Download SilverlightPivotViewerin Scientific Discovery

Silverlight
PivotViewer
in Scientific
Discovery
Jennifer Lin
Sr. SDET Lead
Developer Division
Microsoft Corporation
February 2011
Introducing PivotViewer
PivotViewer Investigates Climate Change
http://gis.team.sdsc.edu/teamimages/
Anatomy of a PivotViewer Application
Web Page
Silverlight Application
CXML or
API
Script
PivotViewer API
PivotViewer
Control
DZC
Server
The human genome (23
chromosomes) is
estimated to be about 3
billion base pairs long
and to contain 20,00025,000 distinct genes.
Chromosomes
A chromosome is a single piece of DNA that contains many genes , regulatory
elements and other nucleotide sequences .
Problem: DNA is 90% noise, so therefore zooming alone is not so useful (e.g. try
some of the conventional viewers in the last slide). Semantic zooming given some
good design ideas would probably work well. In the meantime…
Gene trade cards
• Name
• Band
• Location
• Start base pair within chromosome
• End base pair within chromosome
• Short description
• Link to NIH gene page
• Protein sequence
• each letter represents a codon or aminoacid which
is really a trio of base pairs ATGC
• the color scheme matches some existing colors
used in protein visualization
All data obtained in semi-automated fashion. Plenty of databases around but each
requires different massaging. Most data here is from ENSEMBL’s BioMart.
Other classifications/taxonomies would really help and can be added. For example
protein types like collagen, or other chemical/medical/pharmaceutical
classifications would be useful. MSR?
PivotViewer versus Existing Genome
Viewing Tools
UCSC Genome Browser:
http://genome.ucsc.edu/
Genozoom:
http://131.107.151.123/#/GenoZoom_v1_1
Pivot:
http://lllabsql02/public/PivotViewer/?url=http%3A%2F%2Fllsd2%2Fpublic%2FDemo%2FDNAViewer%2Fpivot%2Fid
eograms.cxml+
PivotViewer API
• Two-way interaction between the control and your
Silverlight application
• Load collections, manipulate the display of the collection
from your Silverlight app
• Receive events from the PivotViewer control to the
Silverlight app as the user uses the control
PivotViewer Collections
•
•
•
•
•
Large groups of related content
Each item contains both an image and meta data
The meta data is stored in a format called CXML
The images are stored in the Deep Zoom format (DZI/DZC)
Collection can range from simple, static content to complex
dynamic systems which are built directly into content
storage systems
PivotViewer Simple Collections
• Up to 5,000 items
• Metadata is static and loaded
all at once
• Visuals are static and contained
in one DZC
• Example:
• Climate Change Data
PivotViewer Linked Collections
• Limited only by storage
complexity
• Metadata is static and loaded
in parts
• Visuals are static and contained
in multiple DZCs
• Example:
• Chromosome Collections
Collection is stored as
static files and multiple
logical units
PivotViewer Resources
PivotViewer Resources:
• Download www.silverlight.net/learn/pivotviewer
• Overview www.microsoft.com/silverlight/pivot
• Tools www.getpivot.com/developer-info/tools.aspx
• Pivot Client App research.microsoft.com/enus/downloads/dd4a479f-92d6-496f-867d-
666c87fbaada/default.aspx
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