The OHBM 2013 Local Organizing Committee (LOC) announces the HBM Hackathon, a meeting-long analysis and resource building competition designed to accelerate the connection between open neuroscience and cloud computing.

Background

OHBM 2013 occurs in a city at the forefront of open neuroscience and information technology. With support from the Allen Institute for Brain Science, Amazon Web Services, and numerous other contributors, the 2013 meeting in Seattle will include an integrated hack room and associated cloud-computing contest called the HBM Hackathon. The hackathon will include a venue on the main poster/exhibit floor space, and prepared cloud-accessible data and software. These resources will be available to participants beginning two months ahead of the meeting, with in-kind support from Amazon Web Services in the form of $100 in cloud computing credits that will be made available to all registered HBM Hackathon participants attending OHBM 2013.

HBM Hackathon Information

• Registration
• Website and Blog
• Discussion Group

Sponsors

HBM Hackathon major sponsors include the Allen Institute for Brain Science and Amazon Web Services.

There are a number of secondary sponsors including:

• NITRC - Neuroimaging Informatics Tools and Resources Clearinghouse
• IBIC - University of Washington Integrated Brain Imaging Center
• INCF - International Neuroinformatics Coordinating Facility
• BIRN - Biomedical Informatics Research Network
• NDAR - National Database for Autism Research
• LONI - Laboratory of NeuroImaging
• HCP - Human Connectome Project
• Frontiers in Brain Imaging Methods
• NIPY - Neuroimaging in Python
• NeuroDebian
• GitHub

Major sponsors made donations specifically to support the HBM Hackathon program.

Secondary sponsors are qualified by making tools and resources AWS-accessible in advance of the meeting, having an on-site presence (flagged consultation table in the Hack Room) during scheduled informal hack time during lunch and poster sessions and/or contributing relevant resources in support of the HBM Hackathon.

Have an open human brain mapping resource you would like to have included?

Just contact us: hbm.hackathon@gmail.com

Venue

OHBM has allocated approximately 3000 square feet of space on the poster/exhibit hall for a Hack Room that will include a podium and presentation equipment. The Hack Room will be used for collaboration as well as formal presentations accommodating up to 300 people. Sponsoring and contributing groups will be present to provide ongoing consultation and assistance with their respective resources, and may optionally make brief presentations at the podium.

Schedule

The HBM Hackathon program will take place during the lunch hour and poster sessions, and includes the Tuesday evening poster reception.

Monday – sponsored by Allen Institute for Brain Science

12:30-1:30pm: HBM Hackathon orientation presentations.

• Shared Allen Institute and AWS presentations
• Light box lunch

1:30-3:30pm: Informal hack activity

• Grassroots responses to contest challenges
• Consultation/assistance from sponsoring groups
• Brief presentations at north wall by participants/sponsors
• Circulating contest judges

Tuesday – sponsored by Amazon Web Services

12:30-3:30pm: Informal hack activity as described under Monday (see above)

6:00-7:30pm: Shared Allen Institute and AWS presentations

Wednesday – sponsor TBD

12:30-3:30pm: Informal hack activity as described under Monday (see above)

1:30-3:00pm: Preliminary pitches to judges (see Judging below)

Thursday – sponsor TBD

10:45-12:15pm: Informal activity as described under Monday (see above)

12:15-1:15pm: Final presentations and community voting

1:15-1:45pm: HBM Hackathon reception

Contest and Challenges

The contest will be organized around three Challenges, two of them pre-announced and open to work in advance of the meeting; and one announced at the time of the meeting. A brief overview of the challenges are provided here and a more detailed post will be provided separately as a post here at the HBM Hackathon Blog.

HBM Hackathon participants are encouraged to work in teams and will receive several incentives:

• $100 in cloud-computing credits per participant registered for OHBM
• Private GitHub Repository for groups of five or more (50 total)

Challenge 1. Best imaging and gene expression relationship discovered via integration of imaging data with the Allen Human Brain Atlas.

Here is a published example that would be responsive to this challenge: Mathias Schroeter from Max Planck Institute will also be one of the speakers at the Imaging-Gene Expression Symposia during OHBM to talk about this paper.

Mueller K, Sacher J, Arelin K, Holiga S, Kratzsch J, et al. Overweight and obesity are associated with neuronal injury in the human cerebellum and hippocampus in young adults: a combined MRI, serum marker and gene expression study. Transl Psychiatry 2: e200. doi:10.1038/tp.2012.121.

Challenge 2. Best neural systems model or visualization based on large-scale integration of resting state fMRI data with other HBM Hackathon accessible datasets.

Here is a published example that would be responsive to this challenge:

Uddin LQ, Supekar K, Amin H, Rykhlevskaia E, Nguyen DA, Greicius MD, Menon V. Dissociable connectivity within human angular gyrus and intraparietal sulcus: evidence from functional and structural connectivity. Cereb Cortex. 2010 20:2636-46.

Challenge 3. To be announced the week of the meeting. This “mystery” challenge is to be addressed entirely during the meeting using resources made openly available to the brain mapping community.

Rules

• Participants must use publicly available data that is listed on the HBM Hackathon Blog. If a public dataset is not listed that you want to use, we would love to add it to the list, just contact us: hbm.hackathon@gmail.com
• Participants can use any computational resources available to them, but judging will take into account innovative use of cloud computing and how openly available the approach is (see Judging)
• At least one team leader/presenter must attend the meeting
• Off-site team members are allowed and encouraged, but will not be eligible for all resources made available to registered OHBM attendees (e.g., cloud computing credits)

Not interested in the challenges?

Cooperative “hackathon” activity outside of the contest is also encouraged. Please feel free to visit the OHBM Hack Room during the meeting to learn about brain mapping community resources and/or work on a project like:

1. Efforts that encourage data sharing and reproducible data processing
2. Dynamically configurable virtual machines (e.g. Amazon Machine Images)
3. Cloud-accessible 3D model library and other standard space atlas resources

Judging

Participants will be judged using a combination of panel judging and peer voting. A committee of three judges not involved in the organization of the HBM Hackathon will be recruited.

The responsibilities of the judges are to:

• Circulate in the Hack Room during informal activity time, and consider self-nominated projects for inclusion in the preliminary judging session scheduled for Wednesday evening.
• Attend the preliminary pitches of hack projects Wednesday 1:30-3:00pm at the north wall presentation space, and decide on 2-3 finalists in each category.

Criteria to be applied include:

• Scientific impact
• Innovative use of cloud services
• Open availability of brain mapping tools, atlases, or datasets
• Extent and diversity of data used

Preliminary judging session: Wednesday 1:30-3:00pm

• Judge-nominated projects pitch for 4 minute (5 slides) with one minute for questions
• A maximum of 15 projects will be presented in this session
• Judges select 2 per Challenge for final session on Thursday
• Finalists may “pour it on” overnight

Final Presentations: Thursday 12:15-1:15pm

• Final projects present for 10 min total (including any questions)
• Winners selected by community voting (i.e., of those attending)

Reception – Thursday 1:15-1:45pm

• Votes will be tabulated and winners will be announced
• Refreshments will be provided

Prizes

Winning entries in each category receive:

• An invitation to submit project to Frontiers in Brain Imaging Methods with Open Access Publication Fees waived (must undergo standard peer review)
• Amazon Kindle Fire and/or Paperwhite (limit 3 per team)
• AWS hosts AMI and/or data resulting from the hackathon free of charge
• Free GitHub Membership with private repositories (Challenge 1: one year silver, Challenge 2: 1 year bronze, Challenge 3: six months bronze)

Thank you and good luck!

The HBM Hackathon Organizers

• Thomas Grabowski, University of Washington, LOC Chair
• Nolan Nichols, University of Washington
• Chinh Dang, Allen Institute for Brain Science
• Elaine Shen, Allen Institute for Brain Science
• Rachel Pizarro, Amazon Web Services
• Jamie Kinney, Amazon Web Services
• Satrajit Ghosh, Massachusetts Institute of Technology
• OHBM 2013 Local Organizing Committee