Training activity information
Details
Develop a strategy to modify or assemble tools, pipelines or processes
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
- Validation and verification – best practices
- Benchmarking and reference standards
- Evaluating and interpreting data
- Data governance
- Effect on patient e.g., clinical safety, confidentiality and incidental findings
- Storage of data in appropriate formats according to local and national standards, taking into consideration patient confidentiality
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 bioinformatics need or challenge are you aiming to address by modifying or assembling tools, pipelines, or processes? What are the desired improvements or outcomes you hope to achieve with your strategy? What is your current understanding of relevant tools, pipelines, or bioinformatics processes that you might modify or combine?
- What will you learn about the process of designing and planning modifications to existing bioinformatics workflows? How will you develop your understanding of integrating different bioinformatics tools or components into a cohesive pipeline? What potential challenges do you expect to encounter in developing this strategy (e.g., compatibility issues, resource limitations)?
- Will you identify specific tools, pipelines, or processes that you could potentially modify or assemble? Will you discuss potential projects or areas for improvement with your training officer or colleagues? Will you research best practices for pipeline development or tool integration? What are your initial ideas for a strategy, and how confident do you feel about developing it?
In action
- Are you starting by outlining the specific need you are addressing, identifying existing tools or components, or sketching a potential workflow? What is your rationale for the initial direction of your strategy?
- Are you encountering any unexpected dependencies or incompatibilities between tools you are considering? Are there specific steps in the modification or assembly process that are proving more challenging than anticipated? What new insights are you gaining about pipeline design or tool integration as you work on your strategy? How does this relate to your previous experience with bioinformatics workflows?
- If you are facing difficulties in connecting different tools or achieving the desired outcome, are you considering alternative tools, different approaches to integration, or breaking down the problem into smaller steps? Are you thinking about seeking advice on specific technical challenges or pipeline design principles?
On action
- Describe the specific goal or need that your strategy aimed to address. What existing tools, pipelines, or processes did you consider for modification or assembly? Outline the main steps in your proposed strategy. What challenges or potential roadblocks did you foresee while developing your strategy?
- What did you learn about the process of designing and planning modifications or assemblies of bioinformatics tools and pipelines? Did you encounter any unexpected complexities or considerations while developing your strategy? What did you learn from these? For example, were there unforeseen dependencies between tools or limitations in their functionality? How did your reflect-in-action during the strategy development influence the final plan? Did you have to revise your approach based on new insights or challenges encountered? How does this experience relate to the development, implementation strategies, and operation of bioinformatic analysis pipelines?
- What aspects of strategy development for tool/pipeline modification or assembly do you need to develop further? How will you apply this learning to future tasks involving pipeline development or process improvement? What ‘next steps’ will you take to further explore or refine your strategy or the tools involved? For example, will you research specific tools in more depth or seek feedback on your proposed strategy? What support or resources would help you in future pipeline development or modification projects?
Beyond action
- Reflect on the strategy you developed in this training activity and how it relates to your subsequent experiences with bioinformatics tools and pipelines. Have you since been involved in projects that required modifying existing pipelines or assembling new ones? How did the strategic thinking in this training activity influence your approach to those projects? Did you encounter similar challenges or discover new considerations? Review your initial reflections on this training activity in the context of the entire S-BG-S1 module and beyond. Have your perspectives on pipeline development and modification evolved as you’ve gained more knowledge and experience? Have you discussed pipeline development strategies with colleagues? Did these discussions provide new insights into different approaches or best practices?
- Consider the broader impact of this training activity on your skills. How has the strategic thinking involved in planning modifications or assemblies contributed to your problem-solving abilities in bioinformatics? In your current work or training, have you applied the principles of strategy development learned in this training activity? For example, when faced with a new analytical challenge, do you now approach it with a more structured plan for identifying and potentially adapting existing resources?
- Identify the transferable skills you gained, such as planning, problem-solving, and understanding the modularity of bioinformatics processes. How might these skills be valuable in future roles involving pipeline development, automation, or service improvement? What future actions will you take to further develop your strategic thinking in the context of bioinformatics tool and pipeline development? Are there specific areas like workflow management systems or scripting languages you plan to focus on?
Relevant learning outcomes
| # | Outcome |
|---|---|
| # 3 |
Outcome
Select appropriate tools for next generation sequencing (NGS) analysis of inherited and acquired disease. |
| # 4 |
Outcome
Analyse NGS data in a clinical setting applying appropriate quality control and data validation. |