Key African Challenges in Critical Mass Development in Bioinformatics

There are various challenges that are encountered within the critical mass development of bioinformatics on the African continent. A shortage of relevant bioinformatics skills has led to ongoing discussions about implementing the appropriate curriculum within the bioinformatics field in Africa [8, 10]. The study of bioinformatics is complex and consists of multiple disciplines essential to biomedical and life science research [8]. Due to the diverse backgrounds of students, it is challenging to improve capacity within bioinformatics and computational biology fields; when students have had a limited exposure to the subject field, there is often a limited grasp [8–10]. This lack of capacity impacts socioeconomic growth, disabling African countries from taking advantage of a knowledge-based economy, compared to other developing countries like China and Brazil [6]. Another confounding factor is limited job opportunities in the field of bioinformatics. This results in graduates opting to apply their technical skills in other sectors of the economy where analytical skills are highly sought after.

Increase in Bioinformatics Demand

Bioinformatics is arguably a recent field of study, but it has developed to a substantial level of importance in the past two decades. The amount of biological data generated by sequencing projects of various species, genome variation studies, and other large data “omics” studies present challenges; demand outstrips supply, and capacity to interpret this complex data is limited in Africa. Ozlem [8, 10–13] argues that in recent decades there has been substantial advancement in the modernization of techniques and established approaches within life sciences, and that continuous development of capacity within the field of computational biology is required.

African Genomic Variation

Researchers in these fields have been interested in studying people in Africa, known as the origin of modern humans, in order to understand the original source of all human genetic diversity [14, 15]. Africa faces a heavy, growing burden of non-communicable diseases [14,16]. The unique environmental impact on medical genetics, as well as genetic factors that contribute to diseases in most African populations, are challenges for African researchers [14,15]. Over the last few years there has been a remarkable growth of African genomic data, starting with the systematic re-sequencing of specific genomic regions [15], followed by next-generation sequencing of the entire genome of an African individual [17,18], leading on to the 1000 Genomes Project (http://www.1000genomes.org/) and the African Genome Variation Project [19]. From a statistical genetics perspective, the high levels of genetic diversity and the burden of complex diseases in African populations offer both challenges and opportunities for genomic analysis [14–16].

While the bioinformatics genomic study of African ethnic groups has commenced, it is still in its infancy and is mostly conducted overseas due to the shortage of practical skills within the research community in Africa. However, the Knowledge Transfer Programme (KTP) aims to match African computational biomedical research questions with knowledgeable experts. This has great benefits, not only for sharing knowledge but also for sustaining further collaborations between local African researchers and the experts.

Lack of Infrastructure As an Emerging Economic Income Continent

African countries share common challenges with other developing countries; however, infrastructure remains central to the problem [6, 20]. The lack of reliable internet connectivity inhibits the growth of bioinformatics in Africa. This challenge creates difficulties in administering certain bioinformatics processes that depend on reliable internet connectivity [6–8]. As a result, most bioinformatics training takes place in shared facilities, either in a university or other tertiary institution [6–8]. Consequently, facilities tend to be oversubscribed and in short supply, while conflicts also arise with other academic fields, such as information technology, which need the facilities for coursework. Overcrowding of multiple software applications on the system provides very little space for related bioinformatics software to support any undertaken studies [21, 22]. Although faced with these challenges, support programmes can mitigate the problem. An example of such an initiative is H3ABioNet, which contributes significantly to project funding and provides training equipment (e.g., eBiokits and Visyo) to local organizations to facilitate quality training and mitigate some of these challenges [20, 22].

The Induced Brain Drain of Bioinformatics Skills in Africa

A substantial number of African scientists, including bioinformaticians, go abroad because of competitive salaries, better job opportunities, and well-resourced institutions. This creates a strain on local, skilled bioinformaticians while the need for bioinformatics capabilities continues to increase [20, 21, 23]. As a result, the brain drain of bioinformatics skills in Africa is alarming; numbers continue to decline in the science and technology statistics averages [20–22]. Moreover, there is a steady decline in leading African experts, who have resorted to collaborating with organizations abroad (mostly in the United States and Europe) to complete research and make use of advanced facilities [1, 8].

Conventional methods of training are initiated by sending researchers to overseas organizations; upon return, they are required to share their learnt knowledge in Africa. However, a lack of mentoring has left many students unable to partake in the field [6, 7]. Although various initiatives are underway to strengthen bioinformatics education in Africa [2, 5, 6, 20], current development capacity in biomedical research is largely based on input from a few isolated senior scientists in Africa and abroad. In addition, disparity across the continent regarding capacity-building in bioinformatics is still a serious concern.

The general approach to international development suggests that developing countries should self-identify their problems and collaborate with developed countries to mitigate these problems [8, 20, 23]. Bioinformatics exists in a rapidly evolving environment. This growth necessitates the equal growth of bioinformaticians to efficiently contribute to ongoing study [2, 20, 23, 24]. If initiatives could be well defined and implemented, they would foster biomedical and life sciences research. However, development in biomedical research is largely based on input from a few isolated senior scientists from Africa, many of whom are based abroad [8, 20, 22–24].

This article describes the KTP, an initiative supported by the Centre for Proteomic and Genomic Research (CPGR) and the NIH-funded H3ABioNet project to strengthen bioinformatics capability-building at local institutions in Africa where life scientists are in need of skilled bioinformaticians. The KTP is an online matchmaking platform that brings together seekers of bioinformatics expertise with experts who are willing to transfer their knowledge in a project-based fashion. These experts physically assist with the development and monitoring of local trainers and trainees through a “train-the-trainer” component associated with every project proposed by the knowledge-seeker.

The KTP and its Review Committee (RC) and Scientific Advisory Committee (SAC) (see Table 1) facilitate the process by identifying and evaluating experts (knowledge providers), projects (proposed by knowledge-seekers, also known as principal investigators [PIs]), and training requirements for potential research associates and trainees, respectively (Fig 1 and S1 Text). Instead of travelling overseas, experts are brought in locally to conduct high-quality research agendas and work on relevant projects, through which the transfer of knowledge and skills is achieved naturally (Fig 1). One of the advantages to this approach is minimized travel and accommodation expenditure. The programme’s success is monitored by the number of local junior and senior bioinformatics trainers created, the number of trainees trained, the number of experts in the expert database, and the number of projects supported (S1 Text). Importantly, the KTP is highly linked to international organizations, including the European Molecular Biology Network (EMBnet), GOBLET, Golden Helix Foundation, and H3ABioNet, amongst others, which contribute significantly toward the goal of increasing bioinformatics capacity and knowledge expansion in Africa, which is essential to the KTP’s objectives (S1 Text).

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Fig 1. Process map of the matchmaking platform.

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Table 1. Description of the KTP’s stakeholders and benefits offered by the KTP to each of the stakeholders.

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Matchmaking Platform

Reviewing activities of the experts includes assessing and validating their skills, experience, and contribution to the scientific community before admitting them into the system and accepting them as either junior or senior experts. S1 Fig illustrates the flow of information during the expert review process (more details in S1 Text). Similarly, the registration of the project includes relevant information about the project, a work package (proposing times and deliverables), and the set of required skills for this project (see S2 Fig and S1 Text for more details). A project PI identifies certain expertise from the KTP skills matrix tree format, adopted from the skills ontology of PLOS Computational Biology. The KTP matchmaking platform (Fig 1) identifies the most suitable expert from the KTP expert database, based on the project requirements submitted by the PI. Based on the number of matching skills requested for a project and the level of skill(s) an expert has, candidates are short-listed and matchmaking is undertaken (see S1 Text for more details). Secondly, the SAC ensures the project is feasible within the timeframe and can be achieved by the selected expert(s). All the expert applications, the review process, and the project selection process are streamlined within the KTP system through an online application process.

An arbitrary scoring system is used to quantify and qualify the skills provided by the individual applying to be an expert (details in S1 Text). In order to manage all the reasoning behind the KTP’s different processes and to retain audit trails (Figs 1, S1 and S2), a web system was designed and implemented (http://ktp.cpgr.org.za/). The KTP is organized around six main stakeholders, whose benefits are shown in Table 1.