Biomedical Data Visualization and User Interfaces using the PIC-SURE API as a backend service

Welcome to the September 2017 Hackathon information page.

Some important links to familiarize yourself with hackathon resources: ___

NHANES

41K individual 1,3K variables

Patel CJ, et al. A database of human exposomes and phenomes from the US National Health and Nutrition Examination Survey. Sci Data. 2016 Oct 25;3:160096

• NHANES i2b2/tranSMART User Interface, a source of data for your visualization (publicly available and open)
• SSC JupyterHub, a powerful server-side computation tool (registration and DUA required) – NHANES JupyterNotebooks

API query examples

101 example by Cartik

Advanced examples by Gabe

Live example UI using PIC-SURE presented by Jason

• Example UI
• The code for the example UI

Slides from opening presentation

• Google Drive Link

Autism Simons Simplex Collection

2,6K probands (affected kid) 6K clinical variables 8.6K full annotated exomes

SSC Clinical Data

• SSC-dev, another source of data for your visualization (registration and DUA required)

• SSC JupyterHub, a powerful server-side computation tool (registration and DUA required)
• SSC PIC-SURE Example, a PIC-SURE API example using SSC data (registration and DUA required)
• PIC-SURE API Information

SSC All Exome annotated in SciDB

SciDB tutorial in Jupyter notebooks Then /readonly/SciDB_tutorial ___

Support

Slack Channel

#hackathon-general

Slack direct messages

PIC-SURE API core developers Jason Gabe

Database developer Ranjay

Docker developer Andre

DevOps AJ

Or find us in the Lounge 4th floor bettewn 423 and 424

Where is my personal Autism SSC-dev PIC-SURE API key?

1) Register here: to SSC i2b2/tranSMART: https://ssc-dev.hms.harvard.edu

2) after approval, log back in https://ssc-dev.hms.harvard.edu

3) Click on your name (top right), then User profile

4) copy/paste your personal BD2K PIC-SURE API key

5) if you want to use JupyterHUB, click here:  https://ssc-hub.hms.harvard.edu