Welcome to the Education Resources page!
Here you will find searchable resources that support educators and instructors teaching microbiome sciences, and individuals new to microbiome research and analyses. Our vision for the page is to provide entry points for microbiome experiments, data, analyses, and past workshops.
To navigate through the resources, filter the content using Categories and Tags.
For example, you are looking for a platform with a graphical user interface. You can search the Categories of ‘Graphical User Interface’ and enter ‘Platform’ in the Search bar to filter through the list and display GUI platforms like Geneious, Nephele, KBase, and Cyverse.
R (Studio)
Statistics/graphing/modeling/command line interface with capability to create markdown files showing workflow.
R Studio Cloud
Cloud based version of statistics/graphing/modeling/command line interface with capability to create markdown files showing workflow.
Anvi’o
Anvi’o is a comprehensive platform that brings together many aspects of today’s cutting-edge computational strategies of data-enabled microbiology, including genomics, metagenomics, metatranscriptomics, pangenomics, metapangenomics, phylogenomics, and microbial population genetics in an integrated and easy-to-use fashion through extensive interactive visualization capabilities.
MicrobiomeDB
MicrobiomeDB was developed as a discovery tool that empowers researchers to fully leverage their experimental metadata to construct queries that interrogate microbiome datasets.
Quantitative Undergraduate Biology Education & Synthesis
The QUBES platform hosts hundreds of teaching materials, reference materials, and cloud-based software free to use and adapts using open Creative Commons licenses.
SimBio
Undergraduate simulation program for virtual labs.
Integrated Microbial Genomes and Microbiomes – JGI
The mission of the Integrated Microbial Genomes & Microbiomes(IMG/M) system is to support the annotation, analysis and distribution of microbial genome and microbiome datasets sequenced at DOE’s Joint Genome Institute (JGI).
MGnify
Submit, analyse, discover and compare microbiome data
The Department of Energy Systems Biology Knowledgebase
KBase is a free and open-access large-scale data science platform that enables users to upload their own data, analyze it alongside collaborator and public data, build increasingly realistic models, and share and publish reproducible workflows and conclusions. KBase integrates data and tools in a unified graphical interface. Users no longer need to do analyses across multiple systems in order to create and run sophisticated systems biology workflows. KBase allows users to perform large-scale analyses and combine multiple lines of evidence to model plant and microbial physiology and community dynamics.
KBase metabolic modeling training
Basics of metabolic modeling in KBase