Partnerships: Myco-Ed

Beyond providing a scalable solution for production of high-quality fungal reference genomes, this program is an important initiative that expands and diversifies workforce training in fungal biology and genomics.

Myco-Ed aims to integrate real scientific contributions/discoveries into undergraduate teaching laboratories with minimal overhead (cost of media, ITS sequencing and tissue preparation), allowing participation from a growing audience. For consistency and to reduce teaching-lab costs, we have partnered with the Arizona Genomics Institute where high molecular weight DNA is extracted from samples, which is then sent to the JGI for genome sequencing, assembly and annotation.

The Mycocosm portal supports the annotation, comparative analysis, and distribution of fungal genome datasets. It includes JGI-sequenced and publicly available datasets encompassing a wide array of fungal genomes, along with curated metadata to enable comprehensive comparative analysis. 

MycoCosm provides data and tools via a graphical user interface, ensuring that no programming knowledge or dedicated compute infrastructure is required to perform computational analyses. The Mycocosm user interface is designed for use by mycologists and researchers, facilitating the transition from genomic sequences to biological inference and understanding of fungal diversity, ecology, and potential applications.

The Department of Energy Systems Biology Knowledgebase (KBase) is involved in the organization and development of Myco-Ed. Eventually assembly exercises will be made available on the platform through the KBase Educators Community. This group enables instructors to create and share teaching resources utilizing KBase.

KBase integrates a variety of data and analysis tools, from DOE and public resources, into an easy-to-use platform that leverages scalable computing infrastructure to perform sophisticated systems biology analyses. The platform is a freely available and developer extensible platform where scientists can analyze their own data alongside public data, using a variety of open-source bioinformatics apps and compute resources to power their workflows. The reproducible and customizable workflows are easily adapted by instructors training their students in computational biology and microbiology topics. 

Learn more in Frontiers.