Strengthening synthetic biology capacity in Kenya through bioinformatics training
This project involved lengthening and adding a synthetic biology module to a bioinformatics course delivered at the icipe institute in Nairobi, Kenya. The course, “Bioinformatics approaches for next generation sequencing analysis” school. was organised by Dr. Jelena Aleksic, TReND in Africa, and Dr. Ben Kulohoma, icipe, Kenya, in collaboration with a group of academics including Richard Smith-Unna (University of Cambridge) and Vicky Schneider (TGAC).
The power of synthetic biology comes in part from the computational tools used for the design up novel biosystems. As such, bioinformatics knowledge is key to harnessing the full power of the field, and building long-term capacity.
As part of this project, we will develop and deliver a novel synthetic biology module, which will be incorporated as part of an 8-day bioinformatics course being delivered in Nairobi, Kenya in November 2015.
Dr Richard Smith-Unna,
Graduate Student, Department of Plant Sciences, University of Cambridge
Dr Vicky Schneider,
Member of Senior Management Team, The Genome Analysis Centre, Norwich
Dr Jelena Aleksic,
Director of Bioinformatics at TReND in Africa (http://trendinafrica.org/)
Mr Richard Pilling,
Director of Big Data and Analytics at Intel
Dr Ben Kulohoma,
Summary of the project's achievements and future plans
The genomics revolution: building bioinformatics capacity in Africa
Blog post by Dr Jelena Aleksic, TReND in Africa
Although Africa accounts for 24% of the global burden of disease, the majority of related biomedical research still happens in Western countries. I believe that the scientific independence of Africa means that scientists on the continent are able to set their own research agenda and develop their own solutions. Given the increase in freely available genomics datasets and low infrastructure requirements, bioinformatics provides a promising field of research for African scientists.
At TReND in Africa, we aim to support scientific capacity development by providing researchers with training, expertise and equipment required for undertaking research. We recently ran a bioinformatics course at the icipe Institute in Kenya, which gave us a fascinating insight into the promises and challenges of bioinformatics as an emerging field of research in Africa.
A thirst for knowledge
As DNA sequencing prices drop and sequencing machines become commonplace at universities around the world, the demand for bioinformatics knowledge and expertise is at an unprecedented high. This is also borne out by the huge demand for training in this area. Bioinformatics continues to be one of our most popular courses and this year alone, we received 430 applications for the 25 spaces in our school in Kenya. TReND in Africa also received applications from 23 different African countries, showing the relevance of the subject across the continent.
The popularity of bioinformatics is perhaps due to its versatility, as well as its low infrastructure requirements. DNA sequencing has transformed many different areas of biology in the last decade, and remains relevant to areas from abstract evolutionary theories to the latest Ebola and HIV research. Furthermore, the advent of open access genomics data means that anyone worldwide can now analyse this information without performing expensive experiments. All they need is the right knowledge, a computer and an Internet connection.
At icipe, we benefited from the Institute’s computing lab and servers, our colleagues at Science Resources Africa inspire us, as they are doing the same work in Sierra Leone on Raspberry Pis. This highlights the potential of bioinformatics for low resource research environments.
All TReND courses are open to students across the African continent, and this is an essential to the way we run training programmes. For our 2015 bioinformatics school, we selected 25 participants who came from nine different African countries. The purpose of this is two-fold. First, it disseminates knowledge further, rather than containing in one geographical area. But importantly, it also creates a network of African scientists who collaborate with and learn from each other. We find that the TReND courses are often a bonding experience for the participants, and training groups often stay in touch and share knowledge long after the course has ended.
In order to meet demand this year, we also opened up 15 overflow spaces to local Nairobi students who could commute to the course daily with their laptops. With 40 spaces in total, this made our 2015 bioinformatics school the biggest TReND course to date in terms of class size. This was somewhat challenging for the instructors, as all of us had to work extra hard to answer questions and support students during the course. A typical day started at 9am and finished around 7pm, with constant teaching and mentoring throughout that time. As always, it was very satisfying to teach students who are passionate, genuinely keen to learn, and have a lot of burning questions.
The Bioinformatics School continues to be a partnership between icipe and TReND, and is taught by a mixture of instructors from the UK (Cambridge University and Imperial College) and Kenya (icipe and BecA-ILRI). We are particularly grateful to Dr Benard Kulohoma from icipe, who was the driving force behind the organisation of this year’s course, despite preparing to move countries. We were also proud to welcome Kelvin Muteru, one of the students on the 2014 course, back as a lecturer.
Ongoing impact and meeting long-term needs
In an environment where all scientists above undergraduate level are expected to lecture regularly, the impact of advanced training courses quickly goes beyond the original participants. All our students hold Masters qualifications or above and work at African research institutions. We estimate that each of our course attendees will have the chance to pass on some of those skills to an additional 200 colleagues within the first year alone, and many more on an ongoing basis from there. For this reason, it is particularly important to improve and update lecturer skills, as well as those of students in the early stages of their scientific careers. Additionally, all our teaching materials are open source and available online, making them easily accessible for future training.
Alongside TReND, a number of excellent initiatives exist in this area including H3ABioNet, a pioneer of this training. We are also very excited about the recent establishment of the Uganda Medical Informatics Centre, an initiative led by the African Partnership for Chronic Disease Research network. We believe that this centre will provide a fantastic bioinformatics infrastructure for the region, and look forward to collaborating. TReND commends these efforts, and firmly believes that more training and infrastructure is needed to unlock Africa’s potential for genomics and bioinformatics research.