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.
The myTea project is lead by
m.c. schraefel from the IAM Group, University of Southampton, with
Robert Stevens, bioinformatics group, University of Manchester.
Co-investigators on the project are
Researcher Assistants on the project:
"featured article" in Nature
"electronic notebooks: a new leaf"
The 'paperless lab' seemed weeks away once, some time in the 1990s. But the prospect receded and labs everywhere are now struggling with an explosion of data. An electronic version of the lab notebook can fully integrate with all these digital data and images, but many researchers still print their gels and data tables, and glue them into a notebook. But we have the technology. The replacement for the trusty lab notebook could be weeks away. News Feature: Electronic notebooks: A new leaf
Record-keeping in the lab has stayed unchanged for hundreds of years, but today's experiments are putting huge pressure on the old ways. Declan Butler weighs up the pros and cons of electronic alternatives to that dog-eared notebook.
schraefel, m. c. and Dix, A. (2007) Within Bounds and Between Domains: Reflecting on Making Tea within the Context of Design Elicitation Methods. International Journal of Human Computer Studies forthcoming, summer 2007 (preprint http://eprints.ecs.soton.ac.uk/8820/).
Gibson, A., Stevens, R., Cooke, R., Brostoff, S. and schraefel, m. c. (2006). myTea: Connecting the Web to Digital Science on the Desktop. Technical Report.
schraefel, m. c., Brostoff, S., Cooke, R., Stevens, R. and Gibson, A. (2005) Transparent interaction; dynamic generation: context histories for shared science. In Proceedings of workshop ECHISE 2005 - 1st International Workshop on Exploiting Context Histories in Smart Environments held in Conjunction with The Third Internationl Conference on Pervasive Computing 2005 (in press), Munich, Germany, May 11 2005.
[De Roure 04] De Roure, D.C. and Hendler, J.A. (eds). IEEE Intelligent Systems, Special Issue on E-Science, Volume 19, Issue 1 (January/February), 2004.
[De Roure 03a] De Roure, D.C. Semantic Grid and Pervasive Computing, GGF9 Semantic Grid Workshop, Chicago, October 2003. See www.semanticgrid.org
[De Roure 03b] De Roure, D., Jennings, N. R. and Shadbolt, N. (2003) The Semantic Grid: A future e-Science infrastructure, in Berman, F., Fox, G. and Hey, A. J. G., Eds. Grid Computing - Making the Global Infrastructure a Reality, pages pp. 437-470. John Wiley and Sons Ltd.
[Flintham 03] Flintham, M., Anastasi, R., Benford, S., Hemmings, T., Crabtree, A., Greenalgh, C., Rodden, T., Tandavanitj, N., Adams, M. and Row-Farr, J. (2003) "Where on-line meets on-the-streets: experiences with mobile mixed reality games", Proceedings of the 2003 CHI Conference on Human Factors in Computing Systems, pp. 569-576, Florida: ACM Press.
[Frey 03] Frey, J. G., Bradley, M., Essex, J. W., Hursthouse, M. B., Lewis, S. M., Luck, M. M., Moreau, L., De Roure, D. C., Surridge, M. and Welsh, A. (2003) Combinatorial chemistry and the Grid, in Berman, F., Fox, G. and Hey, T., Eds. Grid Computing - Making the Global Infrastructure a Reality, pages pp. 945-962. John Wiley and Sons Ltd.
[Goble 02] Carole A. Goble, David De Roure: The Grid: An Application of the Semantic Web. SIGMOD Record 31(4): 65-70 (2002)
[Goble 03a] Goble, C.A., De Roure, D., Shadbolt, N., Fernandes, A.A.A. (2003) Enhancing Services and Applications with Knowledge and Semantics. In (Foster, I. and Kesselman, C. eds.) The Grid: Blueprint for a New Computing Infrastructure (2nd. ed), Ch. 23, pp. 431-458. Morgan Kaufmann.
[Goble 03b] Carole Goble and Stephen Pettifer and Robert Stevens. “myGrid: In Silico Experiments in Bioinformatics," The Grid: Blueprint for a New Computing Infrastructure, edited by Ian Foster and Carl Kesselman, Morgan Kaufmann Publishers, 2003.
[Greenhalgh 02] Chris Greenhalgh, Martin Flintham, Jim Purbrick, Steve Benford, Applications of Temporal Links: Recording and Replaying Virtual Environments, in Proceedings of IEEE Virtual Reality 2002, Orlando Florida, March 24-28, 2002, pp. 101-108, IEEE Computer Society.
[schraefel 04a] schraefel, m.c., Hughes, G., Mills, H., Smith, G., Payne, T. and Frey, J. Breaking the Book: Translating the Chemistry Lab Book to a Pervasive Computing Environment. Proceedings of the 2004 Conference on Human Factors (CHI), 2004. Preprint at http://eprints.ecs.soton.ac.uk/archive/00008641/.
[schraefel 04b] schraefel, m. c., Hughes, G., Mills, H., Smith, G. and Frey, J. (2003) Making Tea: Iterative Design through Analogy. In Proceedings of Designing Interactive Systems, 2004 (forthcoming). Preprint at http://eprints.ecs.soton.ac.uk/archive/00008672/.
[Steed 03] Steed, A, Spinello, S, Croxford, B, Greenhalgh, C, e-Science in the Streets: Urban Pollution Monitoring, Proceedings of the 2nd UK e-Science All Hands Meeting 2003.
[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. http://bioinformatics.oupjournals.org/cgi/content/abstract/19/suppl_1/i302?etoc.
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