Early phases

The development of bioinformatics in South Africa and on the African continent can be traced back to 1996 when Winston Hide founded the South African National Bioinformatics Institute (SANBI) on the University of the Western Cape (UWC) campus. South Africa’s National Research Foundation (NRF) provided the initial funding to establish SANBI, and this was supplemented with funding from what was then Glaxo Wellcome and the United States Department of Energy. The following two years saw investment from the South African telecommunications company, Telkom. During this time, the first four bioinformatics PhD students were enrolled at SANBI, and by 2000, South Africa’s vision for expanding bioinformatics was realized with the establishment of the South African Medical Research Council Bioinformatics Capacity Development Unit at SANBI with committed funding for 2000–2015. In 2003, a regional bioinformatics training center under the umbrella of the World Health Organization’s Tropical Disease Research (TDR) Program was established at SANBI. This program provided a bioinformatics training mechanism for African researchers–a program that subsequently informed training within the International Glossina Genome Initiative [5].

Government support for biotechnology and bioinformatics was formalized in the 2001 Green Paper on the Biotechnology Strategy [6], which highlighted the importance of human capacity development and designated bioinformatics eligible for critical skills work permit applications. Strategic and practical support continued, with ongoing updates of state policies (e.g., [7,8]). Several universities established nascent bioinformatics groups and lobbied collectively, resulting in an influential call to action published in the South African Medical Journal [9].

The National Bioinformatics Network

The first formal call for establishing a nationwide bioinformatics infrastructure came from the South African Medical Research Council in 2002, with funding from the national Department of Arts, Culture, Science, and Technology and later the Department of Science and Technology (DST). While the amount committed was modest, this catalyzed meetings of the bioinformatics stakeholders in South Africa and subsequent formation of a group of scientists promoting the interests of bioinformatics nationally. Shortly thereafter, the DST announced an initiative to establish Biotechnology Regional Innovation Centers (BRICs), including a semiautonomous National Bioinformatics Network (NBN). Planning for the NBN took place during 2002, and the NBN was given a mandate to generate bioinformatics capability and infrastructure and act as a service provider, with specific emphasis on its role in supporting the BRICs. Calls for proposals to set up nodes for the network and for research projects were received in 2003, and a Director was appointed, followed by administrative, technical and scientific staff. Initially, five nodes were funded at Universities across South Africa, with two further nodes added at a later stage. Node funding covered staff appointments, equipment purchases, general running costs, student bursaries, training courses, and research projects. This was followed by five further annual rounds of substantial funding. The NBN funding ended in 2008, and the NBN as an entity was closed in 2009. The NBN initiative vastly expanded bioinformatics capacity in South Africa through the funding of staff positions and through the training of postgraduate students, as well as through extensively taught short courses for researchers. These activities all fell outside of traditional university commitments. The investment in infrastructure provided a very significant boost to the scope of projects that could be executed and the level of bioinformatics research ongoing.

In retrospect, some of the lessons learned from the NBN initiative may be useful for others. These include:

• Splitting of funds into noncompetitive funding for training and initial infrastructure and competitive funding for research-fostered cooperation between bioinformatics groups, while encouraging healthy competition for funding of research projects.
• The use of an independent, international Scientific Advisory Board (SAB) to mediate key funding decisions ensured quality and nonpolitical funding decisions, particularly at the early phases when the South African bioinformatics community was too small to support independent review at a national level.
• Although the state identified bioinformatics as key to supporting health priorities within the biotech industry, the need to build general infrastructure and research capacity was also recognized, and the NBN was given wide autonomy for the type of research funded.
• A very complex governance structure included the NBN Trust Committee, the SAB, and an executive, and this led to a breakdown in accountability when problems did occur.
• Whilst the dedicated funding was very beneficial, the process was poorly integrated into the national funding system and researchers had to source funding from different entities to cover different aspects of a single project. For example, funding for related laboratory work had to be sourced under different initiatives.

Following closure of the NBN initiative, the DST formed a steering committee for Bioinformatics in 2009, which facilitated bioinformatics research and fellowships disseminated through the NRF, commencing in 2010 and repeated every two years. Funding for a national Bioinformatics Service Platform (BSP) was granted in 2013, and the appointment of a coordinator is currently underway (discussed further below). Further support for bioinformatics research has been provided through the DST/NRF South African Research Chairs Initiative (SARChI), and three chairs are currently supported in the broad bioinformatics area (Bioinformatics and Public Health Genomics, Bioinformatics of African Populations, Mechanistic Modelling of Health and Epidemiology). Fig 1 provides a summary timeline of the major events impacting the development of bioinformatics in South Africa.

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Fig 1. The policy, infrastructure, training, and funding landscape of computational biology in South Africa (2000–present).

Government policy on computational biology was driven largely by the DST (above timeline arrow), while bioinformatics training courses have been a constant feature of this landscape since 2003. There was a major period of infrastructure investment from 2002–2007, from the NBN, but national funding has now become available only every two years. National bioinformatics conferences also occur in two-year intervals (details in text).

https://doi.org/10.1371/journal.pcbi.1004395.g001

International influences on the development of bioinformatics in South Africa

Several international initiatives influenced the development of bioinformatics in South Africa. In the early 1990s, the European Molecular Biology Network (http://www.embnet.org/) established the first bioinformatics network in Africa, with nodes similar to EMBNet Nodes in Europe. The first African Node was set up at SANBI, followed by many others (http://www.embnet.org/about/nodes). The World Health Organization’s TDR also provided funding to support establishment of an African Regional Training Centre for Bioinformatics and Applied Genomics in South Africa. As part of this activity, many training workshops were presented across Africa. Another approach to set up a large network within Africa, with leadership in South Africa, was led by the Centre National de la Recherche Scientifique (CNRS) in collaboration with NEPAD. This network funded the start of the ASBCB (African Society for Bioinformatics and Computational Biology) Bioinformatics conferences (ASBCB later joined forces with the International Society for Bioinformatics and Computational Biology [ISCB] to run these conferences) and workshops and mapped the bioinformatics structure in Africa (http://www2.lirmm.fr/france_afrique/20060708_NEPAD.pdf). These international activities helped to establish the initial bioinformatics network structure in South Africa, which in turn attracted national government recognition and commitment to advancing bioinformatics in the country.

More recently, international initiatives are having a profound influence on South African bioinformatics. The NIH-funded H3ABioNet Pan African bioinformatics network (www.h3abionet.org) is part of the Human Heredity and Health in Africa (H3Africa: www.h3africa.org, discussed later) initiative [10] and is coordinated from the University of Cape Town (UCT) with six additional nodes in South Africa. This project is building bioinformatics capacity on the continent and, as a result, is boosting bioinformatics activities in South Africa. The award of funding for H3ABioNet in South Africa prompted the DST to commit funds for bioinformatics support personnel at the Centre for High Performance Computing (CHPC) in Cape Town and to continue funding national bioinformatics courses for postgraduates.

National bioinformatics courses

Bioinformatics was not traditionally part of undergraduate curricula in South Africa, so students registering for postgraduate degrees in bioinformatics tend to start with little formal training in the field. In response, the NBN developed joint courses compulsory for NBN-funded students that introduced them to a range of bioinformatics topics and developed their programming and other technical skills. The first courses were run over two semesters of eight weeks each, but the length and curriculum has been refined over time to account for changing needs, costs, and realistic length of time students can spend away from their research projects. Today, these courses run for seven weeks at the start of each academic year and are aimed at students registered for dissertation-only postgraduate bioinformatics degrees at South African universities. At the start, we relied heavily on international trainers, but now all trainers are based within the country, a testament to the building of local training and skills capacity. In addition to exposure to a range of topics, computer science and mathematics students learn basic molecular biology, while biology-trained students learn programming. All the students benefit from networking opportunities and sharing skills and experience with their peers. These courses, which are supported financially by the DST, are extremely popular and oversubscribed, so we are considering running two such courses in different geographical locations where training is needed, and in the future. The substantial number of applications from bench scientists to attend these courses highlights the current gap in the training of bioinformatics users.

Other bioinformatics training initiatives

In addition to these national courses for training bioinformaticists, different universities and the NBN have run short specialized training courses funded by their own institutions, foreign funding agencies, the NBN or directly by the DST. Some have hosted short courses organized through collaborative grants that individual researchers have with other countries or through funds raised from initiatives such as the NRF Knowledge, Interchange, and Collaboration program. Many of these have focused on training biological scientists in the use of bioinformatics tools, but some have also been tailored towards extending the skills of bioinformaticists. Some examples are provided below but are by no means comprehensive.

Several researchers at South African universities have hosted Ensembl and other roadshows on specific databases or tools, including Galaxy (http://galaxyproject.org/). They have also organized training around specialized topics or techniques, such as microarray, proteomics, or NGS data analysis. These are initiated through personal contacts, and funding sources vary. While such short-course training is not coordinated in South Africa, in many cases funding has been shared, particularly where the course runs in multiple locations in the country. This provides a cost-effective means of training many people in each region. These courses have focused mainly on training researchers in South Africa, but several courses have been hosted in the country and targeted to those both internal and external to the country. For example, SANBI hosted annual WHO TDR workshops for African scientists, and the results of one of these workshops are included in a recent Science publication [13]. UKZN and Medical Research Council in Durban have also served as a hub of education and training on bioinformatics, training people both locally and abroad. International organizations that have had a training presence in the country are the ICGEB (International Centre for Genetic Engineering and Biotechnology), Wellcome Trust, EMBO (European Molecular Biology Organization), EMBNET, and the NIH, through H3ABioNet. Training workshops were also held in 2011 in Cape Town as part of the ISCB Africa ASBCB conference on bioinformatics [14]. In addition to providing training courses, several South African academics are actively involved in GOBLET (Global Organization for Bioinformatics Learning, Education and Training) [15].

The DST, in addition to supporting national bioinformatics courses, has also made provision for financial support of necessary skills development and training needs, in the form of workshops and conferences as required by the bioinformatics community. It extends its training initiative through international cooperation partnership agreements, e.g., EMBO and Cooperation in Science and Technology (COST) training, as well as a number of other DST-driven platforms and Centers of Competence to enhance the bioeconomy of South Africa [8]. Also, as part of the Bioinformatics and Functional Genomics (BFG) program, which is administered through the NRF to fund bioinformatics research, the DST supports the development of human capacity and the creation of BFG skills for bio-based innovation and technology initiatives. Through this, South Africa is creating a growing pool of postgraduate students equipped to support bioeconomy developments, solutions, and knowledge relevant to the South African biotechnology industry, and national initiatives such as the Technology Innovation Agency (TIA), Centers of Excellence, and Research Chairs. It also aims to promote collaboration between academic institutions, science councils, and industry in South Africa, thus linking bioinformatics education to other national initiatives. There are various other training mechanisms to complement as well as to strengthen the training needed to bridge the gap between the academia and industry. Examples include internships offered by the TIA, NRF, and H3ABioNet, train-the-trainer programs, and a Knowledge Transfer Program (KTP) by the Centre for Proteomic and Genomic Research (CPGR).

Bioinformatics in health

Genomics, biotechnology, and specifically bioinformatics were areas that were identified as requisite for addressing the heavy burden of disease in South Africa, particularly diseases of poverty [17]. To date, medical genomics research in South Africa has focused almost exclusively on infectious diseases that include HIV, malaria and tuberculosis. Bioinformatics approaches are used to identify host, vector, and pathogen variation, and to identify variants and biomarkers of pathogenicity and multidrug resistance. Genomic approaches have also been applied to infectious disease control [18]. South Africa, however, is in the process of epidemiological transition from a major disease burden of infectious to noncommunicable diseases [19,20]. Furthermore, the advent of NGS technologies, their increasing accessibility, and decreasing costs have opened new avenues to understanding genotype–phenotype relationships in noncommunicable human disease [20], and the high genetic diversity of sub-Saharan African populations positions South Africa to conduct groundbreaking genomics research towards understanding genetic factors underlying human disease [21].

Establishment of a National Bioinformatics Support Platform

Improved affordability and availability of high-throughput technologies to the South African scientific community has generated increasingly complex genomic datasets, with a concomitant increase in the need for bioinformatics support. Since the dissolution of the NBN, the existing bioinformatics groups have generally been able to secure funding for research, but not for service provision. Despite this, there has been an expectation from peers at their universities that they should play a role in providing support to researchers. This puts them in a difficult situation as salaries for support staff need to be covered and they should derive some benefit from their involvement. The analysis, however, doesn’t always lead to publications. In addition, this may address some of the needs of researchers located near competent bioinformatics groups, but not those of other researchers or the biotechnology community. In response, a proposal for a National BSP was developed by a Steering Committee, and subsequently funded by the DST. The platform is currently being established and staffed, and will provide a bioinformatics support structure for researchers in the academic and commercial sectors throughout the country. The BSP will respond to service requests nationally based on expertise and managed by a central national helpdesk. Although centrally coordinated, BSP staff will be seconded to institutions who demonstrate significant and ongoing need for support. The BSP will also take over custodianship of national bioinformatics training and education that lies outside of university responsibilities. The hope is that the BSP will fill the current gap in bioinformatics service provision that has come to be expected by scientists.

South African Society for Bioinformatics (SASBi)

Local bioinformatics groups were adversely affected by the closing of the NBN, but the impact went beyond the financial, since the NBN also provided a voice and a discussion platform for the bioinformatics community in the country. In order to bring the bioinformatics community together, the community recently established SASBi (http://sasbi.weebly.com/). The aim was to support newly established bioinformatics research groups, to enhance interactions among people related to bioinformatics, and to form a representative body to interact with government. An interim steering committee was formed to establish the national society, and this committee produced a draft constitution. The society was inaugurated on 11 September 2012 at a meeting during the first joint conference of the South African Genetic Society (SAGS) and the bioinformatics community. The second joint SAGS/SASBi conference took place in September 2014. Both DST and BSP have provided financial support which made it possible to support 71 students to attend the conference. SASBi has interacted with the DST on a number of occasions, e.g. it conducted a national survey for bioinformatics needs, and discussed the BSP proposal. During the second joint conference, a SASBi Student Society was formed, and has already been affiliated with the international society (ISCB).

International societies and networks

Many members of SASBi are also members of international societies such as the ASBCB and the ISCB. At least four South African bioinformaticians have previously been or are currently members of the ISCB Board of Directors, and one has served two terms as President of ASBCB. South Africa hosted one of the ISCB Africa ASBCB Bioinformatics conferences in Cape Town in 2011. The SASBi student society was affiliated with ISCB in March 2015, and the affiliation of SASBi with ISCB will be initiated this year now that the society has been in existence for a minimum of two years. Individual bioinformatics researchers also have numerous international collaborators both on the continent and abroad, some of which are described above. A notable example of a large collaborative network is the previously mentioned H3ABioNet network, which links seven local bioinformatics groups with over thirty groups continent-wide and two in the US, and is led from South Africa. The project also links the bioinformatics community with genomics researchers and clinicians in Africa through the wider H3Africa consortium, which consists of over 350 members in 18 African countries.

The EMBNet has been a direct and indirect supporter of bioinformatics initiatives in South Africa. They have, for example, provided numerous reviewers for national grant applications, identified partners for various successful and unsuccessful grant applications, sponsored national conferences, and provided technical support for bioinformatics queries through their mailing lists. They have run training courses in the country and recently facilitated the link between South Africa and the EU COST action, SeqAhead (http://www.seqahead.eu/). South Africa was the first African country to join the Action BM1006 called the NGS network. SeqAhead offered various workshops on NGS data and aimed to galvanize the implementation of efficient workflows for NGS data storage, retrieval, sharing, and analysis.