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Abstract
Bioinformatics skills have become essential for many research areas; however, the availability of qualified researchers is usually lower than the demand and training to increase the number of able bioinformaticians is an important task for the bioinformatics community. When conducting training or hands-on tutorials, the lack of control over the analysis tools and repositories often results in undesirable situations during training, as unavailable online tools or version conflicts may delay, complicate, or even prevent the successful completion of a training event. The eBioKit is a stand-alone educational platform that hosts numerous tools and databases for bioinformatics research and allows training to take place in a controlled environment. A key advantage of the eBioKit over other existing teaching solutions is that all the required software and databases are locally installed on the system, significantly reducing the dependence on the internet. Furthermore, the architecture of the eBioKit has demonstrated itself to be an excellent balance between portability and performance, not only making the eBioKit an exceptional educational tool but also providing small research groups with a platform to incorporate bioinformatics analysis in their research. As a result, the eBioKit has formed an integral part of training and research performed by a wide variety of universities and organizations such as the Pan African Bioinformatics Network (H3ABioNet) as part of the initiative Human Heredity and Health in Africa (H3Africa), the Southern Africa Network for Biosciences (SAnBio) initiative, the Biosciences eastern and central Africa (BecA) hub, and the International Glossina Genome Initiative.
Highlights
High throughput technologies and generation sequencing require the development of new methods to manage the data generated by researchers
The eBioKit is distributed as an affordable and self-contained computing platform and database system containing up to 6 terabytes of biological data and software tools of relevance to bioinformatics researching, including the Ensembl database systems [18, 19], the European Molecular Biology Open Software Suite (EMBOSS) [25], Galaxy [27], National Center for Biotechnology Information (NCBI) Blast [30], and PLINK [31], which are made locally available through a unified web-based user interface
Courses encompass a wide range of bioinformatics disciplines ranging from basic bioinformatics tasks, the UNIX environment, and programming, to more advanced topics such as genome-wide association studies (GWASs), RNA sequencing (RNA-Seq) analysis, genome assembly and annotation, and comparative genomics
Summary
High throughput technologies and generation sequencing require the development of new methods to manage the data generated by researchers. Bioinformatics has been a strategic investment for many countries due to its positive contributions to other fields of life science as well as the comparatively low costs of the discipline. Equipping and running a bioinformatics teaching laboratory cost less than equipping and running a biology laboratory [2] and many developing or formerly socialist countries have access to trained professionals in advanced mathematics and/or computational science [3], which form the basis of the field when combined with biology. An enhanced capacity in bioinformatics allows researchers to conduct advanced analysis inside the country to ensure that the immaterial property rights are retained within the country and can support the development of a national life science industry [3, 4, 5]
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