Efficient Research Workflows with the UNIX Shell

Note: This work­shop is still in pilot mode so the actu­al syl­labus may have slight changes for the work­shop instance, but over­all the learn­ing objec­tives are the same.

Course Instances
Dates and loca­tions are to be announced.

Learning objectives

By the end of this work­shop, par­tic­i­pants will be able to:

1. Access and use the UNIX shell on their own machine for inter­act­ing with the file sys­tem.

2. Nav­i­gate direc­to­ries and man­age files effi­cient­ly using basic shell com­mands .

3. Pre­view and inspect data files

4. Fil­ter and sum­ma­rize data to extract rel­e­vant infor­ma­tion from large datasets.

5. Write sim­ple shell scripts to auto­mate repet­i­tive research tasks, such as batch file pro­cess­ing, renam­ing, and sum­ma­riz­ing datasets.

6. How to use and deposit data in the 4TU.ResearchData repos­i­to­ry, and under­stand how shell work­flows can inte­grate with open data prac­tices.

Syllabus/Curriculum overview

• Morn­ing ses­sion (09:30 – 12:30):
  • Set­up & Intro­duc­tion
  • Nav­i­gat­ing the Filesys­tem
  • Explor­ing & Inspect­ing Files
  • Data fil­terint & sum­ma­riza­tion
  • Basic shell script­ing
• After­noon ses­sion (13:30 – 16:00):
  • Group assign­ments
  • Wrap-up & Dis­cus­sion
  • Get to know $YU.ResearchData

Prerequisites

• No pri­or expe­ri­ence with UNIX shell.
• Par­tic­i­pants should bring their own lap­tops with a Bash shell (Mac/Linux users have it by default; Win­dows users should install Git Bash or WSL).
  
  

Target Audience

This work­shop is designed for any­one inter­est­ed in improv­ing effi­cien­cy in research work­flows with the UNIX shell.

Instructors

Leila Iñi­go de la Cruz

Resources

Par­tic­i­pants are encour­aged to bring their own lap­tops for hands-on exer­cis­es.