Developing and Implementing Cloud-Based Tutorials That Combine Bioinformatics Software, Interactive Coding, and Visualization Exercises for Distance Learning on Structural Bioinformatics

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dc.contributor.authorEngelberger, Felipe
dc.contributor.authorGalaz-Davison, Pablo
dc.contributor.authorBravo, Graciela
dc.contributor.authorRivera, Maira
dc.contributor.authorRamirez-Sarmiento, Cesar A.
dc.date.accessioned2025-01-20T22:20:45Z
dc.date.available2025-01-20T22:20:45Z
dc.date.issued2021
dc.description.abstractThe COVID-19 pandemic has swiftly forced a change in learning strategies across educational institutions, from extensively relying on in-person activities toward online teaching. It is particularly difficult to adapt courses that depend on physical equipment to be now carried out remotely. This is the case for bioinformatics, which typically requires dedicated computer classrooms, as the logistics of granting remote access to a workstation or relying on the computational resources of each student is not trivial. A possible workaround is using cloud server-based computing resources, such as Google Colaboratory, a free web browser application that allows the writing and execution of Python programming through Jupyter notebooks, integrating text, images, and code cells. Following a cloud-based approach, we migrated the practical activities of a course on molecular modeling and simulation into the Google Colaboratory environment resulting in 12 tutorials that introduce students to topics such as phylogenetic analysis, molecular modeling, molecular docking, several flavors of molecular dynamics, and coevolutionary analysis. Each of these notebooks includes a brief introduction to the topic, software installation, execution of the required tools, and analysis of results, with each step properly described. Using a Likert scale questionnaire, a pool of students positively evaluated these tutorials in terms of the time required for their completion, their ability to understand the content and exercises developed in each session, and the practical significance and impact that these computational tools have on scientific research. All tutorials are freely available at https: //github.com/pb3lab/ibm3202.
dc.fuente.origenWOS
dc.identifier.doi10.1021/acs.jchemed.1c00022
dc.identifier.eissn1938-1328
dc.identifier.issn0021-9584
dc.identifier.urihttps://doi.org/10.1021/acs.jchemed.1c00022
dc.identifier.urihttps://repositorio.uc.cl/handle/11534/94632
dc.identifier.wosidWOS:000651525900040
dc.issue.numero5
dc.language.isoen
dc.pagina.final1807
dc.pagina.inicio1801
dc.revistaJournal of chemical education
dc.rightsacceso restringido
dc.subjectUpper-Division Undergraduate
dc.subjectGraduate Education/Research
dc.subjectBiochemistry
dc.subjectPhysical Chemistry
dc.subjectInterdisciplinary/Multidisciplinary
dc.subjectComputer-Based Learning
dc.subjectDistance Learning/Self Instruction
dc.subjectMolecular Mechanics/Dynamics
dc.subjectMolecular Modeling
dc.subjectProteins/Peptides
dc.subject.ods03 Good Health and Well-being
dc.subject.odspa03 Salud y bienestar
dc.titleDeveloping and Implementing Cloud-Based Tutorials That Combine Bioinformatics Software, Interactive Coding, and Visualization Exercises for Distance Learning on Structural Bioinformatics
dc.typeartículo
dc.volumen98
sipa.indexWOS
sipa.trazabilidadWOS;2025-01-12
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