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UCT eResearch
Jason van Rooyen, PhD
eResearch Analyst
www.eresearch.uct.ac.za
Advanced computing and IT for accelerating and transforming research
Libraries Research Week14 April 2015eResearch University of Cape
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Research Week14 April 2015UCT eResearch
eResearch?
Libraries Research Week14 April 2015eResearch University of Cape
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Research Week14 April 2015
http://www.canberra.edu.au/research/ucresearch/e-research
UCT eResearch
• eResearch is 21st century discovery through the application of advanced computing and IT
• It is the transformation of research:
Libraries Research Week14 April 2015eResearch University of Cape
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Research Week14 April 2015
Image courtesy of Dr. Govinda Poudel, with permission.
UCT eResearch
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
Libraries Research Week14 April 2015eResearch University of Cape
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Research Week14 April 2015UCT eResearch
ComprehendVirtual 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
UCT eResearch
• 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
Libraries Research Week14 April 2015eResearch University of Cape
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Data Deluge: some perspective
UCT eResearch
Data Deluge
Libraries Research Week14 April 2015eResearch University of Cape
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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
UCT eResearch
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/
UCT eResearch
• 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
UCT eResearch
“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.”
Libraries Research Week14 April 2015eResearch University of Cape
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Research Week14 April 2015UCT eResearch
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
Libraries Research Week14 April 2015eResearch University of Cape
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Research Week14 April 2015UCT eResearch
Libraries Research Week14 April 2015eResearch University of Cape
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eResearch @ UCT
UCT eResearch
• 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 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.
UCT eResearch
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
Libraries Research Week14 April 2015eResearch University of Cape
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Create a world-class environment for 21st century discovery.
UCT eResearch
UCT eResearch
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
Core capability partnerships
Capability delivery
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As a partner and broker eResearch UCT provides:
• Specialist advice
• Capabilities and infrastructure to:o Collect – capture, store & manage big and small research datao Compute – HPC skills & facilities for modelling, simulation & data
processingo Comprehend – immersive visualisationo Collaborate – virtual labs & collaborative research platformso Communicate – disseminate & promote discovery of research
outcomes & artefactso Customise – resources for planning & building research hardware &
software
• Planning assistance - planning & costing IT personnel, hardware and software
• Seminars and outreach
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Resource Limits
• Requirements for advanced ICT research infrastructure are huge and growing
• Advice and fundamental infrastructure are freely available
• For needs beyond fundamental infrastructure, researchers need to engage early with the UCT eResearch to estimate required funding and to incorporate it into a grant
Imag: permabit.com/data-affordability-gap/
Libraries Research Week14 April 2015eResearch University of Cape
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Research Week14 April 2015UCT eResearch
Libraries Research Week14 April 2015eResearch University of Cape
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Role of eResearch at UCTa partner and broker
UCT eResearch
• 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
Libraries Research Week14 April 2015eResearch University of Cape
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Square Kilometre Array Data
www.skatelescope.org
UCT eResearch
• 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
UCT eResearch
• 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
UCT eResearch
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
UCT eResearch
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Facility Support: Centre for Imaging and AnalysisProvides the instrumental resources and expertise for structural analysis in all disciplines.
acquisition processing interpretation dissemination
Workflow:
UCT eResearch
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
UCT eResearch
Libraries Research Week14 April 2015eResearch University of Cape
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Human Heredity and Health in Africa
• First Pan African Bioinformatics Network in Africa: H3ABioNet & H3Africa Consortium
• UCT eResearch, 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.
UCT eResearch
Libraries Research Week14 April 2015eResearch University of Cape
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Advanced Training
• UCT eResearch is helping to fill the skills gap in data intensive research fields through locally run training programmes.
• More than 80 students participated in the Software Carpentry workshop organized during eResearch Africa 2014.
• 24 graduates of the “Introduction to Linux for HPC” training course and 18 graduates of the advanced programme.
UCT eResearch
Libraries Research Week14 April 2015eResearch University of Cape
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…in summary
UCT eResearch
Monash eResearch Centre• eResearch is 21st century research discovery through the application of advanced
computing and IT
• UCT eResearch partners with research groups to accelerate and transform research, connecting them to the most appropriate hardware, software and services to sustain that capability
UCT eResearchAdvanced computing and IT for accelerating and transforming research
Collect Compute Comprehend
Collaborate Communicate Customise
The Team
Anthony Beitz (Dir.)
Timothy Carr
Andrew Lewis
Jason van Rooyen
Heine de Jager
Ashley Rustin
Anthony
Chris Mtshengu
Natalie Simon
Libraries Research Week14 April 2015eResearch University of Cape
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Research Week14 April 2015UCT eResearch
We look forward to hearing from you
Email: [email protected]
Website: www.eresearch.uct.ac.za
Libraries Research Week14 April 2015eResearch University of Cape
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Research Week14 April 2015
UCT eResearch
UCT eResearch