H3ABioNet Newsletter Issue 31: September 2019


Welcome to the first newsletter in the 8th year of the H3ABioNet grant. We have had a number of recent events which are reported on here. The first was a Bioinformatics Education Summit hosted by H3ABioNet in Cape Town and organized together with ISCB, ELIXIR and GOBLET. The summit brought together bioinformatics trainers and educators to work on resources for the trainer community. It was very much a working meeting and much was achieved. Some of the discussions were continued at the ISCB Education COSI meeting at ISMB. I was honoured to be conference co-chair of ISMB this year, which took place during a heat wave in Basel.

Other recent events include the successful Nigerian Bioinformatics Conference and the H3ABioNet Annual General Meeting and Scientific Advisory Board Meeting. Two of our node PIs, Prof Ezekiel Adebiyi and Dr Oyekanmi Nash were honoured at the Nigerian Bioinformatics Conference in recognition of their contribution to bioinformatics development in Nigeria. The AGM/SAB meeting held at the Breakwater Lodge in Cape Town provided an opportunity for node members to have interactive discussions with each other on the various projects. Progress and highlights were reported to the SAB who provided valuable feedback. With just 3 more years to go there was a focus on sustainability with 2 sessions dedicated to these discussions. The meeting was followed by a hackathon to further the development of some of our workflows and tools.

I will leave it there so you can read further about the details of some of the events.

Nicky Mulder

H3ABioNet PI

1st Bioinformatics Education Summit for trainers held in Cape Town, South Africa, 14 -16 May 2019

By: Verena Ras

H3ABioNet in collaboration with ELIXIR (intergovernmental organisation for life science resources), GOBLET (Global Organisation for Bioinformatics Learning Education and Training) and the ISCB (International Society for Computational Biology) recently hosted the first ever Bioinformatics Education Summit for trainers during May of this year. The three day long summit saw these organisations join forces to advance global standards and resources in bioinformatics education and training. Trainers from across more than 15 countries globally worked tirelessly to make advancements on three main areas which were: a) refining ISCB competencies and mapping courses and degrees to refined competencies, b) developing an ISCB accreditation process for short courses and c) developing a trainer guidelines document and trainer portal which will host training resources for trainers. But… What is an education summit without some training... The summit therefore started and ended with some interesting workshops. A pre-summit workshop on bioschemas was presented by Niall Beard from ELIXIR (TESS) to teach trainers the benefits of using schemas and simple markup on local websites to make their materials and events more findable and searchable. The summit ended with an Ensembl genome browser course presented by Ben Moore from the European Bioinformatics Institute.

Niall Beard presenting a workshop on bioschemas for training materials ahead of the summit.

We thought it was a resounding success but don’t believe us, see a testimony from one of our participants below and read another here.

David P Kateete, Makerere University has the following to say:

In 2016, Makerere University embarked on an ambitious program –establishing Master’s and Doctoral training in Bioinformatics. With support from Fogarty International Center and H3Africa, the curricula were developed, reviewed and accredited by the National Council for Higher Education in January 2019. They have generated a lot of interest and the university has received around 160 applications from interested applicants in Uganda and Kenya to be considered for admission for the next academic year. Although we are proud the university is starting postgraduate degree training in bioinformatics, provision of sound training is an enormous task as bioinformatics is relatively a new discipline in Uganda. As BRECA’s representative from Makerere University, I was fortunate to participate in the recently concluded Bioinformatics Education Summit in Cape Town, co-organized by H3BioNet, ELIXIR, ISCB and GOBLET. It was a timely and well-organized event that provided us with the opportunity to reflect on the curricula and our preparedness for training. Overall, it was a great learning experience full of activities aiming at strengthening bioinformatics training in Africa. From definition of concepts like “curriculum” to a thorough discussion of competencies for bioinformatics degree programmes and non-degree courses, mapping curricula to competencies, trainer’s support and guidelines for endorsing curricula by international bodies. When I returned, I shared this experience with colleagues and we agreed as a department to study the materials and gradually implement all that we find useful. Currently, Makerere University yearns to improve on the number of foreign students it admits as it transitions into being a research-led institution. However, this requires internationalization of degree training programmes. We believe that once implemented, the knowledge gained from the summit will not only improve on quality of bioinformatics training, but it will also increase employability of graduates and contribute to the internationalization of higher degree training at the university. Lastly, beyond bioinformatics, I found the summit to be a great model that can be extended to other disciplines e.g. Immunology.

Highlights of the First Nigerian Bioinformatics Conference

By: Zainab Kashim and Faith Ogbole

#FNBC`19 Group photograph of some participants immediately after the opening ceremony

The Nigerian Bioinformatics and Genomic Network (NBGN) is thrilled to announce the successful completion of her maiden “First Nigerian Bioinformatics Conference” tagged FNBC`19 with the theme “Bioinformatics in the era of Genomics in Africa”. The venue of the two-day conference was Nigerian Institute of Medical Research, (NIMR) Yaba, Lagos, Nigeria. FNBC`19 was host to over 200 delegates from across USA, UK, South Africa, Ghana, Morocco, Ethiopia and the giant of Africa – Nigeria. The conference kicked off on the 25th of June 2019 with an opening ceremony which was well attended by dignitaries from major sectors of the country and was aired on several media channels across Nigeria.

The opening ceremony was immediately followed by invited talks from guest speakers, panel and oral abstract session I, poster session, and two other panel and oral abstract sessions along with coffee and lunch breaks in between the sessions.

The second and last day of the conference, 26th June 2019, began with an inauguration ceremony of the Nigerian Bioinformatics and Genomics Network. The hallmark of the inauguration ceremony was the presentation of award of outstanding recognition to the pioneers of bioinformatics in Nigeria: Prof Oyekanmi Nash and Prof Ezekiel Adebiyi. The inauguration ceremony was again immediately followed by invited talks from guest speakers, panel and oral abstract session I, poster session, and two other panel and oral abstract sessions along with coffee and lunch breaks in between the sessions as on the first day. Overall, FNBC`19 witness speeches / invited talks from fourteen keynote speakers and invited speakers, 25 oral abstract presentations, 90 poster presentations and goodwill messages from major stakeholders in Nigeria. Other highlights of FNBC`19 were interactive sessions, award session, and after conference dinner.

Two FNBC`I9 pre-conference workshops were held on 24th June 2019. The workshops were: A practical guide to writing a grant proposal by Prof Nicki Tiffin and Comparative Genomic Bioinformatics Analysis with Ensembl by Dr Ben Moore. Both workshops ran concurrently with over 60 participants in attendance.

Left: #FNBC`19 Ensembl Browser Workshop participants. Right: #FNBC`19 Grant writing proposal workshop participants.

According to the president of NBGN, Dr Segun Fatumo, “The conference was a melting pot for researchers with overlapping bioinformatics vision and FNBC`19 provided exciting networking opportunities as well as a platform for participants to exchange ideas, foster research collaboration and expand their knowledge on a range of topics at the core of bioinformatics.

FNBC`19 has come and gone but commendations have not ceased to abound concerning the impart and success of the conference. As we look ahead for the greater good of NBGN, here`s hoping we get to see more participants and greater dimension of success in our upcoming conferences.

Outstanding leadership awards to two Nigerian professors in recognition of their contributions to bioinformatics training and research in Nigeria

By: Faith Ogbole and Zainab Kashim

The Nigerian Bioinformatics and Genomics Network (NBGN) is a national initiative to facilitate collaborative activities amongst Nigerian bioinformatics and genomics investigators. After her existence for over a year, NBGN was inaugurated on June 26, 2019 in the presence of invited dignitaries and society leaders in Lagos during the most successful First Nigerian Bioinformatics Conference organized by NBGN. The First Nigerian Bioinformatics Conference 2019 (FNBC`19) provided a unique opportunity for special recognition of distinguished pioneers of bioinformatics in Nigeria. It was with an absolutely tremendous pleasure that two Professors were honoured; Prof Oyekanmi Nash and Prof Ezekiel Adebiyi with an award of excellence leadership in recognition of their pioneering work in bioinformatics in Nigeria and Africa at large. Their outstanding contributions to the growth of bioinformatics in Nigeria and Africa have left footprints in the sand of times. The success and growth experienced thus far in bioinformatics in Nigeria and Africa is largely due to the passion, incredible and consistent work that Prof Oyekanmi Nash and Prof Ezekiel Adebiyi have undertaken since they caught the vision of bioinformatics.

Their success story which they gave at FNBC`19, on how they had to create the non existing environment of bioinformatics in Nigeria coupled with their hard work and relentless effort is highly commendable.

As an organization that is committed to supporting and strengthening bioinformatics and genomics in Nigeria, The pioneer president of NBGN, Dr. Segun Fatumo expressed his gratitude to Prof Oyekanmi Nash and Prof. Ezekiel Adebiyi on behalf of NBGN leaders and over 600 members with the presentation of two awards “Outstanding Leadership Award” to each of them at FNBC`19 in recognition of their leadership, dedication and extraordinary contributions to Bioinformatics Trainings and Research in Nigeria.

Bioinformatics is growing from strength to strength in Nigeria because these pacesetters Professors have set the bar for us in Nigeria, therefore members of Nigerian Bioinformatics and Genomics Network are advised to endeavor to strive onwards and upwards.

H3ABioNet 2019 AGM and SAB Meeting Report

By: Nicky Mulder

Over 80 members of the H3ABioNet Consortium and Scientific Advisory Board Members came together in Cape Town at the end of July for the 2019 Annual General Meeting followed by the Scientific Advisory Board Meeting from the 1st-2nd August. The meetings were held at the Protea Breakwater Lodge near the Waterfront, which offered excellent views of Table Mountain at sunset when the meeting closed each day.

The meeting was attended by participants from 20 different countries, with almost all H3ABioNet nodes represented. The AGM from the 30th-31st July provided opportunities for interactive sessions on many of the individual projects, where they were able to get valuable feedback and input from the consortium. Victor Jongeneel led a session on grant proposals, providing useful tips and highlighting a specific grant opportunity that some of the software development projects should apply for.

The SAB meeting provided us with an opportunity to showcase the progress made on a number of projects, as well as overall network progress and highlights from each node. Projects were framed within the context of work packages presented by the work package chairs or co-chairs. Wherever possible, the co-chairs, who represent the next generation of managers, presented the progress. Each presentation was followed by questions and discussion where we received excellent advice from the 5 SAB members which were present. A second sustainability session was run by Victor, where we discussed what the future network should look like and possible models for funding. To celebrate our achievements we had an AGM/SAB dinner at the popular Gold restaurant in town along with face painting and entertainment.

The meeting was the 2nd AGM of the second round of funding and the 7th overall. We have 3 years left and we need to increase our efforts towards long term sustainability. We have achieved many of our aims and the AGM/SAB meeting highlighted the significant progress made in many of the projects. We look forward to another productive year.

Meet the PI: Nicki Tiffin

By: Deborah Fasesan

1. Tell us a bit about yourself:

I am Zimbabwean, I grew up and attended school there, although I was awarded a scholarship to an International college, the United World College of the Atlantic, in Wales, UK for the last two years of high school. After that I returned to Africa and did my under-graduate degree in Biochemistry, and Honours in Medical Biochemistry at the University of Cape Town (UCT). I returned to the UK and worked as a secretary and a laboratory technician whilst applying everywhere until I found funding to do a PhD, which I did in Paediatric Molecular Oncology at the Institute of Cancer Research (University of London), in genetic laboratory-based genetics research. The human genome was in the process of being sequenced while I was doing my PhD and it was an exciting time to be in genetics and genomics. From there, I did a postdoc fellowship at the University of California San Francisco, also in lab research in paediatric molecular endocrinology, studying signal transduction in muscle development. After that, I went back to South Africa and started bioinformatics research at SANBI (South African National Biodiversity Institute) at the University of the Western Cape (UWC), firstly as a post doc and then as a PI of a research group and I was there for quite some time, apart from some time at UCT, in the Human Genetics department. Whilst at SANBI I also did a Masters in Public Health (part time) in Epidemiology and Biostatistics at UCT. After this, I moved out of research for about 2 years, working on secondment to the Provincial Health Department: I worked with a team building a Provincial health information exchange, which was a wonderful experience of digging into health informatics and understanding routine clinical data and health databases. Now I am back at UCT as an Associate Professor in the Computational Biology Division, and the Data Integration Platform for the Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa). I run a node for H3ABioNet focused on Health Informatics, and I also still work at the Provincial Health Data Centre - so I have got a lot of different things on the go now in my position at UCT.

2. Tell us a bit about your institution:

I work at the Health Sciences faculty at UCT, affiliated with the Wellcome Centre - which is an institution in the Health Sciences Faculty, the Computational Biology Division and the Centre for Infectious Disease Epidemiology Research at the School of Public Health and Family Medicine. UCT is well established, it has been around for a long time, has a great reputation, and the academics get quite a lot of research funding. The academic side of Health Sciences is largely supported by grant funding, so we have a lot of emphasis on getting grants, ensuring we have high research outputs in the form of papers, and we also need to graduate lots of students.

3. How did you get into bioinformatics?

When I worked in the USA and the UK we had large budgets for laboratory work and we could order any cutting edge research molecular tools and kits, and receive them within 24 hours. Returning to Africa this wasn’t going to be the case, so I felt that bioinformatics research could have lower consumable research costs but still generate useful information for improving health outcomes on the Continent. Bioinformatics seemed to me to be a more ethical use of funding, and a less constrained and frustrating way to do research in South Africa.

4. What are your research interests?

In my research, I have a really great research group made up of 3 PhDs and 3 Masters students. I supervise some non-academic staff as well, biostatisticians and database managers and bioinformaticians who are more focused on service provision than primary research. We work on a range of things: my area of interest is around the intersection of all these different data types: clinical data, molecular data, epidemiological data and the kind of data we work with in computational biology - genomics data. We all work on the same research problems and diseases. Specifically in South Africa ,we often look at diseases such as HIV, tuberculosis as well as non-communicable diseases. Each of these different research areas have sets of tools to try and understand these diseases, but we are not that good in bringing all these tools together and working in concert to try and solve these problems. I am really interested in that intersection of the different domains and how they can work together to generate data solutions for managing disease in Africa. In fact my position now is as an Associate Professor in Data Integration.

5. What do you enjoy most about your job?

Being in Academia is a wonderful opportunity when you find unknown things interesting and are curious: you have an environment in which you can pursue your interest and can satisfy your curiosity. You have some freedom to be able to explore things that interest you. I enjoy working with young scientists, and ensuring that they gain the right skills to do good science and be good scientists, because to succeed as a researcher you need good mentorship not only in science. There are also other skills required to succeed in academia: it is not an easy career path and it takes good mentorship to be able to succeed. I believe that I should pass on my own learning experiences for other people to build on in the future, in order to move things forward. I think it is a moral imperative to ensure that we pass our own learning on to help other scientists coming through - and I think some senior scientists forget that they need to support young scientists and share their learned experience with them. Obviously I love the work itself: I love data, and I’m always in-trigued because when you have a dataset, the answers are already in there: it’s up to us to find the right tools and skills to find them and understand what the data is really telling us. I find that a really satisfying challenge.

6. What do you enjoy least about your job?

The administrative burden: the more administrative work you have, the less you engage with actual science, and that can be frustrating as administrative work takes a lot of time.

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

It has been really fantastic to be able to work in Africa. To work on African problems with African scientists. It has really created an opportunity that was quite difficult to arrange before the bioinformatics network: if you wanted to collaborate and get funding, you often had to sell out your control of things to a non-African research group in order to be eligible for funding. So the fact that we have the funding available for within-Africa collaborations and have been able to further those relationships and bring skills and strengths together has been a wonderful opportunity that has become possible with the bioinformatics network.

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

This would be advice in general for those pursuing an academic career: it’s a very hard career to choose and not many people make it to the top. If you want to take on a career in bioinformatics in Academia or research, you have to be prepared to put in a lot of hard work from the beginning in order to be sure that you are the person who gets to the top. It is quite stressful working in academia, and you have to be willing, prepared and understand what you are taking on. You have to be sure you are prepared to work very hard to get what you want.

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

I’m a very practical person: in terms of doing things with my hands. I am good at things like DIY, woodwork, crafts, sewing, baking. It helps me turn off my over-active brain and makes me slow down and relax mentally.

10. Final words

My final words would be again for young scientists who are deciding they want a career in research: it is really important to understand that science requires hard work and rigour. You need to be prepared to do a lot of reading of scientific papers and get your knowledge up to speed, you need to practice scientific writing, you also need to be prepared that when you want to publish papers and apply for grants you will often fail, but you have to be willing to try again as many times as required. If you do decide that this is the career path you want, you have to decide that early on and understand what you are getting into, and you really need to do it properly from the beginning. Nobody is going to force you to do these things, you have to have the discipline to choose and do them yourself.
Interview conducted by: Deborah Fasesan
  • 14th International Congress of Human Genetics • 7 – 11 March 2021, CTICC: DEADLINE: 4 October 2019. More information can be found here: http://www.ichg2021.com/call-for-proposals/
  • Automating access to human genomics datasets: the GA4GH Data Use Ontology in action: WEBINAR: September 27 | 7amPDT, 10am EDT, 3pm BST, 11pm JST. Register for the webinar.
  • 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 on the 11th . The conference will be followed by several workshops on the 14th and 15th of November.
  • The Galaxy Africa meeting will take place on the 14th and 15th of November at the ASBCB meeting at KNUST in Kumasi, Ghana (see above). More information on the GALAXY meeting here: https://www.iscb.org/iscbafrica2019-ps/iscbafrica2019-worktut
  • First international congress of the Moroccan Society of Genomics and Human Genetics (SM2GH), slated in Agadir from the 19th to the 21st of December 2019. This congress represents the joint meeting of the SM2GH and the third edition of the School of Immunogenetic organized in partnership with the faculty of Sciences of Rabat and the faculty of Sciences of Agadir. Under the theme Bridging Gaps between Genomics and Medicine in Africa” the event provides a scientific program of a high standard with prominent speakers. If you have any questions, please don't hesitate to contact the Secretariat of the congress: SM2GH.Agadir@gmail.com
  • HBNU Fogarty Global Health Training Program 2020/2021 Fellowship Year - apply here: https://sites.sph.harvard.edu/global-health-research-partnership/apply/
  • Call for Applications: The Adobe Research Fellowships are open graduate students anywhere in the world carrying out exceptional research in computer graphics, computer vision, human-computer interaction, machine learning and more. DEADLINE: 27 September: https://research.adobe.com/fellowship/
  • Congratulations to Prof. Faisal and his team from the H3ABioNet Node - Centre for Bioinformatics and Systems Biology (CBSB), University of Khartoum for successfully undertaking and completing the GWAS Node Accreditation. The reviewers were very impressed: “The report was outstanding. I am extremely impressed with the quality of the writing and analysis. The QC was the best part. I wish my own students (and some of my postdocs...) had anywhere this level of understanding of GWAS concepts. Great job teaching GWAS well”. Well done to the Centre for Bioinformatics and Systems Biology (CBSB), University of Khartoum for this tremendous achievement.
  • H3ABioNet’s Introduction to Bioinformatics Training Course (IBT) is currently running. It has a record number of 1100 participants and almost 400 staff this year.
  • The first ever H3ABioNet 16S rRNA Intermediate Bioinformatics course is currently running and has over 200 participants with almost 100 local staff. The course provides a new model for advanced training in Africa with each classroom managing infrastructure for the course independently.
  • The 14th H3Africa Consortium Meeting is taking place from 22 to 27 September 2019, at La Palm Royal Beach Hotel, Accra Ghana.
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Verena Ras


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