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
Accepting minutes from last meeting
- accepted
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
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.
-
Edinburgh: notes to be cleaned up key points
Jalview: Jim Procter's presentation (45 mins)
- http://www.jalview.org
- 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)
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,
Any other business (<5 mins)
- "New HCS screen published in JCB DataViewer" (ome-nitpick; Chris)