UTOPIA (User-friendly Tools for Operating Informatics Applications) is a suite of free tools for visualising and analysing

bioinformatics Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combin ...

data. Based on an

ontology In metaphysics, ontology is the philosophical study of being, as well as related concepts such as existence, becoming, and reality. Ontology addresses questions like how entities are grouped into categories and which of these entities ...

-driven data model, it contains applications for viewing and aligning

protein sequences Protein primary structure is the linear sequence of amino acids in a peptide or protein. By convention, the primary structure of a protein is reported starting from the amino-terminal (N) end to the carboxyl-terminal (C) end. Protein biosynthesi ...

, 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.

Utopia Protein Analysis suite

The Utopia

Protein Analysis Proteomics is the large-scale study of proteins. Proteins are vital parts of living organisms, with many functions such as the formation of structural fibers of muscle tissue, enzymatic digestion of food, or synthesis and replication of DNA. In ...

suite is a collection of interactive tools for analysing protein sequence and

protein structure Protein structure is the molecular geometry, three-dimensional arrangement of atoms in an amino acid-chain molecule. Proteins are polymers specifically polypeptides formed from sequences of amino acids, the monomers of the polymer. A single ami ...

. 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 format A file format is a Computer standard, standard way that information is encoded for storage in a computer file. It specifies how bits are used to encode information in a digital storage medium. File formats may be either proprietary format, pr ...

s and web services.

Utopia Documents

Utopia Documents Utopia Documents is a semantic, scientific, web-enabled PDF reader that is part of the Utopia toolset. Utopia Documents can be downloaded for free. Utopia provides links to web resources and metadata. Although Utopia is a PDF-reader, it bridges ...

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.

History

Between 2003 and 2005 work on UTOPIA was funded vi
The e-Science North West Centre
based at

The University of Manchester , mottoeng = Knowledge, Wisdom, Humanity , established = 2004 – University of Manchester Predecessor institutions: 1956 – UMIST (as university college; university 1994) 1904 – Victoria University of Manchester 1880 – Victoria Univer ...

by the

Engineering and Physical Sciences Research Council The Engineering and Physical Sciences Research Council (EPSRC) is a British Research Council that provides government funding for grants to undertake research and postgraduate degrees in engineering and the physical sciences, mainly to univers ...

, UK Department of Trade And Industry, and the European Molecular Biology Network (EMBnet). Since 2005 work continues under th
EMBRACE European Network of Excellence
UTOPIA's CINEMA (Colour INteractive Editor for Multiple Alignments), a tool for

Sequence Alignment In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. Ali ...

, is the latest incarnation of software originally developed at The

University of Leeds , mottoeng = And knowledge will be increased , established = 1831 – Leeds School of Medicine1874 – Yorkshire College of Science1884 - Yorkshire College1887 – affiliated to the federal Victoria University1904 – University of Leeds , ...

to aid the analysis of

G protein-coupled receptor G protein-coupled receptors (GPCRs), also known as seven-(pass)-transmembrane domain receptors, 7TM receptors, heptahelical receptors, serpentine receptors, and G protein-linked receptors (GPLR), form a large group of evolutionarily-related p ...

s (GPCRs). SOMAP, a Screen Oriented Multiple Alignment Procedure was developed in the late 1980s on the

VMS #REDIRECT VMS {{redirect category shell, {{R from other capitalisation{{R from ambiguous page ...

computer operating system, used a monochrome text-based

VT100 The VT100 is a video terminal, introduced in August 1978 by Digital Equipment Corporation (DEC). It was one of the first terminals to support ANSI escape codes for cursor control and other tasks, and added a number of extended codes for special ...

video terminal, and featured

context-sensitive help Context-sensitive help is a kind of online help that is obtained from a specific point in the state of the software, providing help for the situation that is associated with that state.US patent 5285709 Context-sensitive help, as opposed to genera ...

and pulldown menus some time before these were standard operating system features. SOMAP was followed by a

Unix Unix (; trademarked as UNIX) is a family of multitasking, multiuser computer operating systems that derive from the original AT&T Unix, whose development started in 1969 at the Bell Labs research center by Ken Thompson, Dennis Ritchie, a ...

tool called VISTAS (VIsualizing STructures And Sequences) which included the ability to render 3D molecular structure and generate plots and statistical representations of sequence properties. The first tool under the CINEMA banner developed at The University of Manchester was a

Java Java (; id, Jawa, ; jv, ꦗꦮ; su, ) is one of the Greater Sunda Islands in Indonesia. It is bordered by the Indian Ocean to the south and the Java Sea to the north. With a population of 151.6 million people, Java is the world's mo ...

-based applet launched via web pages, which i
still available
but is no longer maintained. A standalone Java version, called CINEMA-MX, was also released but is no longer readily available. A C++ version of CINEMA, called CINEMA5 was developed early on as part of the UTOPIA project, and was released as a stand-alone sequence alignment application. It has now been replaced by a version of the tool integrated with UTOPIA's other visualisation applications, and its name has reverted simply to CINEMA.

References

{{reflist, 2 Bioinformatics software Computational science Engineering and Physical Sciences Research Council Department of Computer Science, University of Manchester Science and technology in Greater Manchester