This is our first session at CGR so the plan is a bit different:

a) We need to explain how Cancer Genomics can be discovered programmatically by non-programmers (now that is a conundrum ;-) )

b) We need to geek-out a little to make sure we know how to "walk the last mile to FAIR" - paving over lack of SSL and compressed downloads in sources like The Broad Institute firebrowse and NCI's GDC, respectively.

Let's start with FireBrowse

https://observablehq.com/@episphere/blca

https://github.com/episphere/blca

firebrowse

• Data Portal: firebrowse.org.
• API documentation: firebrowse.org/api-docs.
• Reference: ncbi.nlm.nih.gov/pubmed/28062517.
• Interoperability issues: lack of SSL.

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What do you want to know? (your turn, but only after you created an account in Observable)

#1 - PSCA mRNA expression in Bladder cancer samples

Started at https://observablehq.com/@episphere/blca

#2 - your turn

your observable notebook

#3 - ...

...

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Heres a notebook with hand rolled pretty viz, really just a POC:

• https://github.com/NCBI-Hackathons/RNA-Seq-in-the-Cloud/tree/master/Visualization
• Also, Im involved in running a conference on data viz in Colorado: https://hackathon.colorado.edu (Come on out if youre interested!)