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1st April-5th April 2024: SCHEDULED DOWNTIME!

1st April - 5th April 2024: Due to major upgrades to our computing infrastructure, our resources (e.g. JPred etc) will be unavailable during this time. Apologies for the inconvenience. For Jalview webservices (ClustalW etc) you can install a local instance of JABAWS and configure Jalview to use it.

Geoff Barton

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 jobs.dundee.ac.uk 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.

    Geoff_Barton_Hot_Paper

  • 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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