Definitions

This section of an SOP should include definitions of scientific, technical, and procedural terms used throughout the document. Providing clear definitions ensures that all staff members interpret terminology consistently and reduces the risk of misunderstanding. Definitions should also cover any abbreviations or acronyms that are specific to the SOP.

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Example content:

🧬 Bioinformatics QC Procedure

DEFINITIONS

Term	Definition
Cron jon	A scheduled task on Unix/Linux systems that runs automatically at specified intervals
Duty bioinformatician	The designated member of the bioinformatics team responsible for executing and monitoring production bioinformatics pipelines and monitoring the bioinformatics inbox
FASTQ	A text-based file format that stores both nucleotide sequences and their associated quality scores
Magnitude	The number of sequencing reads assigned to the expected organism by Centrifuge

👩‍🔬 Staff Training Procedure

Example content from an SOP outlining a training procedure

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Definitions

Term	Definition
Training Module	A structured instructional unit covering a defined skill or topic.
Competency Assessment	Evaluation of a trainee’s ability to perform tasks independently to a defined standard.
Training Matrix	A record showing required and completed training for each staff member.
Tell-Show-Do-Apply	A progressive instructional model used to deliver and assess training.

🌌 Galaxy Training Procedure

Example content from a training SOP detailing the standardised procedure for training on the Galaxy platform

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Definitions

• Galaxy: An open-source web platform for accessible, reproducible, and transparent bioinformatics analysis.

• Workflow: A predefined series of computational steps for processing data.

• Competency Assessment: Evaluation of whether a participant can independently perform the trained task to a defined standard.

🧪 Laboratory Procedure

Example content from a wet-lab SOP outlining the procedure for preparing sequencing libraries using the Illumina DNA Prep kit.

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Definitions

Limited-cyle PCR: A polymerase chain reaction using a reduced number of amplification cycles to minimise bias while amplifying sequencing libraries.

Transposome: A complex of transposase enzyme and adapter sequences used to simultaneously fragment DNA and add sequencing adapters.

Tagmentation: A process in which DNA is fragmented and tagged with adapter sequences in a single enzymatic step using a transposome.

💻 Code Update & Review Procedure

Example content from an SOP outlining the procedure for updating and reviewing code within the Luma Genomics Unit (LGU).

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Definitions

Term	Definition
Version Control System (VCS)	A system used to track changes to code, manage branches, and coordinate collaboration between developers.
Repository	A storage location for code, documentation, and related files managed under version control.
Branch	A parallel version of the repository used to isolate changes until they are ready to be merged.
Assignee	The person responsible for completing or managing a GitLab issue or merge request.
Reviewer Template	A structured document used to record review outcomes and ensure consistency in code review.
Assignee Overview Checklist	A checklist used to track completion of required review steps and responsibilities.
Slack Notification	A communication method used to notify team members of review outcomes or required actions.
Testing Suite / Environment	A set of tests or controlled environment used to verify that code changes function correctly before merging.

✅ Validation Procedure