Introducing Microbiomes In Computational Research Opportunities Network (MICROnet)
Biology and Microbiology instructors gathered May 20-22 for a workshop at University of Massachusetts Amherst in Amherst, MA, as part of NSF RCN-UBE* MICROnet [# 2418285]. One of the primary goals for MICROnet is hosting in-person trainings for undergraduate faculty and educators, where they can discuss their teaching and research goals, build out interesting collaborative projects, and develop a regional MICROnet hub.
*National Science Foundation Research Coordination Network for Undergraduate Biology Education
What is MICROnet?
Microbiomes In Computational Research Opportunities Network or MICROnet was the natural evolution from our RCN-UBE KBase Educators Incubator [# 2316244]. During the Incubator, educators developed and piloted a modularized program for training students in microbiome research skills, while also generating findable, accessible, interoperable, and reusable (FAIR) data and sharing it openly with the research community via the KBase platform. The Microbiome Workforce Development Program consists of five modules: Research Question and Hypothesis Development (Module 1), Experimental Design and Sample Metadata (Module 2), and Sample Collection and Processing (Module 3), to round out Data Analysis (Module 4) and Conclusions and Publishing (Module 5) in KBase. These modules were developed by undergraduate faculty (https://www.kbase.us/news/educator-workshop-jan2024/) alongside collaborators, National Microbiome Data Collaborative (NMDC) and the National Ecological Observatory Network (NEON), in an effort to make reproducible and open materials.
More information and access to modules and resources:
MICROnet was established to train the next generation of microbiome researchers in the process of scientific investigation and give them bioinformatics skills that will better prepare them for the workforce and next steps in their careers. This network of undergraduate faculty across the US teach topics in microbiome science and apply modules in their courses to build skills, while connecting with fellow educators to build national and regional collaborations across institutions.
Participants listening intently during a lecture portion of the workshop.
Training Workshop
Sixteen participants from Connecticut, Maryland, Massachusetts, New York, Pennsylvania, and Vermont joined the first MICROnet in-person workshop. They received an orientation to the modular resources and MICROnet, took part in discussions to develop their course question(s), pondered how to run effective experimental designs and logistics activities with students, and walked through the process of publishing data with students.
Workshop participants at University of Massachusetts Amherst.
Top row (left to right) Gabe Bouchard, Ellen Dow, Kristen DeAngelis, Maureen Morrow, Cam Anderson
Bottom row (left to right: Elisha Wood-Charlson, David Bernstein, Anne Estes, Welkin Pope, Jennifer Goff, Heather Reed, Anna McLoon, Phil Arevalo, Anna Budman, Arianna Krinos, Sara Bolduc (Not pictured: Steve Biller)
Steering Committee members and instructors from the Incubator program joined the workshop to lead training around protocols and best practices for publishing with students. All of our MICROnet modules emphasize the FAIR data principles, especially including metadata related to environmental samples, sample processing, and connecting samples to data to publications and other research products. Participants took an active role in discussing their personal research questions and goals, and how to integrate students’ questions into their courses. They also had a chance to practice sampling a soil core and validating sample metadata using the NMDC Field Notes App and Sample Submission Portal to curate comparable and reusable data.
Conversations during the workshop included how to keep the regional network engaged with one-another. Participants came up with the idea to hold bimonthly check-ins for their hub. There are also several follow-up activities for the network, including virtual coworking sessions on tailoring materials and setting up best practices for sharing data. These in-person discussions also formed a working group to begin developing a collaborative question or framework for working across courses.
Educators at UMass Amherst documenting a sample site and taking soil cores.
Conclusions
Instructors are now preparing to integrate the modules in their courses in the 2025-26 academic year, and the MICROnet team is working to support their network logistics. The workshop was a great opportunity for participants and Steering Committee members to connect, as our first step in establishing a North East regional network. Having everyone together in-person enables more organic discussions and break-outs that lead to conversations on how students can contribute to existing research questions or utilize existing datasets.
If you are an educator interested in using these modules, send an email to engage@kbase.us to connect with us and get on the list for when materials are released.
References & Links
National Science Foundation Research Coordination Network for Undergraduate Biology Education: Microbiomes in Computational Research Opportunities Network (MICROnet) [# 2418285] https://www.nsf.gov/awardsearch/showAward?AWD_ID=2418285&HistoricalAwards=false
National Science Foundation Research Coordination Network for Undergraduate Biology Education Incubator: KBase Educators: Program for Microbiome Workforce Development [# 2316244] https://www.nsf.gov/awardsearch/showAward?AWD_ID=2316244&HistoricalAwards=false
MICROnet Webpage: https://www.kbase.us/engage/microbiome-training/
KBase Educators Community Webpage: https://www.kbase.us/engage/educators/
