Getting Started with Bioinformatics on Tufts HPC

Shirley Li, Bioinformatician

Yucheng Zhang, Senior Bioinformatics Engineer

Tufts Technology Services, Research Technology

October 2, 2025

Welcome

This workshop is designed to help you get started with bioinformatics on the Tufts High-Performance Computing (HPC) cluster. We will cover:

• Introduction to the Linux/Unix Command Line
• Bioinformatics on the Tufts HPC: tools, workflows, and available resources

Prerequisites

You will need an active Tufts HPC account. If you are new to the HPC, we strongly recommend reviewing our recent Intro to HPC workshop.

TIP: To test your account, try logging in to Tufts OnDemand. If you can log in successfully, you’re all set. If not, please reach out to tts-research@tufts.edu for assistance.

Connecting to the Cluster & Starting a Job

You can connect to the cluster either through a terminal application (such as Terminal on macOS or MobaXterm on Windows) or via the web-based Open OnDemand portal.

NOTE: Access to the new cluster and new Open OnDemand is not enabled by default. To apply for access, you must join the HPC Upgrade Early Adopter Program.

Using the Command Line (SSH)

To connect, use the ssh command with your Tufts UTLN.

• New Cluster:

  ssh your_utln@login-prod.pax.tufts.edu
  

• Old Cluster:

  ssh your_utln@login.pax.tufts.edu
  

WARNING: Do not run jobs on login nodes. Login nodes are shared resources with limited CPU and memory. They should only be used for light tasks like submitting jobs, managing files, and editing scripts.

To start an interactive session on a compute node, use the srun command:

srun -N1 -n2 -t2:00:00 --pty bash

This command requests an interactive session with the following resources:

• -N1: 1 node
• -n2: 2 CPU cores
• -t2:00:00: A time limit of 2 hours

Using Open OnDemand

You can also access the cluster through a web browser via Open OnDemand.

• New Open OnDemand: https://ondemand-prod.pax.tufts.edu
• Old Open OnDemand: https://ondemand.pax.tufts.edu

Recording

Getting started with bioinformatics - 2025 Fall

Upcoming Research Technology Workshops

• Introduction to Programming with Python
  • October 9, 2025, 3:00pm - 5:00pm
• Introduction to Git & GitHub
  • October 15, 2025, 1:00pm - 3:00pm
• Introduction to Research Computing Tiered Storage
  • Tuesday, October 21, 2025, 11:00am - 12:00pm
• Using the newly upgraded HPC Cluster
  • Thursday, October 23, 2025, 1:00pm - 3:00pm
• Best Practices for using GPUs in Jupyter for Data Science
  • Wednesday, October 29, 2025, 2:00pm - 3:30pm

For a full list, please visit: https://go.tufts.edu/workshops