1. Award Number
ACI-1547611
Nancy Wilkins-Diehr, San Diego Supercomputer Center, UCSD
Katherine Lawrence, University of Michigan School of Information
How the S2I2-funded
Science Gateways Community Institute
supports scientific discovery and
your directorate’s research
2. What is a science gateway?
2
science gateway /sī′ əәns gāt′ wā′/ n.
1. an online community space for science
and engineering research and
education.
2. a Web-based resource for
accessing data, software,
computing services, and
equipment specific to the
needs of a science or
engineering discipline.
3. Gateways serve many purposes
• Analysis capabilities using up-to-date software optimized for supercomputers
(Neuroscience gateway, SEAgrid, CIPRES)
• Access to instruments and analysis of instrument data (Ultrascan, Slooh)
• Access to sensor data (OOI, NEON)
• Opportunities for citizen scientists willing to help (Foldit)
• A tool to conduct more advanced inquiries, including synthesis from multiple
sources
• A pathway for educators and students to use advanced cyberinfrastructure
tools, regardless of institutional affiliation
Most importantly, gateways allow researchers to “stand on the
shoulders of others” and concentrate on the complexity of their
own work.
We will go quickly through some examples.
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4. Cyberinfrastructure for Phylogenetic Research
(CIPRES)
PI Mark Miller, SDSC, www.phylo.org
• 210 US research universities
• From top-tier research institutions to
non-PhD granting colleges
• 3 K-12 school systems
• 43 non-governmental organizations
• Museums including the Smithsonian
Institution, the American Museum of
Natural History, and the Field Museum
• Botanical gardens, (e.g. Chicago,
Rancho Santa Ana, and New York)
• Institutes (e.g. JCVI and Broad)
• 10 US governmental agencies
• Including NIH, USDA, NOAA, US Forest
Service
• Curriculum delivery (76)
• 2000+ publications since 2010
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5. CIPRES’ reach is deep and wide
Nature, Feb 2016
5
Massachusetts State Science Fair,
July 2012
6. I-TASSER gateway
leads to rapid
influx of XSEDE
users in Q4 2016
PI Yang Zhang, U Michigan
6
I-TASSER “broke” my XSEDE user figure :-)
— David Hart, NCAR
Headline News:
SDSC’s ‘Comet’
Supercomputer Surpasses
‘10,000 Users’ Milestone
7. • Powerful simulators and data analysis
tools widely used by neuroscientists
• > 4.5 million core hours on XSEDE
supercomputers to > 300 neuroscientists
since 2013
• Strong contributor to BRAIN initiative
• Catalyzes and democratizes
computational neuroscience research
• Leading neuroscientists and researchers
plus students from underrepresented minority
institutions
• Tutorials at Society for Neuroscience annual
meetings
• Next phase of NSG recently funded by
NSF and UK Biotechnology and Biological
Sciences Research Council (BBSRC) Simulation
run
on
the
NSG
for
a
55,000
mouse
cell
column
using
30
nodes
(720
cores)
for
25
hours.
Research
and
Image
credit
Mitelut,
Gratiy,
Spacek,
Anastassiou and
the
Allen
Institute
for
Brain
Science
Courtesy: Amit Majumdar
Awards: US NSF 1146949, 1146830, 1458840, 1458495;;
UK BBSRC BB/N005236/1
Neuroscience Gateway (NSG)
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Amit Majumdar, Subha Sivagnanam, Maryann Martone,
Kenneth Yoshimoto, UCSD
Ted Carnevale, Yale University
Angus Silver, Padraig Gleeson, University College London
www.ngsportal.org
8. Some NSF programs even specify the use of gateways.
This is the right direction to go! Gateways are cost-effective infrastructure.
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9. SEAGrid: 10 Years in Service
PI Sudhakar Pamidighantam, IU
• Over 5M XSEDE CPU hours
used in 2016
• 40 Publications since 2015
• 689 Registered Users,
~100 Active
• Web and desktop clients for pre-
and post-processing
• Dynamic information services
• RSS, HPC load, queue prediction
• Workflow support
• Checkpoint/restart, HTC, coupled
applications
• Community account and individual use
• XSEDE, IU systems, Blue Waters,
Raven (Cardiff University)
• Consulting – add requested
capabilities, data archive
• Nek5000
• Gamess
• Molcas
• Gaussian
• CP2K
• Amber
• Quantum Espresso
• NWChem
• Charmm
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• Lammps
• DFTB+
• Tinker
• DDScat
• Abaqus
• Abinit
• PSI4
• PolyUMod
10. Gateway to instruments: Ultrascan
Analytical Ultracentrifugation Data Analysis
• Ultracentrifugation used for
characterization of
macromolecules in the solution
phase
• New multi-wavelength
instruments producing 100’s of
times more data
• Unprecedented accuracy
• Enables new discoveries
• High-resolution analysis
requires supercomputers
• Characterize increasingly
complex mixtures and
interactions between molecules
Courtesy: Borries Demeler 10
PI Borries Demeler, UT Health Sciences Center
San Antonio, uslims.uthscsa.edu
11. The UltraScan science gateway
enables experimental scientists to
analyze data on supercomputers.
Desktop analysis
tools are integrated
with the Web portal.
Launch
analysis and
monitor
through a
browser
UltraScan uses
Apache Airavata for
managing analyses on
HPCs worldwide.
11Courtesy: Borries Demeler
12. Gateways to instruments: Slooh
Members control telescopes and share images
• Over
30
observatories
around
the
world
• 4M
photos
taken
since
2003
• Increases
public
support
for
investment
in
these
facilities
• People
gather
virtually
around
live
telescopes
to
see
space
for
themselves
and
share
perspectives
• “In
seconds
my
computer
screen
was
transformed
into
a
live
telescopic
view”
• Citizen
scientists
and
professional
astronomers
in
70
countries
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14. Citizen Science: Foldit
Crowd sourcing protein folding
• Collaboration between
U. of Washington Center
for Game Science and
UW Dept. of Biochemistry
14
Source: Huffington Post
15. Despite many successes,
we observed challenges in developing
and sustaining gateways
• Two NSF awards allowed us to study the problem and
solutions
• 2009 EAGER
• 2012 S2I2 conceptualization-phase grant
• In 2014, we sent a survey to 29,000 NSF PIs and
academic CIOs and CTOs
• Nearly 5,000 responded
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16. Responses came from across domains
16
2%
9%
10%
14%
16%
16%
16%
22%
30%
0% 10% 20% 30% 40%
Arts
and
Humanities
Professional
Disciplines
Social
Sciences
Environmental
Sciences
Engineering
Computer
and
Information
Sciences
No
Response
Life
Sciences
Physical
and
Mathematical
Sciences
Primary areas of current domain expertise. Respondents could select all that apply;;
84% (4,141 of 4,957) responded, generating 6,689 total responses (mean=1.6 domains per respondent).
17. Specialized Resources Percent
Data collections 75%
Data analysis tools, including visualization and mining 72%
Computational tools 72%
Tools for rapidly publishing and/or finding articles and data
specific to my domain
69%
Educational tools 67%
Platforms for fostering group or community collaboration 63%
Simplified interfaces that eliminate the need to learn coding 62%
Citizen science and other public engagement resources 47%
Workflows that automate or capture tasks or processes 42%
Scientific instruments, such as telescopes, microscopes, or
sensors
39%
88% say Web-based applications important to
their work
n=4,004, or 88% of 4,538 researcher/educators.
Percentage indicates these resources are “somewhat” or
“very” important to their work.
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18. 57% played some role in creating gateways
Used for a variety of purposes
n of application types=7,805,
by 2,756 creators (out of
2,819);; mean=2.8 application
types per application creator
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19. Why is it difficult to build a science gateway?
• Building a gateway takes many types of expertise
• But projects cannot always locate or afford to hire these specialists
• Finding the right people for short-term work is also difficult
• Need for a variety of team members, like a start-up company!
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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
20. Access to
specialized
services can help
20
Proposed Service % Interest
Evaluation, impact analysis, website
analytics
72%
Adapting technologies 67%
Web/visual/graphic design 67%
Choosing technologies 66%
Usability Services 66%
Developing open-source software 64%
Support for education 64%
Keeping your project running 62%
Legal perspectives 61%
Managing data 60%
Cybersecurity consultation 57%
Website construction 57%
Software engineering process
consultation
53%
Source code review and/or audit 51%
High band-width networks 45%
Scientific instruments or data streams 44%
Management aspects of a project 38%
• Many topics well-
suited for short-term
consulting
22. Science Gateways Community Institute
Designed to help the community build gateways more effectively
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Diverse expertise
on demand
Longer-term,
hands-on support
Student
opportunities &
educator resources
Sharing
experiences &
knowledge as a
community
Software & visibility
for gateways
24. Incubator
Expertise for the gateway lifecycle
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Need specialized expertise on a part-term basis?
Want to learn gateway-building, from start to finish?
Project Management
Sustainability Planning
• Nancy Maron, creator of the ITHAKA S+R course
on Sustaining Digital Resources
Business & Strategic Planning
• The Purdue Foundry, national award-
winning entrepreneurship program
Security
• Center for Trustworthy Scientific
Cyberinfrastructure
Impact Measurement & Evaluation
• Ann Zimmerman Consulting
Community Engagement
Development Tools & Processes
Technology Planning, Open-Source Licensing &
Selection
• Indiana University Science Gateways Research
Center, initiators of Apache Airavata
Graphic & User-Interface Design
Usability
• University of Michigan & Purdue University User
Experience Programs
Creating Institutional Resources
• Notre Dame’s Center for Research Computing
• HUBzero® group at Purdue
Incubator
25. Incubator current activities
• Bootcamp 1
• Applications due 2/22/2017
• April 24–28, 2017
• Purdue Research Park, Indianapolis
• Accepting up to 10 projects to participate as a cohort
• http://sciencegateways.org/upcoming-events/
science-gateways-bootcamp/
• Consulting Engagement Requests
• http://sciencegateways.org/request-services
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Incubator
26. Need to build your gateway beyond your team’s capacity?
How We Benefit Our Clients
• Help adapt to new resources, technologies, and users
• Share our deep understanding of community
needs
• Capture and document our support of client’s
gateway
• Co-author papers or present posters
• Strengthen team’s software-engineering practices
• Give hands-on opportunities to students
Extended Developer Support
Enhancing gateways through technical help
from experienced gateway developers
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Flexibility
• Technology agnostic
• Gateways using all types of CI
• Services available for 3 to 12 months
• “Burst” support for smaller issues
• Well-defined engagements with work plans
Request EDS services:
sciencegateways.org/
request-services
Extended
Developer
Support
27. EDS current projects
Consultation Description Discipline Gateway Type/ Content
ChemCompute Helping scale up a chemistry
education gateway.
Chemistry Education
COSMIC^2 Helping extend the SDSC
Workbench framework to support
large Cryo-EM data sets.
Cellular & Molecular
Medicine
Data Analysis
CitSci.org Working with gateway team to
improve efficiency of diverse
queries required by broad range
of citizen science user
communities.
Computer
Science/Multiple
Disciplines
Platform for Creating
Citizen Science Projects
USD
Cybergateway
Developing a campus cluster-
centric gateway with University of
South Dakota.
Computer Science Science Gateway
Platform as a Service
(SciGaP)
QUBES Web interface and user
experience design for quantitative
biology education.
Quantitative Biology Education
Aquavit Using modeling and sharing for
water management.
Freshwater Systems Collaboration Portal
ENIGMA Metadata management and
sharing for bipolar disorder
experiments.
Neuroscience,
Clinical Psychiatry,
and Genetics
Data sharing
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28. Want to find software
solutions?
Have software to share?
Scientific Software Collaborative
Leveraging & promoting existing
investments in gateway technologies
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Scientific
Software
Collaborative
Extend Your Audience
• List your gateway or components
• Offer your technology
• Support gateways as SGCI Affiliate
End-to-End Solutions
• Browse existing gateways
• Identify their technologies
• Use for your research or
teaching
• Identify platforms or components and
use what you need
• Assemble & test in our “sandbox”
Sign up for our newsletter to be notified:
sciencegateways.org/connect-with-us
29. How do you find a gateway?
A marketplace that will interact with other
marketplaces to encourage reuse
Scientific
Software
Collaborative
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31. Eager to share what you know or have created?
Wish you could learn from others’ experience?
Want to grow gateway-building expertise at your institution?
Want to promote research and international exchange?
Community Engagement &
Exchange
Connecting the community through
interaction & professional development
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Community
Engagement &
Exchange
Ways to Connect
• Learn to create your own campus-based
gateway development group
• Share what you know through a guest blog,
webinar, case study, or conference
• Become a partner or affiliate
• Submit your research to our joint special issues
with international workshops
• Offer us your feedback, input, or requests
32. Community Engagement &
Exchange activities
Volunteer!
• Contribute to a guest blog
• Present at a webinar
• Be featured in a case study
Request a campus-based gateway
development group presentation
Contact help@sciencegateways.org
Participate in annual conference
• Gateways 2017: October 23–25, Ann
Arbor, Michigan
• Joint special issue journal with int’l
colleagues
• Submit tutorials, presentations,
posters in June
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Community
Engagement &
Exchange
33. Want to become a gateway builder?
Could you use gateways in your teaching or research?
Interested in supporting career
tracks for gateway developers?
Workforce Development
Nurturing the next generation of
science gateways users and developers
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Workforce
Development
Young Professionals Network
• SPOTLIGHT featuring young professionals
• Young Professional of the Year Award
includes honorarium
• Networking opportunities through virtual
seminars
• Support for professional editing for your
technical publications
• Volunteer to be a mentor
Summer Programs & Internships
• Graduate & undergraduate students
• Domain-focused & gateway-development
topics
• Work on real gateway projects
• Stipend and housing/transportation support
34. Workforce Development current
activities
• Young Professionals Network
• http://sciencegateways.org/yp
• Summer programs and
internships (including financial
support)
• Applications due 3/17/2017,
see
http://sciencegateways.org/yp-
summer-programs
• Conference tutorials — Look for
us at NOBBChE and ADMI
• Travel support to annual
Gateways conference
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Workforce
Development
35. How to engage
• Request a Letter of Collaboration to leverage
existing SGCI offerings
• 23 written to date
• Become a Partner or Affiliate to provide
complementary expertise and cross-promotion
• Write SGCI experts into proposals for
dedicated, continuing expertise
Email help@sciencegateways.org to discuss
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36. Thank you!
• Remember to connect with us
• Mailing list for news and updates:
http://sciencegateways.org/connect-with-us/
• Ready to request our services?
http://sciencegateways.org/request-services
• Have a question? help@sciencegateways.org
• @sciencegateways on Twitter
• http://sciencegateways.org/linkedin
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