Anthony BeitzInterim Director

UCT eResearch Centrewww.eresearch.uct.ac.za

Overview of

eResearch

What is eResearch?

• eResearch is 21st century discovery through the application of advanced computing and IT

• It is the transformation of research:

From this:

To this:

image courtesy of Dr. Govinda Poudel, with permission.

And the acceleration of research:

From this:

To this:

Data: N. Georgiou-Karistianis Visualisation: Y. Benovitski

Brains of ~100 study subjects (controls, pre-symptomatic and Huntington’s Disease sufferers) visualised at once!

Emergence of Research Methodologies

“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.”

MRI Scanner

Collect

GPU Cluster

Compute

CAVE2TM

Comprehend

eResearch version of a microscope

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Research Data Commons

Communicate

Virtual Lab

Collaborate

eResearch version of a microscopeConventional microscope

Compute

Collect

Comprehend

Dat

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m –

Col

lect

Dat

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m –

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Research Data Deluge: Some Perspective

• 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

Research Data Deluge

Data generation rates:

• Next Generation Sequencing platforms 4 TB/week/machine

• Direct electron detectors > 1 TB / day (equivalent to synchrotron beamlines)

• Large Hadron Collider 15 PB/ year

• Square Kilometer Array0.3-1.5 EB / year

Laboratory based

www.skatelescope.org www.fei.com

Large facilities

Data Storage and Management: The story of PlyC

• Drug resistant bacteria a growing concern

• Bacteriophages viruses that infect and kill bacteria

• Potential of PlyC

Data Storage and Management: The story of PlyC

• First round Monash researchers had no luck unraveling PlyC structure

• But MyTardis, the Monash bioscieence research data repository allowed them to store this data in way that made it accessible for future use.

• In 2010 new technological advancements emerged. Researchers could easily find the data and solve the PlyC structure

Accelerating Research: Visualisation

• A next generation hybrid 2D and 3D virtual reality environment

• Renders terascale datasets with unparalleled quality for comprehending and analysing big data

Monash Cave2 Image courtesy Electronic Visualisation Laboratory & Dept of Psychiatry, UIC, with permission. Photo by Philip Chan,

Monash University

eResearch at UCT

eResearch at UCT: The History

• 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

eResearch at UCT: the vision

Create a world-class environment for 21st century

discovery.

How?

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

eResearch Centre

Research Office• Advocacy• Collaboration

ICTS• Data Storage• Compute• Networks

DVC-Research• Leadership• Governance• Strategy• Resourcing

The Library• Research visibility &

discovery• Research data

managementFaculties• Various

capabilities

Researchers

Core capability partnerships

Capability delivery

Role of eResearch at UCT

UCT eResearch Services• Specialist advice• Capabilities and infrastructure to:

Collect – capture, store & manage big and small research dataCompute – HPC skills & facilities for modelling, simulation & data

processingComprehend – immersive visualisationCollaborate – virtual labs & collaborative research platformsCommunicate – disseminate & promote discovery of research

outcomes & artefactsCustomise – resources for planning & building research hardware

& software

• Grant assistance - planning & costing IT personnel, hardware and software

• Seminars and outreach

The eResearch Centre is a:

Partner

Broker

Service Provider

Partner• Square Kilometre

Array (SKA)• 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?

Image: SKA Photo Library

Facility Support: Olympus Virtual Microscope

The old: slide boxes The new: Olympus VS120 Microscope

Facility Support: Olympus Virtual Microscope

eResearch:• Worked with the

department to set up the servers and the database

• Configured the system for various access scenarios including student, departmental and public access

Other examples of facility support engagement

Centre for Imaging Analysis Clinical Research Centre

Broker• CERN and Vidyo Conferencing

• 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

Service Provider• High Performance

Computing

• Storage

• 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

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 eResearch Centre to estimate required funding and to incorporate it into a grant

Imag: permabit.com/data-affordability-gap/

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

UCT eResearch CentreAdvanced computing and IT for accelerating and transforming research

Collect Compute Comprehend

Collaborate Communicate Customise

The Team Timothy Carr

Andrew Lewis

Jason van Rooyen

Heine de Jager

Ashley Rustin

Anthony

Chris Mtshengu

Natalie Simon

We look forward to hearing from you

UCT eResearch CentreEmail: eresearch-support@uct.ac.za

Website: www.eresearch.uct.ac.za