Ctrl+K

Good practices and reproducibility

Good practices and reproducibility#

Topic overview#

In this lesson you will learn about good practices and reproducibility while using Unix-based systems. First, you apply good practices for exploring commands and gaining knowledge about bioinformatics problem solving, with help of browser-based and AI-based searches. To ensure reproducibility, you learn how to control the flow of inputs and outputs to programs and save your commands into a file. Lastly, you learn how to become responsible users of computing servers by using a module system for loading more advanced, pre-installed software.

Learning objectives#

Learning Objective 1 - You are able to gain knowledge and extract more information about commands

  • LO 1.1 - You read command manuals and help page within the command line

  • LO 1.2 - You perform browser-based searches for solving a problem of interest

  • LO 1.3 - You perform iterative AI-based problem solving with ChatGPT

Learning Objective 2 - You can automate computational tasks and construct workflows to obtain reproducible results

  • LO 2.1 - You redirect the output and error streams to files

  • LO 2.2 - You pipe the results of one command to another

  • LO 2.3 - You write simple scripts and execute them

Learning Objective 3 - You are able to use pre-installed software to solve bioinformatic problems

  • LO 3.1 - You load pre-installed software from a module system

Contents