With advancing technologies and ever-increasing availability of data, current researchers and researchers-in-training need computational biology skills early in their careers. The data analysis modules introduce data science skills to researchers and educators using KBase, a free, online, open-access data analysis platform that requires no coding experience or computational resources.
This is the second webinar in a 2-part series and will cover advanced analysis of microbial isolates (using the annotated genomes from the spring series) in a modularized format that uses KBase’s reproducible notebook workflows. The first series, From Bench to Publication: Identification and Analysis of Microbial Isolate Genomes, was held in spring of 2025 and 2026.
MICROnet also offers community-developed teaching resources that enable student exploration of microbiome research questions. Instructors create teaching workflows based on ‘omics data concepts (e.g., genomics, metagenomics, metabolic modeling and transcriptomics) often taught in courses from general biology to microbiology to bioinformatics. Leveraging KBase, these modularized workflows can be quickly customized to any course and can result in student-authored data publications in .
Instructors participating in this series will:
- Use the free, online, open-access KBase platform for data analysis and publication.
- Learn how to apply and adapt advanced isolate analysis workflows for their own research and/or teaching courses, including genome analyses and comparisons, metabolic modeling and RNA-seq.
Thursday, Sept. 17, 12–1:30 p.m. ET | Gene Feature Analysis
Session 1 demonstrates using KBase to identify and characterize gene features in bacterial genomes. This session will cover how to construct feature sets in KBase and build, trim multiple sequence alignments (MSAs) and create hidden Markov models (HMMs) from these MSAs. Finally, participants will use the HMMs to search for and identify genes of interest.
Thursday, Oct. 1, 12-1:30 p.m. ET | Comparative Genomics
Session 2 demonstrates using KBase’s functional profiling and comparative genomics tools to analyze sets of isolate genomes. This session walks through how to compare genomic features across sets of genomes to begin to understand evolutionary relationships between organisms represented in the datasets, in addition to exploring structural and functional variance.
Thursday, Oct. 15, 12-1:30 p.m. ET | Metabolic Modeling
Session 3 introduces the basics of metabolic modeling in KBase. During this session, participants will construct and gapfill metabolic models, perform flux balance analysis and explore metabolic capacity of their organism.
Thursday, Oct. 29, 12-1:30 p.m. ET | RNA-seq and Expression Analysis
Session 4 introduces the RNA-seq tools in KBase for analyzing gene expression patterns across different samples. This session will demonstrate how to import reads and a genome to align and assemble transcripts before performing differential expression analysis. Participants will learn best practices using quality control checks at various steps of the analysis in KBase.
Course Learning Goals
Having completed all sessions, participants will be able to do the following:- Understand how to identify and compare genetic features across isolate organisms.
- Use metabolic modeling tools to investigate metabolism of organisms and form hypotheses about the relationship between genetic features and their biochemical function.
- Use RNA-seq data to understand how experimental conditions affect gene expression of various features.
Format
- Attendance is virtual and required at the live events. The facilitators will be working in real-time during the webinar sessions.
- The live (virtual) sessions will be a 90-min interactive tutorial interspersed with break-out groups for hands-on practice and trouble shooting.
- Participants will receive a link to the recording after the live event. The recording will be available until April 30, 2027.
Eligibility
- As the content is for more advanced users, participants will need to be familiar with the KBase platform. This could be satisfied by completing any of the 91Â鶹ÌìÃÀ-KBase webinar series (offered in 2025 and 2026) or in-person KBase workshops/webinars.
- While coding skills and advanced knowledge of bioinformatics are not required, it is recommended that participants have a general understanding of biological concepts and microbiomes or environmental microbiology.
- For undergraduate educators based in the U.S., there are additional opportunities to support instructor training and undergraduate research within MICROnet. Please reach out if you are interested!
Registration Details
- 91Â鶹ÌìÃÀ members (all categories except supporting members or student member): $250 for the 4 sessions in this fall series.
- 91Â鶹ÌìÃÀ student members: $150 for the 4 sessions in this fall series.
- Non-members (non-members or 91Â鶹ÌìÃÀ supporting members): $350 for the 4 sessions in this fall series.
- No refunds and no discounts will be given.
- All registrants will receive a link to the recording after the live event and will have access until April 30, 2027.
