Vermont Biomedical Research Network

The Metagenomics Workshop Incubator Carpentry
2025-01-07 - 2025-01-08
Workshop info:The Metagenomics Workshop Incubator CarpentryTuesday January 7- Wednesday January 8, 2025 –> in person only 9:00 AM – 4:30 PM each dayUniversity of Vermont campusRegister for the in-person workshop Maximum is 25 participants
What You’ll Learn:Project Organization and Management Learn how to structure your metadata, organize and document your metagenomics data and bioinformatics workflow, and access data on the NCBI sequence read archive (SRA) database.
Introduction to the Command Line Learn to navigate your file system, create, copy, move, and remove files and directories, and automate repetitive tasks using scripts and wildcards.
Introduction to R Use R studio to manage several data types and structures.
Data Processing and Visualization for Metagenomics Use command-line tools to perform quality control, metagenomic assembly, metagenomic binning, taxonomic assignment, and diversity exploration.
Who Should Attend:PUI researchers from various fields with interest in metagenomics research
Why Attend:Increase the efficiency and accuracy of data analysisImprove the reproducibility of your researchTake your first steps in analyzing big dataEnhance your ability to collaborate with programmers and data scientists
Cost:The workshop is free for participants
Requirements:No prior coding experience is requiredBring a laptop that can load required software (Mac or PC)
Contact Information:For inquiries or additional information, please contact Heather Driscoll (hdriscol@norwich.edu
VBRN and UVM Data Science Core Team

Genomics Data Carpentry
2025-03-17 - 2025-03-18
Monday March 17 – Tuesday March 18, 2025, from 8:30 AM – 5:00 PM both days
Registration is open!
Workshop website

This online-only workshop is intended for people working with high-throughput sequencing data and focuses on helping them upgrade their workflow from relying on spreadsheets and GUI platforms to using command-line tools and accessing remote computing power. Learners will be introduced to core Bash commands and will learn to write custom Bash scripts to automate an analysis pipeline. They will be introduced to some commonly used command-line bioinformatics tools and file formats. This workshop does not cover individual methods for working with RNA-seq, ChIP-seq, or other specialized datasets, but instead focuses on core principles for efficient and reproducible research with sequencing data.

Plotting and Programming with Python
2025-05-29 - 2025-05-30
Thursday May 29 – Friday May 30, 2025 – two full days
8:30 AM – 5:00 PM

Registration is open!

In this workshop, learners will gain confidence in using the command-line to navigate their file structure and work with files on their computer, write custom Bash scripts to automate repetitive analyses, learn the core concepts of version control and be able to implement a simple Git workflow for tracking their own work. Additionally, this workshop will cover Python programming basics, focusing on working with core data structures including tabular data, using conditionals and loops, writing custom functions, and creating customized plots. JupyterLab and strategies for getting help will also be introduced. This workshop is appropriate for learners with no previous programming experience.
