H3ABioNet Newsletter Issue 29: February 2019


The February newsletter brings news of some of our recent outreach and networking activities as well as the H3ABioNet helpdesk. The helpdesk was started towards the beginning of the H3ABioNet project as a means to provide a support forum for H3ABioNet and H3Africa researchers that could be monitored. The helpdesk has evolved from predominantly H3ABioNet use to increasing use by H3Africa projects and even researchers outside of the consortium. This demonstrates the need for bioinformatics support in Africa. You can read more about the helpdesk in the first article.

We are pleased to see our nodes engaged in outreach activities within their regions. Below you can read about some of the node capacity building activities and one of the H3Africa activities at the Science Forum in Pretoria last year. We also feature an article on a recent Software Carpentry course we ran at the University of Cape Town. H3ABioNet is developing a coordinated plan for training carpentry trainers and rolling out carpentry courses across Africa. Finally, we present a meet the PI interview with Prof Seydou Doumbia, who I met prior to H3ABioNet during early efforts to boost bioinformatics in Africa.

Nicky Mulder

H3ABioNet PI

I hope you enjoy reading about this and our recent endeavours.

The H3ABioNet Helpdesk

By: Lyndon Zass

During the first round of H3ABioNet, the network established one of the first public and freely available, online bioinformatics helpdesks to support the development of bioinformatics and genomics capacity in Africa and provide rapid bioinformatics support to researchers across Africa and the rest of the world. The following report introduces the H3ABioNet Helpdesk, outlining its function, use, and performance.

The Helpdesk provides support through Helpdesk representatives, with backgrounds and significant experience in various bioinformatics applications. Representatives are voluntary members of H3ABioNet, and range from mid- to late- career scientists, with unique experience in analyzing African genomic data.

The Helpdesk accepts queries, submitted as tickets, through an online interface accessible from the H3ABioNet website. Users are encouraged to create accounts and tickets in order to receive support (see Figure 1). The Helpdesk supports a wide range of bioinformatics and H3ABioNet-specific project queries, including queries with regards to NGS and GWAS data analysis; the Human Mutation Analysis (HUMA) platform, Data Management, REDCap and many more (see Figure 2). Based on the overlap between a Helpdesk representative’s expertise and the query category, a Helpdesk administrator prioritizes queries and assigns them to the appropriate Helpdesk representative.

Figure 1 (left): Figure 1: The H3ABioNet Helpdesk lifecycle; Figure 2 (right): Figure 2: Illustration of the various categories of queries the Helpdesk attends to.

Queries received by the Helpdesk can generally be divided into two broad categories, H3ABioNet-specific queries, and queries which deal with data analysis applications. H3ABioNet-specific queries generally involve H3ABioNet projects, activities and(or) tools (e.g NetCapDB, Node Accreditation, H3Africa Chip), and tend to accumulate during the introduction or high use of these projects or tools. Data analysis queries generally include queries regarding the computing requirements for analysis, software inquiries, comparisons and recommendations, as well as specific analysis support, such as scripting, error identification and correction.

The Helpdesk’s performance is regularly monitored and evaluated. Previous performance analyses have revealed that the Helpdesk performs efficiently and resolves queries in a timely manner. Similarly, user feedback has been equally positive. Previous feedback analyses revealed that the majority of Helpdesk users rated quality of support (77%), query resolution time (74%), and user friendliness of the Helpdesk interface (84%), above average, on a standard 1 – 5 scale. Similarly, 94% of these users also revealed that they would use the Helpdesk again if needed in the future and recommend use of the Helpdesk to other users.

Students, researchers and bioinformaticists are all encouraged to employ the H3ABioNet Helpdesk to gain project-specific support for the issues they may be facing with their analyses and (or) research! The H3ABioNet Helpdesk is actively promoted through outreach material and at H3ABioNet training events! We are happy and eager to assist you wherever we can! If you would like to get in touch with us or have any further questions, please contact Lyndon Zass (lyndon.zass@cpgr.org.za) or Mamana Mbiyavanga (mamana.mbiyavanga@uct.ac.za).

South-South Capacity Building within H3ABioNet: A Case Study of CGRI/NABDA and ACE/ USTTB BAMAKO

By: Deborah Fasesan

In fulfilment of one of the several goals of H3ABioNet, which includes the development of bioinformatics capacity in Africa and facilitation of scientific collaboration across nodes, the CGRI/NABDA Node (Center for Genomic Research and Innovation/ National Biotechnology Development Agency) Abuja, Nigeria, played host to an MSc bioinformatics Student from Bamako, Mali for a project internship in December, 2018.

Mr Abdoulaye Diawara, the student, from ACE (African Center of Excellence in Bioinformatics) Node, Bamako, Mali, was assigned to Dr Segun Fatumo as his project supervisor. Dr Segun Fatumo from CGRI/NABDA node teaches GWAS in the MSc Bioinformatics degree program at ACE, Université des Sciences des Techniques et des Technologies de Bamako USTTB Mali.

For effective project delivery, Prof. Oyekanmi Nash -The PI of CGRI/NABDA Abuja node, arranged a short internship for Abdoulaye Diawara, where he had sufficient time to work on his project with his supervisor- Dr Fatumo. Abdoulaye was able to access CGRI/NABDA computing facilities, and was able to network with members of staff of CGRI/NABDA.

The student, presented his work titled ‘Genome-wide Association Study of Type 2 Diabetes in Uganda’ during CGRI/NABDA Annual symposium event, which took place on the 12th of December, 2018. After a successful internship visit, Abdoulaye returned to Bamako and successfully defended his MSc project.

Figure 1 (left): Mr Abdoulaye Diawara delivering a presentation at CGRI. Figure 2 (center): Dr Segun Fatumo teaching GWAS at ACE, Université des Sciences des Techniques et des Technologies de Bamako USTTB Mali in July 2018. Figure 3 (right): Student listen attentively at the GWAS Practical session at ACE/ USTTB.

Drama of DNA: Exploring Ethical Challenges Related to Genomic Research

By: Marlyn Faure

The Individual Findings in Genetic Research in Africa (IFGENRA), presented the Drama of DNA , a novel approach to community engagement at the annual South African Science Forum, on 13th December 2018, held at the Pretoria International Convention Centre, South Africa. The conference is hosted by the Department of Science and Technology and attracts about 3000 attendees. Members from the broader H3Africa community also volunteered to be part of the event.

The Drama of DNA method uses drama as a means to engage various audiences around ethical challenges related to genomic research and novel technologies. How the process works is that audience members volunteer to act out existing scripts or plays focussing on ethical issues related to specific genomic research studies, such as feedback of findings or technology and its potential impact on a family or research, such as next generation sequencing. What makes this approach so appealing is by using a common narrative, it allows various actors in a research context (doctors, recruiters, participants, family members and so on) to understand the impact of the research on a variety of stakeholders. For example, during one of the scenarios a doctor may have to play the role of a parent or ethics committee member, or a parent or patient may have to play a doctor delivering bad news. Such an approach helps fosters empathy between actors and helps people coming from different vantage points to speak about ethical challenges using a common narrative. Once the audience has watched the scenarios, a facilitator will ask pointed questions about ethical challenges raised in the scenario and how that relates to their own experiences.

This work is part of the larger IFGRENA study which aims to create an evidence base from which to create local policies to help navigate individual genetic findings from genetic studies in African populations. The study is based at the University of Cape Town, South African and is led by Jantina de Vries and Ambroise Wonkam. The Drama of DNA method aims to engage various stakeholders and communities involved in genomic research in South Africa and possibly in other African countries.

The method was developed by two US scholars, Karen Rothenberg, a lawyer and bioethicist at the University of Maryland, and Lynn Bush, a psychologist and bioethicist at Harvard University. Given that this method was initially developed in the US context, the scripts have been contextualised for the South African context. Marlyn Faure, the research assistant in the study and heading up the community engagement has spent time with clinicians, patients, researchers and genetic counsellors at Groote Schuur Hospital and Red Cross Children’s Memorial Hospital to understand local concerns in the genetic research context in South Africa. Scripts have been contextualised for the South African and have been piloted with a variety of audiences including genetic study recruiters, clinicians and geneticist.

It is hoped this method aids lay audiences involved in genomic research with an accessible approach to meaningfully engage with ethical challenges and to bring their own concerns to relevant stakeholders to influence researchers and clinicians. It is also hoped that such a novel approach will also help researchers and clinicians further understand concerns of their patients and families. New scripts are currently being written specifically for to use in research study enrolling children with specific neurological development challenges – schools, family members and support and relevant civil society groups will be included in the engagement activities.

View their first short film below!

Software Carpentry - Teaching Basic Computing Skills to Young Researchers

By: Ziyaad Parker

H3ABioNet hosted its first Software Carpentry workshop at the University of Cape Town, aimed at young researchers looking to learn basic computing skills in Linux, Git and Python. Although the workshop was only two days long, it provided students the opportunity to gain new knowledge and practice their skills. The first day consisted of Linux, Git tutorials and exercises while second day focused mainly on Python tutorials and exercises.

The workshop was headed by Ziyaad Parker (H3ABioNet), who previously attended training in both Software Carpentry and FAIR (Findable, Accessible, Interoperable, Reproducible) Data Carpentry Instructor workshops. Lyndon Zass (H3ABioNet) was a helper who had also previously attended the Software Carpentry Instructor Training. The vision of the Carpentries for H3ABioNet is to have trainers in every H3ABioNet node so when the need for Carpentry workshops arises from students across Africa there are resources available. This, in turn, decreases the cost of travel because instead of getting expertise from other countries, you are able to source trainers locally.

The workshop at the University of Cape Town consisted of just under 20 students with 4 instructors. The 4 instructors consisted of Samar Elsheikh, Kenneth Babu, Mamana Mbyivanga and Ziyaad Parker. All the instructors were positive role models with genders of both male and female. All the teachings were conducted using the Carpentry teaching materials created by other content creators and instructors for previous workshops. All the lessons consisted of hands-on practical sessions where the instructors explained the concepts and topics. The students were provided time to do an example and ask questions. Students worked directly from Github, Bash and Python. Additionally, common tools, workflows and the open science culture were communicated clearly in these workshops. One of the challenges was that two days was too short. Another challenge was that students from other nodes applied and wanted to attend but due to funding shortage it was not possible.

More detailed information about the content of the workshop can be found here.

If you are interested in having a Software, Data or FAIR Carpentry Training done in your region. Please fill in this form.

Meet the PI: Seydou Doumbia

By: Deborah Fasesan

"To the H3Africa and H3ABioNet community - we need to be enthusiastic and fight for our vision. H3ABioNet was built on the common vision of few people from different parts of Africa. We trusted each other and we were persistent to achieve our common goal. I am proud to see that H3ABioNet is such a good example of collaboration in Science in Africa, as a result of high commitment, trust and common vision. I foresee a lot of opportunities coming from this network."

Question: Tell us a bit about yourself.

I am the Dean of Medical School and Dentistry at the University of Sciences, Techniques and Technologies, Bamako (USTTB) Mali. I am also the Director of the University Clinical Research Center (UCRC), and a professor of Epidemiology and Public health.

Question: Tell us a bit about your institution.

USTTB was recently created in 2011 with 3 faculties: Faculties of Science and Technology, Medicine and Pharmacy. It was split from the previous University of Bamako. In terms of research, the University currently hosts the International Center of Excellence in Research (ICER), the Malaria Research and Training Center (MRTC), the African Center of Excellence in Bioinformatics and the University Clinical Research Center. The research programmes were created through a collaborative agreement with the National Institutes of Health (NIH) of the United States of America. Since 2003, the University of Bamako-USTTB has been involved in bioinformatics/genomics capacity building in Africa through bioinformatics/genomics training grants funded by World Health Organization special program on Tropical Diseases Research (WHO/TDR) and the National Institutes of Health of USA.

Question: How did you get into bioinformatics?

I became involved in bioinformatics in 2003 through a Nigerian friend (Raphael Isokpehi), we met when I was about rounding off my PhD in Tulane University, New Orleans. Raphael was invited by my mentor Dr. Donald Krogstad (Chair of the Department of Tropical Medicine at that time) to present a bioinformatics seminar and he spoke about the different training activities in bioinformatics in Africa especially at SANBI. I became interested in bioinformatics, as I have always been involved in informatics for data management and analysis and got the chance to work closely with biologists. Before going to Tulane I was the one running the Epidemiology software to assist Malian medical students with their data analysis. Back home, in collaboration with Prof Charles Taylor from UCLA I developed a proposal for electronic data archiving of research reports and theses thereby creating a database for scientific research. This proposal was submitted to Professor Yeya Toure of WHO/TDR who encouraged us to apply for a WHO/TDR Grant application. Finally I was awarded a WHO/TDR grant to establish a disease vector functional genomics training center for Africa. The goal of this project was to develop and strengthen functional genomics research capacity in Africa through training of young scientists and networking. From 2004 - 2007, the university began developing short term trainings of African junior scientists to apply state-of-art bioinformatics and functional genomics techniques (http://sundjata.biology.ucla.edu/MRTC/Africangenomics/Announcement.htm). This program was among the five research and training centers (in Kenya, South Africa, Tunisia, Nigeria and later Mali) sponsored by WHO/TDR. The program trained more than 50 researchers from a dozen of African research institutions and contributes to career development in bioinformatics and genomics research. Some of those trainees have pursued graduate studies in Bioinformatics (e.g. Segun Fatumo from Nigeria and Paul Mireji from Kenya).

Question: What are your research interests?

As an Epidemiologist, primarily in infectious diseases research, I have basically been working on Malaria, since the early years of my career. My research covers many aspects of infectious diseases including but not limited to: malaria, leishmaniasis, HIV and emerging infectious diseases. I have been Principal Investigator or Co-investigator in several research grants funded by the National Institutes of Health of United States, CDC, the Gates Foundation, WHO and other research funding agencies. I am Program Director of the NIAID/NIH funded Tropical Medicine Research Center (TMRC) Program on Neglected Tropical Infectious diseases and the West African Center of Excellence in Malaria Research. These programmes aimed to understand the epidemiology, transmission and immune mechanism of resistance/susceptibility to the parasites responsible for these diseases. My capacity building activities involve a public health training program in epidemiology and the development of clinical research at the University of Bamako (University Clinical Research Center, UCRC). I am actively involved in the development of a West African Sub-consortium for clinical research, a network including Mali, Guinea Conakry, Liberia and Sierra Leone, aimed to harmonized clinical research for multi-center studies. I have also been involved in several trials/testing of new public health interventions (eg. Ebola vaccine trials, Attractive Targeted Sugar Bait for mosquito control).

Question: What do you enjoy most about your job?

I love teaching, mentoring and competing for grants for research and for capacity building. I enjoy impacting on public health especially in malaria and elsewhere. I enjoy seeing alumni developing successful careers, I like seeing our results being used to improve health, I love seeing collaborators growing to expand research activities and students growing in their careers.

Question: What do you enjoy least about your job?

I don’t enjoy the stress, so many deadlines to catch up with, travels that take me far away from my family, the busy schedule and activities that come with the type of work I’m doing and lastly, I don’t enjoy administrative activities.

Question: How has being a part of the H3ABioNet community impacted your research group?

I’m proud to see the network become a dream come true. I was part of the initiators who worked for the setup of the African Society of Bioinformatics and Computational Biology network. The goal then in the taskforce, was to push Africa to the fore in terms of bioinformatics, computational biology and strategic collaborations, as Africa then, was lagging behind. This basic goal of H3ABioNet, with the leadership of Nicky, has helped us work closely together.

We have been able to get support from NIH to create the first African Center of Excellence in Bioinformatics (established in 2015), which is now been expanded to Uganda. We have also been able to develop a Master training program in bioinformatics for students, and we are now in our third cohort of the program. We were also awarded different grants in bioinformatics such as the Fogarty training grant: “West African Center of Excellence for Global Health Bioinformatics Research Training”. The proposed program will support the NIH-USTTB’s African Center of Excellence in Bioinformatics with the overall goal to build a sustainable bioinformatics research training program that will foster genomics approaches to address global health issues in Africa. Also funded by the NIH isEzekiel Adebiyi of Covenant University in Nigeria for the “West African Sustainable Leadership and Innovation Training in Bioinformatics Research (WASLITBRe)”, which I am a part of. The goal of this project is to support the H3Africa consortium by producing a sustainable network of individuals who are well trained in various aspects of advanced bioinformatics and data science research, ready to assume leadership roles at academic, health care and research institutions in West Africa. Finally we have been awarded a grant from German government (DFG) in collaboration with University of Jena in Germany and Covenant University of Nigeria to “Identify new insecticidal genes targets against infected mosquitoes to fight malaria employing bioinformatics approaches”. The goal of this project is to develop and investigate gene regulatory signaling and metabolic network models to identify genes being central for the induction of the immune response in the midgut of P. falciparum infected An. Gambiae mosquitoes. We are also working to develop a research-training program in genomics medicine in Mali and in Senegal in collaboration with UCT and I am very pleased to see that bioinformatics activity is growing across the African continent.

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

I would encourage anyone that bioinformatics is a growing field, embracing a new field is always challenging especially for young Africans but I believe this new field is also good to secure a job. As the bioinformatics need is growing, large data are been produced, which may be either research data or societal data. If we do get more capacity, it would help us improve our lives not only in the health sector. Bioinformatics could be multidisciplinary and therefore provides the opportunity to work in many fields, for example, in Medicine and Public health. There are also many opportunities for career building in Bioinformatics, therefore, such an individual has to be creative, believe in what he/she is doing, and should be persistent.

  • AGMT: African Genomic Medicine Training has commenced on the 26th of March and will run till the 24th of June.
  • H3ABioNet will host an Education Summit in Cape Town. The event will take place from 14 - 17 May 2019. Please find more information here: https://www.h3abionet.org/categories/training/bioinformatics-education-summit. Closing date for registration is 31 March 2019.
  • The 13th H3Africa consotirum meeting will be held in Tunisia from 8 - 12 April 2019.
  • 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
  • ISCB Wikipedia Competition. Entries are open now; the closing date for entries is 17 May 2019 and the winners will be announced at the Town Hall meeting at the ISMB/ECCB conference in July 2019. Further details are available on-wiki: https://en.wikipedia.org/wiki/Wikipedia:ISCB-WP.
  • 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.
  • The international conference "Africa, the cradle of human diversity" will take place on May 22nd-25th 2019 at Uppsala University (Sweden). Registration is now open until April 22nd. Please register at https://goo.gl/forms/ND4ODgZKYQLrSsFi1. For more information, please visit the official website for the event https://africathecradleofhumandiversity.com.
  • The supreme council of Universities in Egypt approved ZagaZig’s application to provide a two year based Professional Master degree in Bioinformatics. Applications for this programme will start in August 2019. Most of the course will be taught in the Egyptian Center of Bioinformatics and Genomics (ECBAG). Congratulations on this achievement!
  • Congratulations to Dan Masiga, Rosaline and Caleb and the ICIPE Node members who have successfully undergone a node accreditation exercise and are now accredited for Variant calling from NGS data.
  • The 27th conference on intelligent systems for Molecular Biology and the 18th European Conference on computational Biology will take place in Basel Switzerland from 21 - 25 July. for more information, please visit their website: https://www.iscb.org/ismbeccb2019.
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