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.

SKAO Launches

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.

Find out more from SKA and SKA Observatory.

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.

Discovering Giant Radio Galaxies

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.

Dr Matthew Prescott, second author on the paper, is a Post-Doctoral Research Fellow with UWC’s Astrophysics Group . Read an interview with him about his work. UWC eResearch Director Prof Mattia Vaccari and several other UWC researchers are also co-authors.

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.

Gates Foundation open funding call for research studies to accelerate knowledge of COVID-19 through data science

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.

Welcome to Dr Frederic Isingizwe!

eResearch Scientist Frederic Isingizwe

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.

I was born and grew up in Rwanda, where I got my first degree in Physics. Being an avid learner and intrigued by computer technologies, I opted for a postgraduate program at AIMS south Africa which led to a degree in Mathematical Sciences and later on, an MScEng and PhD in Electronic Engineering from Stellenbosch University, South Africa. While a graduate candidate, I was involved in research on superconductor devices, applied spectroscopy and biosystems modelling, managing a postgraduate research laboratory for biological sensors and nanodevices development. Upon completion, I assumed a role for technical advisory and research support for postgraduate students in sensor-based 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.

Some of my work: Google Scholar | Science Communication | Github