UTOPIA (bioinformatics tools): Difference between revisions

Revision as of 17:26, 16 August 2023

Latest revision as of 04:21, 28 November 2023

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| website = {{URL|utopia.cs.manchester.ac.uk}}

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'''UTOPIA''' ('''User-friendly Tools for Operating Informatics Applications''') is a suite of free tools for visualising and analysing [[bioinformatics]] data. Based on an [[ontology (information science)|ontology]]-driven data model, it contains applications for viewing and aligning [[peptide sequence|protein sequences]], rendering complex molecular structures in 3D, and for finding and using resources such as web services and data objects.<ref name="CaFG">{{Cite journal | last1 = Pettifer | first1 = S. R. | author-link1 = Steve Pettifer| last2 = Sinnott | first2 = J. R. | last3 = Attwood | first3 = T. K. | author-link3 = Terri Attwood| doi = 10.1002/cfg.359 | title = UTOPIA—User-Friendly Tools for Operating Informatics Applications | journal = Comparative and Functional Genomics | volume = 5 | issue = 1 | pages = 56–60 | year = 2004 | pmid = 18629035| pmc =2447318 }}</ref><ref>{{Cite book | last1 = McDermott | first1 = P. | last2 = Sinnott | first2 = J. | last3 = Thorne | first3 = D. | last4 = Pettifer | first4 = S. | author-link4 = Steve Pettifer| last5 = Attwood | first5 = T. | author-link5 = Terri Attwood| doi = 10.1109/CMV.2006.3 | chapter = An Architecture for Visualisation and Interactive Analysis of Proteins | title = Fourth International Conference on Coordinated & Multiple Views in Exploratory Visualization (CMV'06) | pages = 55 | year = 2006 | isbn = 978-0-7695-2605-8 | s2cid = 43554573 }}</ref><ref name="rescue">{{Cite journal

| last1 = Attwood | first1 = T. K.

| author-link1 = Terri Attwood

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| pages = S19

| year = 2009

| issue = Suppl 6

| pmid = 19534744

| pmc =2697642

| doi-access = free

}}</ref> There are two major components, the protein analysis suite and UTOPIA documents.

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| pmid = 20823323

| pmc =2935404

}}</ref><ref name="hamburger">{{Cite journal | last1 = Pettifer | first1 = S. | author-link1= Steve Pettifer| last2 = McDermott | first2 = P. | last3 = Marsh | first3 = J. | last4 = Thorne | first4 = D. | last5 = Villeger | first5 = A. | last6 = Attwood | first6 = T. K.| author-link6 = Terri Attwood | doi = 10.1087/20110309 | title = Ceci n'est pas un hamburger: Modelling and representing the scholarly article | journal = Learned Publishing | volume = 24 | issue = 3 | pages = 207 | year = 2011 | s2cid = 29739751 | doi-access = }}</ref>

== History ==

Between 2003 and 2005 work on UTOPIA was funded via [https://web.archive.org/web/20070820201835/http://www.esnw.ac.uk/ 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 (United Kingdom)|Department of Trade And Industry]], and the [[EMBnet|European Molecular Biology Network (EMBnet)]]. Since 2005 work continues under the [http://www.embracegrid.info EMBRACE European Network of Excellence].

UTOPIA's CINEMA (Colour INteractive Editor for Multiple Alignments), a tool for [[Sequence alignment|Sequence Alignment]], is the latest incarnation of software originally developed at The [[University of Leeds]] to aid the analysis of [[G protein-coupled receptor]]s (GPCRs).<ref name="gpcr">{{Cite journal | last1 = Vroling | first1 = B. | last2 = Thorne | first2 = D. | last3 = McDermott | first3 = P. | last4 = Attwood | first4 = T. K. | author-link4= Terri Attwood| last5 = Vriend | first5 = G. | last6 = Pettifer | first6 = S. | author-link6 = Steve Pettifer| doi = 10.1186/1471-2105-12-362 | title = Integrating GPCR-specific information with full text articles | journal = BMC Bioinformatics | volume = 12 | pages = 362 | year = 2011 | pmid = 21910883| pmc =3179973 | doi-access = free }}</ref> SOMAP,<ref name="somap">{{Cite journal | last1 = Parry-Smith | first1 = D. J. | last2 = Attwood | first2 = T. K. | author-link2 = Terri Attwood| doi = 10.1093/bioinformatics/7.2.233 | title = SOMAP: A novel interactive approach to multiple protein sequences alignment | journal = Bioinformatics | volume = 7 | issue = 2 | pages = 233233–235 | year = 1991 | pmid = 2059849}}</ref> a Screen Oriented Multiple Alignment Procedure was developed in the late 1980s on the [[OpenVMS|VMS]] computer operating system, used a monochrome text-based [[VT100]] video terminal, and featured [[Context-Sensitive Help|context-sensitive help]] and [[Pull-down menu|pulldown menus]] some time before these were standard operating system features.

SOMAP was followed by a [[Unix]] tool called VISTAS<ref name="vistas">{{Cite journal | last1 = Perkins | first1 = D. N. | last2 = Attwood | first2 = T. K. | author-link2 = Terri Attwood| doi = 10.1016/0263-7855(94)00013-I | title = VISTAS: A package for VIsualizing STructures and sequences of proteins | journal = Journal of Molecular Graphics | volume = 13 | issue = 1 | pages = 73–75, 62 | year = 1995 | pmid = 7794837}}</ref> (VIsualizing STructures And Sequences) which included the ability to render 3D molecular structure and generate plots and statistical representations of sequence properties.