Delivering blended bioinformatics training in resource-limited settings: a case study on the University of Khartoum H3ABioNet node

Ahmed, Azza E.; Awadallah, Ayah A; Tagelsir, Mawada; Suliman, Maram A.; Eltigani, Atheer; Elsafi, Hassan; Hamdelnile, Basil D; Mukhtar, Mohamed A; Fadlelmola, Faisal M.

doi:10.1093/bib/bbz004

Cited by 10 publications

(12 citation statements)

References 19 publications

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“…When delivering bioinformatics training in an LMIC setting, the classroom infrastructure may be unreliable (although this can also be a non-LMIC issue of course!). Make sure you communicate with local hosts prior to the workshop to fully understand local infrastructure challenges that may impact upon your course delivery [ 24 ]. For some, it may be intermittent electricity, and, for others, internet connectivity and data costs.…”

Section: Introductionmentioning

confidence: 99%

Ten simple rules for organizing a bioinformatics training course in low- and middle-income countries

et al. 2021

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Section: Introductionmentioning

confidence: 99%

Ten simple rules for organizing a bioinformatics training course in low- and middle-income countries

et al. 2021

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“…icipe.org/content/2018-trainees). Other successful training models were in Sudan (Ahmed et al, 2020).…”

Section: Discussionmentioning

confidence: 99%

A Baseline Evaluation of Bioinformatics Capacity in Tanzania Reveals Areas for Training

et al. 2021

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Due to the insufficient human and infrastructure capacity to use novel genomics and bioinformatics technologies, Sub-Saharan Africa countries have not entirely ripped the benefits of these technologies in health and other sectors. The main objective of this study was to map out the interest and capacity for conducting bioinformatics and related research in Tanzania. The survey collected demographic information like age group, experience, seniority level, gender, number of respondents per institution, number of publications, and willingness to join the community of practice. The survey also investigated the capacity of individuals and institutions about computing infrastructure, operating system use, statistical packages in use, the basic Microsoft packages experience, programming language experience, bioinformatics tools and resources usage, and type of analyses performed. Moreover, respondents were surveyed about the challenges they faced in implementing bioinformatics and their willingness to join the bioinformatics community of practice in Tanzania. Out of 84 respondents, 50 (59.5%) were males. More than half of these 44 (52.4%) were between 26–32 years. The majority, 41 (48.8%), were master’s degree holders with at least one publication related to bioinformatics. Eighty (95.2%) were willing to join the bioinformatics network and initiative in Tanzania. The major challenge faced by 22 (26.2%) respondents was the lack of training and skills. The most used resources for bioinformatics analyses were BLAST, PubMed, and GenBank. Most respondents who performed analyses included sequence alignment and phylogenetics, which was reported by 57 (67.9%) and 42 (50%) of the respondents, respectively. The most frequently used statistical software packages were SPSS and R. A quarter of the respondents were conversant with computer programming. Early career and young scientists were the largest groups of responders engaged in bioinformatics research and activities across surveyed institutions in Tanzania. The use of bioinformatics tools for analysis is still low, including basic analysis tools such as BLAST, GenBank, sequence alignment software, Swiss-prot and TrEMBL. There is also poor access to resources and tools for bioinformatics analyses. To address the skills and resources gaps, we recommend various modes of training and capacity building of relevant bioinformatics skills and infrastructure to improve bioinformatics capacity in Tanzania.

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“…This highlights insufficient progress despite the existence of multiple training initiatives, including the African Society for Bioinformatics and Computational Biology founded in 2004 and the H3ABioNet pan-African bioinformatics network founded in 2012 [ 24–27 ]. This may be due to the challenges of online courses, including a relatively high drop-out rate [ 27 , 28 ], or because these courses focus on bioinformatics without hands-on training for the laboratory component of pathogen genomics research.…”

Section: Discussionmentioning

confidence: 99%

Capacity building for whole genome sequencing of Mycobacterium tuberculosis and bioinformatics in high TB burden countries

Rivière

Heupink

Ismail

et al. 2020

Briefings in Bioinformatics

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Background Whole genome sequencing (WGS) is increasingly used for Mycobacterium tuberculosis (Mtb) research. Countries with the highest tuberculosis (TB) burden face important challenges to integrate WGS into surveillance and research. Methods We assessed the global status of Mtb WGS and developed a 3-week training course coupled with long-term mentoring and WGS infrastructure building. Training focused on genome sequencing, bioinformatics and development of a locally relevant WGS research project. The aim of the long-term mentoring was to support trainees in project implementation and funding acquisition. The focus of WGS infrastructure building was on the DNA extraction process and bioinformatics. Findings Compared to their TB burden, Asia and Africa are grossly underrepresented in Mtb WGS research. Challenges faced resulted in adaptations to the training, mentoring and infrastructure building. Out-of-date laptop hardware and operating systems were overcome by using online tools and a Galaxy WGS analysis pipeline. A case studies approach created a safe atmosphere for students to formulate and defend opinions. Because quality DNA extraction is paramount for WGS, a biosafety level 3 and general laboratory skill training session were added, use of commercial DNA extraction kits was introduced and a 2-week training in a highly equipped laboratory was combined with a 1-week training in the local setting. Interpretation By developing and sharing the components of and experiences with a sequencing and bioinformatics training program, we hope to stimulate capacity building programs for Mtb WGS and empower high-burden countries to play an important role in WGS-based TB surveillance and research.

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Delivering blended bioinformatics training in resource-limited settings: a case study on the University of Khartoum H3ABioNet node

Cited by 10 publications

References 19 publications

Ten simple rules for organizing a bioinformatics training course in low- and middle-income countries

Ten simple rules for organizing a bioinformatics training course in low- and middle-income countries

A Baseline Evaluation of Bioinformatics Capacity in Tanzania Reveals Areas for Training

Capacity building for whole genome sequencing of Mycobacterium tuberculosis and bioinformatics in high TB burden countries

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