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Development of the Organonitrogen Biodegradation Database: Teaching Bioinformatics and Collaborative Skills to Undergraduates during a Pandemic.

ABSTRACT: Physical distancing and inaccessibility to laboratory facilities created an opportunity to transition undergraduate research experiences to remote, digital platforms, adding another level of pedagogy to their training. Basic bioinformatics skills together with critical analysis of scientific literature are essential for addressing research questions in modern biology. The work presented here describes a fully online, collaborative research experience created to allow undergraduate students to learn those skills. The research experience was focused on the development and implementation of the Organonitrogen Biodegradation Database (ONDB, z.umn.edu/ondb). The ONDB was developed to catalog information about the cost, chemical properties, and biodegradation potential of commonly used organonitrogen compounds. A cross-institutional team of undergraduate researchers worked in collaboration with two faculty members and a postdoctoral fellow to develop the database. Students carried out extensive online literature searches and used a biodegradation prediction website to research and represent the microbial catabolism of different organonitrogen compounds. Participants employed computational tools such as R, Shiny, and flexdashboard to construct the database pages and interactive web interface for the ONDB. Worksheets and forms were created to encourage other students and researchers to gather information about organonitrogen compounds and expand the database. Student progress was evaluated through biweekly project meetings, presentations, and a final reflection. The ONDB undergraduate research experience provided a platform for students to learn bioinformatics skills while simultaneously developing a teaching and research tool for others.

SUBMITTER: Robinson SL

PROVIDER: S-EPMC8046652 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundCollaborative skills learning in the form of dyad learning compared with individual learning has been shown to lead to non-inferior skills retention and transfer. However, we have limited knowledge on which learning activities improve collaborative skills training and how the number of collaborators may impact skills transfer. We explored the effects of skills training individually, in dyads, triads or tetrads on learning activities during training and on subsequent skills transfer.MethodsIn a randomised, controlled study, participants completed a pre-post-transfer-test set-up in groups of one to four. Participants completed 2 hours of obstetric ultrasound training. In the dyad, triad and tetrad group participants took turns actively handling the ultrasound probe. All performances were rated by two blinded experts using the Objective Structured Assessment of Ultrasound Skills (OSAUS) scale and a Global Rating Scale (GRS). All training was video recorded, and learning activities were analysed using the Interactive-Constructive-Active-Passive (ICAP) framework.ResultsOne hundred one participants completed the simulation-based training, and ninety-seven completed the transfer test. Performance scores improved significantly from pre- to post-test for all groups (p < 0.001, ηp2 = 0.55). However, group size did not affect transfer test performance on OSAUS scores (p = 0.13, ηp2 = 0.06) or GRS scores (p = 0.23, ηp2 = 0.05). ICAP analyses of training activities showed that time spent on non-learning and passive learning activities increased with group size (p < 0.001, ηp2 = 0.31), whereas time spent on constructive and interactive learning activities was constant between groups compared with singles (p < 0.001, ηp2 = 0.72).ConclusionCollaborative skills learning in groups of up to four did not impair skills transfer despite less hands-on time. This may be explained by a compensatory shift towards constructive and interactive learning activities that outweigh the effect of shorter hands-on time.

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Development of the Organonitrogen Biodegradation Database: Teaching Bioinformatics and Collaborative Skills to Undergraduates during a Pandemic.

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