Abstract
Lockdowns and “stay-at-home” orders, starting in March 2020, shuttered bench and field dependent research across the world as a consequence of the global COVID-19 pandemic. The pandemic continues to have an impact on research progress and career development, especially for graduate students and early career researchers, as strict social distance limitations stifle ongoing research and impede in-person educational programs. The goal of the Bioinformatics Virtual Coordination Network (BVCN) was to reduce some of these impacts by helping research biologists learn new skills and initiate computational projects as alternative ways to carry out their research. The BVCN was founded in April 2020, at the peak of initial shutdowns, by an international group of early-career microbiology researchers with expertise in bioinformatics and computational biology. The BVCN instructors identified several foundational bioinformatic topics and organized hands-on tutorials through cloud-based platforms that had minimal hardware requirements (in order to maximize accessibility) such as RStudio Cloud and MyBinder. The major topics included the Unix terminal interface, R and Python programming languages, amplicon analysis, metagenomics, functional protein annotation, transcriptome analysis, network science, and population genetics and comparative genomics. The BVCN was structured as an open-access resource with a central hub providing access to all lesson content and hands-on tutorials (https://biovcnet.github.io/). As laboratories reopened and participants returned to previous commitments, the BVCN evolved: while the platform continues to enable “a la carte” lessons for learning computational skills, new and ongoing collaborative projects were initiated among instructors and participants, including a virtual, open-access bioinformatics conference in June 2021. In this manuscript we discuss the history, successes, and challenges of the BVCN initiative, highlighting how the lessons learned and strategies implemented may be applicable to the development and planning of future courses, workshops, and training programs.
Highlights
As governments across the world began issuing various lockdowns, “stay-at-home” orders, and quarantines to curtail the spread of the coronavirus, academic labs that were considered nonessential were shuttered
In collaboration with Drs Harriet Alexander and Maria Pachiadaki, instructors for a graduate-level course in bioinformatics at the Woods Hole Oceanographic Institution (WHOI), we developed a research task for students to enhance their hands-on bioinformatics skills
We aggregated a number of introductory resources (e.g., the Happy Belly Bioinformatics Unix tutorial (Lee, 2019)) and paired them with lessons that advanced in complexity, allowing learners to see the progression from introduction to practical use
Summary
As governments across the world began issuing various lockdowns, “stay-at-home” orders, and quarantines to curtail the spread of the coronavirus, academic labs that were considered nonessential were shuttered. Access to the growing archive of lessons and short-format tutorials, along with the Slack workspace detailing active lesson deployment, helped to facilitate access to formal support, information exchange, and collaborations This approach aimed to lower the entry barriers between awareness (i.e., promotion) and the use of BVCN content as a resource (i.e., ease of access to archived and ongoing support), which is identified as a key guiding principle for bioinformatics education (Williams et al, 2010). Even after lesson development ended and the BVCN shifted to an asynchronous learning format, the Slack workspace continues to serve as a valuable resource for learners who may have recently completed the coursework and are pursuing follow-up questions regarding how to apply tools to their own datasets. As with many facets of the global pandemic, it appeared that participants became overwhelmed with responsibilities and were more comfortable with using the materials for asynchronous learning
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