Skip to content

1st BD2K 3rd Network of BioThings Hackathon

Andrew Su edited this page May 19, 2015 · 29 revisions

What: 1st BD2K / 3rd Network of BioThings Hackathon (#hackBD2K)

This Hackathon will feature

  • networking and mentoring with leading researchers and experts
  • hacking on exciting projects
  • prizes for the best contributions! ($500 1st place, $300 2nd place)
  • delicious food during the hackathon (Thursday: Dinner; Friday: Breakfast, Lunch, Dinner; Saturday: Breakfast & Lunch). Food will be provided by Phil's BBQ, Bombay Coast, Regent's Pizza ...



When: May 7-9, 2015

Where: This hackathon will be held at The Scripps Research Institute (TSRI) Hazen Campus

See map for details:

Registration: Register Here

Fees: $30.00. Max 50 participants - first come first served! Includes food & drinks, eligibility for prizes, and a fancy t-shirt.

Scholarships: Several scholarships will be available to promote education and diversity. Please fill out this form to be considered for a travel award or scholarship.

**Please contact gstupp at scripps to sponsor a scholarship!

Why: The mission of the BD2K initiative is to enable the biomedical research community to use the various types of Big Data for research. Biomedical research is rapidly becoming data-intensive as investigators are generating and using increasingly large, complex, multidimensional, and diverse datasets. However, the ability to release data, to locate, integrate, and analyze data generated by others, and to utilize the data is often limited by the lack of tools, accessibility, and training.

During this hackathon we will work on projects relating to any of the major challenges of biomedical big data, including:

  • Locating, gaining access to, standardizing, and documenting data, software tools, and APIs
  • Developing effective, robust, reproducible and interoperable means of sharing data and software tools
  • Developing new methods for analyzing biomedical big data
  • Training researchers for analyzing biomedical big data

Who: We’re looking for:

** We welcome participants regardless of programming ability or biological knowledge!! **

  • Hackers and Mentors
  • Biologists, Text Miners and Data Wranglers
  • Developers of visualizations for presenting and understanding large data sets
  • Ontologists, Terminologists, and Data Linkers
  • Semantic Web novices and experts
  • Systems and Network Biologists
  • Crowdsourcing experts and functional game designers
  • Domain experts to advise on motivating use cases

Contact: Please send questions or comments to the Network of Biothings mailing list.!forum/network-of-biothings or gstupp at scripps


Thursday, May 7

6pm-10pm : Welcome social / project team formation

Friday, May 8

9am-? : Hacking !

Saturday, May, 9

9am-2pm : Hacking / presentation preparation

2pm-3pm : Pitches and Demos

3:30pm : Prize announcements

Project ideas

We welcome any project that a) is awesome and b) can be linked back to the mission of generating or facilitating the generation of new biological and medical knowledge. To help spur ideation, a few broad areas of particular interest include:

  • Automated hypothesis generation/testing
  • Network data visualization
  • Crowdsourcing systems for annotation and information extraction
  • Representation and integration of the human variome
  • Development of a comprehensive Network of BioThings (proteins, genes, pathways, mutations, drugs, diseases) extracted from scientific research articles and integrated with public biomedical data (see blog post

Please feel free to either come up with something completely new or take an existing open source project and expand its functionality.

Please visit and contribute your own ideas to the specific list of project ideas.

Participant feedback

We are making this a semi-annual event, so every suggestion you give us this time will improve the experience next time. Please log your feedback here:

Project summaries and presentations

Running minutes here:

You can’t perform that action at this time.