Case Study
Powering a Codeathon for Researcher Collaboration
About the Research
Powering a Multidisciplinary, Multinational Codeathon for Researcher Collaboration
Thomas Stoeger is assistant professor of pulmonary and critical care at Northwestern's Feinberg School of Medicine. He studies aging and age-related disease through systems biology and genome research. He is also a leading member of the University’s Successful Clinical Response In Pneumonia Therapy (SCRIPT) systems biology center.
Research Challenge
Stoeger and SCRIPT was awarded a grant from the National Institute of Allergy and Infectious Diseases (NIAID) and a grant from the Chan Zuckerberg Initiative (CZI) to host a collaborative, in-person codeathon where five teams of researchers from around the world would gather to analyze a new dataset. The researchers would be working with a large collection of unpublished genomics and clinical data from 183 patients to try to improve outcome predictions and treatment responses for patients with pneumonia. To successfully analyze this data, the teams would need access to computing, software, and data storage resources beyond what a laptop can provide.
Solution
Since this Clinical and Single-Cell Transcriptomics for Pneumonia Codeathon was the first one the group hosted, they requested a Research Computing consultation with Northwestern IT’s Research Computing and Data Services (RCDS) team. Stoeger was already familiar with the services offered by RCDS as a Quest user and as a former instructor of a data science workshop for RCDS when he was a postdoctoral fellow at Northwestern. After discussing the needs of the codeathon, the RCDS team designed computing allocations on Quest, Northwestern’s high-performance computing cluster, for each of the codeathon teams. The allocations included specialized software and GPU resources needed for teams to work successfully with the large data set.
RCDS consultants worked with Stoeger to test common analysis workflows with the data to ensure the codeathon teams wouldn’t run into any technical issues that would eat into their limited in-person time together. As a result of the initial tests, they adjusted the dataset to ensure that all five teams would be able to conduct their computationally intensive analysis simultaneously. By the time the codeathon started, everything had been thoroughly stress tested, so the event went smoothly.
It’s incredible to see multidisciplinary, multinational researchers collaborate on data together and learn from each other. This was possible due to the infrastructure set up by RCDS, so the researchers could focus on their work and not be bogged down by technical difficulties.”
Assistant Professor of Pulmonary and Critical Care
Feinberg School of Medicine
Impact
By using existing University GPU and computing resources and working with the RCDS team, the codeathon saved tens of thousands of dollars, which allowed researchers from nine different countries and 12 different institutions to travel to Northwestern to participate. Since the codeathon, three of the teams are continuing their collaborations and working towards presenting their results in papers, posters, and presentations.
Additional Details
- Researchers: Alec Peltikan (Northwestern), Alexander Misharin (Northwestern), Cathy Gao (Northwestern), Ivana Jelic (CZI), Jim Davis (Bacterial and Viral Bioinformatics Resource Center, BV-BRC), Justin Starren (Northwestern), Katie Clepp (Northwestern), Luke Rasmussen (Northwestern), Marcus Nguyen (BV-BRC), Marjorie Kang (Northwestern), Michael Yeaman (UCLA), Nick Markov (Northwestern), Reed Shaman (NIAID), Richard Wunderink (Northwestern), Rogan Grant (Northwestern), Sam Fenske (Northwestern), Slim Fourati (Northwestern), Stanislav Brachtikov (Northwestern), Thomas Stoeger (Northwestern), and Wiriya Rutvisuttinunt (NIAID)
- RCDS Lead Consultant: Scott Coughlin
- RCDS Services Used: