Bringing Bioinformatics Tutorials to Life with sandbox.bio

New web technologies like WebAssembly enable us to build more interactive tutorial environments in sandbox.bio.

The “How I Teach” talk series is an invitation for anyone delivering professional development to life scientists and educators to share their curriculum, tips, technologies, and approaches. Email info@lifescitrainers.org to participate or complete a submission form to sign up to give a short talk and/or demo of the teaching skill you want to share. See full blog post for details.

Time and Date for Talks

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YouTube: To be posted after the talk

June Talk

Robert Aboukhalil , CZI

Format: Short talk and demo

Take home messages

  • New web technologies like WebAssembly enable us to build more interactive tutorial environments in sandbox.bio.
  • A ready-to-use environment is beneficial for demonstrating the value of bioinformatics tools, and leaves students eager to learn how to set up their own environments separately.
  • I’m building sandbox.bio v2 and am looking for community input as to tools I could build that would help life science trainers.

Abstract

Bioinformatics tutorials are essential for getting up to speed with new tools or types of analyses. Despite their utility, students face challenges with installing bioinformatics tools on their local computer or cloud, and there can be hesitation to deviate from tutorial, as making mistakes can be costly (think rm -f or runaway cloud costs).

In this talk, I’ll present sandbox.bio, a free platform for bioinformatics command-line tutorials. To address the challenges mentioned above, sandbox.bio provides learners with a sandboxed command-line environment running inside their browser, where bioinformatics tools are pre-installed and ready to be used. Some tutorials also feature exercises that validate the learner’s understanding of the material.

sandbox.bio was implemented by compiling bioinformatics command-line tools to WebAssembly so they can run in the browser. WebAssembly is a relatively new technology released in 2017 that has been used for bringing tools such as Google Earth and Photoshop to the web. But it can also help us bring bioinformatics tools to the web without rewriting them all in JavaScript!

I’ll also present a sneak peek of sandbox.bio v2, which will support many more bioinformatics tools in its browser environment.

Finally, I would like to spend the bulk of the time discussing with the audience about challenges that life science trainers face while designing bioinformatics tutorials or giving workshops, and whether sandbox.bio could help.

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