jtleek / jhudash

A repository for all things DaSH

Welcome to the JHU DaSH!

tl;dr

• Dates: Sept 21-23
• Location: Baltimore Marriott Waterfront
• Twiter feed: #jhudash

<script>!function(d,s,id){var js,fjs=d.getElementsByTagName(s)[0],p=/^http:/.test(d.location)?'http':'https';if(!d.getElementById(id)){js=d.createElement(s);js.id=id;js.src=p+"://platform.twitter.com/widgets.js";fjs.parentNode.insertBefore(js,fjs);}}(document,"script","twitter-wjs");</script>

• Introduction to the Dash
• Help spreadsheet
• Code of conduct
• Theme areas: Population health, quantified self, current events, Baltimore (civic measurement), Genetics and Genomics
• Goal: Get people in small groups working on problems they are interested in, build simple but useful data products.
• tl;dr plan: M - Getting to know you, gearing up, T - Hacking/working, W - Finishing up/presentations.
• Brought to you by: JHU Data Science Lab, JHU Biostatistics, NIH BD2K
• This website: http://bitly.com/jhudashboard

Tutorials

• Markdown
• Command Line
• Git & GitHub
• R (swirl)
• Webscraping in R
• Shiny tutorial
• Getting help spreadsheet

Tools

• htmlwidgets
• Shiny
• httr

Datasets

Population Health

Introductory presentation

• CMS Data Navigator
• National Health and Nutrition Examination Survey (NHANES)
• National Health Interview Survey
• Behavioral Risk Factor Surveillance Survey
• General Social Survey
• CMS Data on Hospitals and Physicians
• National Immunization Survey
• EPA Air Quality System
• EPA Toxic Release Inventory
• EPA National Emissions Inventory

Quantified Self

Introductory presentation

• Example MyFitnessPal data
• Example Fitbit data
• Quantified self
• Software
  • accelerometry package
  • fitbitScraper

Current Events

Introductory Presentation

• Hillary Clinton's emails
  • State Department Email "Reading Room"
  • PDF dump of emails
  • Code to extract text from PDFs (GitHub)
  • Zip file of data extracted from emails (Kaggle)
  • Code for a few analyses of the emails (Kaggle)
  • The Wall Street Journal's code for analysis of the emails (GitHub)
• Syrian Refugees
  • UNHCR Website
• Cost of College
  • USDOE College Scorecard
• Natural Disasters (The Humanitarian Data Exchange)
  • Ebola
  • Nepal Earthquake

Civic Measurement / Baltimore

Introductory presentation

• Data.gov: http://www.data.gov/
  • http://www.data.gov/states/
  • http://www.data.gov/counties/
  • http://www.data.gov/cities/
• Socrata: http://www.socrata.com/top-open-data-datasets/
• Open city data
  • Open Baltimore: https://data.baltimorecity.gov/
  • Washington D.C.: http://opendata.dc.gov/
  • NYC Open Data: https://data.cityofnewyork.us/
  • Chicago Data Portal: https://data.cityofchicago.org/
  • Seattle: https://data.seattle.gov/
  • Boston: http://www.cityofboston.gov/open/
  • Vancouver: http://vancouver.ca/your-government/open-data-catalogue.aspx
  • Many more, Google "open data cityname"

Genetics + Genomics

Introductory Presentation

• OpenSNP
  • https://opensnp.org/
• Clinvar
  • http://www.ncbi.nlm.nih.gov/clinvar/
• GEO
  • http://www.ncbi.nlm.nih.gov/geo/
• SRA
  • http://www.ncbi.nlm.nih.gov/sra
• CADD
  • http://cadd.gs.washington.edu/
• Software
  • rsnps
  • SRAdb
  • geoQuery
  • BRCA-diagnostic
• GWAS catalog
  • https://www.genome.gov/26525384
• OMIM
  • http://www.ncbi.nlm.nih.gov/omim