SlideShare a Scribd company logo
Award Number
ACI-1547611
Sandra Gesing, Michael Zentner, Maytal Dahan
and Katherine Lawrence
sandra.gesing@nd.edu
19 March 2017
2nd Personalized Medicine Conference, Cancun, Mexico
Gateways to Science:
Harnessing Big Data and Open
Data for Precision Medicine
University of Notre Dame
2
Big Data
3
• Explosion in the quantity, variety and complexity of data
• Questions can be answered impossible to even ask about 10
years ago
• Costs far reduced (e.g., Human Genome project, 15 years, ~
$2 billion; today ~3 days, $1000)
Big Data
4
http://www.genome.gov/images/content/cost_per_genome_oct2015.jpg
Open Data
5
Sharing and analyzing data in genomics and precision
medicine on a large scale enables
•  better diagnoses,
•  treatment options,
•  overall well-being and
•  personalized medicine
for patients around the globe.
•  Initiatives and projects fostering Big Data and Open Data
for health are ongoing
•  Companies address efficient and secure data sharing
•  Novel technologies in genomics allow creating data in
exascale dimensions
Challenges
6
1.  Meaningful data aggregation and analysis
2.  Real-time analytics
3.  Privacy and security demands
4.  Lack of usability of solutions
5.  Missing integration of data
sources and instruments
6.  Complicated US and European
privacy laws on health data
7.  Diversity of stakeholders
è  Technical solutions can
•  address the first five challenges
•  assist with data and measures for easing policies on health data
•  support diverse user roles via easy-to-use end-to-end solutions
Science Gateways
7
•  Increased complexity of
•  today’s research questions
•  hardware and software
•  skills required
•  Greater need for openness
and reproducibility
•  Science increasingly driving
policy questions
•  Opportunity to integrate
research with teaching
•  Better workforce preparation
We need end-to-end
solutions that
provide
broad access to
advanced resources
and
allow all to tackle
today’s challenging
science questions.
8
9
10
It’s a
Science
Gateway
It’s a
Research
Portal
It’s a
Collaboratory
It’s a
Cyber-
infrastructure
It’s
e-Science
eResearch
It’s a
Virtual
Lab
Gateway users are 77% of active XSEDE
users in Q4 2016
11
This is largely due to the CIPRES and I-TASSER gateways, but others are gaining
All users
Gateways
XSEDE users
Login
Science Gateways Survey 2014
12
What services
would be helpful?•  sent out to 29,000 persons
•  4,957 responses from
across domains
•  52% from life, physical or
mathematical sciences
•  32% from computer and
information sciences or
engineering
•  45% develop data collections
•  44% develop data analysis
tools
Science Gateways Survey 2014
13
34% 36%
20%
17%
31%
26%
42%
16%
30%
18%
45% 44%
14% 15%
0%
5%
10%
15%
20%
25%
30%
35%
40%
45%
50%
Usability
Consultant
Graphic
Designer
Community
Liaison/
Evangelist
Project
Manager
Professional
Software
Developer
Security
Expert
Quality
Assurance
and	
  Testing
Expert
Wished	
  we	
  had	
  this
Yes,	
  we	
  had	
  this
Well-designed gateways require a variety of
expertise
Typical Lifecycle of a Science Gateway
14
Early
adopters
Publicity
Wider
adoption
Funding
ends
Scientists
disillusioned
New
project
prototype
Science Gateways Community Institute
15
•  Diverse expertise on
demand
•  Longer term support
engagements
•  Software and visibility
for gateways
•  Information exchange in
a community
environment
•  Student opportunities
and more stable
career paths
Scientific Software Collaborative
16
High-level design of the scientific software collaborative
Opportunities
17
•  Get advice (sustainability, usability, cybersecurity, other) on your
existing gateway
•  Work with SGCI to build a gateway for you
•  Find a working gateway or gateway development software in our
catalog
•  Learn how to set up a gateway group on your campus
•  Keep up to date on gateway developments
•  webinar series, gateways in the news, google scholar feed, case
studies, annual conference, blog posts
•  Enroll a student in an internship program to learn gateway development
•  Partner with SGCI on your own projects, technologies and events
Thanks for your attention!
help@sciencegateways.org
http://sciencegateways.org/
18

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SGCI Science Gateways: Harnessing Big Data and Open Data 03-19-2017

  • 1. Award Number ACI-1547611 Sandra Gesing, Michael Zentner, Maytal Dahan and Katherine Lawrence sandra.gesing@nd.edu 19 March 2017 2nd Personalized Medicine Conference, Cancun, Mexico Gateways to Science: Harnessing Big Data and Open Data for Precision Medicine
  • 3. Big Data 3 • Explosion in the quantity, variety and complexity of data • Questions can be answered impossible to even ask about 10 years ago • Costs far reduced (e.g., Human Genome project, 15 years, ~ $2 billion; today ~3 days, $1000)
  • 5. Open Data 5 Sharing and analyzing data in genomics and precision medicine on a large scale enables •  better diagnoses, •  treatment options, •  overall well-being and •  personalized medicine for patients around the globe. •  Initiatives and projects fostering Big Data and Open Data for health are ongoing •  Companies address efficient and secure data sharing •  Novel technologies in genomics allow creating data in exascale dimensions
  • 6. Challenges 6 1.  Meaningful data aggregation and analysis 2.  Real-time analytics 3.  Privacy and security demands 4.  Lack of usability of solutions 5.  Missing integration of data sources and instruments 6.  Complicated US and European privacy laws on health data 7.  Diversity of stakeholders è  Technical solutions can •  address the first five challenges •  assist with data and measures for easing policies on health data •  support diverse user roles via easy-to-use end-to-end solutions
  • 7. Science Gateways 7 •  Increased complexity of •  today’s research questions •  hardware and software •  skills required •  Greater need for openness and reproducibility •  Science increasingly driving policy questions •  Opportunity to integrate research with teaching •  Better workforce preparation We need end-to-end solutions that provide broad access to advanced resources and allow all to tackle today’s challenging science questions.
  • 8. 8
  • 9. 9
  • 10. 10 It’s a Science Gateway It’s a Research Portal It’s a Collaboratory It’s a Cyber- infrastructure It’s e-Science eResearch It’s a Virtual Lab
  • 11. Gateway users are 77% of active XSEDE users in Q4 2016 11 This is largely due to the CIPRES and I-TASSER gateways, but others are gaining All users Gateways XSEDE users Login
  • 12. Science Gateways Survey 2014 12 What services would be helpful?•  sent out to 29,000 persons •  4,957 responses from across domains •  52% from life, physical or mathematical sciences •  32% from computer and information sciences or engineering •  45% develop data collections •  44% develop data analysis tools
  • 13. Science Gateways Survey 2014 13 34% 36% 20% 17% 31% 26% 42% 16% 30% 18% 45% 44% 14% 15% 0% 5% 10% 15% 20% 25% 30% 35% 40% 45% 50% Usability Consultant Graphic Designer Community Liaison/ Evangelist Project Manager Professional Software Developer Security Expert Quality Assurance and  Testing Expert Wished  we  had  this Yes,  we  had  this Well-designed gateways require a variety of expertise
  • 14. Typical Lifecycle of a Science Gateway 14 Early adopters Publicity Wider adoption Funding ends Scientists disillusioned New project prototype
  • 15. Science Gateways Community Institute 15 •  Diverse expertise on demand •  Longer term support engagements •  Software and visibility for gateways •  Information exchange in a community environment •  Student opportunities and more stable career paths
  • 16. Scientific Software Collaborative 16 High-level design of the scientific software collaborative
  • 17. Opportunities 17 •  Get advice (sustainability, usability, cybersecurity, other) on your existing gateway •  Work with SGCI to build a gateway for you •  Find a working gateway or gateway development software in our catalog •  Learn how to set up a gateway group on your campus •  Keep up to date on gateway developments •  webinar series, gateways in the news, google scholar feed, case studies, annual conference, blog posts •  Enroll a student in an internship program to learn gateway development •  Partner with SGCI on your own projects, technologies and events
  • 18. Thanks for your attention! help@sciencegateways.org http://sciencegateways.org/ 18