An Example of Activity Design for Bioinformatics Training

This activity was designed by Dr Monica Abrudan and was included in a course on Genomic Surveillance of AMR, organised by the Centre for Genomic Pathogen Surveillance and Wellcome Advanced Courses and funded by the National Institute for Health Research in the UK.

This activity supported the following module’s objectives:

• fundamental technical aspects of bacterial genomics informatics, such as common file formats used for storing and processing genomic data, repositories and databases used to store public genomes and antimicrobial resistance genomic determinants and bacterial typing schemes
• querying and retrieving information specific to bacterial genomics from the European Nucleotide Archive ENA (ENA).

The target audience consisted of students, researchers and professionals interested in Bioinformatics, who are already familiar with concepts of microbiology and genomics.

By the end of the module that contained this activity, the learners were expected to be able to: list the names of the major relevant data repositories, describe the particularities of each of them; browse, submit, query and download data from a genomes archive (ENA), using the graphical interface and command line.

The planned activity included hands-on exercises using ENA online portal, where the trainees browsed the ENA database and retrieved specific data.

Some of the exercises asked trainees to practice retrieving genomes and reports from ENA using different query lines, in the browser and on the command line. One such exercise was: “Write a query to retrieve the number of sequences of beta-lactamases in ​Acinetobacter baumannii currently stored in the ENA.”

Learning was assessed using self-evaluated short quizzes. The answers to quiz questions were discussed in the class.

The module that included this activity took one hour and it was split as follows: 25 minute lecture, followed by 20 minutes hands-on work and 10 minute long quizzes.