Software Design Specification: Glossary
Document Type: Reference (Tier 3) Status: Draft Last Updated: 2026-01-25
Purpose
This glossary provides definitions for all terms, acronyms, and domain-specific vocabulary used throughout the PCR.AI system documentation. Terms are organized alphabetically for quick lookup.
A
Acceptance Criteria (AC) - Testable conditions that must be met for a requirement to be satisfied.
Accession - A unique identifier assigned to a patient sample for tracking purposes in the laboratory workflow.
Adjacent Well - Any well vertically, horizontally, or diagonally adjacent to a target well on the thermocycler plate (up to 8 positions).
ADJ Rule - Adjacent well contamination rule that flags potential cross-contamination between neighboring wells.
Alert - Notification triggered when configured thresholds are exceeded in trends data.
Amb (Ambiguous) - An observation classification where the algorithm could not determine a definitive Positive or Negative result.
Amazon Cognito - AWS service providing user identity and authentication services for PCR.AI.
Amazon DynamoDB - AWS NoSQL database service used for session management in PCR.AI.
Amazon ElastiCache - AWS managed in-memory cache service (Redis/Memcached).
Amazon RDS - AWS relational database service.
Amazon S3 - AWS object storage service for file storage in PCR.AI.
Amazon SES - AWS email service for transactional and bulk emails.
Amazon SQS - AWS message queue service for asynchronous processing.
AMB Rule - Rule that handles observations with ambiguous classification.
Analysis - Process of evaluating run data against configured rules.
API (Application Programming Interface) - Interface for software communication between system components.
Associated Wells - Wells sharing the same Mix, Extraction Instrument, Extraction Date, and Batch.
Audit Entry - A single record capturing a change event including timestamp, user, area affected, and before/after values.
Aurora Serverless - AWS serverless database with automatic capacity scaling used by PCR.AI.
Automatic Baseline Check - A boolean property on run targets that determines whether baseline checking is performed automatically or requires manual intervention.
AWS (Amazon Web Services) - Cloud computing platform hosting PCR.AI infrastructure.
B
Backup Mix - Fallback mix assignments when primary mix matching fails.
Baseline - Reference measurements used for curve normalization in PCR analysis.
BCC (Baseline Curve Control) - Rule that validates control CT values against configured bounds.
BPEC (Bad Positive Expected Control) - A rule that validates positive control wells have expected classification.
C
Calibrator - External API (DXAI) providing curve classification and analysis parameters.
CDN (Content Delivery Network) - Distributed content caching service.
Change Type - Classification of an audit modification (e.g., create, update, delete).
Client Configuration - The collection of system-wide settings that control application behavior across all functional areas.
CloudFront - AWS CDN service for content delivery.
Cloudflare - DNS and CDN service for domain management.
CLS (Classification) - Result classification for an observation (Positive, Negative, Ambiguous, etc.).
CLS Discrepancy - A condition where the DXAI classification differs from the machine classification for an observation.
Combined Outcome - A configured mapping specifying conditions for assigning a LIMS outcome based on multiple mix/target results.
concentration_factor - A numeric well property containing the concentration factor value; may be null.
Concurrent Session - An active authenticated user session performing operations on the system.
Configuration Export - Process of extracting configuration data to Excel format.
Configuration Import - Process of importing configuration data from Excel files.
Context-Specific Shortcut - A keyboard shortcut available only on screens where the corresponding action exists.
Control - Sample with known expected result used for quality assurance.
Control Failure - A control well that has failed its quality control validation.
Control Label - Configuration linking runfile sample labels to system roles.
Control Well - A well designated for quality control purposes, containing known reference material.
Cross Contamination - Potential transfer of material between adjacent wells.
Cross-talk - Detection of multiple positive targets in a single well where biological coinfection is unlikely.
CT (Cycle Threshold) - The PCR cycle number at which fluorescence signal crosses a defined threshold. Lower CT indicates higher initial quantity. Standard abbreviation is "CT" (not "Ct" or "ct").
Curve Control Limits - Upper and lower CT bounds for control validation.
CutOff / Upper Boundary - The configured CT threshold used to determine qualitative outcome.
D
Delta CT - The absolute difference between CT values of two targets in a configured pair.
DF (Derivative Factor) - Output parameter from DXAI calibrator analysis.
DFD (Data Flow Diagram) - Software design diagram type.
Diagnostic.ai - Company name providing the PCR.AI platform.
Display Optimization - The process of adjusting visual presentation to ensure readability and usability across different screen sizes and resolutions.
DNS (Domain Name System) - Internet naming service.
Downward Sigmoid - A curve pattern where the middle value is greater than the penultimate value, indicating signal decrease.
Duplicate File - A run file that has already been imported to the system, identified by content matching.
DXAI - External analysis service (Diagnostic.ai eXternal AI) for curve classification.
Dye - Fluorescent reporter molecule used to detect PCR amplification.
DynamoDB - See Amazon DynamoDB. Use capitalization "DynamoDB" (not "dynamodb").
E
Efficiency - Standard curve parameter indicating PCR amplification efficiency.
ERD (Entity Relationship Diagram) - Database design diagram.
Error Code - Unique identifier for an error condition.
Error Resolution - Configured action to address a specific error.
Exact Match Filter - A text filter that only returns results where the value exactly equals the entered text.
Excel - Microsoft Excel spreadsheet format for configuration import/export. Use capitalization "Excel" (not "excel").
Extraction - Process of isolating nucleic acids from samples.
Extraction Instrument - Laboratory device used for nucleic acid extraction.
F
Feature Flag - Configuration toggle controlling application functionality.
FIFO (First-In-First-Out) - Queue ordering method.
Filter Criteria - A constraint applied to a dataset that limits displayed records to those matching specified conditions.
Filter State - The current configuration of all active filter selections.
Final CLS - The resolved Curve-Level Status/Classification value used for analysis and reporting.
Final CT - The resolved Cycle Threshold value used for analysis and reporting.
FL / Fl (Fluorescence) - The emission of light by a substance that has absorbed light.
Fluorescence - Light emission from dye molecules during PCR.
Fluorescence Curve - Plot of fluorescence values across PCR cycles.
FTP (File Transfer Protocol) - File transfer protocol.
FTPS (FTP Secure) - Encrypted file transfer protocol.
G
Global Shortcut - A keyboard shortcut available throughout the application regardless of current screen.
Gradient - The slope of the standard curve (log quantity vs CT), typically negative.
GUI (Graphical User Interface) - Visual user interface.
H
Help Item - A configurable unit of help content consisting of title, description, optional video, and screen associations.
Help Widget - The user interface component that displays help items relevant to the current screen.
HIQ (High Quantity) - Upper quantity reporting threshold.
I
IAM (Identity and Access Management) - AWS access control service.
IC (Internal Control) - A control target used to verify extraction and amplification success.
ICCT - Rule evaluating Internal Control CT values.
IDD (Interface Design Document) - Interface specification document.
IEEE (Institute of Electrical and Electronics Engineers) - Standards organization.
Import - Process of loading run files or configuration into the system.
Inconclusive Result - A sample result pattern where exactly one Non-IC target has a Positive classification.
Inhibited Outcome - A LIMS outcome where is_inhibited: true.
Intercept - Y-axis intersection point on standard curve.
IoT (Internet of Things) - Connected device ecosystem.
IP Whitelist - List of allowed IP addresses for access control.
ISO (International Organization for Standardization) - Standards body.
J
JSON (JavaScript Object Notation) - Data interchange format. Use capitalization "JSON" (not "json").
JWT (JSON Web Token) - Authentication token format.
K
Kit Configuration - Configuration of assay-specific parameters.
Known Issue - A documented discrepancy between SRS requirements and implemented behavior.
Known Quantity - Expected quantity value for control roles in QC calculations.
L
Lambda - See AWS Lambda.
Laravel - PHP web application framework used by PCR.AI backend.
Laravel Vapor - Laravel deployment platform for AWS Lambda.
Levey Jennings (LJ) Chart - A quality control chart that displays control measurements over time with statistical limits.
LIMS (Laboratory Information Management System) - Lab data management system for sample tracking.
LIMS Export - The act of exporting well outcome data to the Laboratory Information Management System.
Linear Regression - Statistical method calculating slope, intercept, R2, and efficiency from standard control coordinates.
LoD (Limit of Detection) - The configured threshold value below which a quantitative measurement is considered undetectable.
Long-running process - A system operation that the system calculates will take more than the configured threshold (default 10 seconds) to complete.
LOQ (Limit of Quantification) - The lowest quantity that can be reliably measured and reported for a given assay group.
M
Maintenance Mode - A system state during deployment where normal application access is suspended and users see a status page.
Max Fl (Maximum Fluorescence) - The highest fluorescence reading value for an observation.
Mean - Statistical average value for Westgard calculations.
Mention - Synonymous with tag; the act of referencing another user in a comment.
MFA (Multi-Factor Authentication) - Two-step authentication requiring multiple verification factors.
MINCONTROL - Rule for general control validation ensuring minimum control requirements.
MINEXTRACT - Rule identifier for extraction controls validation.
Minimum Fluorescence - The lowest acceptable fluorescence reading for a target, configured per target.
Mix - A configured combination of targets and dyes that constitute an assay.
Mix Result - A single analytical result from a mix evaluation.
Mix Results Count - The number of mix results associated with a combined outcome.
MVC (Model-View-Controller) - Software architecture pattern.
N
NC (Negative Control) - Control expected to show no amplification.
NEC (Negative Extraction Control) - Control well used to verify extraction process purity and absence of contamination.
NEG (Negative Control) - A control well type that should not produce positive results.
Non-IC Target - A target that is not an Internal Control; subject targets being tested for the pathogen of interest.
Notification Icon - A visual indicator showing a count of wells in a specific status category.
NTC (No Template Control) - Control without nucleic acid template.
O
Observation - Data point for a specific target/dye combination in a well.
Outcome - Final result classification for a well (e.g., Positive, Negative, Control Passed, Error).
P
Page Load Time - The elapsed time from navigation initiation until the screen is fully rendered and interactive.
Parser - Service that converts thermocycler files to standardized format.
Partial Match Filter - A text filter that returns results where values begin with the entered text (prefix matching).
Passive Target - Reference dye for normalization (not reported as result).
Patient Well - A well in a PCR plate that contains patient sample data (as opposed to control wells).
PC (Positive Control) - Control expected to show amplification.
PCR (Polymerase Chain Reaction) - Molecular biology technique for DNA amplification.
PCR.AI - The SaaS PCR interpretation and QC platform. Standard naming is "PCR.AI" (not "pcr.ai", "Pcr.ai", or "PCRI.AI").
pcr.ai Classification - Classification result produced by the pcr.ai analytical engine.
pcr.ai CT - The CT value calculated by the pcr.ai algorithm.
PEC (Positive Extraction Control) - Extraction process positive control.
PHI (Protected Health Information) - HIPAA-protected health data.
PICQUAL - Rule identifier for qualitative inhibition detection.
PII (Personally Identifiable Information) - Privacy-protected personal data.
POTENTIAL_CONTAMINATED threshold - Upper quantity bound for wells considered "at risk" of contamination.
Precedence - A numeric value that determines rule execution order; lower values execute first.
Print Timestamp - The date and time when the report was printed or exported to PDF.
Problem Files - Folder for run files that failed import/parsing.
Programmatic Rule Name - Internal identifier mapping rule configuration to PHP class (e.g., programmatic_rule_name).
Progress indicator - A visual element displaying process name and percentage completion.
PSR (PHP Standard Recommendation) - PHP coding standards.
Pusher - Real-time communication platform for notifications.
Q
QC (Quality Control) - Quality assurance process for validating results.
QIR (Quantification by Internal Reference) - Quantification calculation method.
QSSC - Rule for quality standard curve calculations.
Qualitative Reporting - Reporting cut-offs for categorical result reporting (Detected/Not Detected).
Quant-as-Qual - A reporting mode where quantitative PCR results are converted to qualitative outcomes.
Quantification - Process of calculating target concentration from CT values.
Quantity - Calculated numeric value representing target concentration.
Quantity Group - A configurable threshold tier (Groups 2-9) that determines formatting rules for quantity values.
quantity_multiplier - A numeric well property populated by rules; used in downstream quantity calculations.
R
R2 / R-squared - Correlation coefficient measuring regression fit quality (0.0 to 1.0). Synonymous with Squared Pearson Correlation Coefficient.
RDS - See Amazon RDS.
Reanalysis - Process of re-executing analysis on existing run data.
Report Contents - A metadata section displaying report identification, creation information, and filter criteria.
Resolution Code - A code assigned to a well during manual intervention that can override automated result processing.
Responsive Design - An approach where the interface automatically adapts layout and sizing based on the display characteristics.
REST (Representational State Transfer) - API architecture style.
RFU (Relative Fluorescence Units) - Fluorescence measurement unit.
Role - Classification of well purpose (Patient, PC, NC, etc.).
Rolling Period - Moving time window for aggregation calculations.
RQUANT - Quantitative reporting rule.
RQUANTASQUAL Rule - Reporting rule for quantitative-as-qualitative results.
RQUAL - Qualitative reporting rule.
RRESOLUTION - Rule that handles resolution code processing.
Rule - A configured analysis operation that evaluates well data and may modify well state (error codes, LIMS status).
Rule Mapping - Configuration that relates a rule ID to a combination of Dye, Target Name, Mix, and optionally Sample Type.
Run - Complete set of PCR analysis data from a single instrument cycle.
Run File - Data file exported from thermocycler instrument containing well and assay data. Standard naming is "run file" (two words, not "runfile" or "Runfile").
Run Target - A configured target within a run that specifies analysis parameters including baseline check mode.
Runfile Threshold - The actual threshold value recorded in the runfile by the lab technician.
RWAC (Resolution Well Affecting Control) - Rule that modifies patient well outcomes based on control well resolutions.
S
S3 - See Amazon S3.
SaaS (Software as a Service) - Cloud software delivery model.
SAML (Security Assertion Markup Language) - SSO protocol.
Sample/Mix Combination - A specific pairing of a sample identifier with a mix/batch context.
Sample Type - See Specimen Type. Clarify distinction in context or treat as synonymous.
SD (Standard Deviation) - Statistical dispersion measure used in Westgard calculations.
SDD (Software Design Document) - Legacy design specification document (predecessor to SDS).
SDK (Software Development Kit) - Development tool package.
SDS (Software Design Specification) - Current design specification document set.
Selectable Row - A table row that can be highlighted to indicate user focus or selection.
SendGrid - Email delivery service.
Sentry - Error tracking and session replay service.
Serverless - Cloud computing model without server management.
SES - See Amazon SES.
Session - User authentication state maintained across requests.
Session Timeout - Automatic termination of a user session after the configured maximum session duration elapses.
Severity - Impact level for known issues: Low (cosmetic/minor), Medium (functional impact), High (critical functionality).
SFTP (SSH File Transfer Protocol) - Secure file transfer protocol.
Sigmoid - S-shaped curve characteristic of PCR amplification patterns.
Sigmoid Curve - The characteristic S-shaped amplification curve produced during PCR.
Sigmoid Direction - The curve shape pattern (Upward or Downward) determined by comparing middle and penultimate reading values.
Sigmoid Pattern - The shape of the amplification curve over time (upward or downward).
SIGMOID_CONTROL - The programmatic identifier for the Downward Sigmoid Control rule in the rules engine.
Site - Organizational unit representing a laboratory location.
SKIP Resolution Code - A resolution code that instructs the system to bypass all further rule processing for a well.
Slope - Standard curve parameter representing the gradient of the regression line.
SOLID - Object-oriented design principles (Single responsibility, Open-closed, Liskov substitution, Interface segregation, Dependency inversion).
Sortable Column - A column whose data can be reordered by the user via header interaction.
Specimen - Sample type classification (e.g., serum, plasma). See also Sample Type.
SQS - See Amazon SQS.
SRS (Software Requirements Specification) - Requirements document.
SSO (Single Sign-On) - Unified authentication allowing single login across multiple systems.
Standard Curve - A calibration curve created from quantitative standard controls with known concentrations.
STDQT - Rule for standard quantity calculations.
Super User - A user with elevated privileges authorized to modify system configuration.
T
Tag - A reference to a user within a comment using @ syntax that triggers notification.
Target - Specific DNA/RNA sequence detected by the assay.
TDD (Test-Driven Development) - Development methodology.
Test Code - Code on sample labels mapping to specimen types.
Thermocycler - Instrument that performs PCR temperature cycling.
Threshold - A numeric value used during PCR analysis to determine cycle threshold (CT) values.
THRESHOLD Rule - Rule that validates threshold values in analysis.
Tissue Weight - A numeric property associated with a well representing the mass of tissue sample.
TLD (Top Level Design) - High-level design document.
TNP (Test Not Performed) - Result status indicator when a test cannot be completed.
toPcrai - S3 folder monitored for incoming run files.
TOTP (Time-based One-Time Password) - MFA method using time-based codes.
Trends Report - Report showing aggregated data over time.
U
UKAS (United Kingdom Accreditation Service) - Accreditation body.
UML (Unified Modeling Language) - Software modeling notation.
Unknown Mix - Auto-created mix entry for unmatched target/dye combinations.
Upward Sigmoid - A sigmoid curve where signal increases over cycles (expected for positive wells).
User Pool - AWS Cognito container for user accounts.
V
Validation - Process of checking data against defined rules.
Vapor - See Laravel Vapor.
Vue - JavaScript framework for frontend (Vue.js).
W
WC - Well Crosstalk rule for detecting multiple positive targets.
WCAF - Rule that handles control affecting failure propagation.
WDCLS (Well Discrepant Classification) - Rule for Patient wells that flags classification discrepancies.
WDCLSC - Well Discrepant Classification for Control wells.
WDCLSC-INVERT-SIGMOID - Rule variant handling inverted sigmoid patterns in control wells.
WDCT - Well Discrepant CT rule for Patient wells.
WDCTC - Well Discrepant CT for Control wells.
Well - A single reaction location on a PCR plate (e.g., A1-H12) containing sample or control material.
Well Position - Grid coordinate identifying a well (e.g., A1, B12).
Westgard - Statistical QC rules for control evaluation. Standard capitalization is "Westgard" (not "westgard" or "WG").
Westgard 1:2S - Rule triggered when control is >2 SD from mean.
Westgard 1:3S - Rule triggered when control is >3 SD from mean.
Westgard 2:2S - Rule triggered when two consecutive controls are >2 SD.
Westgard 7T - Rule triggered when seven consecutive controls trend same direction.
Westgard Event - Generated notification when Westgard rule triggers.
Westgard Limits - Mean and SD parameters for Westgard calculations.
Westgard Rules - Statistical rules for evaluating quality control data, typically using mean and standard deviation bands.
WFINALCLS - Rule identifier for "Set Final Classification Based on Cutoffs".
WG14S Rule - Westgard rule variant (needs explicit definition).
WREP - Rule ID for the Repeat Sample Check rule.
WT Rule (Well Transfer) - The rule identifier for associated well error propagation.
Document Tiers
| Term | Definition |
|---|---|
| SDS | Software Design Specification (this document set) |
| SRS | Software Requirements Specification |
| Domain | A functional area of the system (e.g., NOTIF, KITCFG) |
| Tier 1 | System-level documents (architecture, cross-cutting) |
| Tier 2 | Domain design documents |
| Tier 3 | Reference material (this document) |
| Tier 4 | Traceability artifacts |
Terminology Standardization
For consistency across documentation, use the following canonical forms:
| Canonical Form | Avoid Using |
|---|---|
| PCR.AI | pcr.ai, Pcr.ai, PCRI.AI, PCR.AI System |
| run file | runfile, Runfile, Run File |
| Westgard | westgard, WG |
| CT | Ct, ct |
| LIMS | Lims, lims |
| DynamoDB | dynamodb |
| JSON | json |
| API | api |
| Excel | excel |
| MFA | multi-factor authentication (spell out on first use) |
| SD | standard deviation (spell out on first use) |
References
| Document | Location | Purpose |
|---|---|---|
| SRS | output/srs/ | Requirements source |
| SDD (Legacy) | output/sdd/ | Predecessor documentation |
| SDS Introduction | output/sds/sds-01-introduction.md | Document conventions |