(Bio)Hackathons: What, Why, and How

Benjamin Good TSRI @bgood

Wikimedia

Techcrunch

Hackathons are to:

http://baltimorehackathon.com/

Like an (un)conference

But you create something in the process

Why?

• Collaborative Creativity

• Learning (e.g. new APIs)

• Advertising.. (e.g. pushing your new API..)

• Networking

Hackathons are for:

Key Purpose

PSEA-Quant

MyGene.info

XIPSICQUIC

PINT

IBminer

EGA

Train Online

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Goal: Assemble a network of biomedical entities that is comprehensive, current, and computable.

Pathways Diseases Proteins Variants

Genes Drugs

BioThings (Credit Andrew Su)

An example

Hackathon 1 Stanford• May 2014

• Around 30 participants

• UCSD, TSRI, Stanford, OICR, Buck, Gladstone, SDSU, SRI, WU, Random…

• $500 for best motivating use case, $500 for most sustainable infrastructure design, 2x$500 for best applications

• Panel of experts judged

• Concurrent Hackathon in Maastricht

https://github.com/Network-of-BioThings/nob-hq/wiki/1st-Network-of-BioThings-Hackathon

• Saturday

• 9:00AM: Introductions, Problem Statement, Ideas session

• 10:15AM: Project Pitches and Team Formation

• 11:00AM: Tutorials

• 6:00PM: Progress Reports

• 7:30PM: Dinner at the Left Bank in Menlo Park

• Sunday

• 8:00AM : Breakfast is served

• 4:30PM : Pitches and Demos

• 6:00PM : Winners, prizes awarded, final remarks.

Results• bioDiscoverer

• gettingCrafty

• network of variant annotations

• turned into myvariant.info

• PubMed++

• Whypothesis

• Given a hypothetical drug-disease association, propose a mechanism using known drug-gene and disease-gene interactions. Simplify and visualize the proposed pathway.

Win!

Trish Whetzel UCSD

Robin Haw OICR

Chunlei Wu TSRI

Chris Mungall Berkeley

Ben Ainscough WU

Sean Mooney UW

Hackathon 2: UCSD• Nov. 2014

• Around 30 participants

• UCSD, TSRI, Stanford, STSI, UBC, SDSU, WU, UCSC, Random…

• $500 first place, $400 second place

• Participants voted on winners

• Pre-meeting

• Email spamming, flyers, Google Doc with Ideas List

• Friday

• 6:00pm Drinks and Dinner

• 7:00-10:00pm Project Pitches and team formation

• Saturday (food brought to hackers all day)

• 8:00AM : Doors open for hacking

• 10:30PM : Hackers kicked out.

• Sunday

• 8:00AM : Doors open again

• 11:00AM: Project presentations

• 12:00PM: Winners announced

Projects• BioPolymer: A set of embeddable web components to display and edit bio data. Initially data from MyGene &

MyVariant. Team: Mark Fortner, Keiichiro Ono

• SameSame: a dynamic tool for finding and visualizing the degree of similarity between any set of biomedical concepts. Team: Benjamin Good, Maulik Kamdar, Alan Higgins, Alex Williams

• CIViC - Clinical Interpretation of Variants in Cancer: Crowdsourcing and web interface for curation of clinically actionable evidence in cancer. Team: Obi Griffith, Adam Coffman, Martin Jones, Karthik G, Jon Cristensen, Julianne Schneider

• Citizen Science: An app to enable people to extract structured ‘facts’ (subject predicate object triples) from unstructured text. Here is the project presentation. Team: Richard Good, Hannes Niedner, Andrew Su

• SBiDer: Synthetic Biocircuit Developer: A web-app to search a database of operons [functional biochemical pathways] to use them in new and novel ways [to make synthetic organisms such as the ones used to make this Malaria treatment]. Team Justin Huang, Kwat Yeerna, Fernando Contreras, Joaquin Reyna, Jenhan Tao

• NDex: The NDEx project provides a public website where scientists and organizations can share, store, manipulate, and publish biological network knowledge. Team Dexter Pratt

• fiSSEA: A framework that integrates MyGene.info and MyVariant.info to retrieve functional prediction annotations (or any type of annotation) for knowledge discovery, specifically implement CADD scores for “functional impact SNP Set Enrichment Analysis". Team: Adam Mark, Erick Scott, Chunlei Wu

• MyGene.Info Taxonomy Query: Added detailed taxonomy information to mygene.info. Allows queries based on taxonomy ID and advanced queries based on hierarchies of taxonomic nodes. Team: Greg Stupp, Chunlei Wu

Win!Andrew Su

TSRI

Richard Good goodschooltools

https://github.com/Network-of-BioThings/brat-citizenscience

Hannes Niedner UCSF

Win!Replaced component with mygene.info query during

hackathon (site about to go live)

Win of a different kind

Team of 1 (NDex project) Clearly enjoyed weekend as

a Programmer rather than Project Director..

How - the 6Gs of running a hackathon

• Get people to show up

• Get them to talk to each other

• Get them to pick projects and form teams

• Get them working

• Get them to present their work

• Give out prizes to the best projects