Software —
Training activity: 4

Details

Install new tools or update already installed tools and demonstrate a working version

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

• Reliable resources for software
• Package sources (e.g., R, Python and Perl)
• Source code and compilers
• User level including global
• Software maintainability

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

• Why is the ability to install and update software important in a bioinformatics environment? What considerations are involved in ensuring a working version?
• Are you familiar with different software installation methods (e.g., package managers, source code compilation)? Do you understand the concept of software dependencies?
• What challenges might you encounter during installation or updates? How will you verify that the installed/updated tools are working correctly?
• Will you identify specific tools you might install or update? Will you research their installation procedures and potential issues?

In action

• What method are you using to install or update the tools (e.g., package manager, compiling from source)? Why did you choose this method?
• As you are performing the installation/update, are you encountering any dependency issues or errors? How are you troubleshooting these in the moment?
• Have you considered the use of virtual environments or containerisation tools such as Docker to manage software dependencies and ensure reproducibility across different systems?
• How are you verifying that the tool has been installed or updated correctly? What tests or checks are you performing?
• Is the newly installed/updated tool behaving as expected? Are there any unexpected outputs or issues arising? How are you adapting your approach to address these?
• What resources or documentation are you consulting during the installation/update process? Are they proving helpful?

 

On action

• What tools did you install or update? What method did you use for the installation/update (e.g., package manager)? Were there any issues during the process? What did you notice?
• What did you learn about the process of installing or updating software tools in your environment? Did you encounter any dependency issues or compatibility problems? How did you resolve them? What skills related to software installation and maintenance did you develop or improve? How did your reflect-in-action during the installation/update (e.g., troubleshooting errors) influence the outcome?
• What will you take from this experience regarding best practices for installing and updating software tools? Are there any specific tools or methods you need to become more familiar with?

Beyond action

• Considering your initial experience with software installation and updates, how has your confidence and ability in managing your bioinformatics computing environment evolved through later training activities where you had to install or update software?
• Have you encountered more complex installation scenarios in later activities or observed how experienced bioinformaticians manage software dependencies and compatibility issues? How does your initial experience compare? What have you learned from these later encounters?
• Revisit your reflections on any challenges you faced during the initial installation/update and consider if you would approach those challenges differently now, based on your accumulated knowledge. What new resources or techniques have you learned about since then?
• Think about the implications of software installation and maintenance in a clinical setting, considering patient safety and data integrity. How does your experience in this training activity inform your understanding of these broader responsibilities?
• How will your developing skills in software installation and maintenance contribute to your ability to troubleshoot issues, adopt new technologies, and maintain a robust bioinformatics infrastructure in your future practice?

Relevant learning outcomes

#	Outcome
# 3	Outcome Apply best practice in software development and code testing.
# 4	Outcome Modify, install, update and test software.