Tagged: SKA-Square Millimeter Array Toggle Comment Threads | Keyboard Shortcuts

  • richardmitnick 10:37 am on September 17, 2014 Permalink | Reply
    Tags: , , , , , SKA-Square Millimeter Array   

    About SKA from CIO Australia: “Pawsey rigs up petascale supercomputer” 

    SKA Square Kilometer Array

    SKA

    cio

    09 September, 2014
    Byron Connolly (CIO)

    Cray XC30 system has more than 35,000 cores.

    The $80 million Pawsey Supercomputing Centre in Western Australia has completed the final upgrade of its ‘Magnus’ machine, which provides processing power in excess of a petaflop.

    Magnus, the largest research computer in the Southern Hemisphere, is a Cray XC30 system with more than 35,000 cores using Intel’s new Xeon’s E5-2600 v3 processors. A petaflop machine can complete one quadrillion floating point operations per second.

    cray
    The ‘Magnus’ petscale supercomputer

    It follows the launch in August 2012 of Pawsey’s terascale supercomputer, dubbed Fornax.

    The Pawsey facility is run by iVEC, a collaboration between the CSIRO, the University of Western Australia, Murdoch University, Curtin University, and Edith Cowan University.

    The CSIRO has been eyeing a petascale computer since late 2011 to crunch data for the Australian Square Kilometre Array Pathfinder (ASKAP), and Murchison Widefield Array (MWA) radio astronomy telescopes projects.

    SKA CSIRO  Pathfinder Telescope
    SKA CSIRO Pathfinder Radio Telescope

    ska murch
    SKA Murchison Widefield Array (MWA)

    Magnus will also be used by researchers in the areas of nanotechnology, high energy physics, medical research, mining and petroleum, architecture and construction, and urban planning.

    Pawsey Supercomputing Centre executive director, Dr Neil Stringfellow, said Pawsey currently runs 100 science projects being run by 500 plus users at any one time.

    Read more In pictures: Pawsey Centre

    Dr Stringfellow said researchers from Curtin University had already used the machine – running the earlier Intel Xeon E5-2600 v1 processors – to do lung simulations using a ‘moving mesh’ computational approach.

    “This helps us to understand how the lungs work – it’s the largest lung simulation in the world,” he said.

    This research will help people with asthma, for example, by creating improved aerosol medications, he said.

    Scientific researchers were so keen to get access to computing power provided by this machine that Pawsey was three times oversubscribed in the number of CPU hours that were available to give away.

    There was demand for 250 million CPU hours from researchers in mining, geoscience, bioinformatics, and ‘blue sky’ research in astronomy around galaxy formations.

    “What we have here is a world-class scientific instrument,” he said.

    Dr Stringfellow told CIO Australia that Pawsey had no plans to install a quantum computer in the near future.

    Meanwhile, the Intel Xeon E5-2600 v3 chips include platform telemetry sensors and metrics for CPU, memory and I/O usage, as well as thermal sensors that monitor airflow and outlet temperature.

    A cache monitoring feature also provides data that lets orchestration tools intelligently place and rebalance workloads, resulting in faster completion times.

    It also conducts analysis of performance anomalies due to competition for cache in a multi-tenant cloud environment where there is little visibility into what workloads consumers are running, Intel said.

    See the full article here.

    SKA Banner

    About SKA

    The Square Kilometre Array will be the world’s largest and most sensitive radio telescope. The total collecting area will be approximately one square kilometre giving 50 times the sensitivity, and 10 000 times the survey speed, of the best current-day telescopes. The SKA will be built in Southern Africa and in Australia. Thousands of receptors will extend to distances of 3 000 km from the central regions. The SKA will address fundamental unanswered questions about our Universe including how the first stars and galaxies formed after the Big Bang, how dark energy is accelerating the expansion of the Universe, the role of magnetism in the cosmos, the nature of gravity, and the search for life beyond Earth. Construction of phase one of the SKA is scheduled to start in 2016. The SKA Organisation, with its headquarters at Jodrell Bank Observatory, near Manchester, UK, was established in December 2011 as a not-for-profit company in order to formalise relationships between the international partners and centralise the leadership of the project.

    ScienceSprings relies on technology from

    MAINGEAR computers

    Lenovo
    Lenovo

    Dell
    Dell

     
  • richardmitnick 3:55 pm on September 16, 2014 Permalink | Reply
    Tags: , , , , , SKA-Square Millimeter Array   

    About SKA in Botswana: “Botswana to play part in SKA project ” 

    SKA Square Kilometer Array

    SKA

    From
    bus

    Sept. 15, 2014
    John Churu, Gaborone, Botswana

    Botswana has confirmed its participation in the Square Kilometre Array (SKA) Radio Astronomy project. This was revealed by the Minister of Infrastructure Science and Technology Johnny Swartz during the International Association of Science and Technology for Development Africa (IASTED) conference recently.

    dish

    Swartz told participants that Botswana would “host a subset of radio telescope dishes as part of a 3000-strong compliment of dishes stretching across Southern and East Africa.” According to the minister, taking part in the SKA project will enable the country participate in and contribute to frontier fundamental science research as well as enhance its scientific capacity. In addition, Swartz said this will help build related infrastructure and advance other areas such as high performance computing for the analysis of large data sets generated by telescopes. Swartz has met with the South African minister responsible for Science and Technology more than once, both in Botswana and South Africa.

    Earlier he explained that the government had introduced several programmes in an effort to create an enabling environment for research science and technology as well as innovation.

    “This shows Botswana’s commitment in prioritizing and placing science and technology as a major driver of our economy.” The policies alluded to by the Minister include the ‘Revised National Infrastructure and Communications Policy and the Research, Science, Technology and Innovation Policy of 2012.’

    The government was also in the process of formulating strategies to speed up the transformation of the country from being a natural-resource driven to a technology-driven and knowledge-driven economy.

    Meanwhile, in a related development, the Ministry of Transport and Communication (MTC) through its department of Telecommunications and Postal Services (DTPS) has established collaboration with IST-Africa consortium. IST-Africa consortium is a strategic partnership between international Information Management Corporation of Ireland and Ministries and National Councils responsible for ICT in 18 African countries, supported by the European Union and the African Union Commission.

    “This programme will facilitate the development of Botswana’s research sector through collaboration and funding. Its main objectives are to promote International Research Cooperation, Innovation and entrepreneurship as well as knowledge sharing and Skills Transfer between IST-Africa partners.

    In November 2013 MCT hosted two IST-Africa training workshops focused on Research Collaboration under programmes of Horizon 2020 and Living Labs. “The workshops helped in guiding relevant organisations on processes in place used to acquire funds from European organs during open calls,” said an official from DTPS.

    See the full article here.

    SKA Banner

    About SKA

    The Square Kilometre Array will be the world’s largest and most sensitive radio telescope. The total collecting area will be approximately one square kilometre giving 50 times the sensitivity, and 10 000 times the survey speed, of the best current-day telescopes. The SKA will be built in Southern Africa and in Australia. Thousands of receptors will extend to distances of 3 000 km from the central regions. The SKA will address fundamental unanswered questions about our Universe including how the first stars and galaxies formed after the Big Bang, how dark energy is accelerating the expansion of the Universe, the role of magnetism in the cosmos, the nature of gravity, and the search for life beyond Earth. Construction of phase one of the SKA is scheduled to start in 2016. The SKA Organisation, with its headquarters at Jodrell Bank Observatory, near Manchester, UK, was established in December 2011 as a not-for-profit company in order to formalise relationships between the international partners and centralise the leadership of the project.

    ScienceSprings relies on technology from

    MAINGEAR computers

    Lenovo
    Lenovo

    Dell
    Dell

     
  • richardmitnick 7:54 am on September 16, 2014 Permalink | Reply
    Tags: , , , , , SKA-Square Millimeter Array   

    About SKA from The Register 

    SKA Square Kilometer Array

    SKA

    Register

    Australia’s first pass at the Square Kilometre Array – the Boolardy Engineering Test Array – is about to get commissioned into a fully-live system.

    test

    The test array, known naturally enough as BETA, is part of the science-before-the-science: a proving ground for some of the new technologies being used for the SKA project, in particular, the Phased Array Feeds.

    Those feeds represent a new way of getting signals from the parabolic dishes of the array: instead of the waveguides that collect signals in an old style dish (like The Dish, which recently had to cut back the number of frequencies it would install waveguides for as a cost-saving measure), PAFs put an array of receptors at the focal plane.

    As BETA’s operators explain in this Arxiv paper, that arrangement lets “multiple independently steerable primary beams to be synthesised electronically”, but because it’s never been done before, the test deployment existed for tasks like working out how to form the beams for particular imaging tasks, measuring the pattern stability of the beams, and working out how best to arrange multiple beams into a large field of view.

    Along the way, BETA is also showing off some of the other technologies that’ll be fundamental for the SKA. Once signals from the telescopes have been digitised (using CSIRO-designed boards dubbed DragonFly-2), they’re sent from the telescopes to a central facility for processing.

    With just six antennas in place, the central processing (handled by another board from CSIRO called Redback-2) has plenty to work with: each PAF port on each antenna produces 304 individual 1 MHz channels, with each antenna needing 16 of the Redback-2 boards and 10 GB/second communications.

    Each 12 hour observation run of BETA is good for dumping nearly 154 MB/second on the facility’s disk, for a total of 816 GB. The ASKAP central processor, a 472-node Cray XC30 at Perth’s Pawsey Centre, is currently working hard to fill the 10 PB of Spectra Logic tape storage (duplicated for insurance) available for the facility, and that’s slated for expansion to 50 PB. ®

    See the full article here.

    SKA Banner

    About SKA

    The Square Kilometre Array will be the world’s largest and most sensitive radio telescope. The total collecting area will be approximately one square kilometre giving 50 times the sensitivity, and 10 000 times the survey speed, of the best current-day telescopes. The SKA will be built in Southern Africa and in Australia. Thousands of receptors will extend to distances of 3 000 km from the central regions. The SKA will address fundamental unanswered questions about our Universe including how the first stars and galaxies formed after the Big Bang, how dark energy is accelerating the expansion of the Universe, the role of magnetism in the cosmos, the nature of gravity, and the search for life beyond Earth. Construction of phase one of the SKA is scheduled to start in 2016. The SKA Organisation, with its headquarters at Jodrell Bank Observatory, near Manchester, UK, was established in December 2011 as a not-for-profit company in order to formalise relationships between the international partners and centralise the leadership of the project.

    ScienceSprings relies on technology from

    MAINGEAR computers

    Lenovo
    Lenovo

    Dell
    Dell

     
  • richardmitnick 2:37 pm on September 11, 2014 Permalink | Reply
    Tags: , , , , , SKA-Square Millimeter Array   

    From SKA: “China completes its prototype dish for the SKA” 

    SKA Square Kilometer Array

    SKA

    On 18 August 2014, Professor Philip Diamond, Director General of the SKA Organisation, accompanied by Mrs. Zhao Jing from the SKA China Office of the Chinese Ministry of Science and Technology visited the 54th Research Institute of China Electronics Technology Group Corporation (CETC54) in Shijiazhuang, about 300km south west of Beijing. Professor Diamond, hosted by Mr. Wang Feng, President of the company specialising in antenna construction, was able to see a complete prototype SKA antenna and hold discussions with the CETC54 SKA team.

    chinese
    The completed DVA-C antenna with CETC54′s SKA team and Phil Diamond, Director General of the SKA Organisation

    “The CETC54 crew had worked night and day for weeks to complete the antenna for my visit, and I was personally overwhelmed that they had worked so hard and completely impressed by what they had achieved”, reported Phil Diamond after the visit.

    CETC54, on behalf of the Joint Laboratory for Radio Astronomy Technology (JLRAT), the Chinese member of the SKA DISH consortium, is doing the manufacturing and installation of the Dish Verification Antenna China (DVA-C), one of the three prototype antennas being built as part of the SKA Design phase.

    Two other designs, one Canadian and one South African, are being considered by the DISH consortium to develop the final SKA dish prototype.

    canada
    On Wednesday, May 7th, Canada’s National Research Council (NRC) successfully mounted the DVA-1 Primary Dish onto the telescope pier. DVA-1 is a prototype antenna for the international Square Kilometre Array (SKA) project.

    s.a.
    First night in the Karoo for the first MeerKAT antenna against the backdrop of the Milky Way and the Magellanic Clouds. Credit Photowise
    27 March 2014, Carnarvon, Northern Cape, South Africa – The first of 64 antennas that will make up SKA’s African precursor telescope – MeerKAT – was officially launched today by South Africa’s Minister of Science and Technology, Mr Derek Hanekom. The Minister also officially opened the specialised MeerKAT Karoo Array Processor Building – the cutting edge data centre for the MeerKAT telescope that has been built in an underground bunker at the Karoo observatory site.

    “Manufacturing of DVA-C started in late 2013 and it was a challenge both in terms of technology and fabrication to complete it in only eight months,” said Mr. Wang Feng.

    The DVA-C verification test will be completed in December 2014. The experience in building DVA-C and the tests conducted on it will benefit the SKA to design the final SKA dish prototype. The Chinese antenna is an offset Gregorian dual reflector. The main and sub reflectors were made of Carbon Fiber Reinforced Polymers (CFRP), based on single piece panel and surface metallizing technology. The main reflector size is 18m × 15m, the sub reflector size is 5m × 4.7m.

    See the full article here.

    SKA Banner

    About SKA

    The Square Kilometre Array will be the world’s largest and most sensitive radio telescope. The total collecting area will be approximately one square kilometre giving 50 times the sensitivity, and 10 000 times the survey speed, of the best current-day telescopes. The SKA will be built in Southern Africa and in Australia. Thousands of receptors will extend to distances of 3 000 km from the central regions. The SKA will address fundamental unanswered questions about our Universe including how the first stars and galaxies formed after the Big Bang, how dark energy is accelerating the expansion of the Universe, the role of magnetism in the cosmos, the nature of gravity, and the search for life beyond Earth. Construction of phase one of the SKA is scheduled to start in 2016. The SKA Organisation, with its headquarters at Jodrell Bank Observatory, near Manchester, UK, was established in December 2011 as a not-for-profit company in order to formalise relationships between the international partners and centralise the leadership of the project.

    ScienceSprings relies on technology from

    MAINGEAR computers

    Lenovo
    Lenovo

    Dell
    Dell

     
  • richardmitnick 8:02 am on September 10, 2014 Permalink | Reply
    Tags: , , , , , SKA-Square Millimeter Array   

    From SKA: “Upgrade for SKA precursor telescope in Australia” 

    SKA Square Kilometer Array

    SKA

    On September 4, the first full-size second generation (Mk II) phased array feed (PAF) receiver was installed on an antenna at the Australian SKA site – the Murchison Radio-astronomy Observatory in Western Australia.

    prelim
    The white-coated 2nd generation Phase Array Feed receiver on ASKAP’s antenna 29.

    SKA Murchison Widefield Array
    SKA Murchison Widefield Array

    This marked a new milestone in the development of CSIRO’s Australian SKA Pathfinder (ASKAP) telescope, one of three SKA precursor telescopes.

    path
    CSIRO’s Australian SKA Pathfinder (ASKAP) telescope

    PAFs are a new technology being developed at CSIRO equivalent to “radio cameras”, providing a uniquely large field-of-view to image large swaths of the sky at the same time.

    The development of the second generation PAF system builds on many of the lessons learnt with the design, development, construction and testing of the Mk I receiver. Six Mk I PAFs and their associated electronics, were installed on ASKAP antennas in 2013 and are already producing early science results.

    The design of the Mk II now also incorporates novel components and assembly techniques such as the use of marine composites technology in the PAF casing to manage structural loading, thermal insulation, environmental protection and RFI shielding, as well as specially-designed ground planes that ensure a low and stable operating temperature for increased system reliability.

    The installation has quickly followed the recent preliminary ground-based aperture array tests on the Mk II PAF, which yielded promising system temperature results, confirming the overall system design.

    The Mk II PAF is currently installed on ASKAP Antenna 29 — to follow its progress tune in to the live MRO webcam.

    About ASKAP: one of three SKA precursor telescopes, ASKAP is currently being commissioned. It is using 6 antennas (out of a total of 36) in a test array called BETA, which are equipped with the 1st generation PAF receivers.

    See the full article here.

    SKA Banner

    About SKA

    The Square Kilometre Array will be the world’s largest and most sensitive radio telescope. The total collecting area will be approximately one square kilometre giving 50 times the sensitivity, and 10 000 times the survey speed, of the best current-day telescopes. The SKA will be built in Southern Africa and in Australia. Thousands of receptors will extend to distances of 3 000 km from the central regions. The SKA will address fundamental unanswered questions about our Universe including how the first stars and galaxies formed after the Big Bang, how dark energy is accelerating the expansion of the Universe, the role of magnetism in the cosmos, the nature of gravity, and the search for life beyond Earth. Construction of phase one of the SKA is scheduled to start in 2016. The SKA Organisation, with its headquarters at Jodrell Bank Observatory, near Manchester, UK, was established in December 2011 as a not-for-profit company in order to formalise relationships between the international partners and centralise the leadership of the project.

    ScienceSprings relies on technology from

    MAINGEAR computers

    Lenovo
    Lenovo

    Dell
    Dell

     
  • richardmitnick 9:07 am on September 5, 2014 Permalink | Reply
    Tags: , , , , SKA-Square Millimeter Array   

    From SKA: “French NenuFAR telescope granted SKA Pathfinder status” 

    SKA Square Kilometer Array

    SKA

    The SKA Organisation has officially recognised NenuFAR, a French radio telescope, as a Pathfinder Project of the SKA telescope.

    NenuFAR
    NenuFAR

    NenuFAR, which stands for New Extension in Nançay Upgrading LOFAR, is a new low-frequency radio telescope under construction at the Nançay Observatory near Orleans to extend the existing international LOFAR radio telescope, an array of low frequency antennas spread across eight European countries and centred in the Netherlands.

    “With this announcement, NenuFAR is recognised as an instrument concept paving the way for the new science to be done with the SKA”, said Gilles Theureau, Director of the Nançay Observatory. “It’s excellent news for the project, as well as for the Nançay Observatory.”

    The SKA officially has three precursor telescopes, MeerKAT, ASKAP and MWA. Located at SKA sites in South Africa and Western Australia, these precursors are and will be carrying out scientific studies related to future SKA activities, as well as helping the development and testing of new crucial SKA technologies.

    SKA MeerKAT Telescope Array
    MeerKAT

    askap
    ASKAP

    SKA Murchison Widefield Array
    MWA

    Unlike precursors, pathfinder telescopes and systems are dotted around the globe. They include the famous Arecibo radio telescope in Puerto Rico, which starred in the James Bond movie “Goldeneye”, the LOFAR low frequency array, which is based in Europe, and the JVLA, in North America, which was famously seen in the hit movie “Contact”, amongst others. They are also engaged in SKA-related technology and science studies. A full list is available here.

    NenuFAR will not only be an extension of LOFAR but also a stand-alone instrument. As an SKA pathfinder, the feedback from the design, construction and operation of NenuFAR will be used by the SKA Organisation to facilitate the development of the SKA.

    “NenuFAR is a promising instrument and the SKA’s low frequency array will certainly benefit from the development and lessons learnt on this project”, said Prof. Philip Diamond, Director General of the SKA Organisation. “We are happy to support the French community’s efforts and look forward to working more closely with our colleagues in France in the near future.”

    “The decision by the SKA Organisation to grant NenuFAR the official status of SKA Pathfinder is an important signal for the French community, recognising our expertise in radioastronomy,” added Denis Mourard, Deputy Director for Science of the Institut National des Sciences de l’Univers of CNRS.

    Further reactions from French stakeholders following the announcement:

    “This status as SKA Pathfinder will further increase our motivation and efficiency to complete the construction of NenuFAR Phase 1 as scheduled, and to prepare the next phases, thereby contributing to the development of SKA.” Claude Catala, President of the Observatoire de Paris

    “This recognition confirms our hopes to consolidate between Nançay, Orleans and Paris a world-class pole in radioastronomy in the 21st century.” Youssoufi Touré, President of the University of Orleans

    “This is excellent news. It will encourage us to draw from each step of the development of NenuFAR – starting with the completion of its phase 1 – useful lessons for the design and future operation of the SKA. At the same time it will give us a huge boost in seeking support for the following phases to bring NenuFAR to its full potential. It will contribute to unify the french radio community behind both NenuFAR and the SKA.” Michel Tagger and Philippe Zarka, principal investigators of NenuFAR.

    See the full article here.

    SKA Banner

    About SKA

    The Square Kilometre Array will be the world’s largest and most sensitive radio telescope. The total collecting area will be approximately one square kilometre giving 50 times the sensitivity, and 10 000 times the survey speed, of the best current-day telescopes. The SKA will be built in Southern Africa and in Australia. Thousands of receptors will extend to distances of 3 000 km from the central regions. The SKA will address fundamental unanswered questions about our Universe including how the first stars and galaxies formed after the Big Bang, how dark energy is accelerating the expansion of the Universe, the role of magnetism in the cosmos, the nature of gravity, and the search for life beyond Earth. Construction of phase one of the SKA is scheduled to start in 2016. The SKA Organisation, with its headquarters at Jodrell Bank Observatory, near Manchester, UK, was established in December 2011 as a not-for-profit company in order to formalise relationships between the international partners and centralise the leadership of the project.

    ScienceSprings relies on technology from

    MAINGEAR computers

    Lenovo
    Lenovo

    Dell
    Dell

     
  • richardmitnick 8:43 am on August 29, 2014 Permalink | Reply
    Tags: , , , , , SKA-Square Millimeter Array   

    From SKA: “The big data revolution” 

    SKA Square Kilometer Array

    SKA

    11 August 2014
    Researchers in many fields are now engaging in data-intensive research in which the volume, velocity and variety of data exceed their capacity to extract information from it. What are the challenges for researchers in Africa?

    The modern world is experiencing a data deluge: “The data flow is so fast that the total accumulation of the past two years – a zeIabyte – dwarfs the prior record of human civilisation,” reported Harvard Magazine in March 2014. Popularly known as ‘big data’, this surge of information is set to become as important to business and society as the Internet, providing people with everything from bad-weather warnings to plotting a route home. No-one is immune – least of all researchers, who now work with large data sets that cut across the disciplines, including astronomy, biology, engineering, maths, computer science, archival science, humanities, economics and finance.

    bowl
    Professor Paul Bonnington of Monash University in the Monash CAVE2 (TM), which is used to visualise big data. (CAVE2 is a trademark of the University of Illinois Board of Trustees.) Image: Paul Jones, Coretext.

    In 2001, Gartner, Inc, the world’s leading information and technology research and advisory company, defined big data as “high-volume, -velocity and -variety information assets that require cost-effective, innovative forms of information processing for enhanced insight and decision-making”.

    What this means, in a nutshell, is that the more data there is available, the more potential there is for more accurate analysis. And with more accurate information available, decisions can be made with increasing confidence, while better decision-making leads to greater efficiencies, cost reductions and reduced risks across societies. But this will only happen if the capacity exists to interpret the data correctly. Getting from data to knowledge is not a simple equation, and the need to support data-intensive research at universities in such a way as to manage this is acute. As Professor Russ Taylor, newly awarded joint UCT/University of the Western Cape (UWC) Square Kilometre Array (SKA) Research Chair and big-data champion, says, “Global research leadership requires that we have the capacity to extract information from big data.”

    Increasingly, researchers in several fields are battling to move data sets between collaborator sites, test various sets of parameters to optimise analysis of large data sets, and facilitate access to big-data sets by international research communities. In the last 12 months, UCT researchers have more than doubled their use of central high-performance computer (HPC) facilities for data-intensive research. Demand for research storage is growing substantially each year, and specialist support and analysts are in constant demand.

    “Without the right support, UCT researchers risk diverting time and resources into the development and maintenance of potentially sub-standard or inefficient solutions or just generally taking much more time to do meaningful analysis,” says Professor Danie Visser, Deputy Vice-Chancellor with responsibility for research at UCT. “There is increased potential for valuable data or intellectual property to be lost, stolen or corrupted and for significant interruptions to research activity. A centralised effort is needed to provide a mechanism for researchers to learn from one another and develop institutional best practice.”

    It is partly for this reason that UCT has taken the lead in establishing an eResearch Centre. In line with moves at other leading international research institutions, the centre will provide integrated support across the university research lifecycle and will work in close collaboration with researchers facilitating the delivery of high-impact, locally relevant and internationally competitive research. One of its important roles will be in managing large data sets.

    UCT has also been working with other South African institutions to see what support platforms they have in place and where there are opportunities for collaboration. The first eResearch Africa conference, hosted by the Association of South African University Directors of Information Technology (ASAUDIT), was held in October 2013, based on the Australasia eResearch conference model. A delegate was heard to remark, “This is the first time I have ever seen parallel academic and technical tracks at a conference.” Exactly what the conference organisers were hoping for.

    The purpose of the conference was to bring together practitioners and researchers for a week to share ideas and exemplars on new information-centric research capabilities. eResearch is focused on how information and communications technologies help researchers to collect, manage, share, process, analyse, store, find and re-use information. The success of the event has led to a 2014 conference scheduled for November at UCT that should, judging by the speed of progress, be even bigger and better than the 2013 conference.

    Bioinformatics – a brave new world

    One of the fields at the forefront of big-data research at UCT is bioinformatics (the science of collecting, analysing and interpreting complex biological data), and one of the leading researchers in the field is Nicola Mulder, associate professor of bioinformatics and head of the Computational Biology Group at the Institute of Infectious Disease and Molecular Medicine (IDM). Mulder is managing one of the largest grants at UCT, awarded by the US-based National Institutes of Health (NIH) – a US$13-million grant over five years that is part of the Human Heredity and Health in Africa (H3Africa) Initiative, funded by the NIH and the Wellcome Trust. Its purpose is to set up a bioinformatics network to support H3Africa-funded research projects, which aim to identify the genetic bases for illnesses such as diabetes, rheumatic heart disease, cardiometabolic diseases, tuberculosis pharmacogenetics, kidney disease and strokes.

    Part of the H3Africa initiative involves the creation of biorepositories (places to keep samples). This bioinformatics infrastructure includes a staging area for all data and tools for analysis, and building capacity through training programmes, specialised courses and data-management workshops.

    Mulder says: “H3Africa researchers will generate big-data sets – 500 terabytes at a minimum – and our network, H3ABioNet, has 34 partners: 32 universities and research institutions in 15 African countries, along with two in the United States needed to build the infrastructure necessary to manage the data. At UCT we have a team of four technical posts and have set up a bioinformatics helpdesk for researchers to request support.”

    The project allows Mulder’s team to develop tools, set up pipelines and provide advice about running an analysis, as well as to enable collaborations across research nodes. It also makes provision for internships, which allow H3Africa partners to sit and analyse their data with members of the network.

    “Some impacts of the project include the establishment of a bioinformatics centre at a university in Egypt, giving them space and facilities, as well as one in Tanzania. There are plans to build a bioinformatics centre from scratch in Ghana and we have already started training programmes there. In addition, through the network connections, one of our US partners wrote a successful grant proposal with a Niger partner to do some collaborative work. When we were able to demonstrate what H3Africa is doing for bioinformatics in South Africa, as part of their ongoing commitment, the Department of Science and Technology provided money for local bioinformatics courses.”

    A huge advantage of this – and one of the stated aims of the project – is that it enables African scientists to retain ownership of their data. “Training African scientists in bioinformatics means we can make sure that data stays on the continent, and is analysed on the continent and published in Africa. What has been happening up to now is that researchers have been unable to handle the level and volume of research data, so they would source a collaborator outside Africa and that collaborator would get the material published,” says Mulder.

    Bioinformatics research has lower costs than wet-lab research (where chemicals, drugs or other material or biological matter are tested and analysed, requiring water, direct ventilation and specialised piped utilities). Laboratories, and the need for consumables, can be largely replaced by a computer and an internet connection. This also makes bioinformatics particularly feasible in the African context, where it is easier to come by computers and connectivity than funding for sophisticated infrastructure. The challenge of greater internet connectivity is important and to some extent is already being addressed by groups working to build internet infrastructure, such as UbuntuNet. Stand-alone devices are also in the offing, such as the eBiokit, a Macbased device that has everything a bioinformatician might need, including databases and tools for training and analysis.

    Says Mulder: “It is challenging to do biomedical research today without bioinformatics because so many researchers are generating big data. It is less common now to work on one gene at a time. The new trend is to work on thousands of genes at one time, so you have to have bioinformatics to manage the data. In order to answer genetics questions, it’s becoming more important to generate big-data sets.”

    According to Mulder, the biggest challenge in big data for the biomedical field is the development of next-generation sequencing (NGS) technologies that enable massively parallel sequencing. It is much cheaper than traditional sequencing but it generates millions of short reads, which demand new analysis and storage challenges. With the falling cost of NGS, researchers have the option, for instance, of whole-genome sequencing rather than targeted sequencing. This means one can move towards hypothesis-generating rather than hypothesis-testing science, which has the potential to lead to novel discoveries. New algorithms are being developed to manage this data and for archiving, which makes this sort of research more feasible.

    Particle problems

    Another discipline where big data is playing an increasingly important role is physics. Dr Andrew Hamilton, a lecturer in the Department of Physics at UCT and researcher in high-energy particle physics at the European Organisation for Nuclear Research (CERN), is engaged in one of the world’s most exciting projects – the Large Hadron Collider (LHC). The 27-kilometre LHC is the world’s largest particle accelerator, and it is one of the most important tools available to high-energy physicists in their goal of investigating the fundamental particles that make up the universe. The UCT-CERN Research Centre is part of two of the experiments running at the LHC: the ATLAS experiment, which explores the fundamental particles of the standard model of particle physics, and ALICE, which is aimed at understanding the quark-gluon plasma.

    The Big Data Revolution

    muon
    A simulation of an ATLAS event, which shows a Higgs boson decaying into two Z bosons each of which subsequently decays into two muons (red lines). Image courtesy of ATLAS Experiment © 2014 CERN

    The nature of the LHC’s work means it has been grappling with the problem of big-data sets for 20 years. Many of the particles it investigates (such as the famous Higgs boson) need to be created by colliding protons at speeds approaching the speed of light. Because the particles are very rare, tens of millions of collision events are produced per second, which need to be captured and read by a detector. If researchers were to read out every single event, they would need around 40 terabytes per second, which is way beyond the confines of current technology; using high speed filtering, called triggers, researchers can get this down to hundreds of megabytes per second.

    While this may already sound like a tall order, it is only part of the big data challenge faced by the LHC. In order to define expectations (so that they know what they expect to see), the entire detector is digitally simulated in excruciatingly fine detail, and a computer algorithm is written to simulate the billions of events that might produce a rare particle like the Higgs boson. All of this data then needs to be stored. Factor into this the collaborations involved (just one of the LHC’s seven experiments has 1 000 members belonging to 116 institutions, based in 33 countries), and the scale of the challenge is evident.

    The LHC has created a solution to this very big data problem – the Worldwide LHC Computing Grid (WLCG)., a form of cloud computing that stores and processes information. It currently has 150 centres in 40 countries and operates through a tiered structure that varies in the funding model, the storage space and the number of cores required.

    Creating the infrastructure required to play in this big-data league sounds expensive; however, money is just one of the challenges for UCT, according to Dr Hamilton. “We need the people trained in high-performance computing to operate and administer these facilities,” he says. This is where the WLCG comes in. “It is one of the largest research computing networks in the world.”

    “If UCT wants to be a leader in big-data research, we need to demonstrate that we can operate a big data centre on the global scale. The WLCG gives us the opportunity to contribute to one of the largest research computing networks on the planet and learn from their expertise at the same time.”

    The Big Data Revolution

    Big data from the sky

    Another project that is placing UCT at the centre of international big-data research is the MeerKAT Large Surveys and the Square Kilometre Array (SKA).

    rt
    Africa’s biggest science project, the MeerKAT radio telescope, is a precursor to the SKA telescope. Four key science programmes on MeerKAT are led by UCT astronomers. These research programmes will gather up to one petabyte (1 000 terabytes) of data per year, so advanced tools will have to be developed to process, analyse and store this amount of data.

    rt
    Russ Taylor

    This will be done in collaboration with the SKA South Africa project office. SKA South Africa, UCT and UWC have attracted an eminent role player in this field from Canada, Professor Russ Taylor, who joined the university early in 2014 and will co-ordinate a big-data vision for radio astronomy in South Africa. “The global SKA big science data world is coming to South Africa this decade,” says Taylor, adding that it is probably one of the two projects in the world driving a big data revolution in astronomy.

    There is nothing small about the SKA project. It is the biggest science project ever carried out on African soil. Each MeerKAT antenna, which will be incorporated into the mid-frequency component of SKA Phase 1 when that instrument is constructed, stands 19,5 metres tall and weighs 42 tons.

    When completed, the SKA will be the world’s largest radio telescope, located in Africa and Australia, but shared by astronomers around the globe. Until then, MeerKAT will be the most sensitive and powerful L-Band radio interferometer in the world. In addition to operating as a stand-alone, world-leading imaging radio telescope, MeerKAT will participate in global VL BI (very long baseline interferometry) operations with all major VL BI networks around the world operating at the MeerKAT frequencies, adding considerably to the sensitivity of the global VL BI networks.

    The complete MeerKAT array will have 64 receptors – antennas with receivers, digitisers and other electronics. Connected by 170 kilometres of underground fibre-optic cable, the receptors will operate as a single, highly sensitive astronomical instrument, controlled and monitored remotely from the MeerKAT control room in Cape Town.

    The Big Data Revolution

    When fully operational, the MeerKAT will generate enough data from the antennas to fill about four-anda- half million standard 4.7-gigabyte DVDs in a day. Professor Taylor has served on the board of directors of the international SKA Organisation (representing Canada), and has experience as an observer and observing proposal referee for the US National Radio Astronomy Observatory, Very Large Array. He is the international project leader for the design of the global data-delivery system for the SKA project. This, together with his expertise as a big data specialist, means that he is well positioned to guide UCT toward realising its SKA big data vision. He was the founding international SKA project scientist, and co-authored the first SKA science case.

    A research revolution

    In addition to his own research with SKA, Professor Taylor will also be working to put South Africa – and Africa – on the map in terms of data capacity. He says that there is likely to be a limited window of opportunity to establish national leadership in data-intensive research and a global presence in this emerging field.

    While big data is, by its very nature, a massive challenge to the university, it is also a driver of the transformation of science and, by extension, a driver of global change, and UCT is already part of the revolution. “We are not trying to break into a field where we are absent – we are already there,” says Professor Visser. “If we grasp the opportunity to take leadership in this area we can really make a difference in the country and to science around the world: solving Africa’s issues, but also making Africa part of the global solutions.”

    See the full article here.

    SKA Banner

    About SKA

    The Square Kilometre Array will be the world’s largest and most sensitive radio telescope. The total collecting area will be approximately one square kilometre giving 50 times the sensitivity, and 10 000 times the survey speed, of the best current-day telescopes. The SKA will be built in Southern Africa and in Australia. Thousands of receptors will extend to distances of 3 000 km from the central regions. The SKA will address fundamental unanswered questions about our Universe including how the first stars and galaxies formed after the Big Bang, how dark energy is accelerating the expansion of the Universe, the role of magnetism in the cosmos, the nature of gravity, and the search for life beyond Earth. Construction of phase one of the SKA is scheduled to start in 2016. The SKA Organisation, with its headquarters at Jodrell Bank Observatory, near Manchester, UK, was established in December 2011 as a not-for-profit company in order to formalise relationships between the international partners and centralise the leadership of the project.

    ScienceSprings relies on technology from

    MAINGEAR computers

    Lenovo
    Lenovo

    Dell
    Dell

     
  • richardmitnick 1:32 pm on August 27, 2014 Permalink | Reply
    Tags: , , , , , SKA-Square Millimeter Array   

    From SKA: The Aperture Array Verification System 

    SKA Square Kilometer Array

    SKA

    array
    Image credit: Dr Budi Juswardy (ICRAR), main picture, A. Sutinjo, R. Wayth, T. Colegate (ICRAR) and the ICRAR-Curtin AAVS0.5 and MWA teams, inset.

    The Aperture Array Verification System 0.5 (AAVS0.5) is an engineering prototype for a more advanced low-frequency antenna system that will pave the way for the SKA-Low in Western Australia. Built as an extension to the SKA precursor telescope Murchison Widefield Array (MWA) at the radio-quiet Murchison Radioastronomy Observatory (MRO), AAVS0.5 consists of 16 antennas that are designed by collaborators at the Cavendish Laboratory at Cambridge University, UK. This verification array is an ICRAR/Curtin University engineering initiative. In the inset image, you can even see one of the first images made with AAVS0.5 (made in conjunction with the MWA). ICRAR engineers and scientists are currently planning the next AAVS prototype (AAVS1).

    SKA Murchison Widefield Array
    Murchison Widefield Array

    By 2023, the SKA will feature 250,000 such antennas in Western Australia!

    SKA Banner

    About SKA

    The Square Kilometre Array will be the world’s largest and most sensitive radio telescope. The total collecting area will be approximately one square kilometre giving 50 times the sensitivity, and 10 000 times the survey speed, of the best current-day telescopes. The SKA will be built in Southern Africa and in Australia. Thousands of receptors will extend to distances of 3 000 km from the central regions. The SKA will address fundamental unanswered questions about our Universe including how the first stars and galaxies formed after the Big Bang, how dark energy is accelerating the expansion of the Universe, the role of magnetism in the cosmos, the nature of gravity, and the search for life beyond Earth. Construction of phase one of the SKA is scheduled to start in 2016. The SKA Organisation, with its headquarters at Jodrell Bank Observatory, near Manchester, UK, was established in December 2011 as a not-for-profit company in order to formalise relationships between the international partners and centralise the leadership of the project.

    ScienceSprings relies on technology from

    MAINGEAR computers

    Lenovo
    Lenovo

    Dell
    Dell

     
  • richardmitnick 7:55 am on August 22, 2014 Permalink | Reply
    Tags: , , , , SKA-Square Millimeter Array   

    From SKA: “Zambia to have astronomy centre” 

    SKA Square Kilometer Array

    SKA

    22 August 2014
    BENEDICT TEMBO

    ZAMBIA will accommodate a regional astronomy node to be used as a centre for the study of celestial objects.
    The Copperbelt University (CBU) has, to this effect, signed an agreement with the International Astronomical Union (IAU) to host southern Africa’s regional node of the IAU Office of Astronomy for Development (OAD).

    The centre will be used for the study of astronomical objects such as stars, galaxies, planets, moons and nebulae.

    The node will also be used for the study of physics, chemistry and evolution as well as phenomena that originate outside the Earth’s atmosphere, including supernovae explosions, gamma ray bursts and cosmic microwave background radiation.

    This is the second regional node to be established on the African continent and forms part of the IAU’s plan, which aims to realise the benefits of astronomy.

    This office will also reach out to other countries in Africa which, like Zambia, form part of the Square Kilometre Array (SKA) project.

    The key task is to ensure that all countries involved in the study of astronomical objects have the skills and personnel required both to derive maximum benefit from the major telescope project and to help make the SKA a scientific success.

    According to a statement by the IAU, the signing follows the approval of a proposal from CBU which enjoyed the support of astronomy collaborators in Mozambique, Namibia, South Africa and Zambia.

    This agreement follows the IAU’s invitation to countries that are ready to host similar nodes. The partners of this regional node will establish a steering committee which consists of relevant expertise and representation.

    “Zambia is ideally positioned to play a leadership role in this field. Not only is it a part of the Square Kilometre Array project, but its consistent commitment to develop astronomy capacity nationally serves as an example to other countries in the region. Since the International Year of Astronomy in 2009, we have seen Zambia represented in various global astronomy education and outreach projects. Their experience and dedication to the field of astronomy will be a great benefit to the region,” OAD director Kevin Govender said.

    Dean of the School of Mathematics and Natural Sciences at CBU, F. P. Tailoka also said authorities at the university were happy that educational institution was part the scheme.

    “We are pleased to be part of the implementation of the IAU’s strategic plan. We are a partner country of the Square Kilometre Array which gives us an opportunity to participate in world-class astronomy research. We look forward to see the Zambian community, and the rest of the region, realising the benefits of astronomy,” Professor Tailoka said.

    Signing the agreement on behalf of the IAU, assistant general secretary Piero Benvenuti said astronomy was possibly the most ancient science and the IAU is committed to maintain and spread worldwide this precious heritage.

    “But astronomy is not only pure science, it is a fascinating cultural adventure that engages the entire society and brings many benefits. It has a powerful attraction for young people, encouraging them to follow mathematical and scientific curricula, and it fosters advanced technological developments,” Mr Benvenuti said.

    The establishment of this southern African regional node is significant as this part of the continent is currently very active in terms of the development of world-class astronomy facilities, including the optical Southern African Large Telescope (SALT),

    Southern African Large Telescope

    the radio Karoo Array Telescope (MeerKAT),

    meer

    the gamma-ray High Energy Stereoscopic System (HESS)

    hess

    as well as the Square Kilometre Array. The office in Zambia will exploit all these advantages to benefit the region at large.

    The IAU strategic plan was ratified by its members in 2009, at its General Assembly. Since then a global co-ordinating office (the OAD) was established in Cape Town, South Africa, and has led the implementation of this plan.

    Other regional nodes have already been established in China for the east Asian region, Thailand for the south east Asian region and Ethiopia for the east African region.

    See the full article here.

    SKA Banner

    About SKA

    The Square Kilometre Array will be the world’s largest and most sensitive radio telescope. The total collecting area will be approximately one square kilometre giving 50 times the sensitivity, and 10 000 times the survey speed, of the best current-day telescopes. The SKA will be built in Southern Africa and in Australia. Thousands of receptors will extend to distances of 3 000 km from the central regions. The SKA will address fundamental unanswered questions about our Universe including how the first stars and galaxies formed after the Big Bang, how dark energy is accelerating the expansion of the Universe, the role of magnetism in the cosmos, the nature of gravity, and the search for life beyond Earth. Construction of phase one of the SKA is scheduled to start in 2016. The SKA Organisation, with its headquarters at Jodrell Bank Observatory, near Manchester, UK, was established in December 2011 as a not-for-profit company in order to formalise relationships between the international partners and centralise the leadership of the project.

    ScienceSprings relies on technology from

    MAINGEAR computers

    Lenovo
    Lenovo

    Dell
    Dell

     
  • richardmitnick 7:42 am on August 11, 2014 Permalink | Reply
    Tags: , , , , SKA-Square Millimeter Array   

    From SKA: “India’s National Centre for Radio Astrophysics becomes the 11th full SKA Organisation member” 

    SKA Square Kilometer Array

    SKA

    11 August 2014
    Professor Yashwant Gupta
    National Centre for Radio Astrophysics
    Tata Institute of Fundamental Research
    Pune University Campus, Pune 411007, India.
    Phone: +91-20-25719242/25696105/25691620
    Email: ygupta@ncra.tif.res.in

    Mr Mathieu ISIDRO
    Deputy Communications and Outreach Manager
    SKA Organisation
    Jodrell Bank Observatory, UK
    T: +44 (0) 161 306 9681
    E-mail: m.isidro@skatelescope.org

    Following ratification by the Board of Directors, India’s National Centre for Radio Astrophysics (NCRA) has now become the 11th full member of SKA Organisation.

    “NCRA’s full membership cements India’s intention to play an important part in the SKA, and shows the project is steadily moving forward, with more countries expected to join in the near future,” said Professor Philip Diamond, the SKA Organisation Director General.

    NCRA first joined SKA Organisation in April 2012 as an Associate Member, indicating its intention of becoming a Full Member during the pre-construction phase of the project. NCRA has, in fact, been involved in the SKA project since the project’s earliest days and was one of the institutions that signed an agreement in 1997 to develop technologies for a large-scale radio telescope.

    In November 2013, SKA Organisation attributed 10 work packages representing the various elements of the SKA to 10 international consortia drawn from nearly one hundred institutions, universities and industry around the world to participate in the analysis and design of the components of the SKA during its three year detailed design phase.

    NCRA, a centre of the Tata Institute of Fundamental Research, is leading the Telescope Manager consortium, a key element of the SKA telescope focused on developing all hardware and software necessary to control the telescope, including the software needed to schedule telescope operations and monitor the status of each of the SKA’s thousands of dishes and antenna stations. NCRA is also a participant in the Signal and Data Transport and Central Signal Processing work packages of the SKA.

    Professor Yashwant Gupta, who is leading the Telescope Manager consortium at NCRA, has been appointed as NCRA’s representative on SKA Organisation’s Board of Directors.

    “We are very happy to further strengthen our involvement with the SKA. The SKA is one of India’s key science priorities of the next decade and we are proud to represent our country in this exciting international science collaboration,” he said following the decision.

    Prof. S.K. Ghosh, Centre Director at NCRA further added that “Involvement in the SKA will also benefit next generation improvements in projects in India such as the Giant Metrewave Radio Telescope (GMRT), built and operated by NCRA”.

    GMRT Radio Telescope
    GMRT

    The proposal to transfer NCRA’s full membership status to the Government of India is under active consideration by the Government. The transfer would ensure a wider participation of other interested parties in India and secure the long-term participation of India in the project.

    See the full article here.

    SKA Banner

    About SKA

    The Square Kilometre Array will be the world’s largest and most sensitive radio telescope. The total collecting area will be approximately one square kilometre giving 50 times the sensitivity, and 10 000 times the survey speed, of the best current-day telescopes. The SKA will be built in Southern Africa and in Australia. Thousands of receptors will extend to distances of 3 000 km from the central regions. The SKA will address fundamental unanswered questions about our Universe including how the first stars and galaxies formed after the Big Bang, how dark energy is accelerating the expansion of the Universe, the role of magnetism in the cosmos, the nature of gravity, and the search for life beyond Earth. Construction of phase one of the SKA is scheduled to start in 2016. The SKA Organisation, with its headquarters at Jodrell Bank Observatory, near Manchester, UK, was established in December 2011 as a not-for-profit company in order to formalise relationships between the international partners and centralise the leadership of the project.

    ScienceSprings relies on technology from

    MAINGEAR computers

    Lenovo
    Lenovo

    Dell
    Dell

     
c
Compose new post
j
Next post/Next comment
k
Previous post/Previous comment
r
Reply
e
Edit
o
Show/Hide comments
t
Go to top
l
Go to login
h
Show/Hide help
shift + esc
Cancel
Follow

Get every new post delivered to your Inbox.

Join 330 other followers

%d bloggers like this: