OSFA Station Ideas Flashcards
Requirements gathering for new piece of software. (Programming)
The bioinformatics team has received a request to develop a new piece of software and you are being sent to a meeting to carry out the requirements gathering.
You will have 6 minutes to read an outline of the tool requirements as noted by another team member and make notes and prioritise these based on what is written in the document. You will then have 6 minutes to discuss these with the assessor and refine requirements, add any additional requirements and change priorities.
Skills
- Deciphering requirements
- Task prioritisation
- Software development knowledge
- Communication (asking the right questions)
Review a new piece of software with regards to Information Governance requirements (Introduction to Health Informatics Science)
The lab are planning on implementing anew piece of software and have asked you to review the software with regards to information governance to determine whether meets the requirements to be implemented in a clinical laboratory.
You will have 6 minutes to read an outline of the software and the data which will be stored in it and make notes. You will then have 6 minutes to present your assessment of the software to the head of the laboratory.
Skills
- Knowledge of Information Governance
- Knowledge of IT security
- Critical appraisal
- Communication
Advise a genetics service within a hospital with respect to the bioinformatic requirements of a new clinical service (Advanced Clinical Bioinformatics)
The lab is setting up up a new NGS assay for testing of viruses. You have 6 minutes to read the outline of the test, including the equipment used, the expected output from the analysis, expected TAT etc and make notes on the bioinformatics requirements needed for this. Discuss the outcome of this with the assessor and explain each of the requirements you have made.
Skills
- Sequencing technologies (What type of data?)
- Storage
- Computational power
- Capacity
- Communication
NGS Pipeline Design and Files
You have been asked to explain the bioinformatics pipeline process to a colleague with no prior knowledge of bioinformatics. You have 4 minutes to make notes on the bioinformatics pipeline and then 8 minutes to explain to your colleague.
- Knowledge of NGS pipelines
- Communication (lay mans)
- NGS file types
Code Review (Programming)
You have been asked to code review a small python script which is to be integrated as part of the pipeline to calculate the average coverage for all genes tested.
You have 12 minutes to review the code and make any comments in a text file.
- Good programming practice
- Python knowledge
Databases and SQL (Computing for Clinical Scientists)
You have been given the schema to a database of sequencing results and asked to write queries which provide the answers to the questions below.
1) Number of unique variants in the database
2) The variant which is associated with the patient ID B1111111
3) A list of all patients tested on the ‘BreastCancer’ panel
- Databases
- SQL
Variant Interpretation & MDT
You have been asked to go as representation from the laboratory to discuss a class 3 variant which has been identified in a patient which had an exome test carried out.
You have 4 minutes to look at the evidence on the variant and make notes. You will then explain the variant evidence to the MDT members and then answer questions.
- Variant Analysis
- Communication
- Testing strategies
Pipeline Validation
A pipeline has been built for the analysis of a new NHS assay the lab is setting up. You have been given the information on the results from the pipeline.
Evaluate the performance of the pipeline against best practice guidelines and decide whether the pipeline is fit for purpose.
- Knowledge of NGS pipelines
- Critical evaluation
- Knowledge of validation stats (sensitivity etc)
Develop a Data Capture Strategy
The bioinformatics team have been developing a new variant database. You have been given the outputs from the pipeline and asked to determine a data capture strategy to detail the variants identified and the analysis which was carried out.
You have six minutes to make notes on the pipeline outputs and outline what you would include in the data capture for the variant database.
- Variant Analysis
- Minimum data information
- Data integrity
- Versioning
Gene Panel Design
You have been asked to design a new gene panel for a group of disorders with a similar phenotype. An outline of the disorders has been provided.
You have 5 minutes to make notes on the steps you would carry out to design this panel and discuss why you would do it this way
- Gene panel development
- Ethics (incidental findings)
- Ontologies
SOP Review
You have been asked to review a new SOP for implementation in the lab.
You have 6 minutes to read the SOP and make notes and then discuss with the assessor
- SOP review
- Quality
- Scientific Knowledge
Analysis Requirements
The laboratory is setting up a new assay and you have been given the information on the assay and information on the content of the panel and the of variants etc associated with the disorder.
You have 6 minutes to read the panel details and make notes and a further 6 minutes to outline a bioinformatics analysis strategy for this panel.
- Pipeline knowledge
- Bioinformatics tools
- Gene dossiers
Pathway analysis
The laboratory is investigating a variant of uncertain significance found on an exome test. You have been asked to invedtigate the pathways in which the gene operates and decide whether it is likely or unlikely to be involved with the phenotype of the patient.
You have 6 minutes to read through the provided literature and phenotype information and then 6 minutes to discuss with the assessor and give an overall conclusion.
- Pathway analysis
- Critical evaludation
Programming
Design and code a small program in Java or an alternative object-oriented programming language for bioinformatic application* and proceed to test and debug the program in accordance with good programming practice.* For example for transforming large data sets, which meets simple requirements expressed in plain language.
Programming
Good programming practice
Data transfer (Command Line)
You have been asked to locate and copy a BAM file and get the gene coverage information for the gene listed from a summary text file and output into a new file for a clinical scientist in the laboratory.
You have been given the patient ID, using the command line terminal copy the BAM, its index and the gene coverage to the directory ‘/home/davids/analysis/’
- checksum
- command line - cp etc
- awk
- locate?
