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Staton Lab UTIA Computational Biology Consulting and Resources

Welcome to the UTIA Computational Biology Consulting and Resources wiki!

Consulting

Consulting is offered by Dr. Meg Staton, Associate Professor (EPP) and Ryan Kuster, bioinformatics consultant.

We welcome questions about DNA and RNA data analysis as well as Linux, R, and python. Consulting appointments with Meg Staton (Associate Professor, EPP, [email protected]) and/or Ryan ([email protected]) can also be made via email.

Computational Equipment

This is user and system administration documentation for our two servers - Centaur and Sphinx - and links to guides and documentation on how to install and run programs.

New to this equipment or wondering what this is all about? Start with the FAQs.

A brief overview of this system can be found in our orientation slides; this wiki will go into greater depth on these topics.

Check this page to make sure you have been approved to use our servers.

Calendar to book time

Table of Contents:

1. Getting Started

• Getting Logged In

• UTIA Computational Resource Servers

2. Best Practices

• Calendar - Booking Time for Processes and Server-Usage

• Data Storage, Space Management, and Transferring Data

  • Rclone Google Drive Remote Setup

• Naming Files and Directories

• UTIA-CR Data Usage

3. Package Information

• Installing New Packages

  • Installing Conda, Setting Up Environments, and Installing Packages

  • Spack Modules - How to Find, Install, and Load

• Installed Program Notes

• Running Nextflow Pipelines

Workshops

We regularly offer workshops on getting started with Linux and RNASeq analysis as well as journal clubs focused on computational biology. Registering to receive course credit is optional; all are welcome.

We appreciate feedback on what other topics would be beneficial to students, postdocs, and faculty.

• Fall 2024 - EPP 622 Bioinformatics Applications
• January 2024 - Nextflow and Containers Workshop - 3 day workshop covering the basics of using NextFlow and containers (Docker/Apptainer).
• August 2023 - RNA-Seq Workshop - 5 day workshop covering RNA-Seq essentials, builds directly off of the Command Line Workshop.
• August 2023 - Command Line Workshop - 2 day workshop for absolute beginners to command line.
• January 2022 - RNASeq analysis - All course materials are available including recordings of sessions. If you would like to be added to the servers and follow along at your own pace, please contact Ryan ([email protected]).
• Fall 2021, EPP 604: Journal Club Topic: Genome Evolution.
• Spring 2020, EPP 604: Journal Club Topic: RNA Sequencing.
• Fall 2020 - EPP622 Bioinformatic Applications - Full semester course, 3 credit hours, covering intro to Linux, intro to python, DNA sequence analysis for variants, RNASeq analysis for differential gene expression. All course materials are available including recordings of sessions. If you would like to be added to the servers and follow along at your own pace, please contact Meg ([email protected]). To be offered Fall 2022
• Fall 2019 - workshop or EPP 531, Practicing Python with Rosalind
• Summer 2019 - workshop or EPP 531, Introduction to Python