Educational training technologies provide opportunities for students and professors alike

Sep 25, 2025

Open Frameworks Training the Next Generation of Scientists

The Science

To date, over 160 students participating in Myco-Ed have made more than 800 observations on iNaturalist. Nearly 300 species have been identified since Fall 2024. (Map from the Myco-Ed Fungal Genomics Education Project on iNaturalist)

In PLoS Pathogens, a team of faculty and researchers describe a workforce development program for higher education that develops skills in fungal biology and genomics. Myco-Ed: The Mycological Curriculum for Education and Discovery is a microbiology program that provides training and scientific contributions—including sequencing services and analysis—to participants. Over the past two years, Myco-Ed has been used in 15 individual classrooms across the country, training 316 students in fungal biology, bioinformatics, and genomics.

The Impact

For decades, the Department of Energy (DOE) has invested in training the next generation workforce through funding opportunities managed by the Office of Workforce Development for Teachers and Scientists for both student and faculty researchers. Aligning with this overarching goal, Myco-Ed is a partnership involving academic faculty and researchers at the DOE Joint Genome Institute (JGI), a DOE Office of Science User Facility, and the DOE Systems Biology Knowledgebase (KBase). The JGI and KBase are both supported by the DOE Biological and Environmental Research program.

KBase is a knowledge creation and discovery environment designed for reproducible computational biology analysis. KBase also supports MICROnet (Microbiomes In Computational Research Opportunities Network), a National Science Foundation-funded program, for advancing student research and skill development while curating reusable microbiome data. Undergraduate educators are partnering with the JGI and KBase to tap into their existing infrastructures and technologies, enabling these communities to become trainers for budding scientists and researchers.

Summary

Myco-Ed was started to help expand limited opportunities for students developing skills in fungal biology and genomics. Fungi can be better understood through reference genomes, but unfortunately there are not many available to study. This is because most fungal clades have no reference genomes. It’s a key problem to solve because fungi are very diverse organisms with potential biotechnology applications in a range of fields including agriculture, ecosystem health, and medicine optimization.

Through the Myco-Ed public workforce educational training program, students receive training in laboratory techniques through hands-on experiments and data analysis. Starting with isolating and identifying fungi in the environment, students can prepare samples for sequencing and analysis at the JGI to help produce novel fungal genomes. They manually curate data to connect to the newly generated Myco-Ed reference genomes made available in the public web portal, MycoCosm. These data improve the quantity and quality of fungal gene annotations available to the global research community.

KBase has developed their own educational program in parallel to Myco-Ed: MICROnet. MICROnet facilitates train-the-trainers workshops to connect educators and empower them to utilize program resources. MICROnet is built around a community of instructors training students in microbiome research techniques, including bioinformatics skills, while contributing to current research. The program follows a modularized scientific progress – Research Question and Hypothesis Development (Module 1), Experimental Design and Sample Metadata (Module 2), Sample Collection and Processing (Module 3), Data Analysis in KBase (Module 4), and Conclusions and Publishing (Module 5) – that enables student-curated FAIR (findable, accessible, interoperable, and reusable) data, readily available via the KBase platform. This effort grew from a modularized training program with the aim for future researchers to develop readily applicable skills and curate reusable microbiome data. These instructors teach microbiome science with collaboration and peer-support through regional cohorts and a national network.

Myco-Ed and MICROnet, in theory, are operating in parallel. While KBase does not currently have all the tools for complete processing and analysis of fungal data, the course structures center around the practices of collecting samples and the generation and analysis of reusable and accessible data available on BER-funded platforms.

Both Myco-Ed and MICROnet contribute to workforce development in mycology and microbiome science, respectively. These programs are resources designed to prepare early career researchers with real world science skills and opportunities to contribute to BER research.
Read more on the JGI website.

BER Contact

Ramana Madupu, Ph.D
Program Manager
Biological Systems Sciences Division
Office of Biological and Environmental Research
Office of Science
Department of Energy
Ramana.Madupu(at)science(dot)doe(dot)gov

PI Contacts

Sara Branco, Ph.D.
Department of Integrative Biology
University of Colorado, Denver
sara.branco(at)ucdenver(dot)edu

Stephen Mondo, Ph.D.
Data Scientist
DOE Joint Genome Institute
sjmondo(at)lbl(dot)gov

Ellen Dow, Ph.D.
KBase Educators Program Lead
User Engagement Team
KBase
egdow(at)lbl(dot)gov

Funding

Myco-Ed receives organizational and developmental support from KBase (The Department of Energy Systems Biology Knowledgebase).

Myco-Ed is supported by the JGI Director’s Science Program award #509937. SB was supported by the National Science Foundation Integrative Organismal Systems – Plant Biotic Interactions 2029168 award. This material is based upon work while SB was serving at the National Science Foundation. The work (proposal: 10.46936/10.25585/60008843) conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.
KBase is supported as part of the BER Genomic Science Program. The DOE Systems Biology Knowledgebase (KBase) is funded by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research under Award Numbers DE-AC02-05CH11231, DE-AC02-06CH11357, DE-AC05-00OR22725, and DE-AC02-98CH10886.
MICROnet is supported through KBase under user engagement through the KBase Educators Program and activities supported by the National Science Foundation Research Coordination Network for Undergraduate Biology Education (Award # 2418285) and previously through the NSF RCN-UBE Incubator (Award # 2316244).

Publication

Branco S, Avis PG, Barry K, Bates S, Cobián GM, et al. (2025) Myco-Ed: Mycological curriculum for education and discovery. PLOS Pathogens. 21(7): e1013303. https://doi.org/10.1371/journal.ppat.1013303

Relevant links