Visualization Subgroup

From Evolutionary Informatics Working Group
Revision as of 15:45, 9 March 2009 by Dpc13 (talk) (New page: == Participants == * Greg, Sheldon, Katja, (Matt, Arlin) == Arlin's notes == * categories of users to consider *# user interested only in exploring or displaying data (no editing) *...)
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Participants

  • Greg, Sheldon, Katja, (Matt, Arlin)

Arlin's notes

  • categories of users to consider
    1. user interested only in exploring or displaying data (no editing)
    2. molecular evolution user:
      • study unit is the sequence family (alignment, tree)
      • problems of interest are things like detecting paralogy, function annotation, reconstructing chars
    3. Tree of Life type
      • study unit typically is a taxonomic group
      • wants to discern species relationships
    4. phylogeny producers
      • wants to manipulate data, make supertrees, etc
    5. morphologists
      • study unit is a character complex, OTUs typically are species or higher
      • wants to map characters and so on
  • currently available technologies
    1. PhyloWidget (java applet) - view trees, zoom, limited editing,
    2. mx - view, annotate, solid back end
    3. Nexplorer - view trees with char matrix, limited editing, Bio::NEXUS middleware with functions
    4. ajax wrapper for phylowidget
  • missing technologies
    1. tree manipulation services (and interface standard, e.g,. PhyloWS)
    2. annotation language for "decorations", e.g., extend CDAO
    3. rendering capability for graphic tokens (colors, thickened lines, pie charts, etc)
    4. standards or conventions for rendering
    5. middleware for processing
    6. UI design
  • deliverable: web-based GUI to phylo resources using a standardized API
    • use phylowidget as technology base
    • support visualization of tree decoration
    • support editing or annotation, including
      • free text annotation in key-value pair
      • controlled vocabulary referencing ontology such as CDAO
      • save info in database
      • session management
    • other aspirations (not for this week)
      • plugin architecture