H3ABioNet Newsletter Issue 30: May 2019


This month has been very busy with the H3Africa consortium meeting, H3ABioNet portals hackathon, having the NIH annual report due and many other trips and deadlines. Several H3ABioNet members attended the 13th H3Africa consortium meeting in Tunis, held at the Laico hotel from the 8th-11th April.We had a FAIR competition stand in the poster area, managed by Verena to raise awareness of making data and materials FAIR and at the same time to host a fun competition. This is described further in one of the articles below. H3ABioNet members also contributed to the working group meetings and Paballo and others helped to organize the fellows’ training activities. Immediately after the consortium meeting, our node at Institut Pasteur Tunis hosted a hackathon to develop two portals: a precision medicine portal and a microbiome portal, both aiming to provide resources for African researchers. The hackathon is described further in one of the articles below. Hackathons have become important forums for achieving goals on specific projects and producing tangible outputs. They also provide an excellent opportunity for learning and networking.

H3ABioNet teamed up with the South African Society for Bioinformatics Student Council and MGenAfrica to host a stand at the South African Sci-Fest for high school learners. You can read about the enthusiastic exhibitors and students in this newsletter. These outreach activities are important for generating enthusiasm for bioinformatics and genomics in the youth before they embark on undergraduate studies. This is one of several outreach activities H3ABioNet is embarking on to increase our reach and visibility.

The newsletter concludes with an interview with Dr Victor Jongeneel, a long time supporter and excellent contributor to H3ABioNet and African bioinformatics generally. He has an enormous amount of experience in grant writing and I encourage you all to embrace his willingness to help. I will leave you now to read on as we update you on our activities!

Nicky Mulder

H3ABioNet PI

South Africa’s National Science Festival (Sci-Fest Africa) Clarion Call for learners to Discover their own Elements in Science

By: Paballo Chauke

“DNA! DNA! DNA!” cried pupils who had just discovered knowledge about cells, genetics, diseases, and bioinformatics. “DNA! DNA! DNA!” was a loud chant made by thousands of excited learners who came to our exhibition stand that could be heard reverberating across the 1820 Settlers National Monument building at Scifest Africa 2019.

South Africa’s National Science Festival (Scifest Africa) which is argued to be one of the most popular and well attended Science Festivals in the African continent, was celebrating its 23rd anniversary event from 6th -12th of March 2019. The festival took place in Makhanda (formerly known as Grahamstown), in the Eastern Cape province of South Africa, attracting an estimated number of over 60 000 pupils from across the country but mainly the Eastern Cape. The event has been growing year on year in its 23-year existence, it attracted a total number of 62 000 guests in 2018 and is guestimated to grow even bigger in future years. For the 2019 iteration, the theme was “Discover your element”, linking it to the fact that United Nations has declared 2019 as the International Year of the Periodic Table of Chemical Elements.

Image 1: Jorge da Rocha speaking to students whilst Laura Cottino listens

According to the Scifest Africa website, “Scifest Africa was established in 1996 to promote the public awareness, understanding and appreciation of science, technology and innovation (STI). The project is supported by South Africa’s National Department of Science and Technology and various other cash and in kind sponsors.” At H3ABioNet, Outreach through Science Communication is one of the areas we are passionate about. As a way of giving back, H3ABioNet together with SASBi-SC and MGen Africa attended the week-long event. SASBI which is the South African Society for Bioinformatics - Student Council (Image 1 and 2) was represented by Jorge da Rocha, Laura Cottino, and Bertha Baye while H3ABioNet and MGenAfrica were both represented by Paballo Chauke (Image 3).

Image 2: Laura Cottino playing the protein building game with the students
Image 3: Paballo Chauke, playing a quiz with a group of learners about which organism has the highest number of chromosomes.

H3ABioNet, SASBI-SC and MGenAfrica had an exhibition stand that was littered with nuggets of information, games and some sweets- for the most engaged pupils. We also hosted workshops to teach learners and teachers more about genetic science and how the “elements” and molecules within oneself (DNA), give rise to everything that makes us unique. A lot of learners came to our stand where they would learn more about DNA, how it is packaged to fit inside tiny cells, and how we inherit traits from our parents through inheriting their DNA.

Learners would also play quiz games where they guess who has more chromosomes or genes: pineapples, humans or fruit flies (please see image 3). These were especially great with younger learners. Other games included aligning newly sequenced short reads of DNA with reference sequences with cut outs of these on the table tops. We also understood that most of our audience spoke IsiXhosa as a mother tongue and we appreciated the fact that the English language can be a barrier to learning for those that speak it as a second or third language. As such, we translated our talks, games and teaching to accommodate the many pupils that were awed by how DNA can explain most things in their lives relating to heredity and disease (Image 4).

Image 4: The detective games we played, were translated into three languages

It was a phenomenal experience to be at SciFest Africa interacting with thousands of learners hungry to learn about science, in particular about genetics and bioinformatics, our exhibition stand was always busy with demonstrations, games, questions and teeming with pupils, their siblings and parents. We had great social media coverage this year, please do check our H3ABioNet Twitter and Facebook pages respectively, to see more pictures and videos from the event under #SciFest2019 #SciFestAfrica.

Portals were the focus of the latest H3ABioNet hackathon in Tunisia

By: Melek Chaouch

In fulfilment of one of the several goals of H3ABioNet, which includes the development of databases and resources supporting H3Africa projects, a H3ABioNet African Microbiome and Precision Medicine Portals Design Hackathon was organized in Tunisia. This event took place from 12 to 18 April at the Institut Pasteur de Tunis.

This Hackathon aimed to develop two H3ABioNet Databases and Resources Work Package Portals:

  1. African Precision Medicine Portal (APMP) - a web based portal to collate and curate pharmacogenomics and other genomic medicine metadata specific to African populations, as well as links to existing precision medicine implementation tools and resources in order to support precision medicine initiatives within Africa.
  2. African Microbiome Portal (AMP) - a web based portal to collate, curate and provide primary references for African specific microbiome metadata and resources for African based microbiome research.

The hackathon involved 25 participants that were divided into three teams. Stream A for the African Precision Medicine web portal development and Stream B for the African Microbiome web portal development and one technical team. An additional team for writing and drafting manuscripts about the hackathon was also formed. Graduate and undergraduate students were also involved in the two web portals development.

The hackathon program was based on a series of presentations and talks highlighting the objectives of both portals during the first day and portals design and development breakout group sessions from the 2nd to 6th days.

The Hackathon was an occasion to bring together H3ABioNet project members involved in the design, conception and development of the two H3ABioNet portals. Faisal Fadlelmola and Kais Ghedira as Chair and Co-chair of the Databases and Resources WP were involved in the organization, assisted the participants and ensured the smooth running of the event.

Poster Poster on the wall, who is the FAIR-est of them all?

By: Verena Ras

The 13th H3Africa consortium meeting took place in Tunis, Tunisia from the 7th to the 11th of April earlier this year, where H3ABioNet ran a FAIR data competition. We used the Kahoots platform which allowed us to turn this into a fun, challenging game, with a leaderboard to boot!

The competition ran for 3 days with many consortium members turning up to test their FAIR knowledge. In the end, the fellows proved their digital savviness by outcompeting their PI’s! This was a welcomed surprise. Our future leaders will definitely know how to “FAIR-ify” their data and we may rest assured their data will live on for generations to come.

Below we shine a spotlight on our top three performers, who are all fellows within the H3Africa consortium and we say well done to them all for their knowledge around FAIR.

Top spot went to Noluthando Manyisa:

I am currently working on identifying prevalent pathogenic variations associated with hearing impairment in the South African population. We plan to use bioinformatics analysis to discover the variations and animal models or cell culture to confirm any novel variations that we find. Our aim is to characterise the variations in the South African population and develop a novel panel that is applicable to our population. (Noluthando can be seen on the left of the photo with our 3rd prize winner Khutala)

Second place went to Ajogbasile Fehintola Victoria:

My name is Ajogbasile Fehintola Victoria and I am a Ph.D. student in Molecular Biology and Genomics at the African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria. I also obtained my Master’s degree in Molecular Biology and Genomics from ACEGID, Redeemer’s University finishing with a Distinction grade. My Ph.D. research work involves understanding the intra- and inter-population diversity of Plasmodium falciparum using microsatellite analysis and molecular surveillance of antimalarial resistance of Plasmodium falciparum to Artemisinin Combination Therapy (ACTs) drugs in Nigeria by sequencing.

Our final spot went to Khuthala Mnika:

During my MSc project, I have contributed to the broader scientific community by authoring and publishing three manuscripts as a first author and four manuscripts as a co-author in high impact journals. To highlight, my MSc project has provided a unique insight in clinical predictors of acute painful episodes and the use of hospital services, in a unique group of hydroxyurea and opioid naive participant living with SCD in a sub-Saharan Africa. I also identified specific variants that are associated with pains and health care utilisation, in putative pain- associated genes, and other established Genetic modifiers of SCD. Which open up additional questions on Pharmacogenomics of SCD.

Currently, I am registered as a PhD student under the supervision of Professor Ambroise Wonkam in the division of Human Genetics, University of Cape Town. My project will be a continuation of my MSc project, where I will be exploring hydroxyurea-induced post-transcriptional expression of miRNAs in an African cohort.

We congratulate all our winners!

Meet the PI: Victor Jongeneel

By: Deborah Fasesan

1. Tell us a bit about yourself.

I was born and raised in Switzerland, I am from a Dutch family, I went to college in Switzerland and graduate school in the United States, I did a post doc in the United States as well. I was a group leader at the Ludwig institute for cancer research in Epalinges. I am also one of the founders of the Swiss institute of Bioinformatics. I moved to Cyprus for a couple of years and then returned to the United States to the University of Illinois where I spent 6 years, retired and now in Curaçao.

2. Tell us a bit about your previous institution.

The University of Illinois is a large public university, located in the middle of Illinois. It is the flagship university of the state and has about 40,000 students. It is strong in technical areas such as engineering, computer science and agricultural science which makes it a good place for applying high-performance computing to biological problems. It is among the top 30 or 40 research universities of the world. It is also part of the Big 10 sports league, which groups several high-quality public universities in the Midwestern US. The university was created back in the 1860’s in the era where the federal government would provide pieces of land to establish Universities to educate the majority of the people rather than the rich minority alone.

3. How did you get into bioinformatics?

As an undergraduate in Switzerland, I was already interested in learning computer science. As a biology student, I wrote to the Dean of the College to get permission to take computer science courses but was turned down on the grounds that biologists did not need to use computers. I went to graduate school at the University of North Carolina, where I took elective courses in computer science. I spent the rest of my life working in both biology and computer science. I returned to Switzerland with a solid computer science background, at a time when biologists thought computers were a waste of money, and built up a computational infrastructure in the research campus where I worked. By the time I left people were feeling the impact of the work I had done, and bioinformatics had become a major local strength.

4 What were your research interests?

I was trained as a molecular virologist, and as a graduate student and post-doc I worked in the lab with herpesviruses, phages, and parvoviruses. Once I had my own laboratory, I studied the gene structure, polymorphisms and genetics of the tumor necrosis factor family of genes. When I stopped working in the lab, my main interest was working on joint projects with biologists, engaging with people with needs for data analysis and interrogation, and allow people to make sense of their data.

5. What did you enjoy most about your job?

I enjoyed learning – keeping up with what was going on, such as new developments in the field. I also enjoyed meeting people. Science can be very interactive, and I especially enjoyed bringing together computer scientists and biologists.

6. What did you enjoy least about your job?

Putting together large grant proposals. This can be sometimes be really stressful with deadlines to meet, people not doing their part, and complex guidelines to adhere to.

7. How had being a part of the H3ABioNet community impacted your research group?

University of Illinois has been involved in this network for quite some time now, for everybody in the group, there has been some impact. We have had several interns, participated in lots of projects. I have had the opportunity to visit South Africa, I however wished I had more opportunities to visit other nodes to see how other groups on the African continent worked.

8. What advice would you give a young person that is interested in pursuing a career in bioinformatics?

Find something you are good at, become so good at it that most people would look up to you. However, this takes dedication and focus. A lot of young people think that by pursuing specific degrees, they would become a professional, well –yes, but what really counts is that you can show that you are so good at something that an employer (academic/government/private company) would really want to hire you because you have knowledge that nobody else has or that your presence in the company would make a huge difference.

More specific to bioinformatics- if your basic training has been in biology, learn the language of computer science and understand it, and if your basic training has been in computer science, learn the language of biology and understand it, because in my opinion, bioinformaticians that are good on one side and not good in the other are not good bioinformaticians, the job of a bioinformatician is to be able to talk to both computer scientists and biologists.

9. Tell us something about yourself that not many of your colleagues knew e.g. hidden talent, hobby.

Scuba diving, the time I don’t spend doing bioinformatics, I spend underwater doing underwater photography. I spend a lot of time now doing coral conservation and restoration, and one of the reasons why I live where I live now is that the underwater world is really nice and I can go diving year round.

10. Final words

I have been associated with H3ABioNet for about 8 years now, and one thing that I have noticed a lot is that many African scientists, even though they have received training and they know their field reasonably well, are still finding it very difficult to formulate a real research project, and this is something that I find a little disturbing. This is a problem that I hope the network can do something about. I have helped quite a few people with trying to put together grant proposals and that is basically how I have noticed, usually they have a plan about things they want to do but don’t have a plan about the hypothesis they want to test. As a result they find it very difficult to actually formulate a proposal that can be pushed to funding agencies worldwide. What I am really hoping is that H3Africa more generally can help in this regard and help African scientists formulate competitive research projects. This is something I care about.

Professor Victor Jongeneel dedicating time to his other passion, diving!
  • AGMT: African Genomic Medicine Training has commenced on the 26th of March and will run till the 24th of June.
  • The 2019 iteration of IBT will open it’s call for interested classroom by end of June 2019 and is proposed to run from August - October 2019.
  • Our first ever 16S rRNA intermediate bioinformatics training course will open their call for classroom hosts on 30 May. More information and application details will be hosted on our training page: https://www.h3abionet.org/training/courses-and-events.
  • The H3ABioNet SAB/AGM will take place from 30 July to 02 August in Cape Town.
  • The First Nigerian Bioinformatics Conference is scheduled to take place in the city of Lagos: 25-26 June 2019. The call for abstract is currently on. Additional details about the conference can be found here http://www.ngbioinformaticsconference.com
  • 12th AFMC / AIMECS 2019 Asian Federation for Medicinal Chemistry (AFMC) 12th International Symposium “New Avenues for Design and Development of Translational Medicine” will be held in Istanbul, Turkey on September 08-11, 2019. For more information, please visit the Symposium webpage Programme/Topics section page; http://www.aimecs2019.org/topic.
  • BH2BU, the first comprehensive Ancestry Test performed in Africa is offering the test at a discounted rate of R1299 to the first 1000 participants signing up before the 30th of June 2019. More information here: https://www.behappytobeyou.co.za/
  • The African Society for Bioinformatics and Computational Biology (ASBCB) and the International Society for Computational Biology (ISCB) are organizing the ISCB Africa ASBCB 2019 conference (https://www.iscb.org/iscbafrica2019) that will take place in Kumasi, Ghana from November 11th to 13th including a half-day student symposium. The conference will be followed by several workshops on the 14th and 15th of November. The call for oral and poster presentations proposals is now open and a number of travel fellowships will be available for African based students. They are also accepting workshop proposals: https://www.iscb.org/iscbafrica2019-call/iscbafrica2019-worktutsub
  • ISMB/ECCB 2019 is the largest and most high profile annual meeting of scientists working in computational biology and provides an intense multidisciplinary forum for disseminating the latest developments in computational tools for data driven biological research. The conference will take place between 21 and 25 July in Basel, Switzerland. Further information can be found on their website: https://www.iscb.org/ismbeccb2019
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)
Created By
Verena Ras


creative commons; https://scifest.org/

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