2nd Network of BioThings Hackathon

jgrethe edited this page Nov 6, 2014 · 17 revisions

What: 2nd Network of BioThings Hackathon (#networkofbiothings)

Click here to register!


Contact: Please send questions or comments to the Network of Biothings mailing list. https://groups.google.com/forum/#!forum/network-of-biothings

Chat: We have set up a room in Hall for live conversations for both local and remote participants. Here is the link to join up: https://hall.com/i/UqtUwjby_l4Pe0GbDZ58Sg

When: November 7-9, 2014

Where: This hackathon will be held at:

  • UC San Diego on the 3rd floor of the CALIT2 building. http://www.calit2.net/about/info/ucsd/
  • Note: Rooms have changed at CALIT2. CALIT2 is a secured building - there will be someone in the lobby to let you in and get you to the third floor. On Saturday and Sunday, the student will be available to let people in starting at 8:30am

Why: Despite the massive amount of biomedical literature, only a small amount is available in a form that is readily computable. This hackathon will help develop 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 http://goo.gl/i91ngK). During this hackathon, we will (1) identify motivating use cases, (2) define a shared, sustainable, multi-component infrastructure to build the NoB, and (3) implement common data representations, ontology-based programmatic interfaces, and develop cool applications. We will do this in an open, scalable, responsive manner so that it becomes a major asset for hackers and biomedical researchers worldwide.

This Hackathon will feature

  • networking and mentoring with leading researchers and experts
  • prizes for the best contributions

Who: We’re looking for:

  • Hackers and Mentors
  • Biologists, Text Miners and Data Wranglers
  • Ontologists, Terminologists, and Data Linkers
  • Semantic Web novices and experts
  • Systems and Network Biologists
  • Crowdsourcing experts and functional game designers
  • Skills in Large Text/Data Indexing, Facet Search and Browse, and REST APIs
  • Domain experts to advise on motivating use cases

Come join us for networking, designing, and coding culminating in prize-winning pitches and demos!

Registration: Fees to be determined ($40.00 or less) Max 60 participants - first come first served! Click here to register!

Scholarships: Multiple financial need-based scholarships are available! Please contact ben.mcgee.good at gmail to request one. !


Friday, November 7 6pm-10pm : Welcome social / project team formation

Saturday, November 8 9am-? : Hacking !

Sunday, November, 9 9am-10:30am: Final hacking / presentation preparation

10:30am:11:30am Pitches and Demos

11:45am Prize announcements

Click here to register!

Project ideas

The (#networkofbiothings) is broad and wide-ranging set of ideas. We welcome any project that a) is awesome and b) can be linked back to the core, high-level mission of generating 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

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.

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