The importance of Big Data and Open Data to achieve scientific advancements in precision medicine is beyond doubt and evident in many different projects and initiatives such as the Precision Medicine Initiative (All of Us), ICTBioMed, NCIP Hub, 100K Genomics England Project, NIH Cancer Moonshot, and the Million Veterans Program. In April 2013, McKinsey & Company proclaimed that Big Data has the ability to revolutionize pharmaceutical research and development within clinical environments, by using data for better informed decision making and targeting the diverse user roles including physicians, consumers, insurers, and regulators. Companies from a wide spectrum such as Oracle Health Sciences, Google, and Data4Cure build solutions that help address efficient and secure data sharing with the patient or clinician in mind. Open data can be maintained and shared by patient communities such as PatientsLikeMe.com and build an invaluable resource for further data mining. Even with all these advances there are still challenges to address including a recent Precision Medicine World Conference announcement in November 2016: “We are missing easy-to-use solutions to share patient data.” Science gateways are a solution to fill the gap and help form by definition end-to-end solutions – web-based, mobile or desktop applications - that provide intuitive access to advanced resources and allow researchers to focus on tackling today’s challenging science questions. Science Gateways abstract the complex underlying computing and data infrastructure as far as feasible and desired by the stakeholder and can be tailored to different target groups with diverse backgrounds, demands, and technical knowledge. Science Gateways have existed for over a decade and a wide variety of frameworks and APIs have been developed to support the efficient creation of science gateways and ease the implementation of connections to Cloud infrastructures and distributed data on a large scale. The importance of science gateways has been recognized by NSF by funding the creation of a Science Gateways Community Institute (SGCI) to serve the community with free resources, services, experts, and ideas for creating and sustaining science gateways. To achieve this goal, the SGCI serves the community with five areas that have diverse foci and which also closely interact: Incubator, Extended Developer Support, Scientific Software Collaborative, Community Engagement and Exchange and Workforce Development. The Institute is technology-agnostic and serves the community by offering a wide variety of services and using technologies that are the best fitting solution for the use case. Gateways allow for precision medicine to be more efficiently developed or adapted by lowering the barriers to data sharing and Big Data analysis.

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

2. University of Notre Dame
2

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)

4. Big Data
4
http://www.genome.gov/images/content/cost_per_genome_oct2015.jpg

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