UTOPIA (bioinformatics tools): Difference between revisions

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{{Infobox software

| name =

| title = UTOPIA

| logo =

| logo caption =

| screenshot = [[Image:Utopia-desktop600.jpg
|thumbnail|right|250px| caption = UTOPIA tools on a Mac]]

| collapsible =

| caption =

| author =

| collapsible =

| developer = Steve Pettifer,<br />[[Terri Attwood]],<br />David Parry-Smith,<br />D.N.Perkins,<br />A.W. Payne,<br />A.D. Michie,<br />Phillip W.Lord,<br />J.N.Selley,<br />Phil McDermott,<br />James Marsh,<br />James Sinnott,<br />Dave Thorne.,<br />Benjamin Blundell

| author =

| released = <!-- {{Start date|YYYY|MM|DD|df=yes/no}} -->

| developer = 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.

| discontinued =

| released = <!-- {{Start date|YYYY|MM|DD|df=yes/no}} -->

| discontinued =

| latest release version =

| latest release date = <!-- {{Start date and age|YYYY|MM|DD|df=yes/no}} -->

| latest preview version =

| latest preview date = <!-- {{Start date and age|YYYY|MM|DD|df=yes/no}} -->

| frequently updated = <!-- DO NOT include this parameter unless you know what it does -->

| programming language = C++, JavaPython

| operating system = Linux, Mac and Windows

| platform =

| size =

| language =

| status =

| genre =

| license =

| alexa =

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

}}

'''UTOPIA''' ('''User-friendly Tools for OPeratingOperating Informatics Applications''') is a suite of free tools for visualising and analysing [[bioinformatics]] data. Based on an [[Ontologyontology (computerinformation science)|ontology]]-driven data model, it contains applications for viewing and aligning [[Peptidepeptide 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">{{citeCite journal doi| 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>{{citeCite book doi| 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}}</ref><ref name| chapter ="rescue">{{cite pmidAn Architecture for Visualisation and Interactive Analysis of Proteins |19929850 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="vizrescue">{{citeCite pmid|journal 19534744}}</ref> There are two major components, the protein analysis suite and UTOPIA documents.

| last1 = Attwood | first1 = T. K.

| author-link1 = Terri Attwood

| last2 = Kell | first2 = D. B.

| author-link2 = Douglas Kell

| last3 = McDermott | first3 = P.

| last4 = Marsh | first4 = J.

| last5 = Pettifer | first5 = S. R.

| author-link5 = Steve Pettifer

| last6 = Thorne | first6 = D.

| doi = 10.1042/BJ20091474

| title = Calling International Rescue: Knowledge lost in literature and data landslide!

| journal = Biochemical Journal

| volume = 424

| issue = 3

| pages = 317–333

| year = 2009

| pmid = 19929850

| pmc =2805925

}}</ref><ref name="viz">{{Cite journal

| last1 = Pettifer | first1 = S.

| author-link1 = Steve Pettifer

| last2 = Thorne | first2 = D.

| last3 = McDermott | first3 = P.

| last4 = Marsh | first4 = J.

| last5 = Villéger | first5 = A.

| last6 = Kell | first6 = D. B.

| author-link6 = Douglas Kell

| last7 = Attwood | first7 = T. K.

| author-link7 = Terri Attwood

| title = Visualising biological data: A semantic approach to tool and database integration

| doi = 10.1186/1471-2105-10-S6-S19

| journal = BMC Bioinformatics

| volume = 10

| 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.

==Utopia Protein Analysis suite==

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==Utopia Documents==

'''[[Utopia Documents''']] brings a fresh new perspective to reading the scientific literature, combining the convenience and reliability of the [[Portable Document Format| Portable Document Format (pdf)]] with the flexibility and power of the web. <ref name="rescue"/><ref name="udocs">{{citeCite pmid|20823323}}</ref><refjournal name="hamburger">{{cite doi|10.1087/20110309}}</ref>

| last1 = Attwood | first1 = T. K.

| author-link1 = Terri Attwood

| last2 = Kell | first2 = D. B.

| author-link2 = Douglas Kell

| last3 = McDermott | first3 = P.

| last4 = Marsh | first4 = J.

| last5 = Pettifer | first5 = S. R.

| author-link5 = Steve Pettifer

| last6 = Thorne | first6 = D.

| doi = 10.1093/bioinformatics/btq383

| title = Utopia documents: Linking scholarly literature with research data

| journal = Bioinformatics

| volume = 26

| issue = 18

| pages = i568–i574

| year = 2010

| 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">{{citeCite journal doi| 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 = 233–235 | 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.

}}</ref>. SOMAP<ref name="somap">{{cite doi|10.1093/bioinformatics/7.2.233}}</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">{{citeCite journal doi| 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.

The first tool under the CINEMA<ref name="cinema">{{citeCite journal doi| last1 = Parry-Smith | first1 = D. J. | last2 = Payne | first2 = A. W. R. | last3 = Michie | first3 = A. D. | last4 = Attwood | first4 = T. K. | author-link4 = Terri Attwood| title = CINEMA—a novel Colour INteractive Editor for Multiple Alignments | doi = 10.1016/S0378-1119(97)00650-1 | journal = Gene | volume = 221 | issue = 1 | pages = GC57–GC63 | year = 1998 | pmid = 9852962}}</ref> banner developed at The University of Manchester was a [[Java (programming language)|Java]]-based applet launched via web pages, which is [http://www.bioinf.manchester.ac.uk/dbbrowser/CINEMA2.1/ still available] but is no longer maintained. A standalone Java version, called CINEMA-MX,<ref name="cinemamx">{{citeCite journal doi| last1 = Lord | first1 = P. W. | last2 = Selley | first2 = J. N. | last3 = Attwood | first3 = T. K. | author-link3 = Terri Attwood| doi = 10.1093/bioinformatics/18.10.1402 | title = CINEMA-MX: A modular multiple alignment editor | journal = Bioinformatics | volume = 18 | issue = 10 | pages = 1402–1403 | year = 2002 | pmid = 12376388| doi-access = free }}</ref>, 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.

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{{reflist|2}}

[[Category:Computational science]]

[[Category:Bioinformatics software]]

[[Category:Computational science]]

[[Category:School of Computer Science, University of Manchester]]

[[Category:Engineering and Physical Sciences Research Council]]

[[Category:SchoolDepartment of Computer Science, University of Manchester]]

[[Category:Science and technology in Greater Manchester]]