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AlcoaBase Documentation Index

Welcome to the AlcoaBase user documentation. This index organizes all feature guides by domain, giving you a clear path through the platform from initial setup to advanced AI-powered workflows.

How to Use This Documentation

Each guide is a self-contained reference for a specific feature. Start with the Getting Started section if this is a fresh deployment, then explore guides by domain as you configure and adopt capabilities. Guides are ordered within each section to reflect a natural progression — earlier guides cover prerequisites for later ones.

1. Getting Started

Guide What You'll Learn
Setup Wizard First-run initialization: create admin account, establish your company, configure AI hardware, seed demo data
Document Upload Upload documents via the web UI or bulk CLI tool, manage versions, browse and filter

2. Document Lifecycle & Compliance

Guide What You'll Learn
Workflow Editor Design BPMN document lifecycle workflows with states, transitions, signature gates, and training triggers
Workflow Execution Execute state transitions, understand gate indicators, provide change reasons, review audit history
Electronic Signatures PAdES digital signing, re-authentication, 21 CFR Part 11 compliance, certificate configuration
Training Management View training tasks, complete training, content viewer, records, gate enforcement, admin monitoring
Comprehension Quiz Quiz taking, scoring, pass/fail threshold, dual gate verification, immutable audit trail

3. Search & Knowledge

Guide What You'll Learn
Search & Knowledge Base Hybrid search (BM25+kNN), RAG knowledge chat, document indexing, visual content discovery
AI Inference vLLM integration: RAG queries, embedding generation, OCR, health monitoring, mock mode for development

4. AI-Powered Document Intelligence

Guide What You'll Learn
Agent Management Agent registry, archetypes, personality profiles, tuning parameters, YAML definitions, hot-reload
Multi-Agent Auditing Parallel AI document review, audit profiles, compliance scoring, anomaly detection, missing link reports
AI Document Generator Template-based generation, provenance audit trail, cross-references, mandatory human review workflow
AI Training Ecosystem Personalized schedules, AI material generation, semantic quiz grading, virtual audit role-play, dynamic feedback
Change Impact Analysis Dependency graphs, automatic impact detection, section-level gap analysis, notifications, training resets
Traceability & Gap Discovery Automated traceability matrices, three-pass matching, orphan detection, coverage metrics, stale link alerts

5. Literature Research & Evidence Management

This section covers the complete literature research pipeline — from querying external databases through to managing citation evidence for regulatory submissions. Features build on each other in sequence.

Guide What You'll Learn
Literature Search Engine External database gateways (PubMed, Crossref, arXiv), API key management, rate limiting, proxy routing
Literature Ingestion Pipeline Automated full-text retrieval via Unpaywall, PDF/HTML/XML sanitization, storage quotas, retention policies
Literature Embedding & Hybrid Search Semantic embedding generation, hybrid BM25+kNN indexing, unified cross-corpus search, partition tagging
Literature Review & Synthesis Agents AI-powered SLR screening, PICO criteria, contradiction detection, novelty flagging, inter-rater reliability
Medical Device Vigilance & PMS Product registration, vigilance search profiles, safety signal detection, periodic reports, MDR/IVDR compliance
Literature Search & Citation UI Faceted search dashboard, one-click internalization, citation collections, traceability mapping, PRISMA exports

6. Administration & Governance

Guide What You'll Learn
Admin — User Management RBAC roles, user CRUD, permission templates, company memberships, deactivation, password reset
Admin — System Configuration AI hardware, storage quotas, backup scheduling, health monitoring, service status, rollback
Audit Trail Viewer Centralized audit log, filtering, search, PDF export, immutability enforcement, meta-auditing
AI Risk & Compliance Framework Risk tiers (High/Medium/Low), HITL checkpoints, control gates, operation logging, company risk profiles

7. Corporate Environment & Regulatory Documents

Guide What You'll Learn
ALC Corporate Environment Corporate tenant seeding, user provisioning, regulatory baselines, governance folders, agent activations
Cross-Sector AI Guidelines AI usage policy generation, sector-specific modules (Pharma/MedTech/IVD), risk tier integration
Documentation Suite User Guide & Admin Guide generation, cross-references, versioning, governance workflow integration

Quick Reference

Role Requirements by Feature Area

Area Minimum Role
Document browsing, search, knowledge chat viewer
Document upload, transitions, training member
Literature search, saved searches, export member
Internalization, citation management, traceability document_admin
User management, system configuration system_admin / it_admin
Audit trail access system_admin / doc_admin / it_admin

Key Concepts Across All Features

Concept Description
X-Company-Id Header identifying the tenant context; required on all API calls
X-Change-Reason Header required on all mutating requests (POST/PUT/DELETE) for ALCOA+ compliance
Multi-tenancy All data is scoped to a company; cross-tenant access is impossible
Immutable audit Every state change, access event, and AI operation is logged permanently
Soft-delete Records are archived (status → "archived") rather than physically deleted

8. Manual Testing & Validation

Document Location Purpose
Test Protocols docs/test-protocols/ Reusable step-by-step test procedures (GxP-compliant format)
Test Reports docs/test-reports/ Executed results with pass/fail, tester sign-off, and deviations

Available Protocols (Phase 10)

Protocol Title
TP-10.1.1 Docker Services Health
TP-10.1.2 Setup Wizard — Admin Account
TP-10.1.3 Setup Wizard — Company Creation & Multi-Tenancy
TP-10.1.4 Setup Wizard — AI Mode Configuration

Regulatory Alignment

AlcoaBase documentation and features are designed to support compliance with:

  • 21 CFR Part 11 — Electronic records and signatures (FDA)
  • EU Annex 11 — Computerized systems in GxP environments (EMA)
  • EU AI Act — Risk-based AI governance framework
  • ISO 13485 — Quality management for medical devices
  • MDR 2017/745 — Medical Device Regulation (EU)
  • IVDR 2017/746 — In Vitro Diagnostic Regulation (EU)
  • GMP / GLP / GCP — Good Manufacturing/Laboratory/Clinical Practice

Last updated: June 2026