Skip to Main Content

BIOF 083 | Linux for Biomedical Researchers

May 13, 2020 to May 15, 2020



Registration occurs on a first-come, first-served basis. The deadline for registration is one week before the first day of the course.  If you are unable to register before the deadline, please email: or call 301-496-7977 for space availability. 

NIH Fellows or NIH community members being sponsored by their lab and awaiting payment authorization can tentatively hold a seat using the “Reserve A Seat” option. FAES must receive payment within 7 business days after reserving a seat or 3 business days before the start of the workshop, which ever comes first. If payment is not received in this time frame, your reservation will be cancelled.

Linux is easy, powerful, flexible, secure and cost effective. Linux is ubiquitous, it runs the Android operating system and a whole lot of other smart electronic devices. The world literally runs on Linux for several reasons…. Linux gives the freedom that is needed for the researchers to implement ideas/thoughts/solutions to solve real world problems. This training is fully biologist friendly, taught by-the-biologists to-the-biologists.

Simultaneous access to two screens is highly recommended for adequate learning experience. Examples include two laptops, one computer with two screens, one laptop and one tablet, etc.

Participants will learn to use a Linux based operating system, including basic commands to navigate the system, cleaning/extracting and transforming data, installing and configuring bioinformatics software, learning to setup basic bioinformatic pipelines, learning to program in Linux etc.

Who should attend

  • Researchers and academics interested in learning the tools and methods that would give them freedom to implement their ideas/thoughts/solutions
  • Clinicians, researchers and academics interested in installing, configuring and setting up a Linux based computing system for their own research
  • Program administrators who are interested in getting a firsthand experience working with the opensource system and understanding its potential in biomedical research

Skill sets taught

  1. Basic Linux Commands
  2. Data wrangling in Linux
  3. File manipulations in Linux
  4. Scripting in BASH
  5. Compiling From Source
  6. Installing From Repo
  7. Installation Using .DEB
  8. Creating and Using Profiles
  9. Environmental Variables
  10. Basic Linux System Administration
  11. Intro to R
  12. Intro to Python
  13. Generating and using SSH keys
  14. Setting up and using Git
  15. Setting up a Sequence analysis pipeline using EMBOSS suite
  16. Setting up a Transcriptome analysis pipeline using HISAT2 suite
  17. Setting up a Variant Annotation pipeline
  18. Creating and Using Containers


  • Cloud-based linux environment
  • Training provided by active NIH researchers
  • Cookbook style bound manual for all exercises
  • Continuing Education Credits

Comprehensive file
A PDF file containing all notes, protocols, and reference material will be provided. No additional books are required. 

General Training Rate
Discounted Training Rates
$550.00-NIH Trainees(Fellows, PostDocs, PostBacs working at any NIH Campus ONLY)
$795.00-NIH Community (Working, Appointed, or Assigned to any NIH Campus ONLY)
$899.00-Academia, US Government, US Military

Refund Policy
100% tuition refund for registrations cancelled 14 or more calendar days prior to the start of the workshop.
50% tuition refund for registrations cancelled between 4 to 13 calendar days prior to the start of the workshop.
No refund will be issued for registrations cancelled 3 calendar days or less prior to the start of the workshop.

All cancellations must be received in writing via email to Ms. Carline Coote at
Cancellations received after 4:00 pm (ET) on business days or received on non-business days are time marked for the following business day. 
All refund payments will be processed by the start of the initial workshop.

Return to Workshops & Conferences Calendar