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For 55 hours starting on April 1, 2022, 35 researchers, students, and faculty participated in a patient centered BioHackathon, sponsored by Meharry Medical College and Praxis AI. For one month prior to the event, BioHackers skilled up using Professor Alex Feltus’ Cancer Transcriptomics hands-on journey via the Praxis digital skilling platform.
The Paseman BioHackathon was one of the first such events to integrate automated machine learning curation, cloud-based supercomputing, asynchronous learning journeys, synchronous virtual classrooms, and social collaboration for the purpose of bioscience skilling, research, and workforce development.
Host: Dr. Alex Feltus
Dr. Alex Feltus of Clemson University was the driving force behind the BioHackathon. His opening remarks set the tone for the event:
“I am exceptionally excited about this inaugural free hackathon event brought to you by Meharry Medical School and Praxis AI. This is a 3-day virtual event (in Praxis and Discord) with the goal of presenting (and maybe publishing) novel scientific discoveries in rare kidney cancer and brain tumors. Most importantly, it is all about skilling BioHackers in computational biology techniques so they can team up on Bill’s data.
Who knows, maybe you will find the cure for cancer on this journey. Somebody's gotta do it. However, this doesn't have to happen this weekend. These things take time, but we can make a lot of progress together in 3 days.”
Patient: Bill Paseman
The 35+ participants organized themselves into three distinct teams tackling specific aspects of Bill Paseman’s condition:
Team Name: End of Cancer as We Know It (Patient Led)
Team Approach: Find common genetic lesions between Type I Papillary Renal Cell Carcinoma and meningiomas.
Results: This team asked if Bill’s tumor had been misdiagnosed and was actually a new kidney cancer subtype that was discovered in the scientific literature. After analysis, sufficient evidence was accumulated against the alternative diagnosis which provided assurance that any future treatments could be based on the original diagnosis.
Team Name: RCC1 Immune Microenvironment
Team Approach: The innate immune system's role in kidney cancer.
Results: This team took a top-down approach to mining drug databases for potential therapeutics that target the immune system cells that could have infiltrated Bill’s tumor.
Team Name: Nash Vegas Transcripters
Team Approach: Coding (mRNA) and non-Coding (miRNA. lincRNA) Transcriptome analysis for multi-omics biological network analysis
Results: This team focused on the detection of non-coding genes with altered expression in the tumors.
Workforce-Ready BioHackathon Training
Before, during, and after the event, participating BioHackers used the Cancer Transcriptomics journey to:
- Complete 20+ data-intensive bio-computing labs including Linux, Jupyter Notebooks, and biomedical datasets
- Run fundamental genomics workflows on supercomputer systems
- Add Bill’s open-source patient data to a Gene Expression Matrix (GEM)
- Complete required learning resources including videos, articles, activities, and discussion
- Pass short assessments, and participate in weekly collaboration sessions
- Conduct original research, and publishing results in journals and GitHub repositories
- Earn the valuable, industry-recognized Cancer Transcriptomics digital credential.
BioHackathon Results … Work in Progress
The initial discoveries were encouraging. The BioHackathon continues as teams meet weekly. Our aim is to organize results for the patient and publish a peer reviewed case study with Bill Paseman as lead author. Hopefully, we can help others.
