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Dr David Thorne

Research Associate
School of Computer Science

Doctoral Research

My doctoral thesis put forward a set of software architecture guidelines based on a semiotic investigation of scientific data flow. The complex and evolving data found in many modern areas of science cause significant problems for those who write the software that is used to visualise and analyse them. One implementation of my findings has produced the current incarnation of the Utopia suite of applications, based on a semantically agnostic core framework.


Journal Articles

S. Pettifer, J. Velterop, T. K. Attwood, L. Harland, J. Marsh, D. Thorne, and A. Tunbridge. Reuniting data and narrative in scientific articles. Insights, 25(3):288-293, November 2012. [ DOI ]

B. Vroling, D. Thorne, P. McDermott, T. K. Attwood, G. Vriend, and S. Pettifer. Integrating GPCR-specific information with full text articles. BMC Bioinformatics, 12(362), Sep 2011. [ DOI ]

B. Vroling, D. Thorne, P. McDermott, HJ. Joosten, T. K. Attwood, S. Pettifer, and G. Vriend. Nucleardb: information system for nuclear receptors. Nucleic Acids Research, Nov 2011.

S. Pettifer, P.McDermott, J. Marsh, D. Thorne, A.Villéger, and T. K. Attwood. Ceci n'est pas un hamburger: modelling and representing the scholarly article. Learned Publishing, Jul 2011. [ DOI | http ]

T. K. Attwood, D. B. Kell, P. Mcdermott, J. Marsh, S. R. Pettifer, and D. Thorne. Utopia Documents: linking scholarly literature with research data. Bioinformatics, 26:i540-i546, Sep 2010. [ DOI | http ]

S. Pettifer, J. Ison, M. Kalaš, D. Thorne, P. McDermott, I. Jonassen, A. Liaquat, J. M. Fernández, J. M. Rodriguez, INB-Partners, D. G. Pisano, J. Salzemann, C. Blanchet, V. Breton, M. Uludag, P. Rice, E. Bartaševičiutė, K. Rapacki, M. Hekkelman, O. Sand, H. Stockinger, A. B. Clegg, E. Bongcam-Rudloff, T. K. Attwood, G. Cameron, and G. Vriend. The EMBRACE web service collection. Nucleic Acids Research, 2010. [ DOI | http | http ]

M. L. Hekkelman, T. A. H te Beek, S. R. Pettifer, D. Thorne, T. K. Attwood, and G. Vriend. WIWS: a protein structure bioinformatics web service collection. Nucleic Acids Research, 2010. [ DOI | http ]

S. Pettifer, D. Thorne, P. McDermott, T. Attwood, J. Baran, J. C. Bryne, T. Hupponen, D. Mowbray, and G. Vriend. An active registry for bioinformatics web services. Bioinformatics, 25, 2009. [ DOI | http ]

T. K. Attwood, D. B. Kell, P. Mcdermott, J. Marsh, S. R. Pettifer, and D. Thorne. Calling international rescue: knowledge lost in literature and data landslide! Biochemical Journal, Dec 2009. [ DOI | http ]

S. R. Pettifer, D. Thorne, P. McDermott, J. Marsh, A. Villéger, D. B. Kell, and T. K. Attwood. Visualising biological data: a semantic approach to tool and database integration. BMC Bioinformatics, 16, Jun 2009. [ DOI | http ]

Books and Chapters

S. Pettifer, T. Attwood, J. Marsh, and D. Thorne. Utopia documents: Transforming how industrial scientists interact with the scientific literature. In L. Harland and M. Foster, editors, Open source software in life science research: Practical solutions to common challenges in the pharmaceutical industry and beyond. Springer-Verlag, November 2012. ISBN-10: 1907568972. [ http ]

Workshop and Conference Proceedings

T. K. Attwood, D. B. Kell, P. Mcdermott, J. Marsh, S. R. Pettifer, and D. Thorne. Utopia Documents: linking scholarly literature with research data. In Proceedings of 9th European Conference on Computational Biology, Ghent, Belgium, Sep 2010.

S. Pettifer, K. Wolstencroft, P. Alper, T. Attwood, A. Coletta, C. Goble, P. Li, P. McDermott, J. Marsh, T. Oinn, J. Sinnott, and D. Thorne. mygrid and UTOPIA: an integrated approach to enacting and visualising in silico experiments in the life sciences. Springer, June 2007. 59-70.

P. McDermott, J. Sinnott, D. Thorne, S. Pettifer, and T. Attwood. An architecture for visualisation and interactive analysis of proteins. In Proceedings of 4th International Conference on Coordinated and Multiple Views in Exploratory Visualization (CMV06), pages 55-65, Jul 2006. London, UK.

D. Thorne and S. Pettifer. Unifying abstract and physical molecular model interaction. In Proceedings of EGUK Theory and Practice of Computer Graphics Conference 2005 (TPCG05), pages 75-82, Jun 2005. Canterbury, UK.

Miscellaneous

T. K. Attwood, D. B. Kell, P. Mcdermott, J. Marsh, S. R. Pettifer, and D. Thorne. Utopia Documents and The Semantic Biochemical Journal experiment. EMBNet News, Mar 2010. [ http ]

T. K. Attwood, D. B. Kell, P. Mcdermott, J. Marsh, S. R. Pettifer, and D. Thorne. Knowledge lost in literature and data landslide: calling international rescue! The Biochemist, Dec 2009. [ .pdf ]

S. Pettifer, D. Thorne, P. McDermott, T. Attwood, J. Baran, J. C. Bryne, T. Hupponen, and G. Vriend. The EMBRACE registry. EMBNet News, January 2009. [ .html ]

M. Corpas, J. Sinnott, D. Thorne, S. Pettifer, and T. Attwood. PFF - an integrated database of residues and fragments critical for protein folding. BMC Systems Biology (online journal), 2007. doi:10.1186/1752-0509-1-SI-P48.

Contact Information
Name: David Thorne
Tel.: 0161 275 6148
Room: KB 2.92
Email: thorne@cs.man.ac.uk