UTOPIA (bioinformatics tools): Difference between revisions

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

{{Infobox software

| name =

| title = UTOPIA

| logo =

| logo caption =

| screenshot = Image:Utopia-desktop600.jpg

| caption = UTOPIA tools on a Mac

| collapsible =

| author =

| 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

| 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++, Python

| operating system = Linux, Mac and Windows

| platform =

| size =

| language =

| status =

| genre =

| license =

| alexa =

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

}}

'''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

| 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==

'''UTOPIA''' (User-friendly Tools for OPerating Informatics Applications) is a suite of free tools for visualising and analysing [[bioinformatics]] data. Based on an [[Ontology (computer science)|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.

The Utopia [[Proteomics|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 format]]s and [[web service]]s.<ref name="CaFG"/>

==Utopia Documents==

Between 2003 and 2005 work on UTOPIA was funded via [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, and the European Molecular Biology Network. Since 2005 work continues under the [http://www.embracegrid.info EMBRACE European Network of Excellence].

[[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">{{Cite journal

| 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 [[GPCR]]s. SOMAP<ref>{{cite journal |doi=10.1093/bioinformatics/7.2.233 |author=Parry-Smith DJ, Attwood TK |title=SOMAP: a novel interactive approach to multiple protein sequences alignment |journal=Bioinformatics |volume=7 |issue=2 |pages=233–5 |url=http://bioinformatics.oxfordjournals.org/cgi/content/abstract/7/2/233 |year=1991 |pmid=2059849}}</ref>, a Screen Orientated 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.

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 = 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.

SOMAP was followed by a [[Unix]] tool called VISTAS<ref>{{cite journal |doi=10.1016/0263-7855(94)00013-I |author=Perkins DN, Attwood TK |title=VISTAS: a package for VIsualizing STructures and sequences of proteins |journal=J Mol Graph |volume=13 |issue=1 |pages=73–5, 62 |year=1995 |month=February |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.

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.

The first tool under the CINEMA<ref>{{cite journal |doi=10.1016/S0378-1119(97)00650-1 |author=Parry-Smith DJ, Payne AW, Michie AD, Attwood TK |title=CINEMA--a novel colour INteractive editor for multiple alignments |journal=Gene |volume=221 |issue=1 |pages=GC57–63 |year=1998 |month=October |pmid=9852962 |url=http://linkinghub.elsevier.com/retrieve/pii/S0378-1119(97)00650-1}}</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>{{cite journal |doi=10.1093/bioinformatics/18.10.1402 |author=Lord PW, Selley JN, Attwood TK |title=CINEMA-MX: a modular multiple alignment editor |journal=Bioinformatics |volume=18 |issue=10 |pages=1402–3 |year=2002 |month=October |pmid=12376388 |url=http://bioinformatics.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=12376388}}</ref>, was also released but is no longer readily available.

The first tool under the CINEMA<ref name="cinema">{{Cite journal | 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">{{Cite journal | 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.

==People==

Pre UTOPIA alignment tools: T.K. Attwood, D.J.Parry-Smith, D.N.Perkins, A.W. Payne, A.D. Michie, P.W.Lord, J.N.Selley.

UTOPIA: T.K.Attwood, P.McDermott, J.Marsh, S.Pettifer, J.Sinnott, D.Thorne,

==External links==

*[http://utopia.cs.manchester.ac.uk Official UTOPIA website http://utopia.cs.manchester.ac.uk]

Peer reviewed publications on UTOPIA

*{{cite journal |author=Pettifer SR, Sinnott JR, Attwood TK |title=UTOPIA — User-Friendly Tools for Operating Informatics Applications |journal=Comp. Funct. Genomics |volume=5 |issue=1 |pages=56–60 |year=2004 |pmid=18629035 |pmc=2447318 |doi=10.1002/cfg.359 |url=http://www.ingentaconnect.com/content/jws/cfg/2004/00000005/00000001/art00006}}

*{{cite conference |author=Philip McDermott, James Sinnott, Dave Thorne, Steve Pettifer, Terri Attwood |title=An Architecture for Visualisation and Interactive Analysis of Proteins |booktitle=Fourth International Conference on Coordinated & Multiple Views in Exploratory Visualization (CMV'06) |pages=55–68 |year=2006 |isbn=0-7695-2605-5 |url=http://doi.ieeecomputersociety.org/10.1109/CMV.2006.3 |doi=10.1109/CMV.2006.3}}

==References==

{{reflist|2}}

[[Category:Bioinformatics software]]

[[Category:Computational science]]

[[Category:BioinformaticsEngineering softwareand Physical Sciences Research Council]]

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

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