Let's hack genomics and win prizes!

Presented by HudsonAlpha Institute for Biotechnology and Urban Engine

Goal: Inspire creativity through collaboration, and energize the current and next generation of problem-solvers to conceive and construct innovative solutions to biotech challenges.

The Challenges: use an emerging technology such as machine learning, virtual/mixed reality, or blockchain technology and apply it to BioTech and Life Science.

 

CHALLENGE #1 - Visualizing Overlapping Data Between Replicate Experiments

We perform experiments in the lab that isolate regions of the genome that are interesting in some way. In particular, one assay (Next Generation Capture-C) reports on evidence of physical interactions between one specific region of the genome with all other possible locations. The output of these experiments is a BED file that contains genomic intervals or coordinates.

In order to increase our confidence in the output of the experiment and identify real signal from background noise, we run each experiment multiple times generating a BED file for each replicate. We are interested in visualizing the intervals of the genome where there is a high degree of overlap between the identified contacts within these BED files.

Given a set of BED files, produce and visualize data that characterizes the amount of supporting evidence (number of overlapping intervals) for all locations. Bonus points will be given if the solution is able to accept the amount of overlap as input (e.g. user defines how much overlap they require: more than 1 base of overlap or even allow for negative overlap with a specified distance).

Challenge Details and Example Data

 

CHALLENGE #2 - Augmented Reality to Gamify the Exploration of the Human Genome

This challenge requires teams to develop an internationally useable GenomeCache app that implements augmented reality technology to deliver a highly engaging gamified experience based on the concept of walking through McMillian Park exploring the human genome.

The HudsonAlpha Educational Outreach team designed and built an app in 2012 designed to provide an educational experience on McMillian Park on the HudsonAlpha campus. The app, GenomeCache, is an exploration of the human genome using a geocaching type experience. Using permanent signage, McMillian park has been divided into the 24 chromosomes found in a human genome. Additionally, more than 150 DNA locations have permanent signs indicating the gene name and function of that location in the human genome.

Players of GenomeCache must find signs on McMillian park using a clue provided to them via the app. Once the correct sign is found, a trivia question is delivered to the player that is either based on that specific DNA location or general trivia related to genetics, genomics and biotechnology. Points are awarded for both finding the correct location and for answering the question correctly. An international leaderboard is available online.

Educators using GenomeCache on the HudsonAlpha campus have requested the ability to use GenomeCache at their schools. The approach to meet this goal was to develop a standalone website where educators could print their own signs out on paper and directions for placing them in the correct order and distance apart from one another. This has caused many educators limited ability to use the app as they are limited by the number of copies they are allowed to print in a year. A full GenomeCache printout can be as many as 200 pieces or paper making it impractical for many classrooms.

Challenge Details and Example Data 

 

CHALLENGE #3 - Linking Family History Data through Blockchain

This challenge requires teams to design a tool that can link family medical history data supplied by different family members together to create a ‘master’ family history for all linked family members using blockchain technology. Teams should focus on chain of custody as individual patients should be able to see their own family history data, but not what other members of the family have contributed. Additionally, a medical practice or physician, should have the ability to see both an individual’s contribution to family history as well as the ‘master’ family history generated. As privacy is key, this solution must be decentralized and keep personally identifiable information encrypted and from being accessed by non-authorized individuals. It is recommended that power of work can be ignored in this challenge.

In the United States, there are many laws and regulations about sharing private medical and personal information. Most of these are in place to protect the privacy of any one individual allowing for that individual to decide what information is shared, when it is shared, and with whom. The sense of privacy of our own health information is an important value to the majority of citizens, however this is sometimes in conflict of providing high quality, informed medical care.

One area of a person’s medical record that is used to inform both diagnostic and preventative medicine is the family history of an individual. Family histories are routinely completed by a patient at almost every medical appointment. The family history information that is collected from an individual is filed within a medical record each time it is completed, but is rarely, looked at collectively for that individual over the history of the individual completing the information. For example, if Sue has been going to the same medical practice for the past 5 years for annual visits as well as at least one other visit during the year for illness, she has likely completed a family history form at least 10 times. This data is recorded or copied into her medical record for each visit and is used for only that one visit, requiring Sue to complete a family history form again the next visit. Furthermore, Sue’s maternal aunt, paternal grandfather, and three cousins are also patients at the same medical practice. According to current medical practice, the family history information provided by each of these family members are each recorded in the individual medical records for those patients. Each patient is treated as an individual without any other family medical information than what was supplied by that person regardless of how complete or accurate that information may be.

Challenge Details and Example Data

 

More information can be found on our homepage here.


Schedule:

Friday, February 22:
Kickoff meet and greet (optional)
4:30-7:00 PM

Saturday, February 23:
TECH CHALLENGE BEGINS
8:00 AM through   

Sunday, February 24:
CODE-FREEZE, All coding stops!
2:30pm

Take this 30 mins to submit your projects to Devpost and github
2:30pm - 3:00pm

Teams and Judges breakout for Round 1 Judging
3:00pm - 5:30pm

Final Presentation, Judging, Awards
5:30-7:00 PM

View full rules

Eligibility

High school and college students ages 16 and older, and adults interested in taking on challenges are welcome! There are two categories of teams: high school and college/adult. You don’t have to be a member of a team to sign up. We’ll make sure to get you on one!

How to enter

Click here to register for the event on EventBright

Click here to review agreements and download the legal forms you must fill out to participate.

Judges

No avatar 100

TBD

Judging Criteria

  • Impact
    How much impact (quality and quantity) can this solution have? Does this solution address the problem in a highly significant way?
  • Creativity
    How creative is the team’s approach? Is the solution new? Does the solution represent something that isn't being addressed by the market?
  • Complexity
    How much progress did the team make during the event? Did they start from scratch or build on an existing solution?
  • Product
    How user friendly is the technology? How fully formed/mature is the idea?
  • Presentation
    Did the team effectively communicate their solution? Did they tell the story of the project and why it is important in a compelling way? How well did they respond to questions from judges?