Bioinformatics in Africa

By Goodness Njakoi – Art in Tanzania Internship

African countries have long been disproportionately burdened by the “big three” infectious diseases (HIV/AIDS, tuberculosis, and malaria) and neglected emerging infectious diseases such as EVD and Lassa fever. African populations maintain the world’s highest levels of genetic diversity which decline proportionately with increasing distance from Africa.

The development of bioinformatics as a discipline has provided biological scientists with many important insights into the functioning and composition of biological systems. Together with tools and methods developed within bioinformatics, these insights provide essential foundation.

The establishment of the South African National Bioinformatics Institute in South Africa in the 1990s heralded the development of bioinformatics on the continent. The introduction of bioinformatics to the rest of the African continent was slowed down by several challenges that included limited scope of research encompassing bioinformatics-driven goals, shortage of qualified bioinformaticians, poor access to powerful computer systems, lack of high speed internet, poor access to essential databases and software programs, and unreliable power supply.

Recent funding investments toward large-scale research projects, training, and infrastructure support are helping address the bioinformatics disparities between countries within the continent through establishment of world-class resources and training. The establishment of the African Society for Bioinformatics and Computational Biology (ASBCB) during a World Health Organization Tropical Disease Research workshop in February 2004 led to a sustainable network of researchers across the continent.

A noteworthy initiative with its foundation is the Human Heredity and Health in Africa Bioinformatics Network H3ABioNet network, whose mandate is to provide bioinformatics support for the Human Heredity and Health in Africa (H3Africa) initiative and to develop bioinformatics ability across Africa through funding provided by the National Institutes of Health. H3ABioNet has focused on building infrastructure and implementing tools that enable collaborations and data transfer across the resource-limited continent.

A major focus area of H3ABioNet has been to develop sustainable approaches to develop bioinformatics ability in Africa. Taking into consideration the challenges facing the continent, H3ABioNet has explored various training approaches, including long and short face-to-face training workshops, internships, and data-centered hackathons. Furthermore, H3ABioNet has developed a multiple-delivery-mode learning model comprising elements of distance learning, open educational resources (OER), and face-to-face learning for an Introduction to Bioinformatics IBT course in order to meet the need for bioinformatics training of molecular biologists- as well as individuals from other backgrounds interested in developing skills in bioinformatics- in Africa and to address the specific challenges for this setting.

State of Bioinformatics in Tanzania

Biotechnology industry in Tanzania is still very poor and hardly any bioinformatics is vividly talked about. There are several biotechnologies research works around the country, but no serious investments have been made for bioinformatics. Research groups most likely to apply bioinformatics are the Tanzania Genome Network member groups, the Genome Science Centre at Sokoine University of Agriculture (SUA), IFAKARA Health Institute, Tanzania Society of Human Genetics and the Department of Molecular Biology and Biotechnology at the University of Dar es salaam.

While the government through the National Commission for Science and Technology (COSTECH) understands the potential of R&D in biotechnology to the nation’s economic growth, there is a dare need for awareness campaign on the significance of bioinformatics in biotechnology. It is the role of universities and other higher learning institutions to design programs which also involves Bioinformatics in their curricula. State universities like the University of Dar es Salaam (UDSM) and Sokoine University of Agriculture (SUA) have introduced courses like Introduction to Bioinformatics, Genomics and Bioinformatics, Genomics, Proteomics and Bioinformatics etc. into their curricula.

Teaching bioinformatics is made difficult by the constraints of typical university classrooms. Some areas of basic bioinformatics may be taught using such classrooms, where all that is needed is an internet connection and web browser searches at the NCBI. More in-depth teaching requires the re-creation of a bioinformatics research environment, consisting of a Linux or UNIX operating system, standard GNU utilities, specialist bioinformatics software, and sequence databases. In most cases the available computer laboratories hold few functional computers to train a class, so classes huddle around few working computers. Moreover, the nations’ energy supply would often be cut off, making teaching bioinformatics on a computer rather difficult. But also, there is a serious shortage of skilled personnel to teach bioinformatics in the country. However, even if the power supply is intermittent and the Internet connections run at dial-up speed, it is still possible to conduct bioinformatics activities. Determined bioinformaticians can start a study with just a computer and open-source software downloaded through the Internet. Alternatively, buying an US$3000 wealthy eBioKit system will make a big difference. Meanwhile, awareness campaigns should be constantly stages to appeal to the government and private sector to invest in bioinformatics.

In 2011, three TGN member institutions (MDH, MUHAS and UDSM) joined Human Heredity and Health in Africa Bioinformatics Network (H3ABioNet). The involvement with H3ABioNet is revolutionizing bioinformatics in Tanzania through knowledge transfer and infrastructure improvements. Through H3ABioNet, researchers and technical staff from MDH, MUHAS and UDSM have been attending specialized training courses with the aim that they will teach others at their home institutions.

Future Perspectives

Bioinformatics and data science research thrives on genetically diverse populations as population substructure variation contributes to the identification of true associations in complex disorders and drug response. Research on these topics within Africa supply considerable opportunities for improving health outcomes through their application in infectious disease research vaccine and drug development, and drug resistance patterns.

The completion of the Human Genome Project and technological advances have led to significant cost reductions for genomic data acquisition and also supply immense opportunities for novel insights into etiology, diagnosis and therapy

Although these large volumes of information are valuable resources for the scientific community, the extremely rapid growth in database size also brings difficulties in analyzing and deriving inferences from such data. Computational research has become essential in the post genomic era to help organize and store bioinformatics data, ensuring their retrieval and allowing further processing and analysis. This contributes towards improved understanding of the regulation and functioning of biological processes.

Any country intending to remain up to date in the biomedical, biotechnological and agricultural sectors, cannot disregard bioinformatics. In addition to this general trend, developing countries may also want to manage their own specific data on indigenous biological species, on local epidemiology and biodiversity programs. These tasks clearly require that statisticians and informatics experts become advanced users of bioinformatics software and develop a capability to solve problems locally. This process does not require large resources in it but will allow developing countries to further investigate their own biological resources. To ease this process biomathematics/bio-computing should be introduced to universities, and the establishment of small software groups and companies should be encouraged.

Conclusion

To fully benefit from advances in bioinformatics and data science research, it is imperative to train the next generation of African scientists on their use. It is important to note that the shortage of trained bioinformaticians is among the main obstacles in the development of bioinformatics in Africa. These demands call for building local university programs and infrastructure for setting up environments that are conducive for bioinformatics and data science training. Bioinformatics is known to require less infrastructural investments than other bench science initiatives, but essential resources are necessary such as powerful computer systems, reliable high-speed internet, access to databases and software programs, and reliable electricity. Research infrastructure, research funding, training programs, scientific networking, and collaborations are also important as key elements for developing bioinformatics ability. Other factors affecting the implementation of training programs include teaching laboratories, server systems, airfare cost, timeliness of visas, suitable computational infrastructure, socio-political stability, and availability of open training spots. This ability may be gained through research and training on overlapping computationally intensive topics such as data management and data capture.

It is also of central importance to publish literature on scientific training programs to check and evaluate progress, develop standards, and share training approaches and experiences.

References

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