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UTOPIA

Investigators: Steve Pettifer and Terri Attwood

Researchers: James Sinnott (RA), Neil Vass, Manuel Corpas, Ben Blundell and Alain Coletta (PhD Students)
 

Bioinformaticians routinely analyse vast amounts of information held both in large remote databases and in flat data files hosted on local machines. The contemporary toolkit available for this purpose consists of an ad hoc collection of data manipulation tools, scripting languages and visualisation systems; these must often be combined in complex and bespoke ways, the result frequently being an unwieldy artefact capable of one specific task, which cannot easily be exploited or extended by other practitioners. Owing to the sizes of current databases and the scale of the analyses necessary, routine bioinformatics tasks are often automated, but many still require the unique experience and intuition of human researchers: this requires tools that support real-time interaction with complex data sets. Many existing tools have poor user interfaces and limited real-time performance when applied to realistically large data sets; much of the user.s cognitive capacity is therefore focused on controlling the tool rather than on performing the research.

The UTOPIA project is addressing some of these issues by building re-usable software components that can be combined to make useful applications in the field of bioinformatics. Expertise in the fields of human computer interaction, high-performance rendering, and distributed systems is being guided by bioinformaticians and end-user biologists to create a toolkit that is both architecturally sound from a computing point of view, and directly addresses end-user and application-developer requirements.


CINEMA 5

The first application built with UTOPIA widgets is CINEMA 5, an interactive visual tool for the interpretation, manipulation and construction of multiple protein- and DNA-sequence alignments.

CINEMA 5 aims to provide a highly intuitive, flexible and full-featured interface, with several facilities that are unique to multiple sequence alignment editors. Consistent with the need to avoid the underlying technology getting in the way of effortless interaction, the widgets used to render the protein sequences are optimised so as to efficiently render extremely large sequences, and the means of interaction itself is the familiar 'drag and drop/point and click' metaphor of most office and design applications.

For further information about CINEMA 5, and to download the latest beta version of the application take a look here.




AMBROSIA




The UTOPIA Filing System

At the core of UTOPIA lies the 'UTOPIA Filing System' (UFS), which mediates between the large number of diverse, often complex, and sometimes esoteric remote resources used by biologists in their everyday work, and presents them to the user via the familiar desktop metaphor of 'files', 'folders' and 'applications'.

The UFS blurs the distinction between 'something I found in a remote database' and 'something I have locally on my machine' by making everything appear to be a local resource. It hides all the unsightly plumbing necessary to authenticate and communicate with remote services behind the desktop/filing system metaphor. Retaining metadata ('where', 'when', 'why', 'who', etc.) relating to resources that have been downloaded or referenced, allows the UFS to enter into dialogue with the user when interesting events have occurred ("A new version of this protein is now available; would you like to replace your current one?").

By pushing much of the 'intelligence' of the system into the filing system, it is possible to simplify all the applications that then need to use its resources; file formats can be converted on demand (e.g., by invoking EMBOSS [1] programs 'behind the scenes') to suit whatever the application requires, removing the need for each individual tool to have options for loading multiple types of data; problems with resources such as stale, corrupt, or temporarily unreachable facilities are handled consistently by the filing system, rather than in an ad hoc manner by each individual application.
UTOPIA Software

CINEMA 5

Intuitive sequence alignment editor [More...]

Ambrosia

Structure visualisation tool [More...]

Related publications

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 ]

A. Villéger, S. R. Pettifer, and D. B. Kell. Arcadia: a visualization tool for metabolic pathways. Bioinformatics, 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 ]

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.

S. Pettifer, T. K. Attwood, and J. Sinnott. Integrated approaches for bioinformatics data analysis and visualisation - challenges, opportunities and new solutions. In F. Azuaje and J. Dopazo, editors, Data Analysis and Visualisation in Genomics and Proteomics, pages 137-152. John Wiley and Sons, Ltd, ISBN 0-470-09439-7, January 2005.

S. Pettifer, J. R. Sinnott, and T. K. Attwood. CINEMA - A UTOPIAn sequence editor. CCP11 Newsletter, Jan 2004.

S. Pettifer, J. R. Sinnott, and T. K. Attwood. UTOPIA: user friendly tools for operating informatics applications. Comparative and Functional Genomics, 5:56-60, January 2004.

C. Goble, C. Greenhalge S. Pettifer, and R. Stevens. MyGrid: in-silico experiments in bioinformatics. In I. Foster and K. Kesselman, editors, The Grid: blueprint for a new computing infrastructure (2nd edition), pages 121-134. Morgan Kaufman Publishers, December 2003. ISBN 1558609334. [ http ]