eresearch uctresearchcommonsblog.uct.ac.za/wp-content/uploads/... · swift capability to establish...

eResearch

UCT

Jason van Rooyen, PhD

eResearch Analyst

www.eresearch.uct.ac.za

Libraries Research Week

14 April 2015 eResearch University of Cape

Town

Research Week

14 April 2015 eResearch UCT

Libraries Research Week

14 April 2015 eResearch University of Cape

Town

Research Week

14 April 2015 eResearch UCT

http://www.canberra.edu.au/research/ucresearch/e-research

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

• It is the transformation of research:

Libraries Research Week

14 April 2015 eResearch University of Cape

Town

Research Week

14 April 2015 eResearch UCT

Image courtesy of Dr. Govinda Poudel, with permission.

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 Week

14 April 2015 eResearch University of Cape

Town

Research Week

14 April 2015 eResearch UCT

Comprehend Virtual Lab

Research Data Commons

Communicate

Collaborate

eResearch

version of a microscope

Conventional microscope

Compute

Collect

Libraries Research Week

14 April 2015 eResearch University of Cape

Town

Research Week

14 April 2015 eResearch UCT

Transforming Research Methodologies

Cave

HPC

MRI

• 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 Week

14 April 2015 eResearch University of Cape

Town

Research Week

14 April 2015 eResearch UCT

Data Deluge: some perspective

Data Deluge

Libraries Research Week

14 April 2015 eResearch University of Cape

Town

Research Week

14 April 2015 eResearch UCT

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

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

Libraries Research Week

14 April 2015 eResearch University of Cape

Town

Research Week

14 April 2015 eResearch UCT

Monash’s Dr. Shena McGowan (under the direction of Prof. James Whisstock)

PlyC

http://www.quantumdiaries.org/

• 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)

Libraries Research Week

14 April 2015 eResearch University of Cape

Town

Research Week

14 April 2015 eResearch UCT

Advancing comprehension and collaboration

• Data sharing initiatives

• Open data policies

“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 Week

14 April 2015 eResearch University of Cape

Town

Research Week

14 April 2015 eResearch UCT

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 Week

14 April 2015 eResearch University of Cape

Town

Research Week

14 April 2015 eResearch UCT

• 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

Libraries Research Week

14 April 2015 eResearch University of Cape

Town

Research Week

14 April 2015 eResearch UCT

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.

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 Week

14 April 2015 eResearch University of Cape

Town

Research Week

14 April 2015 eResearch UCT

Create a world-class environment for 21st century discovery.

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

Libraries Research Week

14 April 2015 eResearch University of Cape

Town

Research Week

14 April 2015 eResearch UCT

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.

Libraries Research Week

14 April 2015 eResearch University of Cape

Town

Research Week

14 April 2015 eResearch UCT

Libraries Research Week

14 April 2015 eResearch University of Cape

Town

Research Week

14 April 2015 eResearch UCT

a partner and broker

• 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 Week

14 April 2015 eResearch University of Cape

Town

Research Week

14 April 2015 eResearch UCT

Square Kilometre Array Data

www.skatelescope.org

• 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

Libraries Research Week

14 April 2015 eResearch University of Cape

Town

Research Week

14 April 2015 eResearch UCT

CERN and Vidyo Conferencing

• 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

Libraries Research Week

14 April 2015 eResearch University of Cape

Town

Research Week

14 April 2015 eResearch UCT

High Performance Computing

Facility Support: Olympus Virtual Microscope

The old: slide boxes

The new: Olympus VS120 Microscope

Libraries Research Week

14 April 2015 eResearch University of Cape

Town

Research Week

14 April 2015 eResearch UCT

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

Libraries Research Week

14 April 2015 eResearch University of Cape

Town

Research Week

14 April 2015 eResearch UCT

Facility Support: Centre for Imaging and Analysis Provides the instrumental resources and expertise for structural analysis in all disciplines.

acquisition processing interpretation dissemination

Workflow:

Facility Support:

Libraries Research Week

14 April 2015 eResearch University of Cape

Town

Research Week

14 April 2015 eResearch UCT

• 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

Libraries Research Week

14 April 2015 eResearch University of Cape

Town

Research Week

14 April 2015 eResearch UCT

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.

Libraries Research Week

14 April 2015 eResearch University of Cape

Town

Research Week

14 April 2015 eResearch UCT

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

The Team

Anthony Beitz (Dir.)

Timothy Carr

Andrew Lewis

Jason van Rooyen

Heine de Jager

Ashley Rustin

Anthony

Chris Mtshengu

Natalie Simon

Libraries Research Week

14 April 2015 eResearch University of Cape

Town

Research Week

14 April 2015 eResearch UCT

We look forward to hearing from you

Email: eresearch-support@uct.ac.za

Website: www.eresearch.uct.ac.za

Libraries Research Week

14 April 2015 eResearch University of Cape

Town

Research Week

14 April 2015 eResearch UCT