BEGIN:VCALENDAR VERSION:2.0 PRODID:-//CERN//INDICO//EN BEGIN:VEVENT SUMMARY:HPC insights into chemistry mysteries DTSTART;VALUE=DATE-TIME:20181204T123000Z DTEND;VALUE=DATE-TIME:20181204T125000Z DTSTAMP;VALUE=DATE-TIME:20260807T164614Z UID:indico-contribution-154-910@events.chpc.ac.za DESCRIPTION:Speakers: Jeanet Conradie (University of the Free State)\nThis contribution is aimed to illustrate how chemical computational results\, obtained by density functional theory calculations on high performance com puters\, provides insight into many observed chemical phenomena\, mysterie s or questions\, such as the following:\nThe structure of water clusters i n bulk water is considered one of the unsolved problems in chemistry. Ho w does the structure of water clusters look like at nanoscopic scale? Ho w do the connecting hydrogen bonds render water ideally suited to life pro cesses\, being easily formed but not too difficult to break? A photochrom ic mercury compound has an orange colour in solution\, but turns blue when sunlight shines on it. Why? How do these orange and blue forms differ in structure? Why is conductivity much higher for a certain iridium comp lex\, than for the related rhodium complex with the same ligand? Why is the transient reaction intermediate within a multi-step red blood cell rea ction not experimentally observable? \nThese and many other puzzling chemi cal problems\, can be addressed very efficiently without experimental erro r\, by computational chemistry conducted on high performance computers\, t hereby bypassing tedious or expensive laboratory techniques.\n\nReferences :\n[1] https://en.wikipedia.org/wiki/Water_cluster\n[2] A. Malloum\, J.J . Fifen\, J. Conradie\, The Journal of Physical Chemistry\, submitted\, MS no jp-2018-08976q.R1\n[3] H. Schwoerer\, K.G. von Eschwege\, G. Bosman\, P. Krok\, J. Conradie\, European Journal of Chemical Physics and Physical Chemistry\, 2011\, 14\, 2653-2658.\n[4] K.G. von Eschwege\, J. Conradie\ , J.C. Swarts\, Journal of Physical Chemistry A\, 2008\, 112\, 2211-2218.\ n[5] J. Conradie\, Journal of Organometallic Chemistry\, 2017\, 833\, 88- 94.\n[6] S. Basu\, R. Grubina\, J. Huang\, J. Conradie\, Z. Huang\, A. Je ffers\, A. Jiang\, X. He\, I. Azarov\, R. Seibert\, A. Mehta\, R. Patel\, S.B. King\, A. Ghosh\, M.T. Gladwin\, D.B. Kim-Shapiro\, Nature Chemical B iology\, 2007\, 3\, 785-794.\n\nhttps://events.chpc.ac.za/event/33/contrib utions/910/ LOCATION: Meeting Room 11 URL:https://events.chpc.ac.za/event/33/contributions/910/ END:VEVENT BEGIN:VEVENT SUMMARY:Role of High Performance Computing in the Applications of Bio-econ omically Important Proteins DTSTART;VALUE=DATE-TIME:20181204T113000Z DTEND;VALUE=DATE-TIME:20181204T115000Z DTSTAMP;VALUE=DATE-TIME:20260807T164614Z UID:indico-contribution-154-828@events.chpc.ac.za DESCRIPTION:Speakers: Ozlem Tastan Bishop (Rhodes University)\nThe main re search interest of the Research Unit in Bioinformatics (RUBi) at Rhodes Un iversity is in structural bioinformatics and its applications to bio-econo mically important research questions\, i.e. to drug discovery projects for diseases related to Africa\, and to biodiversity and bioprocessing. Centr e for High Performance Computing (CHPC)\, South Africa\, is regularly used for accelerating computer intensive methods including drug virtual screen ing\, molecular modelling\, quantum mechanics\, molecular mechanics\, mole cular dynamics (MD) and combinations of these techniques. RUBi’s researc h is computationally highly expensive\; i.e. within 3 months (February – April 2018) a total of 7.2 million cpu hours was used. Hence\, CHPC has a great impact on RUBi’s research\, international collaborations and huma n capacity development. This talk focuses on the application of HPC to RUB i’s research projects with some specific examples including analysis of drug resistance of HIV\, identification of new drug targeting sites for ca ncer\, and investigation of proteins related to the production of biofuels . Further\, computational details\, e.g. benchmarking\, compute time\, det ails of software used and/or developed will also be given to demonstrate t he need for HPC resources.\n\nhttps://events.chpc.ac.za/event/33/contribut ions/828/ LOCATION: Meeting Room 11 URL:https://events.chpc.ac.za/event/33/contributions/828/ END:VEVENT BEGIN:VEVENT SUMMARY:Untapped Potential of Computational Material Science In Kenya DTSTART;VALUE=DATE-TIME:20181205T094000Z DTEND;VALUE=DATE-TIME:20181205T100000Z DTSTAMP;VALUE=DATE-TIME:20260807T164614Z UID:indico-contribution-154-713@events.chpc.ac.za DESCRIPTION:Speakers: George Manyali (Masinde Muliro University of Science and Technology)\nComputational material science is taking root in Kenya. Development of big data infrastructure\, high-performance computing facili ties and use of open-source-software will accelerate the growth of this fi eld\, develop competent manpower and improve the economy of the country. T he role played by major public universities in Kenya such as Masinde Mulir o University of Science and Technology\, University of Eldoret\, Kenyatta University and the University of Nairobi in tackling health\, water\, and energy-related issues using computational tools requires long-term funding support. The glaring gap in technology transfer from universities to indu stries in Kenya needs to be addressed in order to harness the full potenti al of computational material science.\n\nhttps://events.chpc.ac.za/event/3 3/contributions/713/ LOCATION: Meeting Room 11 URL:https://events.chpc.ac.za/event/33/contributions/713/ END:VEVENT BEGIN:VEVENT SUMMARY:Simulations of the COSMO model on the CHPC DTSTART;VALUE=DATE-TIME:20181205T100000Z DTEND;VALUE=DATE-TIME:20181205T102000Z DTSTAMP;VALUE=DATE-TIME:20260807T164614Z UID:indico-contribution-154-784@events.chpc.ac.za DESCRIPTION:Speakers: Patience Mulovhedzi (SAWS)\, Mary-Jane Bopape (SAWS) \nThe South African Weather Service (SAWS)\, as a national meteorological service provider for South Africa (SA) and Southern African Development Co mmunity (SADC) communities\, aims to provide useful and innovative weather \, climate\, and related products and services. Part of SAWS services and products are derived from Numerical Weather Prediction (NWP) models\, of w hich Unified model (UM) from the UK Metoffice is the lead model. Weather f orecast models perform differently across different parts of the globe and for different weather phenomena. In order to ensure continuous delivery o f high quality weather forecasts to SAWS stakeholders\, other NWP models a re examined. The Consortium for Small-scale Modelling (COSMO) model is eva luated and analysed in order to investigate whether it is more/less suitab le for predicting high impact weather events over SA.\nThe COSMO model is a European limited area model driven from Icosahedral Non-hydrostatic (ICO N) global model. The ICON model has a grid spacing of 13km globally\, whic h allows the COSMO to be simulated at a fine horizontal resolution of less than 5km. In this study\, the COSMO model is being run with a grid spacin g of 4.4km and 40 vertical levels\, which allows for accurate numerical pr ediction of near-surface weather conditions (e.g. clouds\, fog\, frontal p recipitation) and simulation of severe weather events triggered by deep mo ist convection (supercell thunderstorms\, intense mesoscale convective com plexes\, prefrontal squallline storms and heavy snowfall from wintertime m esocyclones.\nSimulations of five high impact weather events over SA were done on the CHPC system. The COSMO model is run with a grid spacing of 4.4 km (0.036°) over SADC with a domain ranging from 5 – 56 °E and 40 – 5 °S (1276 x 1026 grid points)\, using a timestep of 30 seconds and a 30 hour lead-time. The model is run on a large queue using 1728 cores with u sing default science settings. Both the pre-processing and model run compl eted in +/- 2.5 hours and the model output was in hourly intervals for 86 variables (80 in sigma coordinates and 6 in pressure coordinates).\nThe se lected variables (parameters) from model output are then evaluated against ground observations from SAWS network\, radar data\, satellite observatio ns\, Global Precipitation Measurement (GPM) and National Centers for Envir onmental Prediction (NCEP) Reanalysis data. Selected parameters for evalua tion include wind speed\, surface temperature\, total precipitation\, clou d cover\, mean sea-level pressure\, surface pressure and geopotential heig ht. The outcome of the model evaluation will be discussed in detail at the conference.\n\nhttps://events.chpc.ac.za/event/33/contributions/784/ LOCATION: Meeting Room 11 URL:https://events.chpc.ac.za/event/33/contributions/784/ END:VEVENT BEGIN:VEVENT SUMMARY:An Overview of Modelling at Johnson Matthey DTSTART;VALUE=DATE-TIME:20181205T113000Z DTEND;VALUE=DATE-TIME:20181205T115000Z DTSTAMP;VALUE=DATE-TIME:20260807T164614Z UID:indico-contribution-154-830@events.chpc.ac.za DESCRIPTION:Speakers: Chris Perry (Johnston Matthey)\nOver the past fiftee n years or so\, the number of modellers at Johnson Matthey has grown from one\, to close to twenty\; a firm indication of the importance that JM pla ces in both atomistic\, as well as meso/macroscale modelling. DFT modellin g in particular\, forms an integral part of JM’s research and developmen t efforts in a wide range of areas\, including catalysis\, diagnostic serv ices\, pharmaceutical applications\, and new battery and fuel cell technol ogies. The presentation will provide a brief overview of modelling at JM\, highlighting the types of calculations that we do (with some real world e xamples)\, how modelling fits in with our experimental research programmes \, the HPC resources that we utilize\, and our interactions with the CHPC. \n\nhttps://events.chpc.ac.za/event/33/contributions/830/ LOCATION: Meeting Room 11 URL:https://events.chpc.ac.za/event/33/contributions/830/ END:VEVENT BEGIN:VEVENT SUMMARY:Using High Performance Computing to run large-scale WRFChem Acid D eposition Modelling over the Highveld Region of South Africa DTSTART;VALUE=DATE-TIME:20181205T115000Z DTEND;VALUE=DATE-TIME:20181205T121000Z DTSTAMP;VALUE=DATE-TIME:20260807T164614Z UID:indico-contribution-154-831@events.chpc.ac.za DESCRIPTION:Speakers: Suzanne Cawood (EScience Associates (Pty) Ltd)\nAcid deposition has been studied extensively over the Highveld region of South Africa due to its high density of acid emissions arising mostly from powe r generation and petrochemical production. Although deposition of acid spe cies has been modelled using dispersion models\, the modelling of atmosphe ric chemistry and acid deposition has not been undertaken to any meaningfu l extent in South Africa. Furthermore\, the potential of WRFChem\, the Wea ther\, Research and Forecasting (WRF) model coupled with Chemistry\, has y et to be realized within an African context mainly due to the high computi ng power required to compute even the smallest of domain sizes. With a dom ain size of over 300 000 km2\, which equates to over 75 000 grid cells\, over a two-year modelling period\, computational power was a limiting fac tor to the success of the research. Access to high performance computing a nd more specifically the ability to split the processing across multiple p rocessors is instrumental in running this computationally intensive model. And has been the limiting factor for further research in South Africa on this topic. This presentation provides a review of the benefits of using H igh Performance Computing for running WRFChem when compared with local mic ro-servers.\n\nhttps://events.chpc.ac.za/event/33/contributions/831/ LOCATION: Meeting Room 11 URL:https://events.chpc.ac.za/event/33/contributions/831/ END:VEVENT BEGIN:VEVENT SUMMARY:The role of the interface in binary polymer blends DTSTART;VALUE=DATE-TIME:20181203T094000Z DTEND;VALUE=DATE-TIME:20181203T100000Z DTSTAMP;VALUE=DATE-TIME:20260807T164614Z UID:indico-contribution-154-712@events.chpc.ac.za DESCRIPTION:Speakers: Giuseppe Pellicane (University of Kwazulu-Natal)\nPh ysical techniques for surface modification of plastics use surface-active agents\, which are allowed to self-assemble at the surface. Many technique s\, which are important in modern technologies\, use polymer blends\, and there is considerable interest to understand the extent the composition of the surface layer differs from that in the bulk for molten polymer mixtur es. Dynamical and structural properties of polymers in the melt state are strongly influenced by molecular architecture [1-4] and blending polymers with different molecular topologies could be potentially exploited to cont rol interfacial segregation of the polymer film\, and to achieve optimal m echanical properties of the plastic material [5\,6]. However\, a deep unde rstanding of the role of chain architecture and molecular mass in determin ing which species preferentially adsorb at a given interface is lacking. E xperiments to resolve the matter are typically conducted by mixing polymer s possessing the same repeat chemistry\, but different molecular architect ure [10–14]. Here we show the results obtained in large-scale molecular dynamics simulations of linear-cyclic polymer films\, and we find clear ev idence of enhancement of linear polymers at the interface [7]\, in agreeme nt with recent experimental results [8]. The behavior predicted by the sel f-consistent field theory (SCF)\, i.e.\, enhancement of cyclic polymers at the interface [9]\, emerges for relatively long chains. In our presentati on\, we provide a picture of the microscopic mechanisms through which the chain length arbitrates the competition between the different packing cons traints imposed by the loop and linear geometry of the two polymers. We al so discuss the role of enthalpic and entropic factors of the interfacial f ree energy of the system in determining which species in the blend prefere ntially adsorbs at the interface. \n\n[1] Kapnistos\, M\; Lang. M\; Rubin stein\, M\; Roovers\, J.\; Chang\, T\; Vlassopoulos\, D.\, Soc. Rheol. Ann u. Meeting 2006.\n[2] Robertson\, R. M.\; Smith\, D. E.\, Proc. Natl. Acad . Sci. U.S.A. 2007\, 104\, 4824-4827.\n[3] Iyer\, B. V. S.\; Lele\, A. K.\ ; Shanbhag\, S.\, Macromolecules 2007\, 40\, 5995.\n[4] Subramanian\, G.\; Shanbhag S.\, Macromolecules 2008\, 41\, 7239-7242.\n[5] Wu\, S. L.\; Pol ymer Interface and Adhesion\, Marcel Dekker: New York\, 1982.\n[6] Garbass i\, F\; Morra\, M\; Occhiello\, E.\, Polymer Surfaces: From Physics to Tec hnology\; John Wiley and Sons: New York\,1994.\n[7] G. Pellicane\, M. Megn idio-Tchoukouegno\, G. T. Mola\, and M. Tsige\, Physical Review E Rapid Co mmunications\, 93\, 050501 (2016)\; M. Megnidio-Tchoukouegno\, F. M. Gaith o\, G. T. Mola\, M. Tsige\, and G. Pellicane\, Fluid Phase Equilibria\, 44 1\, 33–42 (2017).\n[8] Wang\, S-F\; Li\, X.\; Agapov\, R. L.\; Wesdemiot is\, C.\; Foster\, M. D.\, ACS Macro Letters\, 2012\, 1\, 1024-1027. (2016 ).\n[9] Wu \, D. T.\; Fredrickson\, G. H.\, Macromolecules 1996\, 29\, 791 9-7930.\n\nhttps://events.chpc.ac.za/event/33/contributions/712/ LOCATION: Hall C URL:https://events.chpc.ac.za/event/33/contributions/712/ END:VEVENT BEGIN:VEVENT SUMMARY:An Evaluation of Galaxy and Ruffus Workflows System for DNA-seq An alysis DTSTART;VALUE=DATE-TIME:20181205T123000Z DTEND;VALUE=DATE-TIME:20181205T125000Z DTSTAMP;VALUE=DATE-TIME:20260807T164614Z UID:indico-contribution-154-719@events.chpc.ac.za DESCRIPTION:Speakers: Olabode Ajayi (South Africa National Bioinformatics Institute)\nFunctional genomics determines the biological functions of gen es on a global scale by using large volumes of data obtained through techn iques including next-generation sequencing (NGS). The application of NGS i n biomedical research is gaining in momentum\, and with its adoption becom ing more widespread\, there is an increasing need for access to customizab le computational workflows that can simplify\, and offer access to\, compu ter-intensive analyses of genomic data. In this study\, the Galaxy and Ruf fus frameworks were designed and implemented with a view to addressing the challenges faced in biomedical research. Galaxy\, a graphical web-based f ramework\, allows researchers to build a graphical NGS data analysis pipel ine for accessible\, reproducible\, and collaborative data-sharing. Ruffus \, a UNIX command-line framework used by bioinformaticians as Python libra ry to write scripts in an object-oriented style\, allows for building a wo rkflow in terms of task dependencies and execution logic. In this study\, a dual data analysis technique was explored which focuses on a comparative evaluation of Galaxy and Ruffus frameworks that are used in composing ana lysis pipelines. To this end\, we developed an analysis pipeline in Galaxy \, and Ruffus\, for the analysis of Mycobacterium tuberculosis sequence da ta. Furthermore\, this study aimed to compare the Galaxy framework to Ruff us with preliminary analysis revealing that the analysis pipeline in Galax y displayed a higher percentage of load and store instructions. In compari son\, pipelines in Ruffus tended to be CPU bound and memory intensive. The CPU usage\, memory utilization\, and runtime execution are graphically re presented in this study. Our evaluation suggests that workflow frameworks have distinctly different features from an ease of use\, flexibility\, and portability\, to architectural designs. Therefore\, in this CHPC Conferen ce\, I will discuss how we composed the NGS bioinformatics data analysis p ipeline in the Galaxy and Ruffus workflow framework and the use of each fr amework in the analysis of Mycobacterium tuberculosis sequence data.\n\nht tps://events.chpc.ac.za/event/33/contributions/719/ LOCATION: Meeting Room 11 URL:https://events.chpc.ac.za/event/33/contributions/719/ END:VEVENT BEGIN:VEVENT SUMMARY:HPC in the De Beers Marine R&D Context DTSTART;VALUE=DATE-TIME:20181204T115000Z DTEND;VALUE=DATE-TIME:20181204T121000Z DTSTAMP;VALUE=DATE-TIME:20260807T164614Z UID:indico-contribution-154-792@events.chpc.ac.za DESCRIPTION:Speakers: Imraan Parker (De Beers Marine)\nThe unique nature o f the underwater mining environment has resulted in R&D playing an import role within De Beers Marine. Physical and numerical simulation methods fo rm an integral part of the R&D concept development pipeline. Computationa l Fluid Dynamics has been increasingly used for concept exploration\, risk mitigation as well as to enhance understanding of physical simulations. HPC has been an enabler for using Computational Fluid Dynamics to solve mu lti-phase problems that were previously deemed to be too large and/or comp lex. Most recently\, this capability has been used in the feasibility sta ge of a new marine mining vessel.\n\nhttps://events.chpc.ac.za/event/33/co ntributions/792/ LOCATION: Meeting Room 11 URL:https://events.chpc.ac.za/event/33/contributions/792/ END:VEVENT BEGIN:VEVENT SUMMARY:On the co-operation between SAWS and CHPC for forecast continuity and Unified Model research in South Africa DTSTART;VALUE=DATE-TIME:20181204T121000Z DTEND;VALUE=DATE-TIME:20181204T123000Z DTSTAMP;VALUE=DATE-TIME:20260807T164614Z UID:indico-contribution-154-715@events.chpc.ac.za DESCRIPTION:Speakers: Stephanie Landman (South African Weather Service)\nW eather forecasting using Numerical Weather Prediction (NWP) models is a we ll-established science and based on the fundamental equations of fluid dyn amics. NWP is therefore an important tool for predicting weather and makin g climate projections. The grid spacing used in models is largely dependen t on the available computational resources and processing speed required f or model output availability for timeous decision making. The direct numer ical simulations that are able to capture all processes explicitly are sti ll too far from our reach for practical purposes such as NWP\, seasonal fo recasting and climate change studies.\nThe available computational resourc es have been improving over time\, which have made possible a decrease in the grid spacing used in models. A number of meteorological organisation a re now using grid spacing of 4 km or less for NWP purposes\, especially ov er limited areas. Models used with such high resolution are called Cloud R esolving Models (CRMs) or convective scale models\, and in these models cl ouds are thought to be resolved explicitly. Similar to other meteorologica l organisations SAWS runs their NWP models with a grid spacing of 4.4 km o ver southern Africa and 1.5 km over South Africa. Both these configuration s are made four times a day\, but with different lead times. These simulat ions are made on a CRAY XC30 machine which was procured in 2014. \nThe SAW S CRAY XC30 has 168 nodes with Ivybridge processors. Each model simulation (4 km and 1.5 km) utilizes 1728 cores to complete. The CRAY is also used for operational seasonal forecasting with a coupled atmosphere-ocean mode l and there are plans for more models on air quality\, ocean wave forecast ing and applications research that will be undertaken on the CRAY. With al l the operational applications on the CRAY\, there is limited processing t ime for research activities such as sub-kilometre grid spacing simulations or ensemble forecasting. Big global operational centres such as the Europ ean Centre for Medium Range Weather Forecasts (ECMWF) maintain two HPC res ources\, with the second one available as a backup to their operational sy stem. Due to budget constraints and the high costs of HPC resources\, SAWS does not have such a failover system in-house\, resulting in no or limite d support for operational NWP at SAWS to operational forecasters if the op erational system fails. \nIn order to deal with HPC shortcomings at SAWS a cooperative partnership agreement was entered into with the Centre for Hi gh Performance Computing (CHPC) to facilitate mutual HPC activities\, and training programs to meet the missions of both SAWS and the CHPC. The CHPC is one of the three national cyber-infrastructure pillars that are suppor ted by the South African Department of Science and Technology (DST). The C HPC currently hosts a Dell cluster\, with a total of 1358 nodes with Intel v3 Haswell processes\, and a 4PB Lustre storage. The main objective of th e CHPC is to enable South Africa to become globally competitive and to acc elerate Africa’s socio-economic upliftment through the effective applica tion of high-end Cyberinfrastructure. The CHPC seeks to become an accompli shed and preferred partner for High Performance Computing solutions.\nThe agreed areas of cooperation between SAWS and the CHPC include 1) the use o f the CHPC cluster as a fail-over system for SAWS operations\, 2) the use of the CHPC HPC system for benchmarking purposes to determine future opera tional needs of SAWS\, 3) Use of the CHPC HPC system for research purposes \, and 4) Training on the use of the CHPC cluster. SAWS has been using UK Met Office Unified Model (UM) as its main Numerical Weather Prediction mo del since 2006. As a result of the agreement between SAWS and the CHPC\, t he UM has now been installed on the CHPC cluster. The CHPC cluster was use d successfully for business continuity purposes when SAWS moved offices\, as well as\, as a failover system when there were power issues at the SAWS premises. Before now the UM had only been available at SAWS and to SAWS e mployees due to license restrictions\, resulting in scientists only gettin g exposure to the UM once employed by SAWS. The installation of the UM on the CHPC infrastructure will allow SAWS and other academic and research in stitutions across South Africa access to the UM for research purposes.\n\n https://events.chpc.ac.za/event/33/contributions/715/ LOCATION: Meeting Room 11 URL:https://events.chpc.ac.za/event/33/contributions/715/ END:VEVENT BEGIN:VEVENT SUMMARY:Advancing Computational Science in South African Academia through Social and Cyber Networks DTSTART;VALUE=DATE-TIME:20181204T090000Z DTEND;VALUE=DATE-TIME:20181204T092000Z DTSTAMP;VALUE=DATE-TIME:20260807T164614Z UID:indico-contribution-154-837@events.chpc.ac.za DESCRIPTION:Speakers: Kevin J. Naidoo (University of Cape Town)\nIn his 20 02 State of the Nation Address\, President Thabo Mbeki identified Informat ion and Communication Technology (ICT) as “a critical and pervasive elem ent in economic development” and recommended the establishment of an “ ICT University”. The establishment of the CHPC in 2005 signalled the fir st pillar in the national research cyberinfrastructure1 and remains a majo r investment that anchors the development and growth of the computational and data sciences stretching across disciplines from science\, through to social science. The recent feverish announcements from pundits through to politicians hailing the onset of the 4th industrial revolution posits a re search landscape where computational science is a central kernel of South Africa’s future economic plan.\n\nLarge parts of the chemical\, biologic al and physical science have had an uptick in production and activity in m odelling\, simulation and data analytics as measured by number of papers p roduced. However\, the challenge of innovative home grown methods to addre ss the national needs of medical science\, the bio-economy and the green r evolution remain unmet. \nI will present a view of the future of computing and data analytics in the biological\, chemical and life sciences. More i mportantly I will discuss a hopeful future scenario where academics across all South African institutions cooperate via the CHPC to advance our inte rnational research profile.\n\nhttps://events.chpc.ac.za/event/33/contribu tions/837/ LOCATION: Meeting Room 11 URL:https://events.chpc.ac.za/event/33/contributions/837/ END:VEVENT BEGIN:VEVENT SUMMARY:High Performance Computing for Nature Inspired Metaheuristics DTSTART;VALUE=DATE-TIME:20181205T090000Z DTEND;VALUE=DATE-TIME:20181205T092000Z DTSTAMP;VALUE=DATE-TIME:20260807T164614Z UID:indico-contribution-154-829@events.chpc.ac.za DESCRIPTION:Speakers: Nelishia Pillay (University of Pretoria)\nGenetic al gorithms and genetic progamming are metaheuristics taking inspi-\nration f rom Darwin’s theory of evolution to solve optimization problems. Ge-\nne tic algorithms explore a solution space to find solutions to problems whil e\ngenetic programming works in a program space to identify a program whic h\nwhen executed will find an optimal solution to the problem. Both these\ napproaches have high runtimes when applied to complex problems and are\nu sually implemented using distributed computing in these instances. More\nr ecently\, genetic algorithms and genetic programming have been employed\nb y hyper-heuristics and have been used for the automated design of machine\ nlearning and search techniques. Hyper-heuristics explore the heuristic sp ace\nrather than the solution space and hence search in the heuristic spac e is\nmapped to the solution space. Automated design of machine learning a nd\nsearch techniques is an emerging field aimed at removing the load of d e-\nsign\, which is a time consuming task\, from the researcher. This will also\nenable non-experts to use machine learning toolkits that automate t he de-\nsign and hence allow the researcher to focus on the problem being solved.\nThe use of genetic algorithms and genetic programming in hyper-he uristics\nand for automated design require additional processing time. The talk will\nfirstly look at the high performance computing architectures i mplemented\nby our research group to reduce the runtimes of genetic progra mming and\ngenetic algorithms\, particularly for hyper-heuristics and auto mated design.\nAn overview of some of the real-world problems that this ha s enabled us\nto solve will then be presented. These include inducing huma n competitive\nheuristics for solving timetabling problems\, network intru sion detection in\nthe area of computer security\, the automated design of techniques for finan-\ncial forecasting\, computer security\, packing and logistics problems and the\nintroduction of multi-space search algorithms that perform search over more\nthan once space with applications in packi ng and forecasting.\n\nhttps://events.chpc.ac.za/event/33/contributions/82 9/ LOCATION: Meeting Room 11 URL:https://events.chpc.ac.za/event/33/contributions/829/ END:VEVENT BEGIN:VEVENT SUMMARY:High performance computing in pyrometallurgy DTSTART;VALUE=DATE-TIME:20181204T094000Z DTEND;VALUE=DATE-TIME:20181204T100000Z DTSTAMP;VALUE=DATE-TIME:20260807T164614Z UID:indico-contribution-154-838@events.chpc.ac.za DESCRIPTION:Speakers: Driaan Bezuidenhout (Mintek)\nPyrometallurgy refers to high temperature (>1600°C) extraction of valuable metals from mineral ore deposits. Most pyrometallurgical processes occur in furnaces of variou s types in which many complex phenomena are occurring simultaneously. Almo st none of these phenomena can be observed directly due to the extreme con ditions inside furnace vessels. Computational modelling is invaluable in u nderstanding the processes in and around furnaces and is often used for de sign and optimization. Problems vary from simple CFD analyses to coupled m ultiphysics applications such as magnetohydrodynamic models of plasma arcs . \n\nHigh performance computing is a valuable tool for developing increas ed understanding and better engineering for these challenging problems. A few case studies are given: DC furnace arc modelling\, multiphase flow thr ough furnace tap-holes\, combustion in a rotary converter and settling of metal and slag.\n\nhttps://events.chpc.ac.za/event/33/contributions/838/ LOCATION: Meeting Room 11 URL:https://events.chpc.ac.za/event/33/contributions/838/ END:VEVENT BEGIN:VEVENT SUMMARY:AI is impacting HPC everywhere DTSTART;VALUE=DATE-TIME:20181203T113000Z DTEND;VALUE=DATE-TIME:20181203T115000Z DTSTAMP;VALUE=DATE-TIME:20260807T164614Z UID:indico-contribution-154-822@events.chpc.ac.za DESCRIPTION:Speakers: Rob Farber ()\nThe convergence of AI and HPC has cre ated a fertile venue that is ripe for imaginative researchers - versed in AI technology - to make a big impact in a variety of scientific fields. Fr om new hardware to new computational approaches\, the true impact of deep- and machine learning on HPC is\, in a word\, “everywhere”. \nJust as technology changes in the personal computer market brought about a revolut ion in the design and implementation of the systems and algorithms used in high performance computing (HPC)\, so are recent technology changes in ma chine learning bringing about an AI revolution in the HPC community. Expec t new HPC analytic techniques including the use of GANs (Generative Advers arial Networks) in physics based modeling and simulation as well as reduce d precision math libraries such as NLAFET and HiCMA to revolutionize many fields of research. Other benefits of the convergence of AI and HPC includ e the physical instantiation of data flow architectures in FPGAs and ASICs plus the development of powerful data analytic services.\n\nhttps://event s.chpc.ac.za/event/33/contributions/822/ LOCATION: Hall C URL:https://events.chpc.ac.za/event/33/contributions/822/ END:VEVENT BEGIN:VEVENT SUMMARY:Computational modelling and capabilities in metal and alloys DTSTART;VALUE=DATE-TIME:20181203T115000Z DTEND;VALUE=DATE-TIME:20181203T121000Z DTSTAMP;VALUE=DATE-TIME:20260807T164614Z UID:indico-contribution-154-793@events.chpc.ac.za DESCRIPTION:Speakers: Hasani Chauke (Univesity of Limpopo)\nThe research i s based on the development and design of metal alloys with special applica tions in various industries\, from automotive and medical to aeronautical. These alloys have unique properties and behaviour under pressure and temp erature conditions. Focus will be on the precious metal\, iron-aluminium\, titanium and titanium-based systems for shape memory alloys\, as well as zirconium-niobium systems. A density functional theory based semi-empirica l approach is employed to explore material properties at zero temperature\ ; while molecular dynamics techniques are also carried out to predict the stability\, strength\, behaviour and the extent of transformation temperat ure. The overview on computational codes and usage of HPC will be discusse d. Furthermore\, the advances on machine learning approaches towards titan ium cluster development and growth will also be indicated.\n\nhttps://even ts.chpc.ac.za/event/33/contributions/793/ LOCATION: Hall C URL:https://events.chpc.ac.za/event/33/contributions/793/ END:VEVENT BEGIN:VEVENT SUMMARY:The CHPC’s role in key projects at Aerotherm DTSTART;VALUE=DATE-TIME:20181205T092000Z DTEND;VALUE=DATE-TIME:20181205T094000Z DTSTAMP;VALUE=DATE-TIME:20260807T164614Z UID:indico-contribution-154-795@events.chpc.ac.za DESCRIPTION:Speakers: Wian Van Der Merwe (Aerotherm)\nComputational Fluid Dynamics (CFD) is a mathematical tool used for commercial and research pro blems\, to predict flow- and thermal characteristics in a wide variety of applications. Aerotherm has been using CFD to improve and design flow-rela ted systems in the South African industry since 1995. The ever increasing demand for higher performance drives the need for more comprehensive CFD m odels. Such high fidelity models\, however\, require sufficient resources to be completed in reasonable timeframes. This talk will discuss how the C HPC plays a crucial role in the success of key CFD projects at Aerotherm.\ n\nhttps://events.chpc.ac.za/event/33/contributions/795/ LOCATION: Meeting Room 11 URL:https://events.chpc.ac.za/event/33/contributions/795/ END:VEVENT BEGIN:VEVENT SUMMARY:Developing Africa's first Earth System Model on the CHPC Lengau cl uster DTSTART;VALUE=DATE-TIME:20181203T092000Z DTEND;VALUE=DATE-TIME:20181203T094000Z DTSTAMP;VALUE=DATE-TIME:20260807T164614Z UID:indico-contribution-154-843@events.chpc.ac.za DESCRIPTION:Speakers: Nicolette Chang (CSIR)\nClimate change is the most s erious collective environmental challenge ever faced by modern humankind. It is a problem with global reach\, but the research effort to address it is disproportionately concentrated in the northern hemisphere and in devel oped countries. Southern hemispheric and African climate issues differ fro m those that drive the research and modelling effort in the north. In part icular\, oceans dominate the southern hemisphere and the land is largely o ccupied by arid systems and tropical forests. African terrestrial ecosyste ms and processes\, Southern Ocean physics\, biochemistry and circulation dynamics as well as Southern Hemisphere atmospheric processes are under-st udied and poorly represented in global models - despite being globally imp ortant contributors to earth system processes. In particular\, of the abou t thirty currently existing coupled ocean-atmosphere global circulation mo dels (CGCMs) and Earth System Models (ESMs) suitable for the projection of future climate change\, only one model had its genesis in the Southern He misphere. Towards addressing this disproportionality\, and in alignment wi th the South African Department of Science & Technology's Global Change Gr and Challenge\, the CSIR and partners are invested in building a Variable- resolution Earth System Model (VrESM)\, with the aim of contributing proje ctions of future climate change to the Coupled Model Intercomparison Proje ct Phase 6 (CMIP6) and Assessment Report 6 (AR6) of the IPCC. VrESM is the first African-based Earth System Model (ESM) and has as component models the variable-cubic atmospheric model (VCAM) of the CSIRO\, a dynamic land- surface model (CABLE)\, the variable cubic ocean model (VCOM) and an ocean biogeochemistry model (PISCES). \nVrESM is formulated on the non-orthogon al\, quasi-uniform cubic grid of Purser and Rancic (1998). Its atmospheric component VCAM has been developed by the Commonwealth Scientific and Indu strial Research Organisation (CSIRO). VCAM is a σ-coordinate model that u ses a semi-implicit semi-Lagrangian approach to solve the hydrostatic prim itive equations. VCAM has inherited the comprehensive physical parameteris ations of the Conformal-Cubic Atmospheric Model (CCAM) (McGregor\, 2005b). The dynamic land-surface model used is the CSIRO Atmosphere Biosphere Lan d Exchange model (CABLE). CABLE includes a dynamic river routing scheme ad apted from the CSIRO Mk3.5 CGCM. The VrESM ocean component VCOM has been d eveloped by the CSIR. This model solves the Boussinesq hydrostatic equatio ns in a z-coordinate in momentum-conservation form\, using a split-explici t solution procedure. VCOM is coupled to the PISCES ocean biochemistry mod el. Coupling of the ocean\, atmospheric and land-surface components takes place every time-step. It is envisaged that VrESM will be applied on a 10 0 km horizontal resolution grid within CMIP6\, with a longer-term plan of performing global eddy-resolving (10 km resolution) simulations depending on the availability of supercomputing resources at the Centre for High Per formance Computing (CHPC) of the CSIR. Our path over the next 5 years (to wards and beyond AR6) is firstly technical\, in further developing and opt imising the VrESM on the computer cluster at the CHPC and secondly scienti fic\, in understanding the underlying mechanisms that are often parameteri zed rather than resolved in global climate models – followed by subseque nt improvements and optimizing the model with this new knowledge. In parti cular\, South Africa has invested significantly in resources to investigat e and undertake long term observations that resolve critical dynamics in t he oceans to our south. From this investment has emerged a competitive edg e in building the first ESM that realistically represent Southern Ocean bi ochemistry and the role of the Southern Ocean in the African and global cl imate systems. In this presentation\, we will present the unique aspects o f the VrESM numerical solution procedure as applied on the cube-based grid . A variety of model applications (including simulations of present-day an d future climate) will also be shown\, with a focus on Southern Hemisphere and African climate processes.\n\nhttps://events.chpc.ac.za/event/33/cont ributions/843/ LOCATION: Hall C URL:https://events.chpc.ac.za/event/33/contributions/843/ END:VEVENT BEGIN:VEVENT SUMMARY:The simultaneous Optimization of the Nose and Tail Geometry of a H igh Speed Train for Drag and Crosswind Stability DTSTART;VALUE=DATE-TIME:20181205T121000Z DTEND;VALUE=DATE-TIME:20181205T123000Z DTSTAMP;VALUE=DATE-TIME:20260807T164614Z UID:indico-contribution-154-832@events.chpc.ac.za DESCRIPTION:Speakers: Andrea Beneke (Prospective Industry and current acad emic user)\, Ken Craig (University of Pretoria)\nThe national rail policy as formulated by the South African government requires that by the year 20 50 all current narrow or Cape gauge main rail lines be replaced by standar d gauge tracks. In addition\, they require that a number of key role playe rs\, of which Transnet is but one\, should work toward the implementation of high speed rail on these new tracks by the same year. The document furt her stipulates that the onus of responsibility of planning and developing the necessary skill in order to achieve the aforementioned\, lies with the se role players.\nThe first step that Transnet is taking to bridge this ga p and move South Africa forward is called the MC25 project\; a medium spee d passenger commuter that will connect Gauteng and Polokwane. The aim of t he project is both economic upliftment as well as a means of addressing a skills deficit with Transnet. The work that was completed was meant to add ress the latter\, with specific focus on the external aerodynamics of a hi gh speed train. \nThis project not only included a study of the external flow field surrounding a high speed train\, but also the simultaneous opti mization of the train nose and tail for drag and crosswind stability which were determined by the aerodynamic investigation to be the primary causes of concern for high speed trains. Due to the flow complexities and sheer magnitude of the simulations\, the computing capabilities that the CHPC of fered was critical to arriving at an optimal solution.\n\nhttps://events.c hpc.ac.za/event/33/contributions/832/ LOCATION: Meeting Room 11 URL:https://events.chpc.ac.za/event/33/contributions/832/ END:VEVENT BEGIN:VEVENT SUMMARY:CORDEX projections of changing tropical cyclones in the IPCC SR1.5 report as performed on the CHPC's Lengau cluster DTSTART;VALUE=DATE-TIME:20181204T100000Z DTEND;VALUE=DATE-TIME:20181204T102000Z DTSTAMP;VALUE=DATE-TIME:20260807T164614Z UID:indico-contribution-154-827@events.chpc.ac.za DESCRIPTION:Speakers: F.A. Engelbrecht ()\, Mavhungu Muthige ()\nThe Paris Agreement which was achieved in December 2015\; holds signatory countries responsible for keeping the increase in global average temperatures well below 2°C with respect to the to the pre-industrial period and to strive to limit the temperature increase to 1.5°C \, recognising that this will reduce the impacts of climate change. Given this impetus at global level\, it is of paramount importance to consider the implications of the 1.5 \, 2\, and 3 °C thresholds in the tropical cyclone activities within the Sou th West Indian Ocean Basin.Using the Coordinated Regional Downscaling Expe riment-Africa (CORDEX) regional climate models\, we downscale six global c limate models of the Coupled Model Inter-comparison Project Phase 5 (CMIP5 ) to high resolution with the aid of computing power from the south Africa n (CHPC) Centre for High Performance Computing’s Lengau Cluster.This ser ves towards studying changes in tropical cyclone tracks over the South Wes t Indian Ocean under different extents of global warming(1.5\, 2 and 3° C of warming with respect to pre-industrial conditions). It is projected th at the number of tropical cyclones making landfalls over southern Africa u nder global warming will decrease\, with 2 °C being a critical threshold\ , after which the rate of cyclone frequency with further temperature incre ases no longer has a diminishing effect.\n\nhttps://events.chpc.ac.za/even t/33/contributions/827/ LOCATION: Meeting Room 11 URL:https://events.chpc.ac.za/event/33/contributions/827/ END:VEVENT BEGIN:VEVENT SUMMARY:Next-generation DNA sequencing: why HPC is becoming a vital compon ent of biological research DTSTART;VALUE=DATE-TIME:20181204T092000Z DTEND;VALUE=DATE-TIME:20181204T094000Z DTSTAMP;VALUE=DATE-TIME:20260807T164614Z UID:indico-contribution-154-898@events.chpc.ac.za DESCRIPTION:Speakers: Peter Teske (University of Johannesburg)\nDuring the past decade\, massive parallel DNA sequencing technologies have completel y changed the way in which genetic data are generated and analysed. Instea d of sequencing a few hundred nucleotides and focusing on a handful of gen es\, it is now possible to generate data from entire genomes. The human ge nome contains about 3 billion nucleotides\, and even this is tiny compared to some plant genomes. The resulting datasets are so large that it is imp ossible to assemble and analyse them without HPC. In this presentation\, I demonstrate some of the HPC pipelines my lab uses to assemble genomic dat a and reconstruct evolutionary relationships between species. These data s ets are small compared to what we have planned for the near future\, highl ighting the necessity to invest more heavily in HPC resources in South Afr ica and help the country’s biologists become internationally competitive . I also focus on the present reluctance of many traditional geneticists t o adopt the new technology\, and suggest that this bottleneck needs to be closed by finding common ground between biologists\, computer scientists a nd other stakeholders. In the near future\, we need to jointly train bioin formatics students who operate at the interface of the different disciplin es.\n\nhttps://events.chpc.ac.za/event/33/contributions/898/ LOCATION: Meeting Room 11 URL:https://events.chpc.ac.za/event/33/contributions/898/ END:VEVENT BEGIN:VEVENT SUMMARY:Modelling Dry Flue Gas Desulfurisation in a Circulating Fluidized Bed. DTSTART;VALUE=DATE-TIME:20181203T121000Z DTEND;VALUE=DATE-TIME:20181203T123000Z DTSTAMP;VALUE=DATE-TIME:20260807T164614Z UID:indico-contribution-154-714@events.chpc.ac.za DESCRIPTION:Speakers: Louis Le Grange (North-West University)\nThe burning of fossil fuels is identified as the biggest source of Sulfur dioxide (S0 2) emissions in South Africa. SO2 is a colourless gas with a nasty smell. It impacts both human health in the form of diminishing lung function and the environment through the effects of acid rain leading to deforestation. In order to meet minimum emissions standards for S02\, as provided by the Air Quality Act of South Africa\, big emitters such as Eskom and Sasol ar e required to implement Flue Gas Desulfurization (FGD) plants. Current FGD plants in South Africa are wet operated – that is\, a sorbent like Calc ium Hydroxide ( Ca(OH)2 ) is mixed with water and sprayed as slurry into f lue gas. In order to save water\, dry FGD processes are considered. One su ch process is called Dry FGD using a Circulating Fluidized Bed (CFB). Duri ng this process dry Ca(OH)2 is introduced into a flue gas stream while wat er is separately introduced as a fine spray. SO2 is then reduced in a reac tion involving the flue gas\, Ca(OH)2 particles and water droplets.\nThe m ain reactor of a Dry FGD CFB plant is the vertical riser\, which can typic ally be 3m in diameter and 20m high. The riser acts as a container in whic h the SO2 in the flue gas is exposed to the Ca(OH)2 particles and water dr oplets. Of importance are the residence time and the riser hold-up\, which forms part of the overall successful design of a dry SO2 scrubber. Comput ational Fluid Dynamics is used to model the gas-solid two-phase mixture. T he two-phase flow regime extends from dense to dilute turbulent flow\, whi ch renders the solution especially challenging. A Probability Density Func tion (PDF) approach is used to represent the microscale dynamics while fil tering methods are used to yield practical solution on the scale of the pl ant. \nTwo codes are used for modelling the two-phase flows namely Neptune _CFD\, which is the research code partly owned by EDF in France\, and Open FOAM\, which allows the user to make fundamental changes in the source cod e. Both these codes are run at CHPC. The results of the study presented fo cus on transient runs performed on CHPC. Optimization of nodes and cores w ere done to yield the most effective solver parallelization for these code s. Hold-up and resident times of particles are predicted inside the riser. The mathematical models of the riser application of two-phase flows repre sent from the biggest computerized parallel models in this field.\n\nhttps ://events.chpc.ac.za/event/33/contributions/714/ LOCATION: Hall C URL:https://events.chpc.ac.za/event/33/contributions/714/ END:VEVENT BEGIN:VEVENT SUMMARY:Effects of Island Shape on Magnetostatic Interactions in Bit Patte rned Media for Data Storage DTSTART;VALUE=DATE-TIME:20181203T123000Z DTEND;VALUE=DATE-TIME:20181203T125000Z DTSTAMP;VALUE=DATE-TIME:20260807T164614Z UID:indico-contribution-154-717@events.chpc.ac.za DESCRIPTION:Speakers: Josephat Kalezhi (Copperbelt University)\nBit patter ned media is one of the promising approaches to extend magnetic recording densities in hard-disk drives beyond recording densities of one Terabit (1 0^{12}) per square inch. In this approach\, the magnetic medium is pattern ed into nanometer-sized magnetic islands where each island can be consider ed to represent a binary digit. The islands are magnetically isolated but experience magnetostatic interactions between them. This study investigate s magnetostatic interactions between islands of various shapes for various island separations using micromagnetic simulations. The shapes range from truncated elliptic cones to cylinders. The computation of magnetostatic i nteractions is a major time-consuming task in a micromagnetic simulation. These interactions scale with O(N^{2}) operations\, where N is the number of interacting mesh elements in discretized islands. To carry out simulati ons\, an open-source finite element micromagnetics package called magpar w as used. The island mesh was generated using netgen\, a tetrahedral mesh g enerator. An open source visualization tool called paraview was used view the outputs of simulations. Open MPI was used in the simulations. Twelve c ores on one node were used in this work. The interactions between islands have been compared against dipole-dipole interactions where each island is assumed to be a dipole. The study has shown that for islands considered\, the effect of island shape is important for island separations less than twice the island width\, centre to centre. The dipole approximation is onl y sufficient for island separations beyond twice the island width. This re sult further suggests an improvement in the computation of time-consuming magnetostatic interactions between large numbers of islands by treating di stant islands as dipoles.\n\nhttps://events.chpc.ac.za/event/33/contributi ons/717/ LOCATION: Hall C URL:https://events.chpc.ac.za/event/33/contributions/717/ END:VEVENT BEGIN:VEVENT SUMMARY:First−Principles Study of Semiconductor-Based Photocatalyst Mate rials for Environmental Remediation DTSTART;VALUE=DATE-TIME:20181203T100000Z DTEND;VALUE=DATE-TIME:20181203T102000Z DTSTAMP;VALUE=DATE-TIME:20260807T164614Z UID:indico-contribution-154-716@events.chpc.ac.za DESCRIPTION:Speakers: Penny Govender (Department of Applied Chemistry\, Un iversity of Johannesburg)\nDue to increasingly global environmental and en ergy crises\, visible light semiconductor photocatalyst with a tunable ban dgap and optical properties have received attention. For this reason\, dev eloping efficient and cost–effective photocatalysts for environmental re mediation is a growing need\, and semiconductor photocatalysts have now re ceived more interest due to their excellent photocatalytic stability and a ctivity. The charge transfer\, catalytic stability\, electronic and optica l properties of several semiconductor–based photocatalyst materials were systematically studied using first–principles study. All the calculatio ns were performed using the Cambridge Serial Total Energy Package (CASTEP) code [1] implemented in Materials Studio 2016 [2] with the plane–wave u ltrasoft pseudopotentials method [3] and Perdew–Burke–Ernzerhof (PBE) functional for the exchange and correlation contribution [4]. All the simu lations were done using the resources provided by the Centre for High Perf ormance Computing (CHPC)\, Rosebank\, Cape Town [5]. The proposed photocat alyst materials show high photocatalytic activity under visible light irra diation with good stability and reduced bandgap compared to the bulk semic onductor. The heterostructures formed a type−II band alignment to accele rate the interfacial charge transfer process and the photocatalytic activi ty. By comparing the relative ratio of effective mass and band alignment r esults\, we could conclude that heterostructures have not only superior mo bility of charge carriers\, but also higher separation of photoinduced ele ctrons and holes.\n\nReferences\n[1] M. Segall\, P.J. Lindan\, M.a. Prober t\, C. Pickard\, P. Hasnip\, S. Clark and M. Payne. First–principles sim ulation: ideas\, illustrations and the CASTEP code. Journal of Physics: Co ndensed Matter 14 (2002) 2717–2744.\n[2] Materials Studio simulation env ironment. Release 2016\, Accelrys Software Inc\, San Diego\, CA (2016) \n [3] D. Vanderbilt. Soft self–consistent pseudopotentials in a generalize d eigenvalue formalism. Physical Review B 41 (1990) 7892–7895.\n[4] J.P. Perdew\, K. Burke and M. Ernzerhof. Generalized Gradient Approximation Ma de Simple. Physical Review Letters 77 (1996) 3865–3868.\n[5] Center for High Performance Computing. CHPC.\n\nhttps://events.chpc.ac.za/event/33/co ntributions/716/ LOCATION: Hall C URL:https://events.chpc.ac.za/event/33/contributions/716/ END:VEVENT BEGIN:VEVENT SUMMARY:High throughput computing considerations for Public Health Genomic s DTSTART;VALUE=DATE-TIME:20181203T090000Z DTEND;VALUE=DATE-TIME:20181203T092000Z DTSTAMP;VALUE=DATE-TIME:20260807T164614Z UID:indico-contribution-154-905@events.chpc.ac.za DESCRIPTION:Speakers: Alan Christoffels (University of the Western Cape)\n Bioinformatics occupies the space between biology and computing and aims t o answer\nquestions in biology using analytical and computing methodology. At the South African\nNational Bioinformatics Institute (SANBI)\, our res earch focus is on methods to store\, retrieve\nand analyze genetic informa tion that spans both communicable and non-communicable\ndiseases. In the c ontext of Public Health\, that is a need to interrogate genetic informatio n\n(DNA) from both hosts (human) and pathogens (bacterial or viruses) to u nderstand\nsusceptibility to diseases and ultimately to track infection tr ends in real time.\nThe ever-increasing volume of data being generated in the public domain places a strain on\nin-house computing resources. While the computing facility at SANBI-UWC is adequate for\ninitial R&D\, these r esources are inadequate to complete projects timeously. The nature of\nthe bioinformatics workflows that require CHPC resources can be grouped into (1) high\nthroughput computing resources that are needed to describe the 1 000s of genetic messages\nin a genome\, versus (2) high performance comput ing resources that is needed to model a\ndrug-protein interaction environm ent - these simulations require days/weeks of dedicated\ncompute time.\nWe have leveraged the CHPC facility in the context of infectious disease res earch with a\nview to analyze genetic variation in bacterial genomes\, and to identify drug targets in\npathogen genomes. These analyzes requires an environment that is able to support\nreproducible workflows and virtualiz ation of the software environment. Examples of these\nuse cases will be de scribed.\n\nhttps://events.chpc.ac.za/event/33/contributions/905/ LOCATION: Hall C URL:https://events.chpc.ac.za/event/33/contributions/905/ END:VEVENT END:VCALENDAR