UCT eResearch

Jason van Rooyen, PhD

eResearch Analyst

www.eresearch.uct.ac.za

Advanced computing and IT for accelerating and transforming research

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Research Week14 April 2015UCT eResearch

eResearch?

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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:

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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

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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

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Data Deluge: some perspective

UCT eResearch

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

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.”

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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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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

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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/

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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

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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

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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

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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

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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

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We look forward to hearing from you

Email: eresearch-support@uct.ac.za

Website: www.eresearch.uct.ac.za

Libraries Research Week14 April 2015eResearch University of Cape

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UCT eResearch

UCT eResearch