UAB Resources

There are resources developed by or provided by UAB scientists, labs, and groups.

Tutorials and Guides by UAB Scientists & Groups

• nf-core tips by Dr. Lara Ianov of U-BDS
• Intro to Docker for RStudio by Dr. Lara Ianov of U-BDS
• Lasseinge Lab Training Guides by the Lasseigne Lab
• UAB’s Research Computing Documentation by UAB Research Computing
• CCTS Informatics Resources by CCTS

High Performance Computing

Cheaha

Cheaha is a High Performance Computing (HPC) resource intended primarily for batch processing of research computing software. We offer a user-friendly portal website Open OnDemand with graphical interfaces to the most common features, all in one place.

Learn more at https://docs.rc.uab.edu/cheaha/getting_started/.

Office Hours

• U-BDS offers weekly data science office hours on Thursdays from 1:30pm-2:00pm.
  • If you are a UAB trainee, staff or faculty please feel free to stop by via zoom.

• Code, Chat, & Collab is hosted weekly on Fridays by the Informatics Club in BBRB 258 at Noon.

• UAB’s Research Computing Office Hours
  • Mondays 10:00 AM to 12:00 PM: Zoom
  • Thursdays 10:00 AM to 12:00 PM: Zoom
• CCTS Biostatistics, Epidemiology & Research Design (BERD) Consultations
  • One-on-One Biostatistics Design Consultation via BERD Clinics and individual appointments (in-person or virtually).
    • Make an appointment: https://redcap.dom.uab.edu/surveys/?s=H7W9EXT38THY7ER9
  • In-person consultations take place in the Shelby Biomedical Research Building (1st floor) on Wednesdays 11:30 am - 1 pm and Fridays 8:30 am - 11:30 am

Community Channels

• Join the UAB Labs Slack and search for the #datascience channel and #informatics-club channel
  • These are great places to ask questions and stay updated on opportunities.

Courses, Workshops, and Events

U-BDS offers bi to tri-annual workshops which cover the fundamentals of programming (R, Python, Unix, git).

External Resources

The Carpentries

The Carpentries is a 501(c)3 non-profit organization dedicated to educating researchers on software and data skills. Using inclusive and accessibly best practices, they build, maintaint and promote high-quality instructional material for a range of software and data-oriented concepts.

• Software Carpentries Lessons: Primary page for the Software Carpentry lessons. The following lessons, and more, are available.
  • The Unix Shell
  • Version Control with Git
  • Programming with Python
  • Programming with R
• Data Carpentries Lessons: Primary page for the Data Carpentry lessons. Instructional material is available for a variety of fields.
  • Genomics Curriculum
  • Image Processing Curriculum

Courses, Tutorials, and Workshops

• EMBL-EBI Training: EMBL-EBI offers a variety of online and in person training resources, including webinars, tutorials, and courses.

Recommended Reading

• Ten simple rules for using public biological data for your research by Oza, V. H., Whitlock, J. H., Wilk, E. J., Uno-Antonison, A., Wilk, B., Gajapathy, M., Howton, T. C., Trull, A., Ianov, L., Worthey, E. A., & Lasseigne, B. N. (2023)
• So you want to be a computational biologist?
• Best Practices for Scientific Computing
• Good Enough Practices in Scientific Computing
• Ten simple rules for biologists learning to program
• Ten Simple Rules for Reproducible Computational Research