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You are here: Home Community Minutes Conference Calls 2013 2013-10-15 Tuesday Team Meeting

2013-10-15 Tuesday Team Meeting

Dundee: Will, Gus, Andrew, Colin, Blazej, Petr, Jean-Marie, Chris, Kenny, Jason, Jim Procter, Geoff Barton Remote: Sebastien, Helen, Roger, Carlos, Curtis, Douglas, Ian, Melissa, Sebastien

Remember: Agenda must be complete (with estimated times) on the day before the meeting. Any additions after that must go at the bottom (AOCB)

Agenda - 2:30pm Start

  1. Accepting minutes from last meeting

    • accepted
  2. 4.4.9 Update Decision

    • Blocker: bfconvert - Melissa looking today (details in standup notes this morning) - discuss later
    • VM change (password) Doc PR 513
    • Delete today's artifacts? Need whole new build - OK to delete.
    • ETA for new release artefacts - will see, hopefully tomorrow
  3. Brief meeting update:

    • Edinburgh: notes to be cleaned up key points
      • Launch 3rd party application from insight (+proposal for storage To be discussed)
      • FLIMfit OMERO 5 compatible+Hudson Job for OMERO 5/4 FLIMfit.
      • MPT: Box it converted to OMERO 5
      • Support for modulo annotation in insight (80% done)
      • Bill/Ian: OPT/FLIM file viewing. @action: Bill to prepare more data.
      • ROI/Annotations and permissions discussion with Bill Hill, Richard Baldock (MRC Edinburgh)
    • Barcelona Report Barcelona Jason: good meeting - see notes. Tag cloud (twitter) for meeting. Rapidly moving field.
  4. Jalview: Jim Procter's presentation (45 mins)

    • Jim: “Jalview coordinator”. BBSRC funded
    • Protein structure & function - data in different places, sequences, alignments, trees, etc
    • Bioinformatics data not nicely human readable - need viz
    • E.g. sequences easier to compare as alignments.
    • E.g. PDB coords viewed as 3D molecule
    • JalView can bring many of these visualizations together
    • Java Alignment Viewer
    • Desktop app - retrieve data from web services etc
    • Applet for viz in browser
    • Jalview - mainly for alignments - highlight various properties / annotations onto alignment.
    • Typical use: load alignment and colour with various schemes / rules. E.g. residue properties, conservation etc.
    • Overview (thumbnail view) for large alignments (many sequences).
    • Tree viewer interactively divide alignments into sub-groups.
    • Jmol viewer allows sequence properties / colours to be seen within the 3D molecule.
    • Javascript API allows selection, highlighting etc.
    • Desktop app has RNA 2ndary structure viewing (from Google summer of code students)
    • Pfam, Rfam look for domains for annotation / classification
    • PDB, UniProt web services supported.
    • Distributed Annotation System
    • Analysis services (SOAP) E.g. Jpred - Protein Secondary Structure prediction (Barton group)
    • JABAWS - Java Bioinformatics Analysis Web Services.
      • Protien Disorder, Alignment & Analysis services behind Tomcat web server.
      • Ships as Virtual Appliance for private use. Includes source code for all packages
      • CLI or use JalView as client - service discovery
      • AAcon - conservation analysis - configurable
    • Future plans - more developers, extensible, sustainable, more structured releases etc
    • 300k lines of code
    • Google analytics for Desktop: 75,000 launches last year
    • Wellcome trust grant just awarded - Now hiring!
    • Jalview 2.8.1 release soon
    • OSGi Modularisation (Jalview 3) - Currently copy & paste UI code to Applet from Desktop. Used by cytoscape & taverna. Open System Gateway Interface - modules dynamically discovered at runtime. Auto gui generation
    • Big Data viz - E.g. COX1 found in 108189 species - PFAM site fails - OOM?
    • Large alignment - E.g. 10,000 columns, 900 sequences. Difficult to see fine features when zoomed out to see context of whole alignment
    • Load alignments from web-services into memory for display etc. Save session as zipped XML (no DB yet - looking at Cassandra for JABAWS, maybe Jalview later)
  5. Plug Jalview into OMERO? Load / save Jalview sessions (XML) to OMERO. Link between - E.g. sequence data for imaging experiments. Annotate sequences with OMERO data.

    • New developer - link cDNA and protein alignments
    • Future - Pure Javascript JalviewLite component, Macros for repeating workflows,
  6. Any other business (<5 mins)

    • "New HCS screen published in JCB DataViewer" (ome-nitpick; Chris)
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