Hackin Omics

The 4th Annual Data Sciences Hackathon was hosted by the Informatics Institute, Informatics Club, the UAB Biomedical Research Information Technology Enhancement Commons Program (U-BRITE), and the Center
Computational Genomics and Data Science (CGDS) over two days on August 5th-6th, providing attendees the opportunity to network with peers in the scientific community. 

With the largest attendance in the event’s history (over 160 registrants), this year’s theme centered around Hackin’ Omics, a multi-omics downstream analysis for discovery of novel translational findings and development of new tools using existing public datasets.

“Although this year’s data science hackathon was virtual, we hoped that we helped biomedical informatics trainees gain hands-on data science experience, learn about UBRITE and other cloud computing platforms, explore biomedical science project ideas, and establish professional relationships." said Jake Chen, Professor and Chief Bioinformatics Officer at the UAB's Informatics Institute, who has been overseeing the data science hackathon series since its inception.

One of the primary purposes of this year’s event was to broaden the collaborative community at UAB and abroad through the development of teams, while allowing researchers to advance existing multi-omics projects and analyze their own datasets. Two pre-Hackathon workshops were conducted leading up to the event: the Computing Resources Workshop, which introduced attendees to various computing resources available for researchers (Cloud computing, High Performance Computing and Code Version Control using Git/GitHub) and the U-BRITE Bootcamp, which provided assistance on the navigation of U-BRITE analysis tools such as PAGER and SEAS.students at hackathon

Over the course of the two-day hackathon, 12 teams were compiled (based on registrants’ top preferences) and tasked with developing new or advancing existing multi-omics projects from the project proposals they developed. The teams were: BiocSwirl, canAI, ImageNomeR, mCIRCrna, MedvAIsor, O-miner, Papaki, ReproCanAtlas, Single-cell-reciter, SNVariome, Team AD Guy, and Team HeriVar. Each project proposal was evaluated based on its approach, scientific rigor and progress, transparency, presentation quality, and other criteria.

“One of the unique aspects of this Hackathon was that while you were given a problem to solve, the methods in which you solved them required unique and innovative thinking through a collaborative team effort,” said Rahul Sharma, Ph.D., a postdoctoral scholar at UAB.

Another key component to this year’s Hackathon was the impact of UAB’s reach and message outside of the United States, with some participants coming from countries in Asia (India, Pakistan), Africa (Nigeria), the Middle East (Iran), and Europe (the Netherlands, France, Poland).

“I believe that this year’s Hackathon was critical in the development of leadership and management skills for professional development,” said Tarun Mamidi, a Ph.D. trainee in the Graduate Biomedical Sciences program at UAB, and chair of the Hackathon.

For the students who were part of organizing this event, it was viewed as a unique opportunity to gain first-hand knowledge of what all goes into constructing an event such as this. "As a student, it provided me the opportunity to learn both leadership and management skills for my professional development,” said Shaurita Hutchins, co-chair and a Ph.D. student in CGDS. “We were fortunate to have mentors from UAB Informatics Institute and CGDS to trust us in our way of organizing the hackathon, a departure from previous UAB hackathons.”

For participants, this year gave an experience that they believe will best help serve them as they go forward in their careers. “I loved the variety of projects from which we were able to choose from. Being part of this Hackathon allowed me to learn about new tools and gain new various skillsets, while also having the chance to work with new individuals in a group for solving the same problem,” said Sayan Bakshi, a Hackathon participant 

This year’s Hackathon has contributed to the overall growth of the U-BRITE web portal, with over 40 projects currently in the works and nearly 190 users, nearly doubling its growth in less than a month. Students having a hand in contributing their work has helped facilitate such a rapid growth.  “With students now leading some of these projects, we are starting to see greater interest in hackathons from individuals outside of UAB, specifically those who want to collaborate with our grad student researchers,” Mamidi said. “Because of this, we have seen some of our teams publish their work from these hackathons to established scientific journals.”Presentation

At the conclusion of the Hackathon, each team presented its findings as part of the Hackin’ Omics Showcase. The winning teams and their projects were:

  • First Place: CanAI, “Comparing Feature Extraction Methods for Biomarker Discovery in Prostate Cancer” (Project Leader – Tarun Mamidi)
  • Second Place: MedvAIsor, “AI-based Personalized Drug Methods for Cancer Treatment Web App” (Project Leader – Rahul Sharma, Ph.D.)
  • Third Place: O-Miner, “Patient Stratification and Molecular Mechanism Identification Using Patient Clinotypes and Transcriptomics Embeddings” (Project Leader - Zongliang Yue,

The winners of the People’s Choice Awards (where all participants could vote for a team other than their own) were:

  • BlocSwirl, “Developing Interactive Tutorials and Tools for Multimodel Workflow in R” (Project Leader – Almas Khan)
  • mCIRCrna, “Integrating Circadian Transcriptomes and snRNA Sequencing to Identify Age and Cell-Type Dependent Gene Signatures” (Project Leader – Shufan Zhang)

With the great success of this year’s Hackathon, future events such as these will serve as a mechanism for the developments of new projects and research, leading to potentially better solutions for real world problems.

“I could not be prouder of the tremendous success of this year’s Hackathon,” said James Cimino, M.D., Distinguished Professor of Medicine and Director of the Informatics Institute. “We have a full suite of biomedical data science training programs that anyone interested in learning more on our Institute's web site, including the new Ph.D program in bioinformatics in conjunction with the department of Biomedical Engineering.”