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Old News

Record of news items from the Barton Group (Legacy Formatting)
  • 22nd Oct  2013:
    Two Job opportunities to join the Jalview Team!  Please see details here.
  • 15th Oct  2013:
    Welcome to Reema Singh who has joined us on a collaborative project with Pauline Schaap’s group.
  • 1st Sept  2013:
    Welcome to Fabio Marques-Madeira who has joined the group as a Wellcome Trust Ph.D. student!
  • 4th July  2013:
    Geoff Barton talking in 2010 about bioinformatics and 10 years of the human genome.
  • 17th June  2013:
     Chris Cole featured on STV news with Hollywood actor Brian Cox  opening the College of Life Sciences Genomic Sequencing Unit.
  • April  2013:
    Update to Geoff Barton’s guide to: “The UK Academic System”.
  • April  2013:
    Visit to the new CTIR building Level 2 which will be our home from January 2014. Photos here.  More photos here, and video here!
  • Mar  2013:
    Welcome to Joe Ward!  New postdoc in NGS sequencing bioinformatics.
  • Jan  2013:
    Happy New Year!  Small updates to People page.
  • Nov  2012:
    Welcome to Thiago Britto Borges who has joined the group on the CAPES Brazil programme.
  • Sep  2012:
    Welcome to Nancy Giang who has joined the group as a Ph.D. student on the Wellcome Trust Programme.
  • Aug 6th  2012:
    Welcome to Konstantinos Moutselos who has joined the DAG as a post-doc/programmer in proteomics.
  • Aug 2012:
    TWO Senior postdoc positions available.  See: Advert1 and Advert2 for details and to apply.  Closing date 30th September 2012.
  • uly 2012:
    BBSRC grant awarded to support development of  JPRED, Kinomer and JABAWS for 5-years! We will shortly be advertising two positions funded off this grant.
  • July 2012:
    Bioinformatics/Data Analysis position to join the Data Analysis Group, to be advertised shortly.
  • July 2012:
    Farewell to Mani who has taken up a new position with the University of Glasgow.  Good luck Mani and thanks for all your contributions to the group.
  • Jan 2012:
    Farewell to Peter Troshin who has taken the plunge as an independent software consultant!  Good luck Peter!
  • Sept 2011:
    Thanks to everyone who attended our mini-symposium on the 8th September!  We are glad so many of you enjoyed it!
  • July 2011:
    Farewell to Michelle Scott who, after a very successful six years in the group has now moved on to start her own group at the Universite de Sherbrooke Canada.
  • May 2011:
    New papers including the Java Bioinformatics Web Services paper and website.

    April 2011:
    Welcome to Manikhandan Mudaliar.  Mani has joined the Data Analysis Group as a research associate.

    November 2010:
    Welcome to Tara Eckenrode.  Tara will be doing her Ph.D. in the group over the next 3.5 years.
  • September 2010:
    Genome Scroller goes live in the College of Life Sciences Atrium.
    GS is a collaboration with the Visual Effects Research Lab in the Duncan of Jordanstone College of Art and Design.
  • August 2010:
    See the video of
     Geoff Barton’s talk on sequence alignment visualisation, given at the Vizbi workshop in Heidelberg.

    August 2010:
    David Martin’s Prophossi paper “Automating expert validation of  phosphopeptide spectrum matches from tandem mass spectrometry” and website published.

    July 2010:
    Michelle Scott’s nucleolar localisation signal predictor published in NAR! - See the database here.
  • June 2010:
    Congratulations to Mark McDowall on his second prize in the ISCB student poster competition at ISMB2010.

    May 2010:
    Welcome to Alexander (Sasha) Sherstnev. Sasha has joined  the group  on a joint BBSRC grant with Gordon Simpson.

    May 2010:
    New release (2.5) of STAMP mulitiple structure alignment and database scanning program.  See here for download.
  • May 2010:
    Updates to Group Information and publications in  2010.
  • Mar 2010:
    Jim Procter co-organised the EMBO VizBi workshop on biological data visualisation at the new Advanced Training Centre EMBL Heidelberg

  • Mar 2010:
    Jim and Geoff  co-authored a review on alignment visualisation and Jim co-authored the commentary in the special issue of  Nature Methods about visualising biological data.

  • Jan 2010: Congratulations to
    Christelle Robert on the successful defense of her Thesis 15/1/10.
  • Jan 2010: Jalview paper rated “Hot” by Thompson Essential Science Indicators.  Read Geoff’s  interview here.


  • Dec 2009:
     Post-doc position in bioinformatics available.  Funded by BBSRC for three years.  See here for the job advert and here for further particulars.  A press release about the grant is here.  Closing date 15th Jan 2010.
  • Oct 2009:
     Two miRNA analysis papers published!  See: here for links.
  • Oct 2009:
     Farewell to Cathy Stephenson.  We thank Cathy for  her efforts over the last four years and wish her all the best in the future.
  • Oct 2009:
     Farewell to Ian Overton.  We wish Ian good luck in starting his own research group at Edinburgh.
  • Aug 2009:
    Press Release about BBSRC Grant joint with Gordon Simpson to apply  massively parallel sequencing to study alternative polyadenylation.
  • July 2009:
     Welcome to Peter Troshin - new Postdoc in the group!
  • May 2009:
    Read the new Data Analysis Group (DAG) web pages to find out how we can now collaborate on more wet/dry research projects.
  • January 2009:
    Paper describing the latest advances in the Jalview multiple alignment editor and analysis workbench published in Bioinformatics.
  • November 2008:
    PIPs protein-protein interaction prediction for Human published in NAR.    See here for details and here to try it.
  • October 2008:
    Kinomer - protein kinase database  published in NAR.  See here for details and here to try it.
  • June 2008:
     SCANPS iterative protein sequence database search site published in NAR.  See here for details and here to try it.
  • April 2008:
    JPRED3 secondary structure prediction server paper now in press.  See here for details and here to try it.

    May 2008:
    Congratulations to Jon Manning on the succesful defense of his Ph.D. thesis.
  • March/April 2008:
    TarO Protein sequence Analysis Pipeline for Structural Genomics Target Selection and General Protein Analysis now Available to try.  See here for details.  And  here for publication.
  • February 2008:
    OB-Score and ParCryst protein crystallisation predictors now available to try. See here for web server, or try them as part of TarO.
  • January 2008: Protein Functional Site Predictions Paper in Print see here for details.
  • June 2008: Two long-term positions in bioinformatics available.  See here for the advert and here for further particulars - APPLICATIONS CLOSED.
  • 7th September 2007: A number of new papers now in print!  See here for the latest!
  • 28th May 2007: Various updates to the site.
  • 3rd May 2007: Congratulations to Diego Miranda-Saavedra on the successful defence of his Thesis.
  • 8th March 2007: A comparison of SCOP and CATH with respect to domain-domain interactions published in PROTEINS. This work describes the identification of  novel domain-domain interfaces important for protein interaction prediction.
  • 25th January 2007: Classification and Functional Annotation of Protein Kinases published in PROTEINS.  This work describes the development and evaluation of a new HMM library for identification and sub-classification of protein kinases.  The library was used in the T. vaginalis analysis.
  • 12th January 2007: Draft sequence of Trichomonas vaginalis published in Science.  Diego and Geoff contributed the analysis of the kinome of this important pathogen.
  • 18th December 2006: Congratulations to Emily Jefferson on the successful defence of her Thesis.
  • 9th October 2006: SNAPPI-DB database and API paper in print with Nucleic Acids Research.
  • 19th September 2006: Two new papers in press - protein-protein interactions and percentage identity in sequence alignments.
  • 27th August 2006: Systems upgrades completed - webservices etc should be back to normal.
  • August 2006: OB-Score structural genomics ranking function software and  data for Pfam and omniome available here.
  • 2007: Applications are invited for the position of Principal Investigator in Bioinformatics or a related computational discipline.
  • 16th June 2006: OB-Score, structural genomics ranking function paper now available.
  • 2nd June 2006: Snf2 paper in print.
    29th May 2006: Updates to About Us and photo gallery pages.
  • Earlier news announcements.
  • 3rd March 2006: EU Network of Excellence “ENFIN” post-doc
  • December 2005: Welcome to Michelle Scott, CIHR Research Fellow.
  • October 2005: Welcome to Cathy Stephenson - SBRN Administrator.
  • 24th August: Congratulations to Jon Barber on the successful defense of his Thesis.
  • 17th June 2005: Jalview multiple alignment analysis system Version 2.0 released!  See the dedicated Jalview web site for details and downloads.
  • 15th June 2005:  OXBench multiple alignment benchmark distribution now available for download.   Read the manual, or the paper describing OXBench for more details.
  • position now available - for details please see here.
  • 1st August 2005: PostDoc VACANCY:  Senior Bioinformatics Research Officer - See here for advertisement and further particulars.  Downloadable advertisement and details of this job are here.  Closing date: 31st August.
  • 15th June 2005:  David Martin’s publication list added to site.
  • 21st March 2005:  Small updates to About Us page.
  • 17th February 2005:  SBF Meeting at Dundee on 17th February, organised by David Martin.  See here for registration details and programme.
  • 28th January 2005:  Minor updates.
  • 10 January 2005: .Geoff quoted on TalentScotland...
  • 5th January 2005: Happy New Year! More updates to images of group and events.
  • 19th November 2004: Updated images of group and events.
  • 18th November 2004:  GOtcha paper published in BMC Bioinformatics.  See paper online here and try the webserver here for predicting protein function.
  • 8th November 2004:  Welcome to Jo van Niekerk new research assistant to work on the “Structural Proteomics of Rational Targets - SPoRT” project, funded by BBSRC.
  • 1st November 2004:  Welcome to Jim Procter new research assistant to work on the “Visualisation and analysis of Biological Sequences Alignments and Structures” project, funded by BBSRC.
  • 28th October 2004:  Re-organisation of this site to put Servers and Software under a single heading.
  • 28th October 2004:  Add links to the RHIMS blast visualisation paper and server.
  • 28th October 2004:  Add links to the GOtcha protein function annotation server.
  • October 2004:  Welcome to Jonathan Manning a new  BBSRC. funded Ph.D. student.
  • September 2004:  Welcome to Andrew Waterhouse new research assistant to work on JalView in the  “Visualisation and analysis of Biological Sequences, Alignments and Structures” project, funded by BBSRC.
  • August 2004:  2.51 Million Scottish Bioinformatics Research Network Funding announced.  See SHEFC Web site for press release (copy here).  New jobs funded by this grant will be announced shortly. 
  • May 2004:  Grant Success!!  Four postdoc/RA positions.  See group pages for more info on new colleagues joining the group.
  • April 2004:  Lab outing to Glen Clova
  • February 2004:  JalView Java Alignment Editor paper published in Bioinformatics
  • 2nd February 2004:  OC Cluster analysis program updated.
    May 2004:  Grant Success!!  Four postdoc positions shortly to be advertised.  Watch this  space.  Also see group pages for more info.
  • April 2004:  Lab outing to Glen Clova
  • February 2004:  JalView Java Alignment Editor paper published in Bioinformatics
  • 2nd February 2004:  OC Cluster analysis program updated.
  • 22nd December 2003: Publications updated.
  • 22nd December 2003: Publications updated.
  • 25th October 2003: Publications updated.
    26th August 2003:
    Publications updated.
    12th August 2003: Welcome to new group members!
    5th August 2003: Publications updated.
  • 18th Feb 2003: New publications added.
  • 19th Nov. 2002: Ph.D. Opportunities in the Group.
  • 14th Nov. 2002: JPred-TNG launched.  Updates to the JPred/JNet back-end that should give more reliable service and faster turn-round.
  • 7th Oct. 2002: Updates to Jalview links.
  • 18th Sept. 2002: Experimental server and software for visualising BLAST output with keyword filtering (RHIMS) available to try.
  • 15th Sept. 2002: Scottish Bioinformatics Forum web site and email list now hosted here.
  • 22nd August 2002: Updates to navigation on this site and more images added.
  • 16th August 2002: Mailing lists for Announcements and user discussion of Group Software.
  • 4th August 2002: Update to OC cluster analysis program now on server.
  • August 2002: Scottish Bioinformatics User Group (BUGS) launched.
  • July 2002: Experimental JPred secondary structure prediction server now availble to try at Dundee
  • Photo Gallery added to this site.
  • June 2002: Post Genomics Centre opened by HRH the Duke of Edinburgh
  • 16th August 2002: Mailing lists for Announcements and user discussion of Group Software.
  • 4th August 2002: Update to OC cluster analysis program now on server.
  • August 2002: Scottish Bioinformatics User Group (BUGS) launched.
  • July 2002:  Experimental JPRED secondary structure prediction server at Dundee.
    Photo Gallery added to this site.
  • July 2002: Deal with Random Computing and Hewlett-Packard supplies 56 2 CPU lp1000r HP netservers.
  • July 2002:  Post Genomics and Molecular Interactions Centre Opened.
  • 1 July 2002:  Tom Walsh joins the group as an EU funded postdoc to work on the TEMBLOR project.
  • 1 June 2002: Goulven Kerbellec joins the group as a 3 month summer student.
  • 1 May 2002: Patrick Audley joins the group as Unix systems administrator.
  • 22 Jan 2002: EC funded senior postdoc position available.
  • 01 Oct 2001: Group expands by 100%!  Jonathan Barber joins the group as a BBSRC funded Ph.D. student.
  • 29 Aug 2001: Phase I of Barton Group  www site relocates to Dundee.
  • 18 Aug 2001: “Estimation of p-values for global alignment of protein sequences - in press.

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