Silverlight PivotViewer in Scientific Discovery Jennifer Lin Sr. SDET Lead Developer Division Microsoft Corporation February 2011 Jennifer Lin Sr. SDET Lead Developer Division Microsoft Corporation February 2011

Introducing PivotViewer

PivotViewer Investigates Climate Change

Web Page Silverlight Application PivotViewer Control DZC Server CXML or API PivotViewer APIScript Anatomy of a PivotViewer Application

The human genome (23 chromosomes) is estimated to be about 3 billion base pairs long and to contain 20, ,000 distinct genes.

Chromosomes A chromosome is a single piece of DNA that contains many genes, regulatory elements and other nucleotide sequences.genes regulatory elements 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 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.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: Genozoom: Pivot: labsql02/public/PivotViewer/?url=http%3A%2F%2Fll- sd2%2Fpublic%2FDemo%2FDNAViewer%2Fpivot%2Fid eograms.cxml+ UCSC Genome Browser: Genozoom: Pivot: labsql02/public/PivotViewer/?url=http%3A%2F%2Fll- sd2%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 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 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

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 Simple 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 Linked Collections

PivotViewer Resources

PivotViewer Resources: Download Overview Tools Pivot Client App research.microsoft.com/en- us/downloads/dd4a479f-92d6-496f-867d- 666c87fbaada/default.aspxresearch.microsoft.com/en- us/downloads/dd4a479f-92d6-496f-867d- 666c87fbaada/default.aspx Download Overview Tools Pivot Client App research.microsoft.com/en- us/downloads/dd4a479f-92d6-496f-867d- 666c87fbaada/default.aspxresearch.microsoft.com/en- us/downloads/dd4a479f-92d6-496f-867d- 666c87fbaada/default.aspx

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