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eResearch@UCT
- 1. Anthony Beitz Interim Director UCT eResearch Centre www.eresearch.uct.ac.za Overview of eResearch
- 2. What is eResearch? • eResearch is 21st century discovery through the application of advanced computing and IT • It is the transformation of research:
- 3. From this:
- 4. To this: image courtesy of Dr. Govinda Poudel, with permission.
- 5. And the acceleration of research: From this:
- 6. 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!
- 7. Emergence of Research Methodologies
- 8. “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.”
- 9. MRI Scanner Collect GPU Cluster Compute CAVE2TM Comprehend eResearch version of a microscope
- 10. Research Data Commons Communicate Virtual Lab Collaborate eResearch version of a microscopeConventional microscope Compute Collect Comprehend
- 11. 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
- 12. 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 Array 0.3-1.5 EB / year Laboratory based www.skatelescope.org www.fei.com Large facilities
- 13. Data Storage and Management: The story of PlyC • Drug resistant bacteria a growing concern • Bacteriophages viruses that infect and kill bacteria • Potential of PlyC
- 14. 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
- 15. 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
- 16. eResearch at UCT
- 17. 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
- 18. eResearch at UCT: the vision Create a world-class environment for 21st century discovery.
- 19. 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
- 20. 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
- 21. Role of eResearch at UCT
- 22. UCT eResearch Services • Specialist advice • Capabilities and infrastructure to: Collect – capture, store & manage big and small research data Compute – HPC skills & facilities for modelling, simulation & data processing Comprehend – immersive visualisation Collaborate – virtual labs & collaborative research platforms Communicate – disseminate & promote discovery of research outcomes & artefacts Customise – resources for planning & building research hardware & software • Grant assistance - planning & costing IT personnel, hardware and software • Seminars and outreach
- 23. The eResearch Centre is a: Partner Broker Service Provider
- 24. 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
- 25. Facility Support: Olympus Virtual Microscope The old: slide boxes The new: Olympus VS120 Microscope
- 26. 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
- 27. Other examples of facility support engagement Centre for Imaging Analysis Clinical Research Centre
- 28. 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
- 29. 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
- 30. 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/
- 31. 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
- 32. The Team Timothy Carr Andrew Lewis Jason van Rooyen Heine de Jager Ashley Rustin Anthony Chris Mtshengu Natalie Simon
- 33. We look forward to hearing from you UCT eResearch Centre Email: eresearch-support@uct.ac.za Website: www.eresearch.uct.ac.za
Notas do Editor
- 1
- We are seeing a change in the way that research is done as information and communication technologies become the lifeblood of research. Transformation of research from one-dimensional, black and white X-ray
- We are seeing a change in the way that research is done as information and communication technologies become the lifeblood of research. Transformation of research from one-dimensional, black and white X-ray
- We are seeing a change in the way that research is done as information and communication technologies become the lifeblood of research. Transformation of research from one-dimensional, black and white X-ray, to 3D multidimensional visualisation/imaging
- We are seeing a change in the way that research is done as information and communication technologies become the lifeblood of research. Transformation of research from one-dimensional, black and white X-ray, to 3D multidimensional visualisation/imaging
- We are seeing a change in the way that research is done as information and communication technologies become the lifeblood of research. Transformation of research from one-dimensional, black and white X-ray, to 3D multidimensional visualisation/imaging
- We are seeing a change in the way that research is done as information and communication technologies become the lifeblood of research. Transformation of research from one-dimensional, black and white X-ray, to 3D multidimensional visualisation/imaging
- We are seeing a change in the way that research is done as information and communication technologies become the lifeblood of research. Transformation of research from one-dimensional, black and white X-ray, to 3D multidimensional visualisation/imaging
- Data deluge: Several large-scale multi-national facilities are challenging the way we do science. The rates of data generation are increasingly massively with LHC requiring 15 PB storage a year. It’s important to realise that these are not acquisition rates but storage rates after post-processing. At the top of the chart is the SKA which promises to challenge our current technologies which will need to catch up in order to process exabytes of data a day and store 1.5 EB per year. The paradigm shift is not limited to massive scale infrastructure installations and similar trends are tacking place at the laboratory scale. Desktop sequencing machines and fast-read-out camera can be purchased from suppliers today which generate in excess of TBs per day. IT departments have traditionally never had the capacity to support such endeavors and will have to work hand-in-hand with researchers to provide the capacity they need.
- You may not necessarily get the best out of your data. Bacteriophages: From 1919 these were investigated as a way to treat bacterial infections but after the 1940’s with the discovery of antibiotics this research was abandoned We are seeing a growing rate of drug resistance in bacteria, with fears that antibiotics may be rendered ineffective Spotlight back on bacteriphages, particularly PlyC, known to be very effective in treating the bacteria Streptococcus – causes throat infections, heart disease, pneumonia, toxic shock syndrome and tropical kind infections
- In order to better understand PlyC, Monash’s Dr. Shena McGowan (under the direction of Prof. James Whisstock) grew crystals from a PlyC solution, placed them in the Australian synchrotron’s protein crystallography beamline and then bombarded them with x-ray radiation. Each crystal’s dataset of diffraction images was then transferred to MyTardis (a bioscience research data repository) and archived. Various crystallography techniques and computer programs were used in an attempt to resolve PlyC’s structure. Unfortunately, these were unsuccessful. In 2010, a new approach enabled Dr. McGowan and Assoc. Prof. Buckle to resolve the structure from the datasets archived in MyTardis. Resolution of the structure was also assisted by Monash’s high performance computing cluster, which expedited computations. The structure was published in the Proceedings of the National Academy of Sciences (USA) in July of 2012 and the raw data and images were made available through MyTardis.
- This virtual environment allows the viewer to not only see but interact with their research data in 3D It combines expertise from high-performance computing, computer graphics and networks This kind if visualisation allows researcher to walk on Mars, see the brain (as in image) or explore ancient structures as they were hundreds of years ago.
- eResearch at UCT probably really began in 2009 when Sakkie Janse van Rensburg joined UCT as Executive Director of ICTS He set about to ensure adequate support for researchers at UCT Built relationships with universities in Australia who were leading the way in terms of eResearch, and slowly but surely began to build up eResearch capacity at UCT
- Partner: we partner with key research groups to help custom design their specialised IT requirements Broker: we connect researchers to the necessary hardware, software and facilities Service Provider: HPC, storage. We provide a free service to all researchers up to a point.
- Key research groups – tend to align with national or institutional research agenda Partner from the beginning to develop solutions For SKA: we provide storage and compute The SKA radio telescope dish array is coming to South Africa toward the end of this decade. When completed it will consist of thousands of radio antennas spread out over thousands of kilometres. The SKA will create 3D maps of the universe 10,000 times faster than any imaging radio telescope array ever built.
- We also engage with facilities which provide technological hubs for researchers Departments across the university are acquiring technology that is changing the face of research, teaching and collaboration For instance: In 2014 the Dept of Clinical Laboratory Services acquired a state of the art Olympus VS120 virtual microscopy system. This effectively digitises old glass slides - so these slide images can now be accessed anywhere with just an internet connection The Olympus VS120 to be used for research, teaching, by pathologists and Groote Schuur
- The Olympus VS120 system features a slide loader that can process up to 100 slides at a time. The images processed by the microscope are of an exceptionally high resolution, which means the server has to handle large file sizes. A single image can be as big as seven gigabytes.
- Centre for imaging analysis: The University of Cape Town plans to establish a world-class visualisation and analysis centre, built largely around electron microscopy. The eResearch team worked with UCT’s Clinical Research Centre to establish one of the few ‘first in human’ clinical trials on African soil.
- Very little of CERN’s research is done on site in Geneva Each project can contain a few thousand researchers who communicate via video conferences that can contain up to 100 people in one conference eResearch put CERN researchers in touch with the Tertiary Education and Research Network of South Africa (TENET) and connected with CERN itself to set up the required infrastructure for effective collaboration This in the form of the Vidyo Router: the engine that enables these advanced video calls This software is now used as not only by all CERN collaborators in SA, but also will be rolled out to other massive projects such as the SKA
- Talk about grants – advise researchers to come to us early to work out their IT requirements and write it into their grants
- At present these services sit within the eResearch Centre – this probably won’t always be the case But for now these services are available to all researchers, up to a point. Limited resources so researchers get so much
- At present these services sit within the eResearch Centre – this probably won’t always be the case But for now these services are available to all researchers, up to a point. Limited resources so researchers get so much