UTOPIA (Bioinformatics tools)

UTOPIA

UTOPIA tools on a Mac
Developer(s)	Steve Pettifer, Terri Attwood, David Parry-Smith, D.N.Perkins, A.W. Payne, A.D. Michie, Phillip W.Lord, J.N.Selley, Phil McDermott, James Marsh, James Sinnott, Dave Thorne, Benjamin Blundell
Written in	C++, Python
Operating system	Linux, Mac and Windows
Website	utopia.cs.manchester.ac.uk, getutopia.com

UTOPIA (User-friendly Tools for OPerating Informatics Applications) is a suite of free tools for visualising and analysing bioinformatics data. Based on an ontology-driven data model, it contains applications for viewing and aligning protein sequences, rendering complex molecular structures in 3D, and for finding and using resources such as web services and data objects. There are two major components, the protein analysis suite and UTOPIA documents.

The Utopia Protein Analysis suite is a collection of interactive tools for analysing protein sequence and protein structure. Up front are user-friendly and responsive visualisation applications, behind the scenes a sophisticated model that allows these to work together and hides much of the tedious work of dealing with file formats and web services.

Utopia Documents brings a fresh new perspective to reading the scientific literature, combining the convenience and reliability of the Portable Document Format (pdf) with the flexibility and power of the web.

Between 2003 and 2005 work on UTOPIA was funded via The e-Science North West Centre based at The University of Manchester by the Engineering and Physical Sciences Research Council, UK Department of Trade And Industry, and the European Molecular Biology Network (EMBnet). Since 2005 work continues under the EMBRACE European Network of Excellence.

UTOPIA's CINEMA (Colour INteractive Editor for Multiple Alignments), a tool for Sequence Alignment, is the latest incarnation of software originally developed at The University of Leeds to aid the analysis of G protein-coupled receptors (GPCRs). SOMAP, a Screen Oriented Multiple Alignment Procedure was developed in the late 1980s on the VMS computer operating system, used a monochrome text-based VT100 video terminal, and featured context-sensitive help and pulldown menus some time before these were standard operating system features.