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1st Network-of-BioThings Hackathon
The 1st NOB Hackathon, scheduled for April 26-27 at Stanford and Maastricht University, aims to develop a comprehensive biomedical network covering diseases, proteins, variants, genes, and drugs. Participants will engage in team formation, project pitches, and tutorials while focusing on building a scalable and interoperable knowledgebase from rapidly growing biomedical literature. Awards totaling $2,000 will be given for innovative use cases, sustainable infrastructure, and application formats during the event.
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1st Network-of-BioThings Hackathon
- 1. 1st NoB Hackathon April26-27 @Stanford University @Maastrict University
- 2. • Michel Dumontier •Natasha Haulman (superadmin) • Mark Musen • Andrew Su • Ben Good • Chris EveloData FAIRport • Mark Wilkinson
- 3. European site @Maastricht University • Chris Evelo (NoB) • Mark Wilkinson (FAIRport)
- 4.
- 5. 5 Pathways Diseases Proteins Variants Genes Drugs Goal: Assemble anetwork of biomedical entities that is comprehensive, current, and computable.
- 6. The biomedical literatureis growing fast 6 In 2013, there were 1,108,920 new articles indexed in PubMed, bringing the current total to over 23 million. 0 200,000 400,000 600,000 800,000 1,000,000 1,200,000 1983 1988 1993 1998 2003 2008 2013 Number of new PubMed-indexed articles
- 7. The biomedical literatureis growing fast 7 In 2013, there were 1,108,920 new articles indexed in PubMed, bringing the current total to over 23 million. 0 200,000 400,000 600,000 800,000 1,000,000 1,200,000 1983 1988 1993 1998 2003 2008 2013 Number of new PubMed-indexed articles k n o w l e d g e
- 8. The Kitchen Sinkapproach • Biocuration • Text-mining • Crowdsourcing • Citizen science • Semantic web • Bio-ontologies • Network biology • Biomedical domain experts • Scientific publishers • Bio-IT • … 8
- 9. 1. Knowledgebase infrastructure •Scaling to billions or trillions of relationships • Efficient query and access • Generic and extensible data model • Interoperability with other resources 9
- 10. 2. Populating theknowledgebase • Scalability with biomedical research • Synergies between methods • Assessing confidence • Preserving provenance 10
- 11. 3. Driving BiologicalProjects • Defining the domain area • N-of-1 cancer • Drug repurposing • Neuroscience • Defining the specific data needed • Defining the mining/analysis strategy • Defining the testable hypotheses 11
- 12. Overarching goals • Demonstratefeasibility • Demonstrate collaboration • Demonstrate synergy • Secure funding for multi-center multi-PI consortium 12
- 13. Schedule Saturday April 26 8:30AM:Registration and Breakfast 9:00AM: Introductions, Problem Statement, Ideas session 10:15AM: Project Pitches and Team Formation 11:00AM: Tutorials 12:15PM: Lunch is served 6:00PM: Progress Reports 7:00PM: Transportation leaves for restaurant 7:15-8:00PM: Cocktails @ Left Bank 8:00PM: Dinner @ Left bank Sunday April 27 8:00AM : Breakfast is served 12:15PM: Lunch is served 4:30PM : Pitches and Demos 6:00PM : Winners announced, prizes awarded, final remarks.
- 14. Prizes • $500 forbest motivating use case • $500 for most sustainable infrastructure design • 2x$500 for best applications
- 15. Format • Form groupsof at most 5 • Must contain at least 2 local participants • Up to 3 additional remote participants (total of 8) • All code must be open and available • GitHub repo https://github.com/Network-of-BioThings/
- 16. Judges • Mark Musen(NCBO) • Bob Stanley (IO Informatics) • Paul Alexander (NCBO) • Manuel Salvadores (NCBO) • Michel Dumontier (NCBO) • Andrew Su (Scripps – Use Cases) • Criteria • Innovation • Integration • Sustainability / Scalability • Impact Potential
- 17. Other Stuff • Wifi •Bathrooms • Room configuration • projectors
- 18. Let’s Get Started! •GitHub • https://github.com/Network-of-BioThings/ • Hackathon repo • Use Cases • Resources • Participant Profiles