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AI Genomics Lab — Progress Tracker

Development Status

Phase 1: Infrastructure — COMPLETED ✅

  • Docker Compose multi-service architecture (7 services)
  • Service Dockerfiles (API, Bio-Pipeline, Frontend)
  • Development helper script (dev.sh)
  • Environment variable configuration
  • Volume management for persistent data
  • Resource limits per service

Phase 2: Bioinformatics Pipeline — COMPLETED ✅

  • Bio container (Ubuntu 22.04 + strobealign + SAMtools + bcftools)
  • Genome indexing pipeline (Nextflow DSL2)
  • Variant analysis pipeline (FASTQ → CRAM → VCF)
  • Streaming pipeline with observability (timestamps, progress, file sizes)
  • Test mode with configurable read limits
  • CRAM output for space efficiency
  • ClinVar annotation support
  • On-demand strobealign index creation

Phase 3: Data Layer — COMPLETED ✅

  • PostgreSQL schema (28 tables with seed data)
  • Neo4j knowledge graph schema + seed data (graph/schema.cypher)
  • MinIO clinical path structure
  • Database initialization and seeding
  • Audit logging

Phase 4: API Layer — COMPLETED ✅

  • FastAPI with 50+ endpoints
  • JWT authentication with Argon2 + RBAC
  • Clinical data CRUD (patients, cases, samples, variants, reports)
  • Pipeline execution management with SSE streaming
  • Genome indexing API
  • Storage management API
  • OpenAPI documentation (/docs)
  • AI provider endpoints (/api/v1/ai/*)

Phase 5: AI Integration — COMPLETED ✅

  • Multi-provider LLM client with caching
  • Anthropic Claude integration
  • OpenAI GPT integration
  • Google Gemini integration
  • DeepSeek integration
  • Xiaomi MIMO integration
  • OpenRouter integration
  • Genetics-specific models (DNABERT, ESM, AlphaFold API)
  • Embedding models (OpenAI, Voyage)
  • Streaming response support
  • Multi-agent system (VariantAgent, GraphAgent, LiteratureAgent, ReportAgent)
  • AnalysisOrchestrator
  • Knowledge graph integration
  • Report generation

Phase 6: Frontend — COMPLETED ✅

  • Next.js dashboard with dark theme
  • Clinical case wizard (10 steps)
  • Cytoscape.js knowledge graph visualization
  • IGV.js genome browser
  • Variant table with filters
  • Real-time pipeline log streaming
  • Design system with Storybook
  • Zustand state management
  • DNA helix animation component (Canvas 3D)
  • Custom SVG pipeline icons (strobealign, samtools, bcftools, etc.)
  • GenomicsPipeline component with progress bars
  • AIModelSelector component
  • Dark theme for all wizard components

Phase 7: Clinical Validation — IN PROGRESS 🔄

  • Validate pipeline against GIAB benchmark samples
  • SNV sensitivity/specificity measurement (target: >99%)
  • ClinVar concordance testing
  • Performance benchmarking on reference hardware

Phase 8: Knowledge Ingestion — PLANNED 📋

  • Automated ClinVar data ingestion
  • gnomAD population frequency integration
  • dbSNP identifier mapping
  • COSMIC cancer mutation database
  • Automated data refresh schedules

Phase 9: Production Hardening — PLANNED 📋

  • Alembic migration system
  • Health check endpoints with real service status
  • Prometheus + Grafana monitoring
  • Log aggregation (Loki)
  • Automated backups
  • Load testing

Phase 10: Advanced AI — PLANNED 📋

  • Fine-tuned variant classification model
  • Graph neural network for variant effect prediction
  • Multi-omics integration
  • Drug response prediction

Recent Updates (June 2026)

AI Provider System

  • Multi-provider configuration with automatic API key detection
  • Support for 7+ providers: Anthropic, OpenAI, Google, DeepSeek, MIMO, OpenRouter
  • Genetics-specific models: DNABERT-2, ESM-3, AlphaFold API, SpliceAI
  • Embedding models for knowledge retrieval
  • Frontend AIModelSelector component with provider/model selection

Dashboard Improvements

  • Professional dark theme (zinc-950 background)
  • Rotating DNA helix animation (Canvas 3D, 45° rotation)
  • Custom SVG pipeline icons matching actual tools (strobealign, samtools, bcftools)
  • GenomicsPipeline component with real-time progress bars
  • Case statistics and demographics panels
  • Services status monitoring

Pipeline Accuracy

  • Updated to reflect actual tools: strobealign → samtools → bcftools mpileup → bcftools call → bcftools filter → ClinVar
  • Removed incorrect references to GATK, minimap2, FastQC, fastp

Wizard Dark Theme

  • WizardSidebar: zinc-900 background, emerald active states
  • WizardHeader: gradient progress bar, step descriptions
  • WizardNavigation: dark buttons with emerald/cyan gradient

Seed Data

Neo4j Knowledge Graph

  • 6 Genes: BRCA1, BRCA2, TP53, EGFR, KRAS, PIK3CA
  • 6 Mutations: pathogenic variants with ClinVar IDs
  • 5 Diseases: hereditary and somatic cancers
  • 3 Drugs: Olaparib, Osimertinib, Sotorasib
  • 4 Pathways: Cell Cycle, Apoptosis, RAS-MAPK, PI3K-AKT

PostgreSQL Catalogs

  • 28 cancer types
  • 30 anatomical sites
  • 12 clinical stages
  • 7 clinical modules (SNV/Indel, CNV, SV, RNA Fusion, MSI/TMB, HRD, Germline)
  • 7 reference species
  • 5 genome sources

Environment Variables

Required

LLM_PROVIDER=deepseek|openai|anthropic|google|mimo|openrouter
DEEPSEEK_API_KEY=
OPENAI_API_KEY=
ANTHROPIC_API_KEY=
GOOGLE_API_KEY=

Optional

MIMO_API_KEY=
OPENROUTER_API_KEY=
VOYAGE_API_KEY=
GENETICS_API_KEY=
LLM_MODEL=  # Override default model