GxP BioInfra Platform

// 01 · ARCHITECTURE & INTENT

GxP BioInfra Platform

A regulated Kubernetes platform architecture and virtual lab implementation designed to demonstrate how cloud-native infrastructure can support reproducible bioinformatics workloads, auditability, access control, GitOps change management, and compliance-ready operations.

This project started as a project tracing document: a full breakdown of the environment, components, risks, controls, and validation evidence required to build the platform correctly. I am now building the virtual lab implementation to test the design and convert the architecture into working proof.

The goal is not to claim a finished production-certified system. The goal is to prove that I understand how to design, document, secure, operate, and validate a Kubernetes-based platform in a regulated context.

Why this project matters

Pharma, biotech, fintech, and regulated SaaS environments need platform engineers who understand more than deployment. They need engineers who can connect infrastructure decisions to auditability, change control, risk, access management, security controls, and operational evidence.

This project is designed to show that bridge:

• Platform engineering: Kubernetes, GitOps, workload placement, storage, ingress, and observability.
• DevSecOps: policy-as-code, secrets management, runtime security, image pinning, and incident response.
• Compliance thinking: GxP-style validation, ISO 27001 alignment, risk registers, supplier assessment, and IQ/OQ/PQ-style documentation.
• Operational maturity: runbooks, disaster recovery plans, patch management, onboarding, and test scripts.

Target architecture

The target platform is designed around a Kubernetes cluster running regulated bioinformatics workloads through a controlled GitOps workflow. Core components:

• Kubernetes / Talos OS — immutable cluster operating system and workload orchestration.
• ArgoCD — GitOps controller enforcing repository-defined cluster state.
• Forgejo — self-hosted Git platform for change control and pull-request-based infrastructure changes.
• Authentik — OIDC/SSO identity provider for centralised access control.
• MinIO — S3-compatible object storage for pipeline input, output, work directories, and audit log persistence.
• OPA Gatekeeper — policy-as-code admission control for resource limits, image pinning, labels, approved registries, and privilege restrictions.
• Falco — runtime security and audit event capture.
• Prometheus / Grafana / Loki — metrics, dashboards, logs, and audit trail visibility.
• Nextflow / nf-core — reproducible bioinformatics pipeline execution.
• Cloudflare Tunnel / Ingress-NGINX / Cert-Manager — secure access, routing, and TLS.

Architecture flow

Horizontal control path from source of truth to validation evidence (virtual lab / target design).

// 02 · WHAT THIS PROVES

Capabilities & evidence

This project demonstrates my ability to think beyond installing tools — designing a platform around operational, security, and compliance requirements from the beginning.

// 03 · DOCUMENTATION

Documentation produced

The project includes a structured documentation set similar to what would be expected in regulated infrastructure environments:

• Architecture Decision Records: key decisions, alternatives, and trade-offs.
• Infrastructure baseline: hardware, network, cluster state, storage, and topology.
• Architecture and component map: how all services connect and why they exist.
• Operational runbooks: daily, weekly, and monthly platform procedures.
• Disaster recovery plan: etcd recovery, storage failure recovery, GitOps restoration.
• Patch management process: CVE severity classification and response windows.
• Security architecture: threat model, protected assets, attack vectors, and layered controls.
• Component hardening guide: verification steps for Talos, ArgoCD, Forgejo, Authentik, MinIO, Gatekeeper, Falco, and other components.
• Incident response playbook: detection, containment, investigation, and recovery procedures.
• Secrets and key management standard: creation, sealing, storage, rotation, and retirement.
• Network security policy: current Flannel limitation and target Cilium enforcement model.
• Compliance matrix: mapping platform controls to Annex 11, Part 11, GAMP 5, and ISO 27001.
• Risk register: formal risks, mitigations, residual ratings, and review triggers.
• Supplier assessment register: third-party software risk and advisory tracking.
• Statement of Applicability: ISO 27001-style control applicability and implementation status.
• IQ/OQ/PQ validation templates: installation, operational, and performance qualification evidence structure.

// 04 · VALIDATION APPROACH

IQ / OQ / PQ-style evidence

Validation-style documentation means structuring evidence the way regulated teams expect: Installation Qualification (IQ) for “built as designed,” Operational Qualification (OQ) for “behaves correctly under defined conditions,” and Performance Qualification (PQ) for reproducible performance under realistic workload assumptions. In the virtual lab, I am aligning test scripts, sync evidence, policy denial cases, and observability exports to that structure — as educational and architectural evidence, not as legal certification.

Phase 7 of the roadmap (validation evidence pack) consolidates IQ baselines, OQ scripted tests (including negative tests where policies must deny bad deploys), and PQ-style reproducibility checks for pipeline runs — always labeled honestly against what the lab can prove today versus target state.

// 05 · ROADMAP

Phased delivery

Status pills reflect honest progress: Complete In progress Not started Roadmap

// 06 · KNOWN LIMITATIONS

Honest constraints

This is a virtual lab and architecture prototype, not a certified production environment.

• Implementation is in progress.
• The design is GxP-aligned but not externally audited.
• The virtual lab is intended to prove architecture and controls, not production scale.
• NetworkPolicy enforcement depends on a future Cilium migration.
• High availability is a target-state concept, not assumed in the first prototype.
• Full bioinformatics workload scale requires larger compute and memory resources.
• Compliance artifacts are educational and architectural evidence, not legal certification.

These limitations are documented deliberately because real platform engineering requires understanding risk, not hiding it.

// 07 · RECRUITER SUMMARY

At a glance

// 08 · TARGET ROLES

Roles this project supports

// 09 · TECH STACK

Tags

Technologies, controls, and frameworks referenced in the architecture and documentation.