Computational Biology and Bioinformatics in Nigeria

Over the past few decades, major advances in the field of molecular biology, coupled with advances in genomic technologies, have led to an explosive growth in the biological data generated by the scientific community. The critical need to process and analyze such a deluge of data and turn it into useful knowledge has caused bioinformatics to gain prominence and importance. Bioinformatics is an interdisciplinary research area that applies techniques, methodologies, and tools in computer and information science to solve biological problems. In Nigeria, bioinformatics has recently played a vital role in the advancement of biological sciences. As a developing country, the importance of bioinformatics is rapidly gaining acceptance, and bioinformatics groups comprised of biologists, computer scientists, and computer engineers are being constituted at Nigerian universities and research institutes. In this article, we present an overview of bioinformatics education and research in Nigeria. We also discuss professional societies and academic and research institutions that play central roles in advancing the discipline in Nigeria. Finally, we propose strategies that can bolster bioinformatics education and support from policy makers in Nigeria, with potential positive implications for other developing countries. © 2014 Fatumo et al.SAF was supported by H3ABioNet NABDA Node, Abuja, Nigeria with NIH Common Fund Award/NHGRI Grant Number U41HG006941 and Genetic Epidemiology Group at Wellcome Trust Sanger Institute.Published versio

Evaluating the Relationship Between Running Times and DNA Sequence Sizes using a Generic-Based Filtering Program.

Generic programming depends on the decomposition of programs into simpler components which may be developed separately and combined arbitrarily, subject only to well- defined interfaces. Bioinformatics deals with the application of computational techniques to data present in the Biological sciences. A genetic sequence is a succession of letters which represents the basic structure of a hypothetical DNA molecule, with the capacity to carry information. This research article studied the relationship between the running times of a generic-based filtering program and different samples of genetic sequences in an increasing order of magnitude. A graphical result was obtained to adequately depict this relationship. It was also discovered that the complexity of the generic tree program was O (log2 N). This research article provided one of the systematic approaches of generic programming to Bioinformatics, which could be instrumental in elucidating major discoveries in Bioinformatics, as regards efficient data management and analysis

Systems Biology and the Development of Vaccines and Drugs for Malaria Treatments

The sequencing race has ended and the functional race has already begun. Microarray technology enables simultaneous gene expression analysis of thousands of genes, enabling a snapshot of an organisms’ transcriptome at an unprecedented resolution. The close correlation between gene transcription and function, allow the inference of biological processes from the assessed transcriptome profile. Among the sophisticated analytical problems in microarray technology at the front and back ends respectively, are the selection of optimal DNA oligos and computational analysis of the genes expression. In this review paper, we analyse important methods in use today in customized oligos design. In the course of executing this, we discovered that the oligos designer algorithm hanged on gene PFA0135w of chromosome 1, while designing oligos for the gene sequences of Plasmodium falciparum. We do not know the reason for this yet, as the algorithm runs on other sequences like the yeast (Saccharomyces cervisiae) and Neurospora crassa. We conclude the paper highlighting the procedures encompassing the back end phase and discuss their application to the development of vaccines and drugs for malaria treatment. Note that, malaria is the cause of significant global morbidity and mortality with 300-500 million cases annually. Our aims are not ends, but a means to achieve the following: Iterate the need for experimental biologists to (i) know how to design their customized oligos and (ii) have some idea about gene expression analysis and the need for cooperation between experimental biologists and their counterpart, the computational biologists. These will help experimental biologists to coordinate very well the front and the back ends of the system biology analysis of the whole genome effectively

DEVELOPMENT AND IMPLEMENTATION OF A BIOINFORMATICS ONLINE DISTANCE EDUCATION LEARNING TOOL FOR AFRICA

Bioinformatics refers to the creation and advancement of algorithms, computational and statistical techniques and theories for solving formal and practical problems arising from the management and analysis of biological data. However, some parts of the African continent have not been properly sensitized to bio-scientific and computing field. Thus, there is the need for appropriate strategies of introducing the basic components of this emerging scientific field to part of the African populace through the development of an online distance education learning tool. This study involved the design of a bioinformatics online distance educative tool an implementation of the bioinformatics online distance educative tool by a programming approach. Design and implementation were done using the Borland Delphi 7 Enterprise edition within its Integrated Development Environment. The advantage of using Delphi programming language in implementing this useful bioinformatics web tool is that Delphi programming language is an object oriented programming language that has a lot of extra facilities for the enhancement of further technical functions, which ordinary HTML cannot handle. The development and use of a bioinformatics distance education software, as a teaching tool, in some African countries holds great promise for accommodating the needs of the populace, who live in cities, small towns and remote areas

MACBenAbim: A Multi-platform Mobile Application for searching keyterms in Computational Biology and Bioinformatics

Computational biology and bioinformatics are gradually gaining grounds in Africa and other developing nations of the world. However, in these countries, some of the challenges of computational biology and bioinformatics education are inadequate infrastructures, and lack of readily-available complementary and motivational tools to support learning as well as research. This has lowered the morale of many promising undergraduates, postgraduates and researchers from aspiring to undertake future study in these fields. In this paper, we developed and described MACBenAbim (Multi-platform Mobile Application for Computational Biology and Bioinformatics), a flexible user-friendly tool to search for, define and describe the meanings of keyterms in computational biology and bioinformatics, thus expanding the frontiers of knowledge of the users. This tool also has the capability of achieving visualization of results on a mobile multi-platform context

Experimental and computational applications of microarray technology for malaria eradication in Africa

Various mutation assisted drug resistance evolved in Plasmodium falciparum strains and insecticide resistance to female Anopheles mosquito account for major biomedical catastrophes standing against all efforts to eradicate malaria in Sub-Saharan Africa. Malaria is endemic in more than 100 countries and by far the most costly disease in terms of human health causing major losses among many African nations including Nigeria. The fight against malaria is failing and DNA microarray analysis need to keep up the pace in order to unravel the evolving parasite’s gene expression profile which is a pointer to monitoring the genes involved in malaria’s infective metabolic pathway. Huge data is generated and biologists have the challenge of extracting useful information from volumes of microarray data. Expression levels for tens of thousands of genes can be simultaneously measured in a single hybridization experiment and are collectively called a “gene expression profile”. Gene expression profiles can also be used in studying various state of malaria development in which expression profiles of different disease states at different time points are collected and compared to each other to establish a classifying scheme for purposes such as diagnosis and treatments with adequate drugs. This paper examines microarray technology and its application as supported by appropriate software tools from experimental set-up to the level of data analysis. An assessment of the level of microarray technology in Africa, its availability and techniques required for malaria eradication and effective healthcare in Nigeria and Africa in general were also underscored

Aligning Multiple Sequences with Genetic Algorithm

The alignment of biological sequences is a crucial tool in molecular biology and genome analysis. It helps to build a phylogenetic tree of related DNA sequences and also to predict the function and structure of unknown protein sequences by aligning with other sequences whose function and structure is already known. However, finding an optimal multiple sequence alignment takes time and space exponential with the length or number of sequences increases. Genetic Algorithms (GAs) are strategies of random searching that optimize an objective function which is a measure of alignment quality (distance) and has the ability for exploratory search through the solution space and exploitation of current results

Establishment of computational biology in Greece and Cyprus: Past, present, and future.

We review the establishment of computational biology in Greece and Cyprus from its inception to date and issue recommendations for future development. We compare output to other countries of similar geography, economy, and size—based on publication counts recorded in the literature—and predict future growth based on those counts as well as national priority areas. Our analysis may be pertinent to wider national or regional communities with challenges and opportunities emerging from the rapid expansion of the field and related industries. Our recommendations suggest a 2-fold growth margin for the 2 countries, as a realistic expectation for further expansion of the field and the development of a credible roadmap of national priorities, both in terms of research and infrastructure funding

The Nigerian Bioinformatics and Genomics Network (NBGN): a collaborative platform to advance bioinformatics and genomics in Nigeria

Africa plays a central importance role in the human origins, and disease susceptibility, agriculture and biodiversity conservation. Nigeria as the most populous and most diverse country in Africa, owing to its 250 ethnic groups and over 500 different native languages is imperative to any global genomic initiative. The newly inaugurated Nigerian Bioinformatics and Genomics Network (NBGN) becomes necessary to facilitate research collaborative activ�ities and foster opportunities for skills’ development amongst Nigerian bioinformatics and genomics investigators. NBGN aims to advance and sustain the fields of genomics and bio�informatics in Nigeria by serving as a vehicle to foster collaboration, provision of new oppor�tunities for interactions between various interdisciplinary subfields of genomics, computational biology and bioinformatics as this will provide opportunities for early career researchers. To provide the foundation for sustainable collaborations, the network organises conferences, workshops, trainings and create opportunities for collaborative research studies and internships, recognise excellence, openly share information and create opportunities for more Nigerians to develop the necessary skills to exceed in genomics and bioinformatics. NBGN currently has attracted more than 650 members around the world. Research collabora�tions between Nigeria, Africa and the West will grow and all stakeholders, including funding partners, African scientists, researchers across the globe, physicians and patients will be the eventual winners. The exponential membership growth and diversity of research interests of NBGN just within weeks of its establishment and the unanticipated attendance of its activ�ities suggest the significant importance of the network to bioinformatics and genomics research in Nigeria