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Pathology Hackathon

"The Edge of Chaos sits at the intersection between disciplines - the intersection of people's minds and the disciplines that preoccupy them. And it is therefore the perfect place for a Pathology Hackathon at a time when the study of disease has become trans-disciplinary. The Pathology Hackathon is a weekly workshop run by graduate students that provides a place where people can walk in with a problem in their domain of expertise. The shared knowledge base for the hands-on exercise is programming. That is, we allow Information and Communication Technology (ICT) to define the share scientific table where we are all sitting.

Several publications have resulted from these sessions. The most visible ones focus on cancer genomics, precisely because there is a public repository of tumor data on more than 7,000 patients (the Cancer Genome Atlas, TCGA). Shared access to a data source provides the watering hole where people can drink from the wealth of reference population data about cancer. This data-driven exercise allows computational statitsticians, biologists, and physicians to jointly translate this information into new therapies."

Dr Jonas Almeida, Professor, Director of Pathology Informatics, UAB




A service of the Division of Informatics, this is a hands on activity that takes place every Wednesday where participants bring their laptops, code, and systems biology / integrative biomedicine problems to an "extreme programming" environment. Each participant is encouraged to maintain his or her own version-controlled repositories, ideally cloned from the shared repository at

The ultimate goal of the Pathology Hackathon is to solve wicked integrative biomedicine problems through a collaborative process.


[TCGA club - in response to multiple requests, the third hour of the hands-on workshop, (i.e. 11-noon) is focused on the cancer genome atlas.]