Implementing a web‐based introductory bioinformatics course for non‐bioinformaticians that incorporates practical exercises

Vincent, Antony T.; Bourbonnais, Yves; Brouard, Jean-Simon; Deveau, Hélène; Droit, Arnaud; Gagné, Stéphane M.; Guertin, Michel; Lemieux, Claude; Rathier, Louis; Charette, Steve J.; Lagüe, Patrick

doi:10.1002/bmb.21086

Cited by 9 publications

(8 citation statements)

References 32 publications

(31 reference statements)

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“…Conferences and workshops also serve as essential sources of bioinformatics skills for some respondents (28.6%), while a small percentage (15.5%) used online resources to learn bioinformatics skills. These later may have benefitted from the opportunity provided by the H3ABioNet (Gurwitz et al, 2017) in addition to other training opportunities such as those used in other countries (Cattley and Arthur, 2007;Ding et al, 2014;Vincent et al, 2018).…”

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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Section: Discussionmentioning

confidence: 99%

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

et al. 2021

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“…Conferences and workshops also serve as essential sources of bioinformatics skills for some respondents (28.6%), while a small percentage (15.5%) used online resources to learn bioinformatics skills. These later may have bene tted from the opportunity provided by the H3ABioNet [19] in addition to other training opportunities such as those used in other countries [20][21][22].…”

Section: Discussionmentioning

confidence: 99%

Baseline Evaluation of Bioinformatics Capacity in Tanzania

Sangeda¹,

Mwakilili²,

Masamu³

et al. 2020

Preprint

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BackgroundEven though the genomics technologies have grown to a large extent, Sub Saharan Africa countries have not entirely reaped the benefits due to the lack of enough capacity to use these technologies. The lack of documentation on existing bioinformatics capacity in these countries hinders the guidance on leveraging the resources and in the identification of areas for improvement. The main objective of this study was to map out the interest and capacity for conducting bioinformatics and related research in Tanzania. Our findings identify critical areas for skills and infrastructure development for bioinformatics research. The study is a cross-sectional, explorative, descriptive study, among Tanzanian researchers in public and private academic and research institutionsResultsOut of 84 respondents, 50 (59.5%) were males. More than half of these 44 (52.4%) were in the age 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%) of respondents was the lack of training and skills. The most used resources for bioinformatics analyses were the BLAST, PubMed and GenBank. Most performed analyses include sequence alignment and phylogenetic, which was reported by 57 (67.9%) and 42 (50%) of respondents, respectively. The most frequently used statistical software packages were SPSS and R. A quarter of the respondents were conversant with computer programming.ConclusionEarly career and young scientists were the largest group 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. As a way to address the skills and resources gaps, we recommend various modes of training and capacity building of relevant bioinformatics skills and provision of infrastructure so as to improve bioinformatics capacity in Tanzania.

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“…Langheinrich and Bogner [67] reported that computer-supported gene technology module increased the students' conceptual understanding of the structure of DNA. It has been reported that the web-based bioinformatics module not only provides bioinformatics information, but also develops specific knowledge (informatics, biological sequence analysis, and structural bioinformatics) and skills [68]. In this study, virtual laboratory (Polymerase Chain Reaction) and web-based teaching (Bioinformatics: Phylogenetic Prediction) were used in biotechnology teaching within the scope of innovative teaching approaches.…”

Section: Discussionmentioning

confidence: 99%

The Impact of Innovative Teaching Approaches on Biotechnology Knowledge and Laboratory Experiences of Science Teachers

Orhan

Sahin

2018

Education Sciences

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The current study presents an evaluation of the laboratory instructional tasks prepared based on innovative teaching approaches (research-inquiry, problem solving, project, argumentation and web-based interdisciplinary learning approaches) designed to enhance science teachers’ biotechnology knowledge, awareness and laboratory experiences. The laboratory instructional tasks developed by the researchers aim to improve the laboratory experiences, as well as support the teaching of biotechnology through innovative teaching approaches. For this purpose, in-service training course titled Biotechnology Education Practices was conducted with the voluntary participation of science teachers (n = 17). The current study employed the embedded design. The quantitative part of the embedded design is designed as the single group pretest-posttest model and the qualitative part of it is designed as the case study. The data of the current study were collected through the Biotechnology Awareness Questionnaire, Biotechnology Evaluation Questions, The Laboratory Self-Evaluation form and worksheets. The results obtained from the analyses revealed that the instructional tasks conducted within the context of the Biotechnology Education Practices resulted in significant effects on the science teachers’ biotechnology knowledge and awareness and that the innovative teaching approaches were effective in developing the science teachers’ laboratory experiences. It would be useful to use laboratory instructional tasks enriched with innovative teaching approaches in teaching biotechnology subjects.

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Implementing a web‐based introductory bioinformatics course for non‐bioinformaticians that incorporates practical exercises

Cited by 9 publications

References 32 publications

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

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

Baseline Evaluation of Bioinformatics Capacity in Tanzania

The Impact of Innovative Teaching Approaches on Biotechnology Knowledge and Laboratory Experiences of Science Teachers

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