Fall 2025
Introduction to Python Programming
Led by Jesse Sandberg & Helen Stott, certified Software Carpentries instructors
Workshop Description
Are you an experimental student who wants to break your dependence on Excel for plotting? Are you a new student rotating in a computational lab? This workshop is designed to cover the basics of programming in Python, with a special emphasis on manipulating data and plotting.
Over the course of 8 hours (spread across two days), we will cover:
- Jupyter notebooks
- Variables and assignment
- Data types and type conversion
- Built-in functions and how to get help
- Libraries (NumPy, pandas, matplotlib)
- Data manipulation and plotting
Learning Goals
- Lower the barrier to entry for students considering a computational lab
- Provide experimental students with enough Python to make a plot using NumPy & matplotlib
Who Should Attend
Open to all STEM students.
Additional Information
Codes for Life trainees: this workshop counts as 2 toward your semester requirement
Please register by October 5
This workshop is 2 sessions — plan to attend both days
Snakemake for Bioinformatics
Hosted by Anthony Geneva & Sunil Shende
Dates and Times
- Wednesday, October 22, 12:00–2:00 PM | JHSC 202
- Wednesday, October 29, 12:00–2:00 PM | JHSC 202
Workshop Description
This hands-on workshop will introduce Snakemake, a workflow management system that enables reliable, scalable, and reproducible scientific workflows. We will work through a Software Carpentry tutorial to build a Snakemake workflow to perform a basic bioinformatics analysis. Later episodes will focus on workflow design, debugging, and configuration.
Learning Goals
- Gain familiarity with the use and benefits of workflow management systems generally and Snakemake specifically
- Complete a worked example using Snakemake to manage and perform basic bioinformatics analyses
- Learn about extensions and options in Snakemake that could apply to coding and scripting
Who Should Attend
This workshop is suitable for STEM trainees who:
- Have familiarity working with Bash or other command line shell environments
- Have an active Amarel account prior to the start of the workshop
No prior experience with Python, R, or bioinformatics is needed to participate.
Additional Information
We will collectively work through a Software Carpentry tutorial to build a Snakemake workflow in the context of a typical analysis task, aligning short cDNA reads to a reference transcriptome. Later episodes will focus on workflow design, debugging, and configuration.
Flashtalk Feedback Workshop
Led by Grace Brannigan
Dates and Times
- Wednesday, November 19, 2025, 12:00–2:00 PM | JHSC 202
- Wednesday, December 3, 2025, 12:00–2:00 PM | JHSC 202
Workshop Description
In this workshop, participants will practice and refine 3-minute “flashtalks” on their research for a general scientific audience. Participants should have a draft of their talk prepared prior to the workshop.
Learning Goals
- Become more comfortable and confident while delivering a short format flashtalk for a general scientific audience
- Practice providing meaningful and actionable feedback to peers
- Refine the content of a flashtalk based on feedback received
Who Should Attend
Open to STEM graduate students preparing to present their research in short formats.
How to Publish Your Paper Workshop
Led by Andrey Grigoriev
Dates and Times
- Wednesday, November 12, 2025, 12:00: 1:00 PM | Virtual
Workshop Description
Publishing your results is a key part of a scientific career. This session covers how to prepare, what to expect, and how to plan next steps. We’ll discuss timing, journal selection, and other factors that influence successful publication.
Learning Goals
- Understand the publication process
- Plan and organize the steps for submitting a publication
Who Should Attend
Any STEM graduate student or trainee interested in learning how to publish scientific work, including junior researchers (undergraduates, master’s, or Ph.D. students).ts.