Training activity information
Details
Use Linux command line and command line tools to:
- Change a file owner and permissions
- Change the content of a file
- Count the number of lines in a file
- Identify the process taking up the most memory
- Check file system disk space usage
Type
Developmental training activity (DTA)
Evidence requirements
Evidence the activity has been undertaken by the trainee​.
Reflection on the activity at one or more time points after the event including learning from the activity and/or areas of the trainees practice for development.
An action plan to implement learning and/or to address skills or knowledge gaps identified.
Considerations
- For example: grep, awk, sed, cat, find, xargs, ls and mkdir
- Navigating the file system
- Manipulating directories and files on command line
- File system structure and permissions, including mounting drives
- Managing file and user permissions
- Escalating user permissions, for example: sudo
- Inspecting and managing processes and storage
- Redirection and piping
- File types
Reflective practice guidance
The guidance below is provided to support reflection at different time points, providing you with questions to aid you to reflect for this training activity. They are provided for guidance and should not be considered as a mandatory checklist. Trainees should not be expected to provide answers to each of the guidance questions listed.
Before action
- What specific Linux commands and tools are relevant to these tasks? How do these skills contribute to safe software solutions?
- What is your current level of familiarity with the Linux command line? Do you understand file permissions, process management, and disk space concepts in Linux?
- What specific commands or techniques do you hope to master? How will this enhance your ability to work in a bioinformatics environment?
- Will you review basic Linux command tutorials? Will you practice these commands in a test environment?
In action
- What commands are you currently using to achieve each task? Why did you choose these specific commands?
- As you are executing the commands, are they producing the expected output? If not, what adjustments are you making to the syntax or approach?
- Which aspects of using the command line feel intuitive, and which require more conscious effort?
- Are you encountering any challenges with permissions, file access, or understanding the output of commands? How are you troubleshooting these issues in the moment?
- How does this practical application of Linux commands connect with any previous knowledge or experience you have with operating systems?
On action
- What were the key commands you used for each task? Were there any commands that you initially tried that didn’t work as expected? What did you notice about that?
- What did you learn about Linux command syntax and the specific tools used (e.g., chmod, chown, grep, ps, df)? Were there any unexpected behaviours or outputs from these commands? What skills or knowledge related to Linux command line did you develop or improve through this activity? How did your experience of reflect-in-action (as discussed previously) influence how you approached or completed these tasks?
- What will you take from this experience regarding your approach to using Linux command line tools in the future? Are there any specific commands or techniques you want to practice further?
Beyond action
- Have you revisited your initial reflections on using Linux command line tools? Consider if your understanding of these commands and their utility has changed as you’ve gained more experience with software development and system administration in subsequent training activities or experiences.
- How have the skills developed in this training activity impacted your approach to later activities? For instance, have you found yourself more comfortable navigating file systems or monitoring resource usage when working on pipelines or installing software in later training activities?
- Can you compare your experience with these fundamental Linux commands to other training activities and experiences, where you might have observed colleagues or mentors using similar commands in a clinical bioinformatics context? What observable behaviours and practices have you assimilated into your own practice as a result?
- Consider engaging in professional storytelling with peers about a situation where these Linux skills were particularly useful (or where a lack of these skills hindered progress). Has analysing this with others changed your view of the situation or the importance of these skills?
- How might the foundational understanding of Linux gained in this activity contribute to your future practice in clinical bioinformatics, even in areas beyond direct software development? For example, how might this knowledge help you understand system logs or troubleshoot issues with bioinformatics tools in a clinical setting?
Relevant learning outcomes
| # | Outcome |
|---|---|
| # 1 |
Outcome
Process data in a Linux environment. |