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Poster SGCI Science Gateways: Harnessing Big Data and Open Data


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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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Poster SGCI Science Gateways: Harnessing Big Data and Open Data

  1. 1. Gateways  to  Science:     Harnessing  Big  Data  and  Open  Data  for  Precision  Medicine      Sandra  Gesing1,  Michael  Zentner2,  Maytal  Dahan3,  and  Katherine  Lawrence4     1University  of  Notre  Dame,  Notre  Dame,  IN,  USA,  2Purdue  University,  West  LafayeLe,  IN,  USA,  3University  of  Texas,  AusOn,  TX,  USA,  4University  of  Michigan,  Ann  Harbor,  MI,  USA   contact:   h"p://   Background   •  Ini7a7ves  and  projects  fostering  Big  Data  and  Open  data  for  health  are   ongoing   •  Companies  address  efficient  and  secure  data  sharing   •  Novel  technologies  in  genomics  allow  crea7ng  data  in  exascale   dimensions   Stakeholders  of  Big  Data  and  Open  Data  for  Precision  Medicine   •  Scien8sts   •  Physicians     •  Pa8ents     •  Pharmacy   •  Insurers     •  Regulators     Challenges   Summary   Sharing  and  analyzing  data  in  genomics  and  precision  medicine  on  a  large   scale  enables  be"er  diagnoses,  treatment  op7ons,  overall  well-­‐being  and   personalized  medicine  for  pa7ents  around  the  globe.     Science  gateways  form  a  solu7on  to  address  the  challenges  on  usability  of   tools  and  sharing  data  under  considera7on  of  data  security  and  privacy.   They  hide  the  complex  underlying  compu7ng  and  data  infrastructure  as   far  as  feasible  and  desired  by  the  user  communi7es  and  are  in  general   tailored  to  different  target  groups  with  diverse  backgrounds,  demands  and   IT  knowledge.     The  Science  Gateways  Community  Ins7tute  (SGCI)  as  an  online  and   physical  resource  for  community  building  supports  science  gateways   via  sharing  exper7se,  such  as  experiences,  technologies,  and  prac7ces.   It  enables  gateway  creators  to  leverage  efforts  across  projects  and  can   step  in  with  supplemental  exper7se  when  needed  by  a  project.   1.  Meaningful  data  aggrega7on  and  analysis   2.  Real-­‐7me  analy7cs     3.  Privacy  and  security  demands   4.   Lack  of  usability  of  solu7ons   5.   Missing  integra7on  of  data  sources  and  instruments   6.   Complicated  US  and  European  privacy  laws  on  health  data   7.   Diversity  of  stakeholders   è Technical  solu-ons  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  solu7ons   Science  Gateways   •  Are  tailored  to  a  targeted  community   •  Form  end-­‐to-­‐end  solu7ons:  web-­‐based,  mobile  or  desktop  applica7ons     •  Provide  intui7ve  access  to  advanced  resources     •  Allow  to  tackle  today’s  challenging  science  ques7ons   Science  Gateways  Community  Ins9tute   •  sent  out  to  29,000  persons   •  4,957  responses  from  across  domains   •  52%  from  life,  physical  or  mathema7cal  sciences   •  32%  from  computer  and  informa7on  sciences  or  engineering     •  45%  develop  data  collec-ons   •  44%  develop  data  analysis  tools   Science  Gateway  Survey   What  services  would  be  helpful?   Which  exper7se  is  needed?   The  SGCI  serves  the  community  with  free  resources,  services,  experts  and   ideas  for  crea7ng  and  sustaining  science  gateways.   ! NSF  Award  Number  ACI-­‐1547611   References:   Gesing,  S.,  Wilkins-­‐Diehr,  N.,  Dahan,  M.,  Lawrence,  K.,  Zentner,  M.,  Pierce,  M.,  Hayden,  L.B.,  and  Marru,  S.  “Science   Gateways:  The  Long  Road  to  the  Birth  of  an  Ins7tute”.  Proc.  of  HICSS-­‐50  (50th  Hawaii  Interna7ona  Conference  on   System  Sciences),  4-­‐7  January  2017,  Hilton  Waikoloa,  HI,  USA.       Lawrence,  KA,  Zentner,  M,  Wilkins-­‐Diehr,  N,  Wernert,  JA,  Pierce,  M,  Marru,  S,  Michael,  S.  “Science  gateways  today   and  tomorrow:  Posi7ve  perspec7ves  of  nearly  5,000  members  of  the  research  community,”  Concurrency  and   Computa7on:  Prac7ce  and  Experience,  2015.     Proposed Service % Interest Evaluation, impact analysis, website analytics 72% Adapting technologies 67% Web/visual/graphic design 67% Choosing technologies 66% Usability Services 66% Visualization 65% Developing open-source software 64% Support for education 64% Community engagement mechanisms 62% Keeping your project running 62% Legal perspectives 61% Managing data 60% Computational resources 59% Mobile technology 59% Database structure, optimization, and query expertise 59% Data mining and analysis 58% Cybersecurity consultation 57% Website construction 57% Software engineering process consultation 53% Source code review and/or audit 51% High-bandwidth networks 45% Scientific instruments or data streams 44% Management aspects of a project 38% High-­‐level  design  of  the  scien7fic  somware  collabora7ve   Conceptual  overview  on  the  five  service  areas  of  the  SGCI