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18/12/13 ProCKSI has a new home
  • After a bit of a downtime our cluster is finally hosted at the Newcastle University.
05/08/11 New release: 8.7.1
  • Maintenance release including several bug fixes
  • Updated similarity comparison method: TM-align (30/01/2011)
  • Updated similarity comparison method: DaliLite (3.3)
  • Updated PDB parser: ParsePDB (2011-02-13)
  • Updated list of obsolete PDB entries (2011-08-05)
29/08/08 New release: 8.7
  • New analysis method: Receiver Operator Characteristics (ROC)
    • Compare the performances of all available similarity comparison methods for a given dataset.
    • Generate ROC curves in JPG or EPS format
    • Produce an overview of AUC values in XML or TEX format
    • SCOP database (1.73) is used as the gold standard
    • Obsolete PDB codes are translated automatically into currently available structures
  • New visualiser for phylogenetic-like trees: ProCKSI-Viz (1.0)
    • Tight integration of ProCKSI-Viz into ProCKSI:
      • Visualise all trees that have been selected in the browser in a client-side application
      • Automatic update of new results of the current experiment
    • Use Java WebStart technology for a quicker start
    • Signed Java Application for more security
    • Future plans:
      • Comparison of trees
      • New and better visualisation formats
  • New similarity comparison method: URMS (22/procksi-8.7)
  • Updated similarity comparison method: MaxCMO-MSVNS (1.2)
  • Updated PDB parser: ParsePDB (2.1)
  • New consensus mode: Consensus/Median
    • Similar to Consensus/Average, but the median is taken in order to produce more robust results that depend less on outliers
  • More control of your experiments:
    • Restart failed tasks
    • Delete your entire experiment manually in addition to auto-deletion after expiration
  • Better usability in "New Experiment" and "My Experiment":
    • Actions in the browser that are likely to take a long time are sent into the background
    • All-against-Target comparison mode allows more structures to be compared than All-against-All comparison mode
  • Extended Terms and Conditions with data protection commitment
17/03/08 New release: 8.6
  • Direct login into My Experiment with experiment ID and email address
  • Updated similarity comparison method: DaliLite (2.4.5)
  • New comparison mode: All-against-Target in addition to All-against-All comparisons
    • Mark target for comparison
  • New consensus mode: Consensus/Greedy in addition to Consensus/Average
    • The best (smallest) values from the Standardised Distance Matrices/Vectors (SDM/SDV) from different methods are taken
    • A second matrix holds the method/measure names of the best values
  • Separate method for Standardisation, Combination, Clustering, Linearisation, and Deletion; depending on comparison mode
    • Linearisation produces input for the generation of ROC curves
06/12/07 New release: 8.5.2
  • Maintenance release including several bug fixes
  • "Standardised Similarity Matrix" (SSM) was renamed into "Standardised Distance Matrix" (SDM)
23/11/07 New release: 8.5
  • New similarity comparison method: Vorolign (1.0)
  • New design with improved user interface and navigation
  • Customisable visualisations for contact maps as images and graphs
  • Customisable notification emails for finished experiments/tasks
  • Improved data security with authentication
  • Improved scheduling of all tasks
26/10/07 New Publication (publisher)
  • "ProCKSI: a decision support system for Protein (Structure) Comparison, Knowledge, Similarity and Information"
    Barthel D., Hirst J.D. , Blazewicz J., Burke E.K., and Krasnogor N.,
    BMC Bioinformatics
    2007, 8:416
16/10/07 Major hardware and operating system upgrade
  • The ProCKSI cluster was extended to 5 compute nodes providing in total 14 cores.
  • The operating system was upgraded to Centos5 and and ProCKSI was reinstalled on all machines.
01/10/07 New internal news history
  • The news history has started (internally).