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H3ABioNet Newsletter Issue 37: February 2022

FOREWORD

This newsletter was originally planned to be the last for 2021, but as usual, time flew and the end of year came and went all too quickly. Therefore, welcome to the first issue of 2022! This has a strong focus on training and capacity development, describing activities from training young school learners to training trainers and developing new leaders. It is great to see the impact of the H3ABioNet training and the passion of both the trainers and trainees to use their skills to make a difference.

We also celebrate the award of grants within the new NIH Harnessing Data Science for Health in Africa (DS-I Africa) Initiative to H3ABioNet and H3Africa members. We were awarded the DS-I Africa Open data Science Platform and Coordinating Centre (the latter led by Dr Michelle Skelton). Our success was tied very closely to the lessons learnt and successes achieved during the H3ABioNet grant. Learning and capacity development through H3Africa and H3ABioNet also prepared African scientists for rapidly responding to the COVID-19 pandemic which has affected all our personal lives and academic activities. The first article describes the role of some of these scientists in fighting COVID-19. I invite you to read on to find out more about this and our other activities.

Nicky Mulder

H3ABioNet PI

The Importance of H3ABioNet Researchers in the Fight Against COVID-19

By: Edward Lukyamuzi, UVRI

Africa reported its first incidence of COVID-19 over a year ago. In comparison to its population of approximately 1.3 billion people, Africa has a low COVID-19 case count: 5,781,699 cases and 140,755 deaths as of mid-September 2021, accounting for about 3% of global cases. In light of the catastrophic situation on other continents and the global death toll of almost 4.5 million, Africa has fared well in the fight against COVID-19. Scientists in Africa are taking a proactive approach to this fight, performing genome sequencing, laboratory testing, and devising new ways to combat this global threat, while leveraging surveillance systems in place for the HIV pandemic and other viral epidemics to enable the rollout of COVID-19 testing as the first line of defense.

Polymerase Chain Reaction (PCR) techniques are commonly used to test for COVID-19. Nigeria, for instance, initially performed about 3,000 tests per day, a minute fraction of what’s required. To address this, Professor Christian Happi of the African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), developed a COVID-19 fast-track test. It costs around $3, far cheaper than $100 for a PCR test. His lab was the first to sequence the genome of SARS-CoV-2 in Africa proving that African scientists can generate critical data in the global fight against Covid-19. Since then, it has identified 55 variants of the virus, including the B.1.1.7 UK variant, tested more than 80,000 samples from Nigeria, sequenced 216 COVID-19 samples from Cameroon and trained frontline health personnel in PCR diagnostic techniques. In addition, the ACEGID produced a COVID-19 vaccine candidate with over 90% efficacy in preclinical studies and is working on a rapid molecular diagnostic test to detect SARS-CoV-2 using CRISPR gene-editing technology.

In September 2020, the World Health Organization (WHO) designated the ACEGID as one of eleven regional reference sequencing research laboratories for emerging pathogens, including the SARS-CoV-2. Among others include H3ABioNet nodes in Uganda & South Africa; Uganda Virus Research Institute (UVRI) and Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP) respectively. On 5th April 2020, UVRI confirmed the first person in Uganda to have contracted Covid-19. Since then the institute has been designated as the Covid19 national reference lab for which it has: conducted over 200,000 tests, validated and approved five antigen based RDTs, performed 6 sets of genomic sequencing of confirmed positive SARS-CoV-2 samples; samples collected from across the country and points of entry to track distribution of variants and possible entry of new variants, validated 6 new PCR platforms and protocols as well as accrediting 11 local laboratories to test for COVID-19. With WHO accreditation, neighbouring countries with limited testing capabilities can now send COVID-19 samples to be examined to the institute.

Another exciting development is the ground-breaking work at KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP) led by Prof Tulio de Oliveira who identified new variants of COVID-19 in South Africa and has also established a new institute at Stellenbosch University aimed at understanding and controlling epidemics and pandemics in Africa and the global south. His discovery of a new SARS-CoV-2 variant – 501Y.V2 (Beta variant), and more recently, Omicron, led to the discovery of other variants all over the world and enriched understanding of the effectiveness of vaccines. These developments demonstrate that African scientists can significantly contribute to the global fight against COVID-19. Who wouldn’t feel inspired to be a part of this new narrative!

Boost Foundation: Helping Kids Learn Coding with Play

By: Verena Ras & Gerrit Botha, UCT

Our resident Bioinformatician, Gerrit Botha has been assisting the BOOST foundation [https://boostafrica.com/programmes/] to teach kids coding through play. The boost foundation focuses on delivering unique, community based, learning experiences and has established computer labs, after school coding programs as well as a sewing centre and job readiness program, with many other programmes as well. Their main aim is to uplift the primary informal settlement within which they work, Dunoon, which is located just out of the Cape Town CBD in South Africa.

In the below image, Gerrit can be seen teaching kids circuit diagrams with a video showing what the kids have built at the end of the lesson – a vibrating creature made from washing pegs, paper clips, a 1.5 V battery, a ~1.5 V motor and cool decorations made by the kids [link to post with video]. On the top left of the image, you can also see Gerrit’s 7 year old daughter, Sufi. Sufi often helps Gerrit when she is not too busy with her own extra mural activities and Gerrit says she loves coming along with him.

Image taken from Boost Foundation's Instagram page @boostfoundation
Gerrit says: “My plan was to start with unplugged/functional coding this week with material that I got from a Professor at Nelson Mandela University. I'm however noticing the kids require some attention in regard to their math abilities. Think I'm going to contact numeric.org and see if we can get some curriculum worked out and rather focus on this for now. Learning as I go.”

Gerrit aims to help the kids improve their Maths skills and to get the kids doing robotics by the second quarter of next year. He hopes to acquire some funding in the future to purchase some kits for some more practical work with the kids.

Let’s give a round of applause to H3ABioNet’s commitment inside and outside of the office, to advancing data and IT skills on the continent! Anyone that is interested in finding out more information about the project/initiative or who would like to donate can find out more here.

Bioinformatics Incubation and Mentorship Program at ICIPE

By: Festus Nyasimi & Caleb Kibet, ICIPE

The Bioinformatics Incubation and Mentorship Program is part of the H3ABioNet in collaboration with the Eastern African Network for Bioinformatics Training (EANBIT) at the international centre of insect physiology and ecology. The program offers highly motivated graduate students interested in bioinformatics with an opportunity to learn hands-on problem-solving skills through an internship usually between 4 and 6 months.

The program is designed to first introduce the students to the bioinformatics field and the basics of programming languages such as Unix, python, and R relevant in genomics data analysis in three phases, i.e. learning phase, mini-projects and implementation/application phase. The learning phase entails intensive training where the interns are taken through the basics of bioinformatics, including but not limited to programming language, computational thinking, sequencing technology, data management, HPC modules, collaborative working and version control. These are designed to give them a basic understanding of the core concepts. In the mini-projects phase, they work on reproducing a paper or a study for skills retention. The mini-projects help them learn about how to apply different tools. It also boosts their confidence in their ability to use the skills gained. In the final phase, the interns are plugged into ongoing projects where they assist in data analysis through the guidance of the lead bioinformaticians. The project phase allows them to grow their skills and choose a career pathway in Bioinformatics.

The program offers interns blended learning through various on-campus training and online training courses overlapping their internship period. The online courses and workshops range from scientific communication to pipeline development organised by groups like H3A BioN et and Galaxy.

Besides the core bioinformatics training, the interns are also trained in communication, writing and presentation skills through weekly code review presentations, participation in journal clubs, project reports and monthly reports. There is a weekly Monday morning update within the team where they get to share what they are working on to update the team on their progress.

This incubation program lays a solid foundation to graduate students interested in bioinformatics and genomics, thus helping them venture and transition quite well in this field as well-trained bioinformaticians. Moreover, such graduates can also proceed with their future studies in Masters and PhD related bioinformatics and genomics programs. From the past three cohorts (16 trainees), we have 9 students who have been awarded full scholarships for their masters or are employed in reputable organisations.

Grants Give African Data Science a Boost

Originally published by: https://www.news.uct.ac.za/article/-2021-11-12-grants-give-african-data-science-a-boost | 12 NOVEMBER 2021 | STORY BY NOBHONGO GXOLO

Infrastructure and capacity development are a big focus of boosting health research on the African continent. This work will be facilitated through five-year grants awarded by the United States National Institutes of Health (NIH) Common Fund’s Harnessing Data Science for Health Discovery and Innovation in Africa, to three data scientists at the University of Cape Town’s (UCT) Institute of Infectious Disease and Molecular Medicine (IDM), based at the Faculty of Health Sciences (FHS).

Professor Nicky Mulder [http://www.idm.uct.ac.za/Nicola_Mulder], Department of Integrative Biomedical Science, Faculty of Health Sciences. Photo Supplied.

Professor Nicky Mulder and Dr Michelle Skelton, the project manager at the Human Heredity and Health in Africa (H3Africa) Coordinating Centre, have been awarded an NIH grant to run the Open Data Science Platform (ODSP) and Coordinating Centre (CC) for the NIH’s DS-I Africa (Harnessing Data Science for Health Discovery and Innovation in Africa) Consortium.

“The application of data science methodologies to large-scale, diverse and complex biomedical data sets for novel discoveries requires access to data, tools, workflows and computing infrastructure, along with training and support. With many of these lacking in Africa, including the skills for execution, there is a need to develop new infrastructure that considers the African context and addresses barriers present in low- and middle-income countries,” explained Mulder, a principal investigator at H3ABioNet (the Pan African Bioinformatics Network for H3Africa).

The ODSP will develop a flexible, scalable open data science platform for the DS-I Africa consortium to find and access data, select tools and workflows, and run analyses on a choice of computing environments – all through easy-to-use workspaces. Administration and support of the core resources and consortium activities will be coordinated by the CC. Together, the ODSP and CC will provide infrastructure for researchers to use data science technologies to deliver cutting-edge biomedical research for health, while promoting cohesion, collaborative cross-consortium activities, and engagement with external stakeholders to facilitate innovation and translation.

According to Mulder, the ODSP is a natural progression of their work at H3ABioNet. She explained: “The CC will draw on the experience of the H3Africa CC in coordinating activities of a pan-African consortium. H3ABioNet has developed bioinformatics capacity in Africa to enable scientists from the continent to analyse their genomics data. We developed tools and workflows, managed H3Africa data through the archive and catalogue, and created data portals to ease access to African data.”

The ODSP will draw on these outputs, extending the tools to incorporate more data science applications and implement some of the standards and workflows developed through H3ABioNet/H3Africa. The award will help ensure longer-term sustainability for their outputs and enable them to broaden their scope-of-work across more diverse data types and applications, while expanding their team to include more data scientists.

The ODSP component has 11 partners in Africa, the United States and the United Kingdom.

Associate Professor Emile Chimusa [http://www.idm.uct.ac.za/Emile_Chimusa], Department of Pathology, Faculty of Health Sciences. Photo Je’nine May.

Associate Professor Emile Chimusa, the convenor of the Human Genetics and Forensic Genetics Honours programme within the Division of Human Genetics, has also been awarded a DS-I Africa grant from the NIH, for a project titled Computational Omics and Biomedical Informatics Programme (COBIP).

Despite the significant human health and disease burden in Africa, no biomedical data science graduate degree programmes in computational omics, clinical informatics and translational research are offered on the continent. To foster research training that will cultivate graduates who are able to respond with agility to future biomedical data science needs and develop innovative solutions to address African health challenges, formal interdisciplinary training in biomedical data science is key.

“This award will add significant value to my work by enabling me to be part of the DS-I Africa consortium.”

COBIP will provide innovative educational infrastructure and research opportunities as well as links between clinicians, researchers and biomedical industries through placements and internships. Through its graduates the programme will impact African biomedical data science research and stimulate diagnostics, therapeutic selection and drug development to support improved healthcare on the continent and globally.

“This award will add significant value to my work by enabling me to be part of the DS-I Africa consortium, while allowing me to train the next generation of biomedical scientists through interdisciplinary training around data science, computational omics and imaging data science,” said Chimusa.

For this research training programme, UCT will partner with the Oregon Health and Science University. The programme will place strong emphasis on training graduate students and faculty from participating African institutions. This will be done through a combination of contact and online teaching, research projects and internships to foster biomedical data science research, aiming to build critical capacity in data science while driving the development of innovative solutions to African health challenges.

Professor Ambroise Wonkam [http://www.idm.uct.ac.za/Ambroise_Wonkam], Departments of Pathology and Medicine, Faculty of Health Sciences. Photo Je’nine May.

Professor Ambroise Wonkam has been awarded a grant from the NIH for a project titled Public Understanding of Big Data in Genomics Medicine in Africa (PUBGEM-Africa).

The project aims to explore and establish some major trends on emerging issues, particularly those related to models of public engagement in big data use for genomics healthcare and innovation in Africa.

There is growing acceptance that the greater availability to scientists of genomes from people from Africa will improve understanding globally of genomic variations, both for complex disease conditions and for monogenic diseases (those arising from a variation in a single gene). However, there remain concerns that the scientific imperative associated with increasing the information on African genomic variations in public databases won’t necessarily translate into enhancing genetic medicine implementation in Africa.

“It is our expectation that PUBGEM research outcomes will inform the continent’s development of appropriate and urgently needed guidelines and regulations.”

“We will investigate [the] perspectives of various stakeholders of the research ecosystem: data providers, data users, funders, [the] ethical review board, etc. It is our expectation that PUBGEM research outcomes will inform the continent’s development of appropriate and urgently needed guidelines and regulations, as we enter the third decade post the completion of the Human Genome Project, in which African genomics research will take centre stage.”

With a focus on big data in genomics medicine, PUBGEM-Africa aims to use empirical methods to address some of the pertinent ethical, legal and social implications (ELSI) of data science research from an African perspective, while contributing to policy discussion on the continent – especially as this relates to models of public engagement in big data use for healthcare and innovation, and particularly in South Africa, Cameroon and Ghana, where the project will be carried out. PUBGEM-Africa will set up an ELSI helpdesk for data science in health in Africa, and provide small grants and mentorship support to emerging data science bioethics scholars in Africa.

Wonkam, the director of Genetic Medicine of African Populations (GeneMAP), explained that the grant will “consolidate the strengths of our research ideas and underscore the sustainable international competitiveness of our work, while recognizing the urgency of the research agenda in the questions around ELSI when it comes to data sciences in genomics in Africa that are not being addressed adequately. It will provide us [with] resources to investigate some aspects of this agenda through research across the continent, while increasing capacity development.”

Image above from: Getty Images

Carpentries Instructor Training Certifies New Cohort of Trainers

H3ABioNet, supported by the South African Centre for Digital Language Resources (SADiLAR), hosted a Carpentries instructor training workshop which ran from 28 June to 2 July during 2021. The course was attended by 18 budding trainees who have all since worked on becoming fully fledged instructors! For those who don’t know, The Carpentries is a non-profit organisation whose overall aim and goal is to increase capacity in foundational coding skills across the world. The community works on community approved lessons which certified instructors may then use to run independent workshops. Lessons are well formulated with the help of educational and coding experts and since it is a voluntary effort, is open to just about anyone to get involved.

Of those who attended the workshop, most have already completed their instructor training assessments and have already received their instructor certification, with the remaining all working on completing their certifications. Our training also allowed the first ever instructor from Tunisia to become certified, Dr. Melek Chaouch who is from the IPT node of H3ABioNet.

Instructors sprang into action quickly, already hosting their first workshop as a team In October of 2021 [please see https://verena90.github.io/2021-10-05-online-NGS_Academy/] and aim to have their next workshop toward the end of March 2022.

The instructors already certified from the recent training have been listed below:

“Learning on the Job”

By: Afolabi Owoloye. PhD Scholar, University of Lagos, Nigeria

A bit about myself:

My name is Afolabi Owoloye, a PhD student of Bioinformatics and Parasitology at the University of Lagos, Nigeria. I have an MSc. (Distinction) in Molecular and Applied Parasitology. I am also a Research Assistant on a European Union-funded project under the European and Developing Countries Clinical Trials Partnerships (EDCTP) grant awarded to my Principal Investigator and Supervisor, Dr. Kolapo Oyebola who is the Head of the Genomic Research in Biomedicine Laboratory, Nigerian Institute of Medical Research. When I applied for the EDCTP-funded PhD Scholarship, Dr Oyebola told me that more than 35 applications competed for just one award and the interviews were tough. What gave me an edge over all my contemporaries was the experience I had garnered from H3A Bio Net IBT 2020 and my data analysis skills (e.g., Python, R programming, GraphPad, etc.). I have now acquired additional skills in molecular biology, bioinformatics, biostatistics and genomic data analysis. I have attended more workshops and courses to improve my skills. For instance, I was a participant at the H3ABioNet Introduction to Bioconductor 2021, H3ABioNet NGS 2021, VEupathDB Workshop 2021, NGD Linux unhatched etc.

My Bioinformatics voyages:

I am versatile in Computer-Aided Drug Design (CADD) using sophisticated software like Maestro Schrodinger, AutoDock Vina, etc., but H3Abionet IBT 2020 opened me up to the world of genomic data analysis. Having realised the importance of the H3ABioNet IBT 2020 workshop, I knew I was never going to miss H3ABioNet NGS 2021. I was added as an observer, thanks to the coordinator who gave me the opportunity. The workshop was highly impactful. My supervisor (Dr Oyebola) is so passionate about building Africa-based capacity for genomics and bioinformatics. As such, our laboratory (Genomic Research in Biomedicine) has established a genomics and data science hub in Nigeria. Our laboratory, through the EDCTP grant, successfully organised the first Bioinformatics and Genomic Data Analysis Workshop at the Nigerian Institute of Medical Research, Lagos, Nigeria. It was an on-site workshop involving 31 participants (including postdoctoral scientists, faculty, PhD and MSc students). Thanks to H3ABioNet for permitting us to use the NGS2021 data for the step-down training. The workshop covered; Introduction to Python and R programming, Introduction to Biological Databases, Unix/Linux Operating System, in silico Drug Design, Genome Assembly and Variant Calling Workflow.

Learning on the job

“Learn on the job”, my supervisor always says this whenever he gives a task that I know little or nothing about. What I am today is a result of learning on the job. We were meant to perform a meta-analysis on “Prevalence of potential mediators of artemisinin resistance in African isolates of Plasmodium falciparum” which has recently been accepted by Malaria Journal for publication. The article is the second of its type in Africa. What makes ours unique is the fact that we dissected more than one potential mediator of artemisinin resistance. Lastly, to everyone scouting to be part of a cutting-edge research group or looking for a scholarship, don’t forget that the job of learning precedes that of earning. For you to earn such an opportunity, I will suggest you take your time to learn the basics.

Image from Wikimedia commons

Courses/Training

  • H3ABioNet’s African Genomic Medicine Training is set to start in March 2022! The course has had >30 hosts sign up and are currently finalizing participant registrations. The course will be extended to clinicians and pathologists this year! The course will run from 14 March until 08 June 2022.
  • H3ABioNet is teaming up with the Wellcome Trust’s Wellcome Connecting Science team to offer our Next Generation Sequencing, blended learning course again in 2022. Classroom hosts have been finalised and we will see 39 classrooms host the course this year. The course will commence on 22 March 2022 and run until 20 June 2022.

Grants and Awards

  • Investigator-initiated research in computational genomics and data science (R01 clinical trial not allowed). For more info, click here. Application deadline – May 2022.
  • Digital Technology Development Awards (Climate-Sensitive Infectious Disease Modelling). This scheme provides funding for software developers from any career stage and discipline to develop digital tools that will improve climate sensitive infectious disease modelling. By the end of the award, successful applicants will have delivered a piece of open-source digital technology that will increase the impact of research in addressing this threat to health. For more info, click here. Application deadline – 31 Mar 2022.
  • The Early Career Grants Programme 2022 is open for applications from early career researchers and global health professionals based anywhere in the world, who have not had research funding in their own name before. For more info, click here. Application deadline – 29 April 2022.
  • ICGEB Research Grants. Grants are awarded to contribute to the implementation of outstanding scientific research projects. An important element of successful applications is the feasibility of the proposed project within the designated time-frame (maximum 36 months). The maximum annual contribution from ICGEB is Euro 25,000. For more info, click here. Application deadline – 30 Apr 2022.
  • Request for Applications: Two Patient-Partnered RFAs with Rare Disease Focus. For more info, click here. Application deadline – 22 May 2022.
  • OWSD PhD Fellowships. For more info, click here. Application deadline – 15 Apr 2022.
  • EMBL International PhD Programme. For more info, click here. Application deadline – 19 Apr 2022.
  • Call for expressions of interest: Engaged Scholarship Programme. More details and information can be found here. Application deadline - 18 March 2022.

Other Announcement/Events

  • Save the date! 19th H3Africa Consortium Meeting 29 May- 1 June 2022. For updates watch this space.
  • 2nd International symposium on Human Genetics, 30-31 March 2022. For more info, click here.
  • SASBi-SC/SAGS 2022 Student Symposium, 24 April 2022. For more info, click here. Abstract submission deadline – 25 Mar 2022.
  • More funding calls here
Visit our website or simply follow us on social media to stay updated with everything that is H3ABioNet, from workflows to courses, you will find them all! (click on any link below) [Image: Wikimedia commons]
Created By
Verena Ras
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Credits:

creative commons, Getty Images, Je’nine May