U-BRITE “Pilot Case Study” Hackathon
Dates/Times
- Sept 13-14, 2018 at 9am-5pm;
- Sept 12th is the Pre-hackathon Day (optional) at 10am-4pm.
Location
- Tinsley Harrison Tower (THT) Vault Conference (unless otherwise specified)
Informatician Contacts
- Amy Wang (Primary) amywang@uabmc.edu
- Jake Chen (overall) jakechen@uab.edu
- Jelai Wang (system implementations) jelaiw@uab.edu
- Wayne Liang (data governance) wliang@uabmc.edu
- Matthew Wyatt (clinical data repository and queries) mwyatt@uabmc.edu
- John Osbourne (design of data portal) josborne@uabmc.edu
- Nafisa Ajala (web site) nafisahsani@uabmc.edu
Mission
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
