Challenges and Considerations for Delivering Bioinformatics Training in LMICs: Perspectives From Pan-African and Latin American Bioinformatics Networks

Ras, Verena; Carvajal-López, Patricia; Gopalasingam, Piraveen; Matimba, Alice; Chauke, Paballo Abel; Mulder, Nicola; Guerfali, Fatma Z.; Angel, Victoria Domínguez Del; Reyes, Alejandro; Oliveira, Guilherme de; Rivas, Javier De Las; Cristancho, Marco

doi:10.3389/feduc.2021.710971

Cited by 8 publications

(7 citation statements)

References 9 publications

(9 reference statements)

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“…Today, the great technological progress of the last decades has provided the means for collecting huge data masses with lower cost and effort to analyse and interpret, and Nigeria, as well as other developing countries, must not be left out [ 91 ]. Bioinformatics training in low–medium income countries has a lasting positive impact if done well, paying attention to the trio, planning, development and implementation, to tackle the major challenges of shortage of infrastructure, lack of training facilities and poor Internet, lack of local expertise and funding [ 44 ].…”

Section: Discussionmentioning

confidence: 99%

“…A group from the same laboratory or institution can be trained in a specific topic or software from time to time [ 43 ]. Training for microbiologists can be tailored for relevance and application to topics of interest in the country or region where the training is taking place rather than a broad bioinformatics subject [ 44 ].…”

Section: Bioinformatics and Computational Biologymentioning

confidence: 99%

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Integrating computational skills in undergraduate Microbiology curricula in developing countries

Adenaike,

Olabanjo,

Adedeji

2023

Biology Methods and Protocols

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The employability of young graduates has gained increasing significance in the labour market of the 21st century. Universities turn out millions of graduates annually, but at the same time, employers highlight their lack of the requisite skills for sustainable employment. We live today; in a world of data, and therefore courses that feature numerical and computational tools to gather and analyse data are to be sourced for and integrated into life sciences’ curricula as they provide a number of benefits for both the students and faculty members that are engaged in teaching the courses. The lack of this teaching in undergraduate Microbiology curricula is devastating and leaves a knowledge-gap in the graduates that are turned out. This results in an inability of the emerging graduates to compete favourably with their counterparts from other parts of the world. There is a necessity on the part of life science educators to adapt their teaching strategies to best support students’ curricula that prepare them for careers in Science. Bioinformatics, Statistics and Programming are key computational skills to embrace by life Scientists and the need for training beginning at undergraduate level cannot be overemphasized. This paper reviews the need to integrate computational skills in undergraduate Microbiology curricula in Developing Countries with emphasis on Nigeria.

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Section: Discussionmentioning

confidence: 99%

Section: Bioinformatics and Computational Biologymentioning

confidence: 99%

Integrating computational skills in undergraduate Microbiology curricula in developing countries

Adenaike,

Olabanjo,

Adedeji

2023

Biology Methods and Protocols

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“…These limitations thus hinder the ability to engage in cutting-edge research in the continent. Poor internet connectivity and a lack of high-performance computing facilities which is still rife especially in sub-Saharan Africa also impede bioinformatics research and learning opportunities for students ( Ras et al, 2021 ). Downloading large data sets and accessing free online courses or tutorials which are essential for bioinformatics education also becomes a problem when engaging in bioinformatics training.…”

Section: Current State Of Bioinformatics Literacy Among African Studentsmentioning

confidence: 99%

Bioinformatics proficiency among African students

Akintola,

Aborode,

Hamza

et al. 2024

Front. Bioinform.

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Bioinformatics, the interdisciplinary field that combines biology, computer science, and data analysis, plays a pivotal role in advancing our understanding of life sciences. In the African context, where the diversity of biological resources and healthcare challenges is substantial, fostering bioinformatics literacy and proficiency among students is important. This perspective provides an overview of the state of bioinformatics literacy among African students, highlighting the significance, challenges, and potential solutions in addressing this critical educational gap. It proposes various strategies to enhance bioinformatics literacy among African students. These include expanding educational resources, fostering collaboration between institutions, and engaging students in research projects. By addressing the current challenges and implementing comprehensive strategies, African students can harness the power of bioinformatics to contribute to innovative solutions in healthcare, agriculture, and biodiversity conservation, ultimately advancing the continent’s scientific capabilities and improving the quality of life for her people. In conclusion, promoting bioinformatics literacy among African students is imperative for the continent’s scientific development and advancing frontiers of biological research.

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“…As such, while deep sequencing can be used to characterize metagenomic resistomes, it entails a high cost per sample, most of which will be spent sequencing background DNA. The associated volume of data also increases equipment costs and computing power needed to parse the data, further constraining this technique’s use in resource-limited settings (31).…”

Section: Introductionmentioning

confidence: 99%

CARPDM: cost-effective antibiotic resistome profiling of metagenomic samples using targeted enrichment

Hackenberger,

Imtiaz,

Raphenya

et al. 2024

Preprint

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Better interrogation of antimicrobial resistance requires new approaches to detect the associated genes in metagenomic samples. Targeted enrichment is an ideal method for their sequencing and characterization. However, no open-source, up-to-date hybridization probe set targeting antimicrobial resistance genes exists. Here we describe CARPDM, a probe design software package made to run alongside all future Comprehensive Antibiotic Resistance Database releases. To test its efficacy, we have created and validated two separate probe sets: AllCARD, which enriches all genes encoded in the Comprehensive Antibiotic Resistance Database's protein homolog models (n = 4,661), and clinicalCARD, which focuses on a clinically relevant subset of resistance genes (n = 323). We demonstrate that allCARD increases the number of reads mapping to resistance genes by up to 594-fold. ClinicalCARD performs similarly when clinically relevant genes are present, increasing the number of resistance-gene mapping reads by up to 598-fold. In parallel with this development, we have established a protocol to synthesize any probe set in-house, saving up to 350 dollars per reaction. Together, these probe sets, their associated design program CARPDM, and the protocol for in-house synthesis will democratize metagenomic resistome analyses, allowing researchers access to a cost-effective and efficient means to explore the antibiotic resistome.

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Challenges and Considerations for Delivering Bioinformatics Training in LMICs: Perspectives From Pan-African and Latin American Bioinformatics Networks

Cited by 8 publications

References 9 publications

Integrating computational skills in undergraduate Microbiology curricula in developing countries

Integrating computational skills in undergraduate Microbiology curricula in developing countries

Bioinformatics proficiency among African students

CARPDM: cost-effective antibiotic resistome profiling of metagenomic samples using targeted enrichment

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