eResearch UCTresearchcommonsblog.uct.ac.za/wp-content/uploads/... · Swift capability to establish...
Transcript of eResearch UCTresearchcommonsblog.uct.ac.za/wp-content/uploads/... · Swift capability to establish...
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eResearch
UCT
Jason van Rooyen, PhD
eResearch Analyst
www.eresearch.uct.ac.za
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Libraries Research Week
14 April 2015 eResearch University of Cape
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Research Week
14 April 2015 eResearch UCT
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Libraries Research Week
14 April 2015 eResearch University of Cape
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Research Week
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http://www.canberra.edu.au/research/ucresearch/e-research
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• eResearch is 21st century discovery through the application of advanced computing and IT
• It is the transformation of research:
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Image courtesy of Dr. Govinda Poudel, with permission.
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IMPLICATIONS
Storage, data management and tools
Pace and scale increasing
• Technology is accelerating the pace and scale of research
• Large-scale data requires more structured approach data management approach
KEY CHANGES
Expert guidance on leveraging new approaches
New tools and methodologies
• New and more powerful instruments
• Digital recognition of text, speech and imagery
• Crowdsourcing and citizen science
Swift capability to establish and support collaborations
Internationalisation
• Research funding is increasingly based on strong international collaborations
• Internationalisation is introducing new complexities in health, ecology and economy (epidemics, climate change, Global Fin. Crisis)
Research Acceleration & Transformation
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Comprehend Virtual Lab
Research Data Commons
Communicate
Collaborate
eResearch
version of a microscope
Conventional microscope
Compute
Collect
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Transforming Research Methodologies
Cave
HPC
MRI
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• 2 gigabytes = twenty metres of bookshelves
• 2 terabytes = an entire academic research library
• 2 petabytes = the contents of all US academic research libraries
• 5 exabytes = all words ever spoken by human beings
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Data Deluge: some perspective
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Data Deluge
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Data generation rates
(post- capture processing) :
• Square Kilometer Array 0.3-1.5 EB / year
• Large Hadron Collider 15 PB/ year
• Direct electron detectors > 1 TB / day
(equivalent to synchrotron beamlines)
• Next Generation Sequencing platforms 4 TB/week/machine
Large facilities
Laboratory based
www.skatelescope.org
http://www.fei.com
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Data Storage and Management:
• Unsuccessful structure solution of PlyC structure
• But data stored in MyTardis, the Monash bioscieence research data repository
• New technological advancements in 2010 led to a solution of the PlyC structure from the data
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Monash’s Dr. Shena McGowan (under the direction of Prof. James Whisstock)
PlyC
http://www.quantumdiaries.org/
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• A next generation hybrid 2D and 3D virtual reality environment for interrogating and sharing data
Monash Cave2 Image courtesy Electronic
Visualisation Laboratory & Dept of Psychiatry, UIC (Philip Chan)
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Advancing comprehension and collaboration
• Data sharing initiatives
• Open data policies
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“Scholarly practices across an astounding wide range of disciplines have become profoundly and irrevocably changed by the application of advanced information technology. This collection of new and emergent scholarly practices was first widely recognized in the science and engineering disciplines….humanities continue to showcase some of the most creative and transformative examples of the use of information technology to create new scholarship.”
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Enhancing research outcomes through the use of
information & communication technology, data
management and key partnerships
Supporting a more research-intensive UCT:
New research strategy (2015-2025) • Resourcing research • Supporting research • Internationalising research • Increasing the visibility of our research • Enhancing interdisciplinary and transdisciplinary research (IDTD) • Supporting engaged scholarship • Bringing research into teaching
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• eResearch at UCT began with ICTS executive director Sakkie Janse van Rensburg
• His goal at UCT was to ensure researchers had the IT support they require to stay ahead of the game
• UCT eResearch Centre established March 2014
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The history
• Joint initiative between the Office of the Deputy Vice Chancellor for Research and Internationalisation, Information and Communication Technology Services, the Libraries, the Research Office.
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How?
eResearch UCT partners with research groups to accelerate and transform research, connecting them to the most appropriate hardware, software and services to sustain that capability
Collect Compute Comprehend
Collaborate Communicate Customise
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Create a world-class environment for 21st century discovery.
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eResearch Centre
Research Office
• Advocacy
• Collaboration
ICTS
• Data Storage
• Compute
• Networks
DVC-Research
• Leadership
• Governance
• Strategy
• Resourcing
The Library
• Research visibility & discovery
• Research data management
Faculties
• Various capabilities
Researchers
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As a partner and broker eResearch UCT will connect researchers with world-class expertise (local or external) and facilities in: • The collection and management of research data;
• modeling, simulation and data processing through HPC
• comprehension of big data through visualisation and data science
techniques
• dissemination of research outcomes (including data and workflows)
• promotion of collaborative research through virtual labs and cloud resources;
• development of customised research software, hardware and services.
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a partner and broker
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• One of the largest scientific projects ever undertaken to answer questions such as:
• What is dark energy?
• Was Einstein right about gravity?
• Is there life elsewhere in the universe?
• eResearch is supporting storage and compute
• Exascale arriving soon…
Image: SKA Photo Library
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Square Kilometre Array Data
www.skatelescope.org
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• CERN is made up of a massive globally dispersed community of researchers
• eResearch connected CERN collaborators with national providers to set up necessary software infrastructure required
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CERN and Vidyo Conferencing
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• Key research projects e.g. SKA and space geodesy
• Use of HPC facilities have tripled in the past year
• 300 researchers across campus assisted by HPC
• 33 citations (and counting)
Image: Stephen Williams Photography
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High Performance Computing
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Facility Support: Olympus Virtual Microscope
The old: slide boxes
The new: Olympus VS120 Microscope
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eResearch:
• Worked with the CLS department to set up the servers and the database
• Configured the system for various access scenarios including student, departmental and public access
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Facility Support: Centre for Imaging and Analysis Provides the instrumental resources and expertise for structural analysis in all disciplines.
acquisition processing interpretation dissemination
Workflow:
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Facility Support:
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• Nikon fluorescent microscope for live cell imaging
• eResearch supported storage, remote data analysis and collaboration
Clinical Research Centre Molecular and Cell Biology Tissue Culture Facility
• Clinical, laboratory and data management systems needed to pass an FDA or EMA audit.
• Software and computational requirements met by eResearch
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Human Heredity and Health in Africa
• First Pan African Bioinformatics Network in Africa: H3ABioNet & H3Africa Consortium
• UCT eResearch Centre, in collaboration with Information and Communication Technology Services (ICTS) and the Computational Biology Group, will be developing a data storage archive solution
• The data will include genomic data and access will be controlled according to internationally accepted standards.
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Monash eResearch Centre
• eResearch is 21st century research discovery through the application of advanced computing and IT
• The UCT eResearch Centre partners with research groups to accelerate and transform research, connecting them to the most appropriate hardware, software and services to sustain that capability
Collect Compute Comprehend
Collaborate Communicate Customise
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The Team
Anthony Beitz (Dir.)
Timothy Carr
Andrew Lewis
Jason van Rooyen
Heine de Jager
Ashley Rustin
Anthony
Chris Mtshengu
Natalie Simon
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We look forward to hearing from you
Email: [email protected]
Website: www.eresearch.uct.ac.za
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