The Forensic DNA Lab (FDL, UWC) will be running an eWorkshop (online workshop) on using the Command Line Interface, Unix, shell and other tools for genomics.
The course will run from 10 June to 15 July with once a week lessons. The course is aimed at graduate students and research scientists who will work with genomic and bioinformatic datasets for the first time. We will help attendees get started in using the CLI for performing genomic workflows. Attendees require no previous experience in CLI tools.
More about the eWorkshop
Command line interface (CLI) and graphic user interface (GUI) are different ways of interacting with a computer’s operating system. The CLI allows you to control your computer using commands entered with a keyboard instead of controlling graphical user interfaces (GUIs) with a mouse/keyboard combination.
The CLI is important for proficiency in genomics as most bioinformatics tools use the shell and have no graphical interface. Importantly, CLI is essential for using remote high performance computing centers e.g. ILIFU, CHPC.
After the course, participants should be able to:
Discuss practical differences between Unix and Windows;
Navigate and manipulate files and folders using standard bash commands;
Write basic scripts for bash including piping between commands;
Access the ILIFU HPC and submit simple scripts to SLURM; and
Discuss folder/directory structure for genomic projects.
The NIH (US National Institute of Health) Common Fund’s Bridge to Artificial Intelligence (Bridge2AI) program is designed to help propel biomedical research forward by setting the stage for widespread adoption of artificial intelligence (AI) and machine learning (ML) that tackles complex biomedical challenges beyond human intuition. It is a new NIH Common Fund program, and will tap into the power of AI to lead the way toward insights that can ultimately inform clinical decisions and individualize care. AI, which encompasses many methods, including modern machine learning (ML), offers potential solutions to many challenges in biomedical and behavioral research.
The Bridge2AI program plans to support several interdisciplinary Data Generation Projects (OTA-21-008) and one complementary cross-cutting Integration, Dissemination and Evaluation (BRIDGE) Center (NOT-RM-21-021) to generate flagship data sets and best practices for the collection and preparation of AI/ML-ready data to address biomedical and behavioral research grand challenges.
It also plans to support the formation of teams richly diverse in perspectives, backgrounds, and academic and technical disciplines. The current Research Opportunity Announcement (ROA) for Data Generation Projects for the Bridge to Artificial Intelligence (Bridge2AI) Program (OT2) (OTA-21-008) requires a Plan for Enhancing Diverse Perspectives (PEDP)—a summary of strategies to advance the scientific and technical merit of the proposed project(s) through inclusivity. Visit the Bridge2AI Program Resources page and Program FAQs for additional information on building diverse teams and for PEDP guidance. To facilitate team building across communities and ensure responsiveness of proposals, NIH strongly encourages potential proposers to participate in the Grand Challenge Team Building Activities taking place in June 2021, please save the date for these upcoming events:
Bridge2AI Program Town Hall June 9, 2021 2:00-3:30pm ET Bridge2AI Data Generation Project Module Microlabs June 14, 16, and 18, 2021 2:00-4:00pm ET each day Bridge2AI Grand Challenge Team Building Expo June 23, 2021 11:00am-5:00pm ET
Further information about how to register and participate in these events, as well as an online networking platform, will be coming soon. Please check the Bridge2AI Scientific Meetings page for updates. Please refer to the research opportunity announcement (OTA-21-008) for additional information on application submission and review. A Letter of Intent (LOI) is required, LOIs must be emailed to bridge2ai@od.nih.gov by 11:59 PM ET on or before July 20, 2021. We encourage you to share the Bridge2AI listserv signup with your contacts and networks so they will receive updates on future funding announcements and the latest news from the Bridge2AI program. You can also keep up to date with the latest information by visiting the Bridge2AIwebsite. Questions can be sent to bridge2ai@od.nih.gov.
Read more about the vision for this new program in a recent NLM Director’s blog.
SKIES (SKilled, Innovative and Entrepreneurial Scientists) is an EU-funded project launched at the beginning of March. It aims to provide PhD and young doctoral researchers in the field of astronomy with new transferable skills for academia and industry, integrating open science, social innovation and entrepreneurship topics.
Leiden University in the Netherlands is leading the project, and local PI Dr Lucia Marchetti (from UCT’s Astronomy department) is the lead for the South African involvement of the initiative. eResearch Director and Astroinformatics Research Professor Mattia Vaccari is involved in the project too, along with SARAO. The project will run for 18 months.
“While an advanced degree in STEM subjects has long been an excellent basis for a career e.g. in the tech industry, most graduates still have to pick up additional skills along the way. The SKIES project aims to bridge this gap by enabling Astronomy PhD students to build upon their strengths to develop into well-rounded scientists and professionals. This is particularly important for SA in the increasingly global talent search of the 4IR era”, says Prof Vaccari.
SKIES will be implemented in astronomy research organisations around the world, including South Africa, Germany, The Netherlands, Poland and Portugal, reaching 500 astronomy graduate students and young researchers. A Train-the-Trainer programme will build the capacity of the teaching staff in each partner country so that they have the knowledge and tools to continue the programme beyond the lifetime of the project.
“I am thrilled to be able to offer this opportunity to our PhD candidates. Their astronomy training already provides them many theoretical skills they can apply into a job outside academia, like programming and problem-solving. With this training, we will now show them how they can best exploit and translate their knowledge into a job beyond astronomy. In this way we will ensure that all our astronomy students are fully equipped for whichever path they decide to take after their PhD”, says local PI Dr Lucia Marchetti.
“The South African Radio Astronomy Observatory (SARAO) supports this exciting collaboration, which gives doctoral students the necessary skills for a smoother transition from academia to industry. It is expected that the SKIES project will lead to increased employability of doctoral students in industry or through entrepreneurship, who will be effectively working on high-impact areas to benefit broader society on the African continent. We look forward to implementing this training and development opportunity with our South African and European partners.”, says Dr Bonita de Swardt, SARAO Programme Manager: Strategic Partnerships for Human Capital Development.
The European Astronomical Society virtual meeting EAS 2021 will hold a Special Session on 28 June – SS5 Data-intensive radio astronomy: bringing astrophysics to the exabyte era. It will feature UWC’s eResearch Director Mattia Vaccari, a member of the organising committee.
The session will cover the current status and challenges faced by radio astronomy in handling large data volumes, and technical solutions and applications within and outside astronomy.
The aim of the session is to bring together different communities (astrophysics, high-energy physics, research institutes, industry) to discuss current tools and ideas for the future development of data management. The meeting hopes to enhance the broader knowledge base through various approaches to tackling the challenges SKA radio telescopes are facing, now and in the future.
The topics that will be covered include Data-intensive radio astronomy, current facilities and challenges; Data science and the exa-scale era: technical solutions within astronomy; Data science and the exa-scale era: applications and challenges outside astronomy.
Scientific Organising Committee – Special Session 5 EAS2021
chair – Eleni Vardoulaki (TLS, Germany) co-chair – Marta Dembska (DLR, Germany) co-chair – Alexander Drabent (TLS, Germany)
The SKA Observatory (SKAO) is an intergovernmental organisation dedicated to radio astronomy and was launched on 4 February following its first council meeting. SKAO is tasked with “building and operating the two largest and most complex radio telescope networks ever conceived to address fundamental questions about our universe”.
SKAO has headquarters in the UK, and sites in South Africa and Australia. It is the world’s second inter-governmental organisation that is solely dedicated to astronomy, and other members include Italy, the Netherlands and Portugal. Observers include France, Germany, India, Spain and Sweden. SKAO will begin recruitment in Australia and South Africa in the next few months, working alongside local partners CSIRO and SARAO to supervise construction, which is expected to last eight years, with early science opportunities starting in the mid 2020s.
South Africa’s MeerKAT telescope, currently operated by SARAO (South African Radio Astronomy Observatory), will become part (and make up approximately 25%) of the SKA1-Mid telescope or Phase 1 of the SKA mid-frequency telescope.
MeerKAT, situated in the Karoo, consists of a 64 dish-shaped antennas. It is an SKA precursor or ‘pathfinder’ telescope, and is the most powerful radio telescope in the southern hemisphere. The MeerKAT antennas, each 13.5 metres in diameter and standing about four stories high, are distributed over 8 km and are connected by buried power lines and optical fibre connections to very fast computers in the underground Karoo Array Processor Building (KAPB) on the Losberg site.
Image: Nighttime composite image of the SKA combining all elements in South Africa and Australia. Credit: SKAO, ICRAR, SARAO / Acknowledgment: The GLEAM view of the centre of the Milky Way, in radio colour. Credit: Natasha Hurley-Walker (Curtin / ICRAR) and the GLEAM Team.
Astronomers from UWC are part of an international team responsible for the remarkable discovery of two giant radio galaxies. These galaxies were spotted in new radio maps of the sky created by the MeerKAT International Gigahertz Tiered Extragalactic Exploration (MIGHTEE) survey. It is one of the largest survey projects underway with South Africa’s impressive MeerKAT radio telescope and serves as a precursor to the Square Kilometre Array (SKA) due to become fully operational in the mid-2020s.
The discovery has made waves in the astronomical community around the world. Read articles from CNN, SciNews, Phys.org and Tech Times to find out more.
Image: The giant radio galaxy MGTC J095959.63+024608.6; in the background is the sky as seen in optical light; overlaid in red is the radio light from the giant radio galaxy, as seen by MeerKAT. Image credit: I. Heywood, University of Oxford / Rhodes University / South African Radio Astronomy Observatory / CC BY 4.0.
The Bill & Melinda Gates Foundation continues to work with the public and private sectors in the global response to COVID-19.
The International COVID-19 Data Alliance (ICODA) and the Bill & Melinda Gates Foundation’s Grand Challenges initiative, supported by the COVID-19 Therapeutics Accelerator, are announcing an open funding call for research studies to accelerate knowledge of COVID-19 through data science: Grand Challenges ICODA COVID-19 Data Science. Register for an informational workshop to be held on January 7, 2021 (14:00 UTC), and the grant application deadline is January 19, 2021
Researchers can register for an informational workshop to be held on January 7, 2021 (14:00 UTC), and the grant application deadline is January 19, 2021.
“We invite you to read summaries of the grants awarded to date through Grand Challenges initiatives with the Gates Foundation as funder or co-funder and to explore an interactive world map of projects across the broader Grand Challenges funding partner network.If you have a great idea for one of the open opportunities, please apply. If you know someone else who has a great idea, please forward this message so they can apply and sign up on our Grand Challenges website for email updates with the latest opportunities. We look forward to receiving innovative ideas from around the world.”
To learn more about the foundation’s broader work and how COVID-19 is being addressed across the foundation, visit the foundation’s website and sign-up for The Optimist newsletter. See videos of the plenary sessions at the 2020 Grand Challenges Annual Meeting, for the first time in virtual format and with a focus on addressing the current pandemic and using partnerships and lessons learned to speed progress across a broad range of global health and development goals.
My name is Frederic Isingizwe, I am a research scientist and science communicator, most specifically within the area of modern computational methods to enable carrying out data-driven research efficiently. I have a special interest in the application of data science methods and artificial intelligence in any way that helps improve the quality and sustainability of life in the world.
My higher education span Physics, Mathematical Sciences and Electronic Engineering (MScEng and PhD). While a graduate candidate, I was involved in research on superconductor devices, applied spectroscopy and bio-systems modelling, managing a postgraduate research laboratory for biological sensors and nano-devices development. Upon completion, I assumed a role for technical advisory and research support for postgraduate students in sensors development and applications research projects.
Since then, I was a postdoctoral research fellow under the South African research chair in postharvest technology at Stellenbosch University. While there, I applied machine learning methods on spatial and multi-wavelength spectral data to advance non-destructive techniques for quality testing and control in postharvest production environments.
I have now joined the eResearch Office at UWC as an eResearch Scientist, and my comprehensive role is to help bring its mission to a success.
It’s International Open Access Week (19-25 October), and UWC Library is celebrating with libraries around the world under the theme Open with a purpose: Taking action to build structural equity and inclusion.
During this week the library will host a number of webinars and presentations, and UWC has entered the international Figshare upload competition, where the individual researchers can win prizes for uploading their research data. For more information about the competition email us on rdm-support@uwc.ac.za.
Tuesday 20th October 2020 10:00 – 11:00
Welcome by Dr Shirlene Neerputh, UWC Library Director Data Intensive Research at UWC by Prof M Vaccari, Director eResearch at UWC The Carpentries in Africa by Dr Angelique van Rensburg, The Carpentries Facilitators: Sarah Schafer & Mattia Vaccari
Wednesday 21st October 2020 10:00 – 11:00
Introduction to Figshare by Megan Hardeman, Head of Engagement at Figshare
UWC RDM Services by Mark Snyders, Manager Scholarly Communications, UWC Library Services
Thursday 22nd October 2020 10:00 – 11:30
The value of open access publishing in the times of Covid-19 pandemic infected research environment by Alfred Nqotole, Deputy Director Research Support & Scholarly Communications, UWC Library Services Open Access Publishing: UWC Editor’s Perspectives by Prof M Dinbabo and Prof R Shambare
Facilitator: Alfred Nqotole
Register in advance for this webinar: https://uwc.zoom.us/webinar/register/WN_jIWs08KGS4CiDJRKzMGgUA
About the speakers:
Angelique van Rensburg, PhD (Educational Psychology), is the Regional Consultant for Southern Africa at The Carpentries and an Extraordinary Researcher at Optentia Research Focus Area, North-West University, Vaal Triangle Campus. Angelique aims at developing strategies and workflows to adapt The Carpentries’ membership and workshop programs to function optimally in Southern Africa. In addition, her role aims to assist and advise in developing a plan to create and support a strong team of volunteer instructors across Africa.
Megan Hardeman is head of engagement at Figshare. For the last four years, she has helped researchers make the most of storing, sharing, and collaborating using Figshare and has written case studies, delivered talks and training, leads the ambassador programme, and more. Previously, she was a Product Manager at Emerald Publishing.
Mattia Vaccari is Director of eResearch and AstroInformatics Research Professor at UWC, and he coordinates UWC’s Data Intensive Research emerging niche, which brings together researchers from different fields to foster multi-disciplinary collaboration in big data science. He has worked as a Research Scientist at Imperial College London, the University of Padova and UWC, working at the junction between astronomical instrumentation, big data processing technologies and extragalactic astrophysics.
Mulugeta Dinbabo is the Chief Editor of the African Human Mobility Review (AHMR), an accredited Journal by the Department of Higher Education and Training (DHET). AHMR is an interdisciplinary journal created to encourage and facilitate the study of all aspects (i.e. socio-economic, political, legislative and developmental) of human mobility in sub-Saharan Africa.
Richardson Shambare is an Associate Professor in the School of Business and Finance (SBF) at the University of the Western Cape. Prof Shambare has a keen interest in entrepreneurship and marketing in SMMEs. He has published several peer-reviewed articles, books, and book chapters and presented research at numerous international conferences. Prof. Shambare is the co-founding editor of the Journal of Entrepreneurial Innovations. The JEI specialises in publishing research and analyses pertaining to entrepreneurship trends and particularly innovations in the small, medium, and micro enterprises (SMMEs). The JEI is an Open Access, free to publish online journal.
In addition to the webinars and sessions available, UWC has entered the international Figshare upload competition, where the individual researchers can win prizes for uploading their research data. For more information about the competition email us on rdm-support@uwc.ac.za.
On 23 September, the DVC Research and Innovation hosted a webinar titled ‘An impetus for Social Innovation and Development and Data Intensive Research: Higher Education, Food Security, Big Data and the Fourth Industrial Revolution’. The session demonstrated various niche areas at UWC, including Social Innovation and Development and Data Intensive Research. Presentations on research projects included the following:
University as a Vehicle to Achieve Social Innovation and Development: Repositioning the Role of the University in Society.
Dr Lwando Mdleleni works at UWC as a researcher in the office of the Deputy Vice Chancellor: Research and innovation. His particular research focus is on social innovation and development. The underlying notion around his position is to foster the role that the university plays in collaborating with communities. He is the founding director of Zenzeleni Networks, where he focused on research and community development in rural South Africa.
Can social innovation provide solutions to relieve economic vulnerability and address food (in)security in the context of natural disaster? Critical analysis of the influence of social innovation during uncertain times of crisis.
Shehaam Moosa is a Master’s student at the Institute for Social Development. She is affiliated to the DSI-NRF Centre of Excellence in Food Security and the Office of the Deputy Vice-Chancellor: Research and Innovation. She is a graduate of the University of Cape Town holding a Bachelor of Social Science, as well as a Bachelor of Development Studies Honours from the University of the Western Cape. Her research focuses on the influence of social innovation during uncertain times of natural disaster, particularly whether crisis culminates collaboration, in terms of addressing economic vulnerability and food (in)security. She is passionate about sustainable development, social transformation and enabling the most vulnerable.
A deeper look at the Fourth Industrial Revolution (4IR) and what it means for the marginalized, a Social Innovation perspective.
Sihle Maphukatha is a Master’s student in Computer Science, his research focus on Fourth Industrial Revolution and Social Innovation. He has a BSc degree in Environmental and Water Science with honours in Integrated Water Resource Management and he has recently obtained his postgraduate diploma in Software Development, all at UWC.
Data Intensive Research for Drug Development, Therapeutics and Precision Medicine.
Dr Samuel Ayodele Egieyeh is a seasoned and highly experienced pharmacist (qualified in 1997) with B.Pharm (UNILAG), M.Pharm (UWC) and PhD in Bioinformatics (UWC). He also has a post-graduate diploma in clinical research and drug development from the University of Basel, Switzerland. He started his research career as a research fellow in 2001 at the Department of Pharmaceutics and Pharmaceutical Technology, National Institute for Pharmaceutical Research and Development (NIPRD) in Abuja, Nigeria, where he was involved in the formulation, production and quality control of herbal medicinal products and raw material development. He is currently a senior lecturer at the School of Pharmacy at UWC. He leads the Computational Pharmacology and Cheminformatics Group (CPCG). His research focuses on computational drug discovery and design; data science (including cheminformatics, bioinformatics, machine learning and biostatistics techniques) for predictive drug development and precision medicine. His presentation will show the use of data science in drug discovery and development, therapeutics, and precision medicine. The presentation will also introduce the “University of the Western Cape’s Computational Pharmacology and Chemoinformatic Platform”, which analyses hit compounds from high-throughput assays (HTS) available in public bioactivity databases. The platform provides data analytics and data mining tools for researchers in drug discovery and design to analyse and mine useful data from their in-vitro experiments in order to make rational and viable drug discovery and design decisions.
Machine Learning for Data Intensive Applications in Communication Networks
Dr Clement N. Nyirenda joined UWC as a Senior Lecturer in Computer Science in October 2018. He received a PhD in Computational Intelligence and Systems Science from Tokyo Institute of Technology in 2011 and spent one year as a postdoctoral researcher at Keio University, Japan. His research efforts revolve around Artificial Intelligence techniques and their applications in Communication Networks and Smart Environments. In this presentation, he will give an overview of three machine learning projects that he has been working on over the past few years. The first project focuses on human position determination in indoor environments using Hierarchical Reservoir Computing (HRC) based on Array Antenna signals. The second one involves radio signal strength prediction using Echo State Networks (ESN), and the third application involves the detection of data anomalies in smart water metering networks using unsupervised learning techniques.