e-Science: CombeChem

 
 
 

End-to-End Digital Support for Chemical Research

http://www.combechem.org


Recently I have been able to take these ideas forward in the context of the explosion of data from combinatorial & high-throughput chemical techniques.  In the CombeChem project we have shown how the growth in the power of modern computing, together with new software techniques, make an essential contribution to meeting the demands of dealing with the exponential growth in data.  It allows the data to be combined with the appropriate metadata and to be made available in a verifiable and auditable manner.  The demonstrations have been based around the National Crystallography Service (NCS) laser experiments and a synthetic chemistry laboratory, all in pursuit of smart interconnected chemical investigations.  This approach has resulted in demonstrations of digitally aided design of experiments, and integrated data generation with properly designed human-computer interactions for both collection and analysis of the data.  These developments have involved considerable work in computer science and adapting concepts and processes to the needs of chemists and vice versa


The CombeChem and e-Bank projects have already made a huge impact on the worldwide crystallography community (our chosen initial demonstrator area) through ‘instruments on the Grid’ and dissemination of data (as exemplified by the success of the e-Bank project).  Similarly, my major interest in the usability of the computer systems means we have been very concerned with the human-computer interface, particularly for use directly in the laboratory. This has been a significant focus of our work on the Smart Laboratory Electronic Notebook.


Taylor, K., Essex, J.W., Frey, J.G., Mills, H.R., Hughes, G. and Zaluska, E., The semantic grid and chemistry: experiences with CombeChem. J. Web Semantics, 4 (2), 2006, 84-101.
http://dx.doi.org/doi:10.1016/j.websem.2006.03.003

Taylor, K.R., Gledhill, R.J., Essex, J.W., Frey, J.G., Harris, S.W. and De Roure, D.C., Bringing chemical data onto the semantic web. Journal of Chemical Information and Modeling, 46 (3), 2006, 939-952. http://dx.doi.org/doi:10.1021/ci050378m

Coles, S.J., Frey, J.G., Hursthouse, M.B., Light, M.E., Milsted, A.J., Carr, L.A., De Roure, D.C., Gutteridge, C.J., et al., An e-science environment for Service Crystallography - from submission to dissemination. Journal of Chemical Information and Modeling, 46 (3), 2006, 1006-1016. http://dx.doi.org/doi:10.1021/ci050362w.

Rousay, E.R., Fu, H.C., Robinson, J.M., Essex, J.W. and Frey, J.G., Grid-based dynamic electronic publication: A case study using combined experiment and simulation studies of crown ethers at the air/water interface. Philos. Trans. R. Soc. London, A, 363 (1833), 2005, 2075-2095.

Welsh, A.H., Mansson, R.A., Frey, J.G. and Danos, L., Statistical analysis of second harmonic generation experiments: a phenomenological model. Chemometrics and Intelligent Laboratory Systems, 75 (1), 2005, 45-54.

Hughes, G., Mills, H., De Roure, D.C., Frey, J.G., Moreau, L., Schraefel, M.C., Smith, G. and Zaluska, E., The Semantic Smart Laboratory: A system for supporting the chemical eScientist. Organic & Biomolecular Chemistry, 2 (22), 2004, 3284-3293.

Frey, J.G., Bradley, M., Essex, J.W., Hursthouse, M.B., Lewis, S.M., Luck, M.M., Moreau, L., De Roure, D.C., et al., Combinatorial chemistry and the Grid, In: Berman, F., Hey, A.J.G. and Fox, G.C. ed. Grid computing: making the global infrastructure a reality, John Wiley & Sons Ltd., 2003, 945-962.

Frey, J.G., De Roure, D.C., Taylor, K., Essex, J., Mills, H. and Zaluska, E., CombeChem: A Case Study in Provenance and Annotation using the Semantic Web. Provenance and Annotation of Data, International Provenance and Annotation Workshop, IPAW 2006, 2006, 288.
http://www.springer.com/uk/home/generic/search/results?SGWID=3-40109-22-173681711-0

Heery, R., Duke, M., Day, M., Lyon, L., Coles, S., Frey, J.G., Hursthouse, M., Carr, L., et al., Integrating research data into the publication workflow: eBank experience. PV-2004: Ensuring the Long-Term Preservation and Adding Value to the Scientific and Technical Data, European Space Agency, 2004, 135-142.

schraefel, m.c., Hughes, G., Mills, H., Smith, G., Payne, T. and Frey, J.G., Breaking the Book: Translating the Chemistry Lab Book into a Pervasive Computing Lab Environment. CHI 2004, ACM Press, 2004.