Utilizing protocols.io for teaching

4 min readOct 5, 2020

The protocols.io platform offers a place to organize all of your class materials in one place, while keeping students engaged, and providing the necessary resources to teach either remotely or in person.

Get a look at some of the key functions in which you can structure your class, plus explore how Dr. Bonnie Hurwitz, an Associate Professor of Biosystems Engineering at the University of Arizona, utilizes protocols.io for teaching.

Getting Started

There are three key elements to the protocols.io platform: the File Manager, Workspaces, and Editor

These features allow you to structure your class by creating and sharing class materials effectively, enabling teamwork and communication, and keeping your work organized by having your materials in one central and secure place.

In the File Manager, which is the central place on protocols.io, you can organize all of your class materials and structure it as you see fit. The File Manager supports any file type, which allows you to upload any documents. You can also sync with Google Drive, One Drive, Box, and more.

Workspaces on protocols.io can be used across many fields by lab students, for at home lab experiments, computational work, or field classes. Workspaces can also be utilized as a virtual classroom, providing a place to ‘meet’, regardless if it’s in person or virtual.

  • Central and secure location
  • Protocol sharing
  • Sharing of resources
  • Discussions
  • Collaboration

Another way to stay organized is through our Task Manager in Workspaces. In the Task Manager, you can assign tasks, highlight lectures, or keep your students up to date and informed about what’s happening in your class.

In the editor on protocols.io, you can actively create content for students, and provide step by step instructions that are easy for students to follow. You can also include images and videos, components, and group steps into sections to add more visuals. If a student has a question, they can leave a comment and you will receive a notification. A discussion will then occur on the document.

Students can also utilize the editor to create documents, while also taking advantage of the concurrent editing feature. For example, if a group of students are on a team, they can all work on the same document together.

Another feature that can benefit students, is the run functionality. The run functionality allows students to run a protocol, giving them a step by step checklist, in which they can check off each step as they complete it. A run record will then be recorded, and can be used to make any notes. If you would like to modify a protocol, you can create a new version at any time. The older versions will still be available but will be marked as outdated. Multiple versions of a protocol can also be compared to each other using the Compare button, which highlights the differences between the two versions.

A conversation with Dr. Bonnie Hurwitz

Dr. Bonnie Hurwitz is an Associate Professor of Biosystems Engineering at the University of Arizona. She has worked as a computational biologist for nearly two decades on interdisciplinary projects in both industry and academia. Her research on the Earth and human microbiome incorporate large-scale –omics datasets, high-throughput computing, and big data analytics to answer questions in systems biology. A core focus of her lab is in developing bioinformatics algorithms and cyberinfrastructure for microbial ecology.

We were recently joined by Dr. Bonnie Hurwitz for a webinar to discuss how she has been utilizing protocols.io for teaching.

In this webinar, Bonnie dives into how she has been utilizing protocols.io to develop coursework, onboard students, and how her classes use step by step protocols to run different bioinformatics analysis’.

Bonnie discussed a class that is currently in development, that will be focused on reproducible protocols and teaching undergraduate students how to understand and define what reproducible research is. In this class, they will do a research project, which will then be implemented into protocols.io for future generations to explore. Bonnie also explained, that in another class they use protocols.io as part of their students homework. In this, the students have to go through the protocols and work with example data sets. This is useful as they can see real time comments and interactive videos such as demos and examples.

You can click here to watch our full webinar with Dr. Bonnie Hurwitz detailing how she utilizes workspaces for teaching.

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