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


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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 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.

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

  1. 1. Award Number ACI-1547611 Sandra Gesing, Michael Zentner, Maytal Dahan and Katherine Lawrence 19 March 2017 2nd Personalized Medicine Conference, Cancun, Mexico Gateways to Science: Harnessing Big Data and Open Data for Precision Medicine
  2. 2. University of Notre Dame 2
  3. 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. 4. Big Data 4
  5. 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. 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. 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.
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  10. 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. 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. 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. 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. 14. Typical Lifecycle of a Science Gateway 14 Early adopters Publicity Wider adoption Funding ends Scientists disillusioned New project prototype
  15. 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. 16. Scientific Software Collaborative 16 High-level design of the scientific software collaborative
  17. 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. 18. Thanks for your attention! 18