ilifu-supported Africa CDC course at SANBI

SANBI are currently teaching a course on SARS-CoV-2 (COVID-19) bioinformatics to visitors from public health labs across Africa. The course is taking place at the University of the Western Cape from the 23 to 27 May 2022, and is using ilifu, South Africa’s big data infrastructure for data-intensive research. 

Africa CDC aims to strengthen capacities and capabilities at public health institutions in Africa in order to detect and respond quickly and effectively to disease threats and outbreaks. They have data-driven interventions and programmes, and SANBI has been working with Africa CDC since 2018. 

In 2020, the Africa CDC launched its Institute of Pathogen Genomics (IPG), which has been at the forefront of supporting SARS-CoV-2 sequencing on the African continent. SANBI is one of the specialist centres assisting Africa CDC in its work developing pathogen genomics and bioinformatics. As part of this role, they are running a week-long course on SARS-CoV-2 sequence analysis for people from public health labs in 9 African countries – Morocco (Institut Pasteur du Maroc), Egypt (Central Public Health Laboratory), Ethiopia (Ethiopian Public Health Institute), Uganda (Center Public Health Institute), Kenya (National Public Health Laboratory), Senegal (Institut Pasteur de Dakar), Zambia (Zambian National Public Health Institute), Ghana (Noguchi Memorial Institute for Medical Research) and South Africa (National Institute for Communicable Diseases). Nigeria (Nigeria CDC) and DRC (Institut National de Recherche Biomédicale) could not attend in-person, but are participating online. 

Back row (L-R): Ziphozakhe Mashologu, Wael Saif, Harris Onywera, Peter van Heusden, Alan Christoffels, Leonard Kingwara, Ayitewala Alisen, Abebe Negeri, Abdelmajid Eloualid, Amadou Diallo. Front row (L-R) Susan Alicia Fernol, Michelle Lowe, Annie Chan, Tracey Calvert-Joshua, Quaneeta Mohktar, Francis Ahiakpah, Moussa Diagne. Not present: Mpanga Kasonde, Akil Prince, Emmanuel Lokilo . 

SANBI have been ilifu partners since its inception, and Peter van Heusden, Senior Bioinformatician at SANBI, is one of the organisers of the workshop. He says that participants have found it to be “an excellent resource to support public health bioinformatics”. ilifu is a node in the South African national data infrastructure which enables South African researchers to be leaders in the strategic science domains of astronomy and bioinformatics. 

Course participants working on data analysis in SANBI’s Aaron Klug seminar room, 23 May 2022.

The training relies on cloud infrastructure provided by Ilifu – each lab gets their own installation of SANBI’s SARS-CoV-2 Workbench to work on, and gets hands-on experience with uploading data, doing data analysis and visualising their results. While the current training has focused on SARS-CoV-2, the discussions have ranged across a number of other infectious diseases that these public health labs are responding to: HIV, TB, hepatitis, malaria, influenza and other pathogens. SANBI sees this training as feeding into Africa CDC’s efforts to build a Community of Practice in public health bioinformatics and genomic surveillance.

Training Opportunity : Data Science and Machine Learning

A training opportunity for data science and machine learning is available and registration closes on 25 May.
 
Makerere University School of Public Health (MakSPH) in Kampala, Uganda, is working in partnership with four other African universities to research the COVID-19 response in Africa. Through the collaboration, a community of practice (COP) has been establised. It is aimed at developing the capacity of African institutions to prepare, analyse and respond to disease epidemics successfully.
 
As part of the COP, and in partnership with IBM Research Africa (IBMRA) scientists, who have expertise in artificial intelligence (AI), data science, and machine learning, the project has organised a capacity-building opportunity on data science and machine learning.
 
Participants interested in or with a background in data science, artificial intelligence, machine learning and cloud computing are encouraged to register. There is no minimum skill requirement aside from computer literacy.

Topics that will be covered include analysing the impact of COVID-19 on essential health services using time series analysis; learning from COVID-19 models to support what-if scenario analysis; and intervention planning and descriptive statistics to analyse NPIs implemented in African countries.

The training will be conducted online through Webex, with an expected engagement of about 2 hours every week. Facilitation will be in both English and French, and the programme will run until October 2022.

Interested participants can register herehttps://shorturl.ae/Gd3EC
by 25 May 2022.

Africa Women in Data Science: Online Event

DARA Big Data (Development in Africa through Radio Astronomy), in partnership with the Office of Astronomy for Development (OAD), IDIA (Inter-University Institute for Data Intensive Astronomy) and SARAO (South African Radio Astronomy Observatory) is hosting a free 3-day Africa Women in Data Science online event. The event will coincide with International Women’s Day 2022 and will also mark the one year anniversary of the publication of the SARAO Women in Data Science report.

The event organisers hope to help build a thriving African community of female data scientists and promote skills development for women who are interested data science careers. Registration for the event closes January 31 2022.

The event will take place from 8-10 March 2022, which coincides with International Women’s Day. It aims to increase African women’s participation in the 4th Industrial Revolution (4IR) to build a prosperous, resilient Africa of the future. The integral role of African women for the 4IR will be discussed and various opportunities will be showcased for young women hoping to get into the field of data science.

Africa Women in Data Science is free to attend and will be split into a conference on Day 1 (March 8) and a hackathon on Days 2 and 3 (March 9-10). The conference will feature inspiring female panel discussions, presentations from leading industry experts and question and answer sessions. Day 1 is open to anyone across Africa with a keen interest in data science. To register for the conference, only complete the first section of the registration form.

Register here: https://www.astro4dev.org/2022/01/11/registration-open-for-africa-women-in-data-science-event-iwd2022/

Enquiries can be emailed to linzi.stirrup@manchester.ac.uk

Using machine learning for food quality and safety assurance

The latest research published by eResearch Office’s Dr Frederic Isingizwe on detecting defects in fresh agri-food products dealt with detecting soft damage to apple fruit while they are still invisible to the naked eye.

Damage to fresh agri-food products due to brute impact or compression force can occur during handling and transport, can be invisible at an early stage but becomes more pronounced with time, either in the consumer’s hands or on a retailer’s shelf. Such damage to fresh produce accelerates the deterioration of fruit and vegetables and can facilitate infections by micro-organisms, which makes products unsafe to consume.

The research was conducted to aid with sorting and grading fresh products, either at an industrial or smaller scale. We demonstrated that these invisible defects can be detected using shortwave hyperspectral imaging techniques and by using machine learning algorithms, we established the degree to which the differentiation of defective from sound apple fruits is feasible.

Read more about this work here.

eWorkshop: Command Line Interface for Genomics Beginners

Forensic DNA Lab UWC

UWC’s Forensic DNA Lab (FDL) hosted an eWorkshop (online workshop) on using the Command Line Interface, Unix, shell and other tools for genomics.

The course was aimed at graduate students and research scientists who will work with genomic and bioinformatic datasets for the first time and ran from 10thJune to 15thJuly in two hours weekly sessions.

Seventeen (17) participants were registered, including staff, Honours, Masters and PhD students from different institutions including the South African Biodiversity Institute; University of the Western Cape; Stellenbosch University; University of Johannesburg; University of Pavia (Italy) and ICGEB/UCT.

More about the eWorkshop

Command line interface (CLI) and graphic user interface (GUI) are different ways of interacting with a computer. The CLI ‘is a text-based interface used to interact with software and operating system by typing commands into the interface and receive a response in the same way’. The GUI on the other hand, is a visual-based interface featuring the use of graphic images such as windows, icons and menus, and is navigated mostly using a mouse and the keyboard sometimes.

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.

The course was designed to impart the following knowledge and skills to the participants:

  1. Discuss practical differences between Unix and Windows;
  2. Navigate and manipulate files and folders using standard bash commands;
  3. Write basic scripts for bash including piping between commands;
  4. Access the ILIFU HPC and submit simple scripts to SLURM; and
  5. Discuss folder/directory structure for genomic projects.

The ilifu cluster computing infrastructure was used for training tasks, which included lessons on basic Unix bash commands and practical activities which required specialised Singularity containerized software.

X-ray Observations Supporting MIGHTEE MeerKAT Science Project Unveiled

New X-ray map reveals the growing supermassive black holes in next-generation MeerKAT survey fields 

One of the largest X-ray surveys using the European Space Agency’s XMM-Newton space observatory has mapped nearly 12,000 X-ray sources across three large, prime regions of the sky. The X-ray sources represent active galactic nuclei and galaxy clusters, and the survey captures the growth of the supermassive black holes at the cores of these galaxies. This X-ray survey complements previous X-ray surveys, allowing the researchers to map active galactic nuclei in a wide range of cosmic environments.

The XMM-SERVS survey lays key groundwork for studying the cosmic history and physical  properties of active galaxies 

Figure 1: XMM-Newton image of the 4.6-square-degree W-CDF-S field reveals the wide, sensitive view of the X-ray sky provided by XMM-SERVS. The detected sources, most of which are growing supermassive black holes, are color coded according to the energies of the X rays detected (with red having the lowest energies and blue the highest). The white outline indicates the area of the Chandra Deep Field-South, a well-known ultradeep pencil-beam X ray survey. The image highlights how XMM-SERVS has now provided sensitive panoramic X ray imaging around this survey. The XMM-Newton image covers an area about 20 times larger than the apparent size of the full moon, shown to scale at upper left.
Figure 2: XMM-Newton image of the 3.2-square-degree ELAIS-S1 field, which is about 15 times larger than the apparent size of the full moon (shown to scale at lower right). XMM SERVS provides a wide, sensitive X-ray view of this region.

These X-ray observations will be invaluable to study the active galactic nuclei (i.e. black holes) and galaxy clusters (the largest cosmic structures bound together by gravity) detected by the MIGHTEE MeerKAT Large Survey Project (led by UWC Visiting Professor Matt Jarvis and UWC Research Chair Russ Taylor) in its ongoing mission to study the faint radio sky.

Qingling Ni and W. Niel Brandt from Penn State presented the results of the XMM-Spitzer  Extragalactic Representative Volume Survey (XMM-SERVS) at a press briefing during the 238th meeting of the American Astronomical  Society on 7 June. A paper describing the survey, authored by an international team of astronomers including UWC’s eResearch Director Prof Mattia Vaccari, has been accepted for publication in The Astrophysical Journal Supplement. A pre-print is also available on arxiv.org.

“X-ray surveys are the best way to find growing supermassive black holes, which are located at  the cores of many large galaxies,” said Ni, a graduate student at Penn State and lead author of  the paper. “With this massive new survey, we can access population data about growing  supermassive black holes to better understand their physical properties and evolution over cosmic history.” 

“This survey represents key foundational work upon which, I suspect, hundreds of studies will  be built over the next decade or two,” said Brandt, Verne M. Willaman Professor of Astronomy  and Astrophysics and professor of physics at Penn State, and one of the leaders of the study.  “XMM-Newton was the best mission to gather these data, and we needed to invest a lot of  observation time for this study—with a total combined exposure of nearly 60 days—because it  will be so important for active galaxy studies, galaxy cluster studies, and for understanding  large-scale structures in the universe. It required a multiyear, multinational effort and it’s  incredibly gratifying to get it done. We are most grateful to the European Space Agency and  NASA for their long-term support of this work.” 

Caption from featured image: XMM-Newton image of the 5.3-square-degree XMM-LSS field, which is about 25 times  larger than the apparent size of the full moon (shown to scale at lower right). XMM-LSS was the  first XMM-SERVS field to have been observed by XMM-Newton. Chien-Ting Chen, a former postdoctoral researcher at Penn State who is now an astronomer at USRA, led the work for this  field (see Chen et al. 2018, Mon. Not. Roy. Ast. Soc.). XMM-SERVS provides a wide, sensitive X ray view of this region

eWorkshop: Command Line Interface for Genomics Beginners

Forensic DNA Lab UWC

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:

  1. Discuss practical differences between Unix and Windows;
  2. Navigate and manipulate files and folders using standard bash commands;
  3. Write basic scripts for bash including piping between commands;
  4. Access the ILIFU HPC and submit simple scripts to SLURM; and
  5. Discuss folder/directory structure for genomic projects.

The course registration is now closed.

Research Opportunity Announcement: Data Generation Projects for the Bridge to Artificial Intelligence (Bridge2AI) Program

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

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.

Madagascar Astronomy Python Workshop 2017. Credit: IAU Office of Astronomy for Development archive
Madagascar Astronomy Python Workshop 2017. Credit: IAU Office of Astronomy for Development archive

“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 project summary can be viewed here.

European Astronomical Society Special Session

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)

Mattia Vaccari (UWC, South Africa)
Roberto Pizzo (ASTRON, Netherlands)
Hans-Rainer Kloeckner (MPIfR, Germany)
Giuliano Taffoni (INAF, Italy)
Matthias Hoeft (TLS, Germany)

Find out more about EAS 2021 European Astronomical Society Annual Meeting 2021

The deadline for abstract submission is 2 March 2021. Researchers can submit abstracts here. The organising group will accept oral and poster presentations. Please also note that the same deadline applies for applications for fee waivers.

SS5 Data-intensive radio astronomy: bringing astrophysics to the exabyte era will be an afternoon session at CET (Central European time) on 28 June.