At the heart of this new technology-supported endeavor sits very traditional practices: a human scientist writing notes during an experiment into a paper lab book.
To move this crucial data from paper, where only one person can see it at a time, to the Web, where the community can benefit from it, we need innovative means of data capture that support how scientists work.
The myTea Best Practice project is about taking the lessons learned from the Smart Tea project in CombeChem (about capturing previously paper-based information into new digital forms) and applying that within the myGrid eScience project's work to support Bioinformaticians.
About the project
The myTea project is a year long collaboration between Smart Tea/CombeChem (University of Southampton) and myGrid (University of Mancher) eScience projects to develop an integrated experimental capture system for bioinformatitians. The project is funded by EPSRC.
In the Smart Tea project of Combechem, we developed an innovative method of analysis in order to understand the cultural, affective and functional processes and artefacts of experimental annotation by users. The results have been two-fold: (1) a well-received prototype of a replacement lab book system and (2) a design method for investigating such highly expert, loosely structured work as chemists running experiments in a wet lab.
Application Context: moving from Analytic Chemistry to BioInformatics
Our focus for this project is the bioinformatics domain. This focus gives us a two degrees shift from the original Smart Tea work. First, we move from chemistry to biology. The experimental practice in both communities, while sharing artefacts for recording practices, is culturally distinct in its method of recording. Second, we move from the "wet" in virto lab of synthetic organic chemistry to the dry, in silico lab of bioinformatics. This shift provides an opportunity to engage related problems in a new context - new in two levels: the domain (biology) and the lab type (in silico).
In this project, with myGrid's expertise in services to support experiment workflows, we plan to extend the design method developed in Smart Tea to investigate the needs for the above described, dynamic annotation support in bioinformatics.
This Best Practice project, therefore, has as its primary goal:
To transfer best practice design methods from
Smart Tea to myGrid in order to design an effective, integrated experiment
annotation capture system for bioinformaticians. The application will
integrate myGrid’s experiment workflow processes with new mechanisms
for annotation capture and review/sharing of those annotations in the
context of the associated experiment workflow results.
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[Stevens 04] Stevens, R. and Hannah J. Tipney and Chris Wroe and Tom Oinn and Martin Senger and Phil Lord and Carole Goble and Andy Brass & May Tassabehji Exploring Williams-Beuren Syndrome Using myGrid. Accepted for publication at Intelligent Systems for Molecular Biology (ISMB), Glasgow, UK, August 2004.
[Stevens 03] Robert D. Stevens and Alan J. Robinson and Carole A. Goble myGrid: Personalised bioinformatics on the information grid. Bioinformatics 19(2003): i302-i304. .
myTea virtual Lab software: pre release candidate We've added new pages to describe the myTea Software Framework and virtual Lab to support in silico bioinformatics. The alpha release candidate will be available there for download. Please take a look and let us know what you think.
A paper overviewing the latest software framework and toolset for the myTea virtual Bench and Lab-book is now available on EPRINTS. The paper is called "myTea: connecting the Web to Digital Science on the Desktop"
EPSRC, myGrid, CombeChem