COVID-19 Data-Driven Medicine Competition
The UAB Informatics Institute is hosting a hackathon June 15-16, 2020 from 9 a.m. to 5 p.m. to bring together teams of scientists to address problems related to COVID-19 through the use of biomedical and health data. The focus will be on ways to access and analyze data available through the U-BRITE COVID-19 portal. Collaborate and learn with other researchers to help tackle the greatest challenge of our generation. All from UAB are welcome, including trainees, faculty, and staff in biomedical, bioinformatics, computer, and data sciences. We can match individuals with teams based on your background and interests.
The hackathon will take place online over two days (June 15 – 16th). Hackathon topics will be made openly available prior to the event, check out the information below to propose an idea. Actual coding, analysis, and research will not start until the first day of the hackathon. The hackathon will take place virtually through Zoom meetings and breakout rooms. The event will be guided by a panel of UAB experts consisting of faculty geneticists, virologists, clinicians, informaticians, epidemiologists, and other educators, who will serve as either mentors or judges. All teams will be invited to a short Hackathon presentation on a special UAB Informatics Institute PowerTalk event afterward. After the Hackathon, the winners will be announced.
The hackathon represents a culmination of the recent UAB COVID-19 data science initiative, a project jointly supported by the UAB Informatics Institute, UAB Center for Clinical and Translational Science, and the UAB AI.MED lab since mid-March 2020. The initiative has been built on a UAB biomedical data science infrastructure called U-BRITE and collaborated on by more than 70 researchers, informaticians, trainees, and scientists across campus. The aims of the COVID-19 data science initiative are to curate rapidly accumulating public data sets, software tools, and research articles, build a COVID-fight multi-disciplinary knowledge curation team and join the fight against COVID-19 with “data-driven medicine.”
Check out this Hackathon Guide for information on participating and running a hackathon
Click the button below for more information on the Hackathon Showcase today from 10 a.m. to 12 p.m.
COVID-19 Data Science Hackathon Contest Evaluation Guidelines
We encourage teams to select a topic from the list of recommended ones, although teams can also design a topic and submit it by the posted deadline. All COVID-19 Data Science Hackathon topics should be rooted in a recently published paper with the potential to impact the prevention, diagnosis, treatment, or research of COVID-19 caused by SARS-CoV-2. A panel of data science experts (“judges”) will be asked to evaluate and improve the submitted topics.
In the end, a successful hackathon team will be expected to develop answers to a particular COVID-19 hypothesis/problem using data science approaches, by following these evaluation criteria:
- Does it involve a highly-interesting hypothesis, phrased as a question statement? All good topics should be firmly grounded in at least one recent COVID-19 published in the biomedical literature.
- Does it have the potential to advance public biomedical knowledge/understanding of COVID-19? The advancement may be defined broadly, from epidemiology to treatment, including basic, translational, and clinical, and population impacts.
- Does it involve the innovative use of data science tools from GitHub/GitLab? At least one of the team members should be skilled in deploying the software tools and designated as a technical contact in the team’s roster before the Hackathon.
- Does it leverage on existing publicly available data sets, particularly those on the U-BRITE platform? If additional data sets are needed, beyond what is already available (see COVID-19 Featured Data), the team should work ahead of time (some of these data require non-trivial effort to stage) to communicate with the Hackathon IT Architect (Jelai Wang), who will assess whether we can bring them to U-BRITE before the Hackathon.
- Is the project feasible to perform with 50-80 hours of total team efforts within the 2-day Hackathon period? The team should stay focused on collecting key evidence to address the hypothesis with the understanding that future work may be needed to clear all doubts.
- Does the informatics approach adopted demonstrate rigor? Is the sample set too small or biased? What statistical techniques are used to quantify the biases or validity of conclusions made?
We will not evaluate the hackathon project based on these factors:
- Experimental validation of findings. In silico validations, using cross-validations, statistics, independent literature search, or unbiased separate data sets, are sufficient.
- Comprehensiveness of subject problem examined. Due to time constraints, preliminary conclusions that can help answer the question are adequate.
- Publication-readiness. We understand that reaching a point for publishing findings requires additional effort, especially by testing multiple alternative hypotheses.
- Provide scientific guidance on the overall project design, data to be used, and choices of analytical tools necessary to complete the project on time
- Facilitate constructive and critical discussions among the teams to improve the overall rigor and reproducibility of the approach
- Coordinate tasks and different roles to be performed by different team members
- Help overcome obstacles as they arise before and during the Hackathon
- Help the team prepare a final presentation to compete in the contest
- Form a team at least one week before the Hackathon and send us a list of team members
- Discuss and pick a topic for the Hackathon
- Prepare for the Hackathon by installing necessary software, attending training sessions, ensuring readiness, and working with organizers to bring in necessary public data sets or software tools into U-BRITE beforehand.
- Divide up roles: data cleaning, programming, informatics approach design, data analysis, technical writing, etc.
- Develop your solution during the Hackathon
- Prepare and deliver a presentation about your work (see below). Start preparing after the Hackathon is complete so you can focus on your project during the two days of the Hackathon. Presentations will be recorded.
- Attend presentations as assigned by organizers, either live Zoom or watch the recording.
- Judges may also be mentors but will need to recuse themselves from evaluating teams they are mentoring.
- Evaluate presentations based on scientific rigor, innovation, and presentation
- Submit evaluations to organizers
- Each team will have 10min (less than ten slides) to report their problem solved, approach, and conclusions.
- Prepare your presentation after (not during) the Hackathon
- Teams presentations will be held via Zoom Friday, June 19 at 10:15 am.
- Judges will rate the team based on the criteria specified above.
- The codes, results, and documentation all need to be deposited in U-BRITE. Participants agree to make their work open-source and openly accessible to U-BRITE users.
Reach out if you have questions.
We look forward to an innovative, productive, and fun hackathon!
Thanks to all mentors, judges, and participants!
Schedule of Events
The below schedule is subject to change.
Tuesday, June 9 from 3:00 – 4:00 pm
Wednesday, June 10 from 1:00 – 2:00 pm
Friday, June 12
An Introduction to U-BRITE for Hackathon
Amy Wang & Jake Chen
Hackathon Readiness Check, Live Walkthrough & U-BRITE Q&A with Troubleshooting
Accessing UAB COVID19 Clinical Data for Hackathon
12:00-1:00 pm: Virtual Lunch & Discussions of “getting ready” among participants
Q&A sessions with expert panelists
Monday, June 15 – Hackathon Day 1
9:00 AM – 9:05 AM
Director, Informatics Institute and Professor of Medicine
Jake Chen, Amy Wang, and Jelai Wang
9:05 AM – 9:30 AM
· Opening Remarks
· The Case for Hackathons
· Mission and Goals
· Ground Rules
· Team Science and Collaboration
· Seeking Help: Expert Panelists and Office Hours
· Technical Readiness
9:30 AM – 10:00 AM
Breakout/Work Sessions/Office Hours
See Office Hours Airtable for schedule
10:00 AM – 4:55 PM
Day 1 Wrap-up
4:55 PM – 5:00 PM
Tuesday, June 16 – Hackathon Day 2
Report from Day 1
9:00 AM – 9:30
· Reports from teams
Breakout/Work Sessions/Office Hours
See Office Hours Airtable for schedule
9:30 AM – 4:30 PM
Day 2 Wrap-up
4:30 PM – 5:00 PM
· Observations, lessons learned, and feedback
· Next steps
Friday, June 19 from 10:00 a.m. – 12:00 p.m.
Experts & Office Hours
List of Experts
Experts Office Hours for Hackathon
Images from the Hackathon
Preparation Instructions for COVID-19 Data Science Hackathon
- Sign up for an Airtable account at https://airtable.com/if you don’t already have one.
- We will send out instructions and/or invitations on how to access the Hackathon base in Airtable to view and edit information there.
- Click on the link to access the information.
- In the Participants table, review and update your information as necessary, including your preferred/available roles.
- Open the Projects table and review the projects there. in the Projects table. See if any interest you and think of how to use/revise it to develop a project. Or you can enter a new project idea. See attached guidelines for development of projects.
- Look for people you may want to team up with in the Projects and Teams tables. You can join an existing team or form one of your own. Teams should have about 2-4 people and have people from different backgrounds and fields.
- You can also look in the Participants Grouped by Title table to help you find potential team member.
If you are from outside UAB and we have not yet been in contact with us about XIAS so you can access Cheaha/High-Performance Computing (HPC) at UAB, please email me and Jelai Wang (email@example.com) right away to set up an account.
Obtain a Cheaha account if you plan to do data wrangling or software development and have not done so already. See instructions on requesting one. It is not necessary for all team members to have an account. Users from outside UAB will need to be sponsored for outside access (see #2).
Obtain a GitLab account (https://gitlab.rc.uab.edu). Go to the LDAP tab, use your BlazerID login and password. See #2 if you are from outside UAB. Use the GitLab for code sharing.
Use Box for sharing files and documents (not necessarily code to be shared with the wider community. Box is especially useful for transferring or sharing files that are too large send via email. You can store files for your team here (login UAB BlazerID. We will send you a link to view and edit documents for your team.
Note that if you plan to participate as a expert, panelist, or mentor in a field of expertise but not involving technical aspects such as software development, coding, data wrangling (I am not a technical person), then it may be optional for you to complete all the technical preparations. However, you may learn something, improve your ability to understand and collaborate on technical aspects, and perhaps even move toward becoming technically savvy yourself.
Detailed patient data for UAB patients will be available to participants from UAB for whom that data sharing is permitted. Unfortunately, participants from institutions outside UAB will not be able to access this data.
The datasets will not include overt identifiers (name, medical record number, etc) but may include zip codes and dates related to clinical values. This form of dataset is considered to be a HIPAA Limited Dateset and requires some restrictions on access and use. As such, per IRB and institutional policy, release of of datasets requires HIPAA training, IRB Human Subjects Protection training and an Acknowledgement of Restrictions on the Use of Limited Datasets.
Prior to the Hackathon any participant from UAB seeking access to Clinical datasets from UAB Medicine must complete the following (if you have not previously done so or if your training is out of date). If you are from outside UAB, we will work with you to gain access to necessary resources (see #3). If IRB Human Subject Protection training and HIPAA Training have not been completed those are required as well, but those are typically in place as a matter of normal practice for those involved in research. See below for instructions on how to access and receive training for these resources:
- See the CCTS i2b2 web page, has more information about i2b2 and how to Complete HIPAA training in the UAB Learning Management System. The link can be found here.
- Complete IRB Human Subjects Protection training. You can complete this through the UAB Learning Management System or CITI. See information and options for IRB initial training or IRB continuing training. If you are new to UAB, you can use training from your previous institution or other approved organizations. We recommend taking the CITI course, which has modules that are common to many research institutions.
- Complete the “Acknowledgement of Restrictions on the Use of Limited Data Sets” in the UAB Learning Management System. This link will take you to the course in the campus-side training system. Email the certificate to firstname.lastname@example.org.
We’d like to get everyone thinking about and preparing their projects for the upcoming hackathon. See attached guidelines document which describes characteristics of good projects. See the Projects table in the Hackathon Airtable base for projects and project ideas. The table includes detailed information about the project and individual(s) who submitted the project. Researchers have also indicated the suitable of the project and assessments of readiness of the project. Feel free to take any of these and revise as you wish (e.g., narrow the scope, focus on one aspect or use case).
If you have your own project in mind, you can enter it directly in the Projects table on the Covid-Hackathon Airtable base, or you can submit it through our project submission form or to me via email. Please include detailed information about the project, such as what your research question is and how you would answer the question. Also include any relevant publications and datasets (from UAB and/or publicly available).
Please sign up for teams in the Teams table in Airtable. Teams will ideally have about 2-4 members and have a mix of backgrounds and areas of expertise. You may wish to pair up with people you know, people with common interests, and/or people with complementary backgrounds.
Each team will work on one project, but multiple teams may work separately on the same project – they may use different approaches.
Sign up for your project and team and/or invite others to join your team (preferred). If you do not organize or join a team, we, will do our best to match people with projects and teams.
Put the following dates on your calendars:
- Q&A Sessions – Tuesday, 6/9 from 3-4 pm or Wednesday, 6/10 from 1-2 pm
- Pre-Hackathon Workshop – Friday, June 12 from 9 am-4 pm
- Hackathon – Monday, June 15 and Tuesday, June 16 (Core hours 9 am-5 pm)
- Hackathon Showcase – Friday, June 19 from 10 a.m. – 12:00 p.m.
- Awards Ceremony – Friday, June 26 10 – 11 a.m.
While there will be a competition and awards, remember to learn and have fun as we promote team science and combat the real enemy, SARS-CoV2. Let the hacking begin!