U-BRITE “Pilot Case Study” Hackathon


  • Sept 13-14, 2018 at 9am-5pm;
  • Sept 12th is the Pre-hackathon Day (optional) at 10am-4pm.


  • Tinsley Harrison Tower (THT) Vault Conference (unless otherwise specified)

Informatician Contacts


The U-BRITE hackathon is an intensive 2-day developers gathering event hosted by the U-BRITE informatics team. The primary goal is to help each of the scientific team in completing their scientific case studies by leveraging data hosted in the U-BRITE data portal and scripts/pipelines run in the U-BRITE analysis gateway. In addition, we will help teams with their final result sharing and publication through the use of U-BRITE expo repository. Lots of on-site tutorials, workshops, and Q&A will be provided. Each team is expected to have the whole development team be present on-site throughout the whole time periods. FREE boxed lunch for the 15 participants will be provided.

Preparation Self-Check Before the Hackathon
  • Complete the “U-BRITE Project Readiness” Form (Link) and make sure all data, scripts, and permissions for your project is set prior to coming to the hackathon
    • Data Portal
    • Analysis Gateway
    • Data Governance Policy
    • Expo Gallery
  • Review the Jupyter on Cheaha Quick Start tutorial (Link)
  • Bring a laptop computer with all the right tools
  • Bring your case study design
  • Be open to learn skills, solve your case study specific problems, code, debug, and show us what you have!

We expect every team to have completed the U-BRITE project readiness before the Hackathon to work on case studies. In case that some of you have not been ready or need to be ensure that you’re fully ready (or “compliant”), you’re invited to the Pre-hackathon Workshop on Sept 12th at 10am-4pm.

Planned Agenda
 “Pre-Hackathon Workshop” 9/12 Wednesday
Morning 10:00–10:30am Readiness Self-check: An Introduction Jake Chen & Jelai Wang
10:30–11:30am iNoteBook (Jupyter web notebook) team scripting setup Jelai Wang
11:30am-noon Readiness Check Interactive
12:00pm-1:00 pm: Box Lunch & Discussions of “getting ready” among participants
Afternoon 1:00-2:30pm HPC/Cheaha training Wednesday registration required[1] Lister Hill Library – Edge of Chaos Cafe
3-5pm On-site help for data loading and project script loading Jelai, Amy, Matt?
 “Hackathon Day I” 9/13 Thursday
Morning 9:00–9:30am Welcome and Introduction of Expectations Jake Chen
9:30–10:00am Data Governance Worksheet Wayne Liang
10:00–11:00am Clinical data repo and i2b2 workspace query demo Matt Wyatt
11:00am-noon Case study using clinical data and omics data: an iNotebook demo Tim, Alex, and Jelai
12:00pm-1:00 pm: Box Lunch & Discussions of “pain points” among participants
Afternoon 1:00-5:00pm Team programming, interactive query demos, and case study feedback All
Evening 5-7pm Group dinner (optional) Amy and participants
 “Hackathon Day II” 9/14 Friday
Morning 9:00–9:15am Summary and Review for Day I Jake / Amy
9:15-10:15am Packaging results for dashboards Jelai
10:15–11:30am Break. Bioinformatics PowerTalk: “Computational prediction and modeling for protein-drug and protein-protein interactions” Prof. Daisuke Sahara (Purdue), Shelby 105, 1825 University Blvd.
12:00pm-1:00 pm: Box Lunch & Discussions of “initial success experience” among participants
Afternoon 1:00-4:30pm Team programming, interactive query demos, and case study presentations Each team (category I & II queries)
4:30-5pm Summary and Wrap-ups Jake & Teams
Event Pictures