agentic-flow 1.9.0 → 1.9.1

package/agentic-flow/examples/crispr-cas13-pipeline/docs/ARCHITECTURE.md

@@ -1,2964 +0,0 @@
-# CRISPR-Cas13 Pipeline - System Architecture
-
-## Executive Summary
-
-This document describes the complete microservices architecture for the CRISPR-Cas13 bioinformatics pipeline, designed to analyze off-target effects and immune responses from non-human primate gene editing experiments.
-
-**Architecture Principles:**
-- **Scalability**: Horizontal scaling with Kubernetes orchestration
-- **Fault Tolerance**: Circuit breakers, retry policies, graceful degradation
-- **Security**: Zero-trust architecture with OAuth2/JWT authentication
-- **Maintainability**: Clean separation of concerns, comprehensive monitoring
-- **Performance**: Distributed processing with Apache Kafka, Redis caching
-
-## Table of Contents
-
-1. [System Context](#1-system-context)
-2. [Container Architecture](#2-container-architecture)
-3. [Data Layer](#3-data-layer)
-4. [Processing Layer](#4-processing-layer)
-5. [API Layer](#5-api-layer)
-6. [UI Layer](#6-ui-layer)
-7. [Security & Authentication](#7-security--authentication)
-8. [Monitoring & Observability](#8-monitoring--observability)
-9. [Deployment Strategy](#9-deployment-strategy)
-10. [Technology Stack](#10-technology-stack)
-11. [Scalability & Performance](#11-scalability--performance)
-12. [Trade-off Analysis](#12-trade-off-analysis)
-
----
-
-## 1. System Context
-
-### C4 Context Diagram
-
-```
-┌─────────────────────────────────────────────────────────────────────┐
-│                         External Systems                             │
-│  ┌──────────────┐  ┌──────────────┐  ┌──────────────┐             │
-│  │   Research   │  │     NCBI     │  │   Ensembl    │             │
-│  │     Team     │  │   Database   │  │   Genome     │             │
-│  └──────┬───────┘  └──────┬───────┘  └──────┬───────┘             │
-│         │                  │                  │                      │
-└─────────┼──────────────────┼──────────────────┼──────────────────────┘
-          │                  │                  │
-          ▼                  ▼                  ▼
-┌─────────────────────────────────────────────────────────────────────┐
-│                 CRISPR-Cas13 Analysis Pipeline                       │
-│                                                                       │
-│  ┌─────────────────────────────────────────────────────────────┐   │
-│  │                    Web Application                           │   │
-│  │        (Experiment Setup, Monitoring, Visualization)         │   │
-│  └─────────────────────────────────────────────────────────────┘   │
-│                              │                                        │
-│  ┌─────────────────────────────────────────────────────────────┐   │
-│  │                    API Gateway (Axum)                        │   │
-│  │           (Authentication, Rate Limiting, Routing)           │   │
-│  └─────────────────────────────────────────────────────────────┘   │
-│                              │                                        │
-│  ┌───────────────────┬──────┴───────┬──────────────────────────┐   │
-│  │                   │              │                          │   │
-│  ▼                   ▼              ▼                          ▼   │
-│ ┌────────┐     ┌──────────┐  ┌──────────┐            ┌─────────┐  │
-│ │Alignment│     │Off-Target│  │  Diff    │            │  Data   │  │
-│ │ Service │     │  Predict │  │  Expr    │            │ Storage │  │
-│ │(Bowtie2)│     │  Service │  │ (DESeq2) │            │         │  │
-│ └────────┘     └──────────┘  └──────────┘            └─────────┘  │
-│                                                                       │
-└───────────────────────────────────────────────────────────────────────┘
-```
-
-### System Users
-
-1. **Research Scientists**: Design experiments, submit samples, analyze results
-2. **Bioinformaticians**: Configure pipelines, validate results, export data
-3. **System Administrators**: Monitor health, manage resources, configure deployments
-4. **External Systems**: NCBI (reference genomes), Ensembl (annotations), institutional HPC clusters
-
-### Key Requirements
-
-- **Throughput**: Process 50-100 samples/day (200GB-1TB sequencing data)
-- **Latency**: Real-time status updates (<1s), full pipeline completion (2-6 hours)
-- **Availability**: 99.9% uptime during business hours
-- **Security**: HIPAA-compliant data handling, role-based access control
-- **Scalability**: Auto-scale processing nodes 1-50 based on queue depth
-
----
-
-## 2. Container Architecture
-
-### C4 Container Diagram
-
-```mermaid
-graph TB
-    subgraph "Client Layer"
-        WEB[React SPA<br/>TypeScript + Vite]
-        CLI[CLI Tool<br/>Python/Rust]
-    end
-
-    subgraph "API Gateway Layer"
-        NGINX[Nginx Ingress<br/>Load Balancer]
-        API[Axum API Server<br/>Rust + Tower]
-        WS[WebSocket Server<br/>Real-time Updates]
-    end
-
-    subgraph "Processing Layer - Kubernetes"
-        ALIGN[Alignment Service<br/>Bowtie2 + Samtools]
-        OFFTARGET[Off-Target Predictor<br/>Custom ML Model]
-        DIFFEXPR[Differential Expression<br/>DESeq2/EdgeR]
-        IMMUNE[Immune Response Analyzer<br/>ImmuneSigDB]
-    end
-
-    subgraph "Message Queue"
-        KAFKA[Apache Kafka<br/>Job Orchestration]
-    end
-
-    subgraph "Data Layer"
-        POSTGRES[(PostgreSQL<br/>Metadata + Results)]
-        MONGO[(MongoDB<br/>Genomic Annotations)]
-        REDIS[(Redis<br/>Cache + Sessions)]
-        MINIO[(MinIO S3<br/>FASTQ + BAM Files)]
-    end
-
-    subgraph "Monitoring Layer"
-        PROM[Prometheus<br/>Metrics Collection]
-        GRAFANA[Grafana<br/>Dashboards]
-        JAEGER[Jaeger<br/>Distributed Tracing]
-    end
-
-    WEB --> NGINX
-    CLI --> NGINX
-    NGINX --> API
-    NGINX --> WS
-
-    API --> KAFKA
-    API --> POSTGRES
-    API --> REDIS
-
-    KAFKA --> ALIGN
-    KAFKA --> OFFTARGET
-    KAFKA --> DIFFEXPR
-    KAFKA --> IMMUNE
-
-    ALIGN --> MINIO
-    ALIGN --> POSTGRES
-    OFFTARGET --> MONGO
-    DIFFEXPR --> POSTGRES
-    IMMUNE --> MONGO
-
-    API --> PROM
-    ALIGN --> PROM
-    OFFTARGET --> PROM
-    DIFFEXPR --> PROM
-
-    PROM --> GRAFANA
-    API --> JAEGER
-    ALIGN --> JAEGER
-```
-
-### Container Communication Patterns
-
-| Source → Target | Protocol | Purpose | Security |
-|----------------|----------|---------|----------|
-| Web → API Gateway | HTTPS (TLS 1.3) | REST API calls | JWT Bearer Token |
-| API Gateway → Services | HTTP/2 + gRPC | Service mesh | mTLS |
-| Services → Kafka | TCP (SASL/SSL) | Job submission | API Key |
-| Services → Databases | TCP (TLS) | Data persistence | Role-based credentials |
-| Services → MinIO | HTTPS | Object storage | IAM access keys |
-| Prometheus → Services | HTTP | Metrics scraping | Service account |
-
----
-
-## 3. Data Layer
-
-### 3.1 PostgreSQL - Relational Data
-
-**Purpose**: Store structured metadata, experimental designs, analysis results, user accounts
-
-**Schema Design**:
-
-```sql
--- Database: crispr_cas13_pipeline
-
--- Users and Authentication
-CREATE TABLE users (
-    id UUID PRIMARY KEY DEFAULT gen_random_uuid(),
-    email VARCHAR(255) UNIQUE NOT NULL,
-    full_name VARCHAR(255) NOT NULL,
-    password_hash VARCHAR(255) NOT NULL,
-    role VARCHAR(50) NOT NULL DEFAULT 'researcher', -- researcher, bioinformatician, admin
-    institution VARCHAR(255),
-    created_at TIMESTAMPTZ DEFAULT NOW(),
-    updated_at TIMESTAMPTZ DEFAULT NOW(),
-
-    INDEX idx_email (email),
-    INDEX idx_role (role)
-);
-
--- Experiments
-CREATE TABLE experiments (
-    id UUID PRIMARY KEY DEFAULT gen_random_uuid(),
-    user_id UUID NOT NULL REFERENCES users(id) ON DELETE CASCADE,
-    name VARCHAR(255) NOT NULL,
-    description TEXT,
-    organism VARCHAR(100) DEFAULT 'Macaca mulatta', -- rhesus macaque
-    target_gene VARCHAR(100),
-    cas13_variant VARCHAR(50), -- Cas13a, Cas13b, Cas13d
-    guide_rna_sequence TEXT NOT NULL,
-    status VARCHAR(50) DEFAULT 'pending', -- pending, processing, completed, failed
-    created_at TIMESTAMPTZ DEFAULT NOW(),
-    completed_at TIMESTAMPTZ,
-
-    INDEX idx_user_id (user_id),
-    INDEX idx_status (status),
-    INDEX idx_created_at (created_at)
-);
-
--- Samples
-CREATE TABLE samples (
-    id UUID PRIMARY KEY DEFAULT gen_random_uuid(),
-    experiment_id UUID NOT NULL REFERENCES experiments(id) ON DELETE CASCADE,
-    sample_name VARCHAR(255) NOT NULL,
-    sample_type VARCHAR(50), -- control, treatment, timepoint_0h, timepoint_24h
-    fastq_r1_path TEXT NOT NULL,
-    fastq_r2_path TEXT,
-    sequencing_platform VARCHAR(100), -- Illumina NovaSeq 6000
-    read_count BIGINT,
-    quality_score FLOAT,
-    created_at TIMESTAMPTZ DEFAULT NOW(),
-
-    INDEX idx_experiment_id (experiment_id),
-    INDEX idx_sample_type (sample_type),
-    UNIQUE (experiment_id, sample_name)
-);
-
--- Analysis Jobs
-CREATE TABLE analysis_jobs (
-    id UUID PRIMARY KEY DEFAULT gen_random_uuid(),
-    experiment_id UUID NOT NULL REFERENCES experiments(id) ON DELETE CASCADE,
-    job_type VARCHAR(50) NOT NULL, -- alignment, off_target, diff_expr, immune_response
-    status VARCHAR(50) DEFAULT 'queued', -- queued, running, completed, failed
-    priority INT DEFAULT 5, -- 1-10
-    worker_pod VARCHAR(255), -- Kubernetes pod name
-    started_at TIMESTAMPTZ,
-    completed_at TIMESTAMPTZ,
-    error_message TEXT,
-    metrics JSONB, -- execution time, memory usage, etc.
-
-    INDEX idx_experiment_id (experiment_id),
-    INDEX idx_status (status),
-    INDEX idx_priority (priority),
-    INDEX idx_created_at (created_at)
-);
-
--- Off-Target Predictions
-CREATE TABLE off_targets (
-    id UUID PRIMARY KEY DEFAULT gen_random_uuid(),
-    job_id UUID NOT NULL REFERENCES analysis_jobs(id) ON DELETE CASCADE,
-    chromosome VARCHAR(50) NOT NULL,
-    position BIGINT NOT NULL,
-    strand CHAR(1) CHECK (strand IN ('+', '-')),
-    target_sequence TEXT NOT NULL,
-    mismatch_count INT NOT NULL,
-    cfd_score FLOAT, -- Cutting Frequency Determination score
-    mit_score FLOAT, -- MIT specificity score
-    gene_symbol VARCHAR(100),
-    annotation TEXT,
-
-    INDEX idx_job_id (job_id),
-    INDEX idx_chromosome (chromosome),
-    INDEX idx_mismatch_count (mismatch_count),
-    INDEX idx_cfd_score (cfd_score)
-);
-
--- Differential Expression Results
-CREATE TABLE differential_expression (
-    id UUID PRIMARY KEY DEFAULT gen_random_uuid(),
-    job_id UUID NOT NULL REFERENCES analysis_jobs(id) ON DELETE CASCADE,
-    gene_id VARCHAR(100) NOT NULL, -- Ensembl ID
-    gene_symbol VARCHAR(100),
-    base_mean FLOAT,
-    log2_fold_change FLOAT NOT NULL,
-    lfcse FLOAT, -- log2 fold change standard error
-    pvalue FLOAT NOT NULL,
-    padj FLOAT, -- adjusted p-value (Benjamini-Hochberg)
-    significant BOOLEAN GENERATED ALWAYS AS (padj < 0.05) STORED,
-
-    INDEX idx_job_id (job_id),
-    INDEX idx_gene_symbol (gene_symbol),
-    INDEX idx_padj (padj),
-    INDEX idx_significant (significant)
-);
-
--- Immune Response Signatures
-CREATE TABLE immune_signatures (
-    id UUID PRIMARY KEY DEFAULT gen_random_uuid(),
-    job_id UUID NOT NULL REFERENCES analysis_jobs(id) ON DELETE CASCADE,
-    signature_name VARCHAR(255) NOT NULL, -- e.g., "Interferon Response"
-    signature_source VARCHAR(100), -- ImmuneSigDB, MSigDB
-    enrichment_score FLOAT NOT NULL,
-    normalized_enrichment_score FLOAT,
-    pvalue FLOAT NOT NULL,
-    fdr FLOAT, -- false discovery rate
-    leading_edge_genes TEXT[], -- array of gene symbols
-
-    INDEX idx_job_id (job_id),
-    INDEX idx_signature_name (signature_name),
-    INDEX idx_fdr (fdr)
-);
-
--- Audit Log
-CREATE TABLE audit_log (
-    id BIGSERIAL PRIMARY KEY,
-    user_id UUID REFERENCES users(id) ON DELETE SET NULL,
-    action VARCHAR(100) NOT NULL, -- login, create_experiment, submit_job, download_results
-    resource_type VARCHAR(100),
-    resource_id UUID,
-    ip_address INET,
-    user_agent TEXT,
-    metadata JSONB,
-    created_at TIMESTAMPTZ DEFAULT NOW(),
-
-    INDEX idx_user_id (user_id),
-    INDEX idx_action (action),
-    INDEX idx_created_at (created_at)
-) PARTITION BY RANGE (created_at);
-
--- Create monthly partitions for audit log
-CREATE TABLE audit_log_2025_01 PARTITION OF audit_log
-    FOR VALUES FROM ('2025-01-01') TO ('2025-02-01');
-```
-
-**Connection Pooling** (via `sqlx` in Rust):
-```toml
-[database]
-max_connections = 100
-min_connections = 10
-connection_timeout = 30s
-idle_timeout = 10m
-max_lifetime = 30m
-```
-
-**Migration Strategy**:
-- Use `sqlx-cli` for schema migrations
-- Versioned migrations in `migrations/` directory
-- Blue-green deployment for zero-downtime updates
-- Automated rollback on migration failure
-
----
-
-### 3.2 MongoDB - Genomic Annotations
-
-**Purpose**: Store flexible, document-based genomic annotations, gene ontology terms, and analysis metadata
-
-**Collections**:
-
-1. **genes** - Gene annotations from Ensembl
-2. **transcripts** - Transcript variants
-3. **immune_signatures** - ImmuneSigDB reference data
-4. **go_terms** - Gene Ontology annotations
-5. **analysis_cache** - Cached intermediate results
-
-**Example Document** (genes collection):
-
-```json
-{
-  "_id": ObjectId("..."),
-  "ensembl_id": "ENSMMUG00000012345",
-  "gene_symbol": "IFNB1",
-  "description": "interferon beta 1",
-  "chromosome": "chr9",
-  "start": 21077035,
-  "end": 21078018,
-  "strand": "+",
-  "biotype": "protein_coding",
-  "species": "Macaca_mulatta",
-  "transcripts": [
-    {
-      "transcript_id": "ENSMMUT00000012345",
-      "biotype": "protein_coding",
-      "length": 1783,
-      "exons": [
-        {"start": 21077035, "end": 21077248, "number": 1},
-        {"start": 21077790, "end": 21078018, "number": 2}
-      ]
-    }
-  ],
-  "go_terms": [
-    {"id": "GO:0051607", "term": "defense response to virus", "evidence": "IDA"},
-    {"id": "GO:0045071", "term": "negative regulation of viral genome replication", "evidence": "IMP"}
-  ],
-  "orthologs": {
-    "human": "ENSG00000171855",
-    "mouse": "ENSMUSG00000048806"
-  },
-  "indexed_at": ISODate("2025-01-15T10:30:00Z")
-}
-```
-
-**Sharding Strategy**:
-- **Shard Key**: `chromosome` (distributes data evenly across 24 shards: chr1-chr22, chrX, chrY)
-- **Config**: 3 replica sets × 3 shards = 9 nodes minimum
-- **Indexes**:
-  - `{gene_symbol: 1}` - Fast gene lookups
-  - `{chromosome: 1, start: 1, end: 1}` - Range queries for genomic regions
-  - `{go_terms.id: 1}` - Gene Ontology searches
-
----
-
-### 3.3 Redis - Caching & Job Queues
-
-**Purpose**: High-performance caching, session management, real-time job status
-
-**Use Cases**:
-
-1. **Session Storage** (TTL: 24 hours)
-```redis
-SET session:a1b2c3d4 "{\"user_id\": \"uuid\", \"role\": \"researcher\"}" EX 86400
-```
-
-2. **Job Status Cache** (TTL: 1 hour after completion)
-```redis
-HSET job:uuid status "running"
-HSET job:uuid progress "45.2"
-HSET job:uuid worker_pod "align-worker-7f8d9"
-EXPIRE job:uuid 3600
-```
-
-3. **API Rate Limiting** (sliding window)
-```redis
-ZADD rate_limit:user:uuid timestamp1 timestamp2 timestamp3
-ZREMRANGEBYSCORE rate_limit:user:uuid 0 (timestamp-3600)
-ZCARD rate_limit:user:uuid  # count requests in last hour
-```
-
-4. **Cached Query Results** (TTL: 10 minutes)
-```redis
-SET cache:experiments:user:uuid "[{...}, {...}]" EX 600
-```
-
-**Cluster Configuration**:
-- **Mode**: Redis Cluster (6 nodes: 3 masters + 3 replicas)
-- **Persistence**: AOF (Append-Only File) + RDB snapshots every 5 minutes
-- **Eviction Policy**: `allkeys-lru` (least recently used)
-- **Max Memory**: 16GB per node
-
----
-
-### 3.4 MinIO (S3-Compatible Object Storage)
-
-**Purpose**: Store large sequencing files (FASTQ, BAM, VCF) and analysis artifacts
-
-**Bucket Structure**:
-
-```
-crispr-cas13/
-├── raw-data/
-│   ├── {experiment_id}/
-│   │   ├── {sample_id}_R1.fastq.gz
-│   │   └── {sample_id}_R2.fastq.gz
-├── aligned/
-│   ├── {experiment_id}/
-│   │   ├── {sample_id}.bam
-│   │   └── {sample_id}.bam.bai
-├── results/
-│   ├── {job_id}/
-│   │   ├── off_targets.csv
-│   │   ├── diff_expr.csv
-│   │   └── immune_signatures.json
-└── reports/
-    └── {experiment_id}/
-        ├── qc_report.html
-        └── final_report.pdf
-```
-
-**Lifecycle Policies**:
-- **raw-data**: Retain for 180 days, then transition to Glacier
-- **aligned**: Retain for 90 days, then delete (can regenerate)
-- **results**: Retain indefinitely
-- **reports**: Retain for 365 days
-
-**Data Integrity**:
-- MD5 checksums for all uploads
-- Versioning enabled on all buckets
-- Replication to secondary datacenter (disaster recovery)
-
-**Access Control**:
-- IAM policies per service (principle of least privilege)
-- Pre-signed URLs for temporary file access (TTL: 1 hour)
-- Server-side encryption (SSE-S3) for all objects
-
----
-
-## 4. Processing Layer
-
-### 4.1 Kubernetes Cluster Architecture
-
-**Cluster Specifications**:
-- **Nodes**: 10-50 worker nodes (auto-scaling)
-  - **CPU-optimized**: 16 vCPU, 32GB RAM (alignment, off-target prediction)
-  - **Memory-optimized**: 8 vCPU, 64GB RAM (differential expression, R/Bioconductor)
-- **Namespaces**:
-  - `crispr-production` - Production workloads
-  - `crispr-staging` - Pre-production testing
-  - `crispr-dev` - Development experiments
-  - `monitoring` - Prometheus, Grafana, Jaeger
-  - `kafka` - Message queue infrastructure
-
-**Node Affinity Labels**:
-```yaml
-node-role: compute-intensive  # for alignment, off-target prediction
-node-role: memory-intensive    # for DESeq2, R workloads
-node-role: gpu-enabled         # future ML model inference
-```
-
----
-
-### 4.2 Microservice Containers
-
-#### 4.2.1 Alignment Service (Bowtie2)
-
-**Responsibilities**:
-- Align FASTQ reads to reference genome
-- Quality control (FastQC, MultiQC)
-- BAM sorting and indexing (Samtools)
-
-**Technology Stack**:
-- **Base Image**: `ubuntu:22.04` with Bioconda
-- **Tools**: Bowtie2 2.5.1, Samtools 1.17, FastQC 0.12.1
-- **Language**: Python 3.11 (orchestration scripts)
-
-**Resource Limits**:
-```yaml
-resources:
-  requests:
-    cpu: "4"
-    memory: "16Gi"
-  limits:
-    cpu: "8"
-    memory: "32Gi"
-```
-
-**Dockerfile** (see `docker/alignment-service/Dockerfile`):
-```dockerfile
-FROM ubuntu:22.04
-
-# Install Bioconda and tools
-RUN apt-get update && apt-get install -y \
-    wget curl git build-essential python3.11 python3-pip
-
-# Install Miniconda
-RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
-    bash Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda && \
-    rm Miniconda3-latest-Linux-x86_64.sh
-
-ENV PATH="/opt/conda/bin:$PATH"
-
-# Install bioinformatics tools
-RUN conda install -c bioconda bowtie2=2.5.1 samtools=1.17 fastqc=0.12.1 -y
-
-# Install Python dependencies
-COPY requirements.txt /app/
-RUN pip3 install -r /app/requirements.txt
-
-COPY alignment_worker.py /app/
-WORKDIR /app
-
-CMD ["python3", "alignment_worker.py"]
-```
-
-**Python Worker** (alignment_worker.py):
-```python
-import os
-import subprocess
-from kafka import KafkaConsumer, KafkaProducer
-import boto3
-import logging
-
-logging.basicConfig(level=logging.INFO)
-logger = logging.getLogger(__name__)
-
-def align_sample(sample_id, fastq_r1_s3, fastq_r2_s3, reference_genome):
-    """
-    Download FASTQ from MinIO, align with Bowtie2, upload BAM to MinIO
-    """
-    s3 = boto3.client('s3', endpoint_url=os.getenv('MINIO_ENDPOINT'))
-
-    # Download FASTQ files
-    logger.info(f"Downloading {fastq_r1_s3} and {fastq_r2_s3}")
-    s3.download_file('crispr-cas13', fastq_r1_s3, f'/tmp/{sample_id}_R1.fastq.gz')
-    s3.download_file('crispr-cas13', fastq_r2_s3, f'/tmp/{sample_id}_R2.fastq.gz')
-
-    # Run Bowtie2 alignment
-    logger.info(f"Aligning sample {sample_id}")
-    cmd = [
-        'bowtie2',
-        '-x', reference_genome,
-        '-1', f'/tmp/{sample_id}_R1.fastq.gz',
-        '-2', f'/tmp/{sample_id}_R2.fastq.gz',
-        '-p', '8',  # threads
-        '--very-sensitive',
-        '-S', f'/tmp/{sample_id}.sam'
-    ]
-    subprocess.run(cmd, check=True)
-
-    # Convert SAM to BAM, sort, and index
-    logger.info("Converting SAM to BAM")
-    subprocess.run(['samtools', 'view', '-bS', f'/tmp/{sample_id}.sam', '-o', f'/tmp/{sample_id}.bam'], check=True)
-    subprocess.run(['samtools', 'sort', f'/tmp/{sample_id}.bam', '-o', f'/tmp/{sample_id}.sorted.bam'], check=True)
-    subprocess.run(['samtools', 'index', f'/tmp/{sample_id}.sorted.bam'], check=True)
-
-    # Upload BAM to MinIO
-    logger.info("Uploading BAM to MinIO")
-    s3.upload_file(f'/tmp/{sample_id}.sorted.bam', 'crispr-cas13', f'aligned/{sample_id}/{sample_id}.bam')
-    s3.upload_file(f'/tmp/{sample_id}.sorted.bam.bai', 'crispr-cas13', f'aligned/{sample_id}/{sample_id}.bam.bai')
-
-    # Cleanup
-    os.remove(f'/tmp/{sample_id}_R1.fastq.gz')
-    os.remove(f'/tmp/{sample_id}_R2.fastq.gz')
-    os.remove(f'/tmp/{sample_id}.sam')
-    os.remove(f'/tmp/{sample_id}.bam')
-
-    return f's3://crispr-cas13/aligned/{sample_id}/{sample_id}.bam'
-
-def main():
-    consumer = KafkaConsumer(
-        'jobs.alignment',
-        bootstrap_servers=os.getenv('KAFKA_BROKERS'),
-        group_id='alignment-workers'
-    )
-
-    producer = KafkaProducer(bootstrap_servers=os.getenv('KAFKA_BROKERS'))
-
-    for message in consumer:
-        job = json.loads(message.value)
-        logger.info(f"Processing alignment job {job['job_id']}")
-
-        try:
-            bam_path = align_sample(
-                job['sample_id'],
-                job['fastq_r1_s3'],
-                job['fastq_r2_s3'],
-                job['reference_genome']
-            )
-
-            # Send completion message
-            producer.send('jobs.completed', json.dumps({
-                'job_id': job['job_id'],
-                'status': 'completed',
-                'bam_path': bam_path
-            }).encode())
-
-        except Exception as e:
-            logger.error(f"Alignment failed: {e}")
-            producer.send('jobs.failed', json.dumps({
-                'job_id': job['job_id'],
-                'error': str(e)
-            }).encode())
-
-if __name__ == '__main__':
-    main()
-```
-
----
-
-#### 4.2.2 Off-Target Prediction Service
-
-**Responsibilities**:
-- Extract guide RNA sequences from BAM files
-- Predict off-target sites using custom ML model
-- Score off-targets with CFD and MIT algorithms
-
-**Technology Stack**:
-- **Base Image**: `python:3.11-slim`
-- **ML Framework**: PyTorch 2.1 (pre-trained transformer model)
-- **Libraries**: Biopython, NumPy, Pandas
-
-**Resource Limits**:
-```yaml
-resources:
-  requests:
-    cpu: "2"
-    memory: "8Gi"
-  limits:
-    cpu: "4"
-    memory: "16Gi"
-```
-
-**Dockerfile** (see `docker/off-target-service/Dockerfile`):
-```dockerfile
-FROM python:3.11-slim
-
-RUN apt-get update && apt-get install -y \
-    build-essential libssl-dev
-
-COPY requirements.txt /app/
-RUN pip install --no-cache-dir -r /app/requirements.txt
-
-COPY off_target_worker.py /app/
-COPY models/ /app/models/
-
-WORKDIR /app
-CMD ["python", "off_target_worker.py"]
-```
-
-**Python Worker** (off_target_worker.py):
-```python
-import torch
-from transformers import AutoModelForSequenceClassification, AutoTokenizer
-import pysam
-from kafka import KafkaConsumer, KafkaProducer
-import logging
-
-logger = logging.getLogger(__name__)
-
-class OffTargetPredictor:
-    def __init__(self, model_path='/app/models/cas13_off_target.pt'):
-        self.device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')
-        self.model = AutoModelForSequenceClassification.from_pretrained(model_path).to(self.device)
-        self.tokenizer = AutoTokenizer.from_pretrained(model_path)
-
-    def predict_off_targets(self, guide_rna, bam_path, genome_fasta):
-        """
-        Scan genome for potential off-target sites
-        """
-        off_targets = []
-
-        # Open BAM file and extract aligned reads
-        bamfile = pysam.AlignmentFile(bam_path, "rb")
-
-        # Scan for sequences with mismatches to guide RNA
-        for read in bamfile.fetch():
-            if read.is_unmapped:
-                continue
-
-            seq = read.query_sequence
-            mismatches = self.count_mismatches(guide_rna, seq)
-
-            if 1 <= mismatches <= 4:  # Potential off-target (1-4 mismatches)
-                # Score with ML model
-                cfd_score = self.calculate_cfd_score(guide_rna, seq)
-                mit_score = self.calculate_mit_score(guide_rna, seq)
-
-                off_targets.append({
-                    'chromosome': bamfile.get_reference_name(read.reference_id),
-                    'position': read.reference_start,
-                    'strand': '+' if not read.is_reverse else '-',
-                    'target_sequence': seq,
-                    'mismatch_count': mismatches,
-                    'cfd_score': cfd_score,
-                    'mit_score': mit_score
-                })
-
-        bamfile.close()
-        return off_targets
-
-    def count_mismatches(self, seq1, seq2):
-        # Implementation details...
-        pass
-
-    def calculate_cfd_score(self, guide, target):
-        # Cutting Frequency Determination score
-        # Implementation based on Doench et al. 2016
-        pass
-
-    def calculate_mit_score(self, guide, target):
-        # MIT specificity score
-        # Implementation based on Hsu et al. 2013
-        pass
-
-def main():
-    predictor = OffTargetPredictor()
-
-    consumer = KafkaConsumer(
-        'jobs.off_target',
-        bootstrap_servers=os.getenv('KAFKA_BROKERS'),
-        group_id='off-target-workers'
-    )
-
-    producer = KafkaProducer(bootstrap_servers=os.getenv('KAFKA_BROKERS'))
-
-    for message in consumer:
-        job = json.loads(message.value)
-        logger.info(f"Processing off-target job {job['job_id']}")
-
-        try:
-            off_targets = predictor.predict_off_targets(
-                job['guide_rna'],
-                job['bam_path'],
-                job['genome_fasta']
-            )
-
-            # Store in MongoDB and PostgreSQL
-            # ... (implementation)
-
-            producer.send('jobs.completed', json.dumps({
-                'job_id': job['job_id'],
-                'off_target_count': len(off_targets)
-            }).encode())
-
-        except Exception as e:
-            logger.error(f"Off-target prediction failed: {e}")
-            producer.send('jobs.failed', json.dumps({
-                'job_id': job['job_id'],
-                'error': str(e)
-            }).encode())
-
-if __name__ == '__main__':
-    main()
-```
-
----
-
-#### 4.2.3 Differential Expression Service (DESeq2/EdgeR)
-
-**Responsibilities**:
-- Count gene expression from BAM files (featureCounts)
-- Perform differential expression analysis (DESeq2 or EdgeR)
-- Generate visualizations (MA plots, volcano plots, heatmaps)
-
-**Technology Stack**:
-- **Base Image**: `bioconductor/bioconductor_docker:RELEASE_3_18`
-- **R Packages**: DESeq2 1.42, edgeR 3.44, ggplot2 3.4
-- **Language**: R 4.3 with Rserve for API integration
-
-**Resource Limits**:
-```yaml
-resources:
-  requests:
-    cpu: "4"
-    memory: "32Gi"  # R requires significant memory
-  limits:
-    cpu: "8"
-    memory: "64Gi"
-```
-
-**Dockerfile** (see `docker/diff-expr-service/Dockerfile`):
-```dockerfile
-FROM bioconductor/bioconductor_docker:RELEASE_3_18
-
-RUN R -e "BiocManager::install(c('DESeq2', 'edgeR', 'Rsubread', 'ggplot2', 'pheatmap', 'EnhancedVolcano'))"
-
-COPY diff_expr_worker.R /app/
-WORKDIR /app
-
-CMD ["Rscript", "diff_expr_worker.R"]
-```
-
-**R Worker** (diff_expr_worker.R):
-```r
-library(DESeq2)
-library(edgeR)
-library(Rsubread)
-library(ggplot2)
-
-# Kafka consumer setup (using rkafka package)
-library(rkafka)
-
-consumer <- rkafka.createConsumer(
-  list("metadata.broker.list" = Sys.getenv("KAFKA_BROKERS"))
-)
-
-while (TRUE) {
-  message <- rkafka.consume(consumer, "jobs.diff_expr")
-
-  if (!is.null(message)) {
-    job <- jsonlite::fromJSON(message$payload)
-
-    tryCatch({
-      # Step 1: Count reads with featureCounts
-      bam_files <- job$bam_files
-      gtf_file <- job$gtf_annotation
-
-      counts <- featureCounts(
-        files = bam_files,
-        annot.ext = gtf_file,
-        isGTFAnnotationFile = TRUE,
-        GTF.featureType = "exon",
-        GTF.attrType = "gene_id",
-        nthreads = 8
-      )
-
-      # Step 2: Create DESeqDataSet
-      col_data <- data.frame(
-        condition = job$conditions,  # e.g., c("control", "control", "treatment", "treatment")
-        row.names = job$sample_names
-      )
-
-      dds <- DESeqDataSetFromMatrix(
-        countData = counts$counts,
-        colData = col_data,
-        design = ~ condition
-      )
-
-      # Step 3: Run differential expression analysis
-      dds <- DESeq(dds)
-      res <- results(dds, contrast = c("condition", "treatment", "control"))
-
-      # Step 4: Extract significant genes
-      res_df <- as.data.frame(res)
-      res_df$gene_id <- rownames(res_df)
-      sig_genes <- res_df[res_df$padj < 0.05 & !is.na(res_df$padj), ]
-
-      # Step 5: Generate plots
-      pdf(paste0("/tmp/", job$job_id, "_plots.pdf"))
-
-      # MA plot
-      plotMA(res, main = "MA Plot")
-
-      # Volcano plot
-      EnhancedVolcano::EnhancedVolcano(
-        res_df,
-        lab = res_df$gene_id,
-        x = 'log2FoldChange',
-        y = 'padj'
-      )
-
-      # Heatmap of top 50 genes
-      top_genes <- head(sig_genes[order(sig_genes$padj), ], 50)
-      pheatmap::pheatmap(
-        assay(dds)[rownames(top_genes), ],
-        cluster_rows = TRUE,
-        cluster_cols = TRUE,
-        show_rownames = TRUE
-      )
-
-      dev.off()
-
-      # Step 6: Upload results to PostgreSQL and MinIO
-      # ... (implementation)
-
-      # Send completion message
-      rkafka.produce(
-        producer,
-        "jobs.completed",
-        jsonlite::toJSON(list(
-          job_id = job$job_id,
-          significant_genes = nrow(sig_genes)
-        ))
-      )
-
-    }, error = function(e) {
-      rkafka.produce(
-        producer,
-        "jobs.failed",
-        jsonlite::toJSON(list(
-          job_id = job$job_id,
-          error = as.character(e)
-        ))
-      )
-    })
-  }
-
-  Sys.sleep(5)  # Poll every 5 seconds
-}
-```
-
----
-
-### 4.3 Apache Kafka - Message Queue
-
-**Purpose**: Decouple API layer from processing layer, enable fault-tolerant job orchestration
-
-**Topics**:
-
-| Topic | Partitions | Replication | Purpose |
-|-------|------------|-------------|---------|
-| `jobs.submitted` | 10 | 3 | New analysis jobs from API |
-| `jobs.alignment` | 10 | 3 | Alignment tasks |
-| `jobs.off_target` | 10 | 3 | Off-target prediction tasks |
-| `jobs.diff_expr` | 5 | 3 | Differential expression tasks |
-| `jobs.immune` | 5 | 3 | Immune response analysis tasks |
-| `jobs.completed` | 10 | 3 | Successfully completed jobs |
-| `jobs.failed` | 5 | 3 | Failed jobs for retry/alerting |
-| `jobs.progress` | 10 | 3 | Real-time progress updates |
-
-**Producer Configuration** (Rust API):
-```rust
-use rdkafka::producer::{FutureProducer, FutureRecord};
-use rdkafka::config::ClientConfig;
-
-let producer: FutureProducer = ClientConfig::new()
-    .set("bootstrap.servers", "kafka-broker-1:9092,kafka-broker-2:9092,kafka-broker-3:9092")
-    .set("message.timeout.ms", "5000")
-    .set("acks", "all")  // Wait for all in-sync replicas
-    .set("retries", "3")
-    .create()
-    .expect("Producer creation error");
-
-// Produce message
-let payload = serde_json::to_string(&job)?;
-producer
-    .send(
-        FutureRecord::to("jobs.alignment")
-            .payload(&payload)
-            .key(&job.job_id),
-        Duration::from_secs(0),
-    )
-    .await?;
-```
-
-**Consumer Configuration** (Python workers):
-```python
-from kafka import KafkaConsumer
-
-consumer = KafkaConsumer(
-    'jobs.alignment',
-    bootstrap_servers=['kafka-broker-1:9092', 'kafka-broker-2:9092', 'kafka-broker-3:9092'],
-    group_id='alignment-workers',
-    auto_offset_reset='earliest',
-    enable_auto_commit=True,
-    max_poll_records=10,
-    session_timeout_ms=30000,
-    heartbeat_interval_ms=10000
-)
-```
-
-**Monitoring**:
-- Consumer lag alerts (Prometheus + Grafana)
-- Throughput metrics (messages/sec per topic)
-- Partition rebalancing events
-
----
-
-### 4.4 Horizontal Scaling Strategy
-
-**Auto-Scaling Policies** (Kubernetes HPA):
-
-```yaml
-apiVersion: autoscaling/v2
-kind: HorizontalPodAutoscaler
-metadata:
-  name: alignment-service-hpa
-  namespace: crispr-production
-spec:
-  scaleTargetRef:
-    apiVersion: apps/v1
-    kind: Deployment
-    name: alignment-service
-  minReplicas: 2
-  maxReplicas: 20
-  metrics:
-  - type: Resource
-    resource:
-      name: cpu
-      target:
-        type: Utilization
-        averageUtilization: 70
-  - type: Resource
-    resource:
-      name: memory
-      target:
-        type: Utilization
-        averageUtilization: 80
-  - type: External
-    external:
-      metric:
-        name: kafka_consumer_lag
-        selector:
-          matchLabels:
-            topic: jobs.alignment
-      target:
-        type: Value
-        value: "100"  # Scale up if lag > 100 messages
-  behavior:
-    scaleUp:
-      stabilizationWindowSeconds: 60
-      policies:
-      - type: Percent
-        value: 100  # Double pods
-        periodSeconds: 60
-    scaleDown:
-      stabilizationWindowSeconds: 300
-      policies:
-      - type: Percent
-        value: 50  # Reduce by half
-        periodSeconds: 60
-```
-
----
-
-## 5. API Layer
-
-### 5.1 Axum (Rust) RESTful API
-
-**Why Rust + Axum?**
-- **Performance**: ~10x faster than Node.js for I/O-bound operations
-- **Memory Safety**: No null pointers, data races, or buffer overflows
-- **Concurrency**: Tokio async runtime for efficient request handling
-- **Type Safety**: Compile-time guarantees for API contracts
-
-**Project Structure**:
-```
-api/
-├── src/
-│   ├── main.rs              # Entry point, server setup
-│   ├── routes/
-│   │   ├── mod.rs
-│   │   ├── auth.rs          # POST /api/v1/auth/login, /logout
-│   │   ├── experiments.rs   # CRUD for experiments
-│   │   ├── samples.rs       # Upload FASTQ files
-│   │   ├── jobs.rs          # Submit and monitor jobs
-│   │   └── results.rs       # Query analysis results
-│   ├── models/
-│   │   ├── mod.rs
-│   │   ├── user.rs
-│   │   ├── experiment.rs
-│   │   ├── sample.rs
-│   │   └── job.rs
-│   ├── middleware/
-│   │   ├── auth.rs          # JWT validation
-│   │   ├── rate_limit.rs    # Redis-backed rate limiting
-│   │   └── logging.rs       # Structured logging
-│   ├── services/
-│   │   ├── database.rs      # PostgreSQL connection pool
-│   │   ├── kafka.rs         # Kafka producer
-│   │   ├── storage.rs       # MinIO S3 client
-│   │   └── cache.rs         # Redis client
-│   └── error.rs             # Custom error types
-├── Cargo.toml
-└── Dockerfile
-```
-
-**Main Server** (src/main.rs):
-```rust
-use axum::{
-    Router,
-    routing::{get, post},
-    middleware,
-    Extension,
-};
-use tower::ServiceBuilder;
-use tower_http::trace::TraceLayer;
-use sqlx::PgPool;
-use std::net::SocketAddr;
-
-mod routes;
-mod models;
-mod middleware as mw;
-mod services;
-mod error;
-
-#[tokio::main]
-async fn main() {
-    // Initialize tracing
-    tracing_subscriber::fmt::init();
-
-    // Database connection pool
-    let db_pool = PgPool::connect(&std::env::var("DATABASE_URL").unwrap())
-        .await
-        .expect("Failed to connect to database");
-
-    // Redis client
-    let redis_client = redis::Client::open(std::env::var("REDIS_URL").unwrap())
-        .expect("Failed to connect to Redis");
-
-    // Kafka producer
-    let kafka_producer = services::kafka::create_producer();
-
-    // Build API router
-    let app = Router::new()
-        // Health check
-        .route("/health", get(health_check))
-
-        // API v1 routes
-        .nest("/api/v1", api_v1_routes())
-
-        // Middleware layers
-        .layer(
-            ServiceBuilder::new()
-                .layer(TraceLayer::new_for_http())
-                .layer(middleware::from_fn(mw::logging::log_requests))
-                .layer(Extension(db_pool))
-                .layer(Extension(redis_client))
-                .layer(Extension(kafka_producer))
-        );
-
-    // Start server
-    let addr = SocketAddr::from(([0, 0, 0, 0], 3000));
-    tracing::info!("Listening on {}", addr);
-
-    axum::Server::bind(&addr)
-        .serve(app.into_make_service())
-        .await
-        .unwrap();
-}
-
-fn api_v1_routes() -> Router {
-    Router::new()
-        .nest("/auth", routes::auth::routes())
-        .nest("/experiments", routes::experiments::routes())
-        .nest("/samples", routes::samples::routes())
-        .nest("/jobs", routes::jobs::routes())
-        .nest("/results", routes::results::routes())
-}
-
-async fn health_check() -> &'static str {
-    "OK"
-}
-```
-
-**Authentication Route** (src/routes/auth.rs):
-```rust
-use axum::{Router, Json, routing::post, Extension};
-use serde::{Deserialize, Serialize};
-use sqlx::PgPool;
-use jsonwebtoken::{encode, EncodingKey, Header};
-use bcrypt::verify;
-
-pub fn routes() -> Router {
-    Router::new()
-        .route("/login", post(login))
-        .route("/refresh", post(refresh_token))
-}
-
-#[derive(Deserialize)]
-struct LoginRequest {
-    email: String,
-    password: String,
-}
-
-#[derive(Serialize)]
-struct LoginResponse {
-    token: String,
-    refresh_token: String,
-    user: UserInfo,
-}
-
-#[derive(Serialize)]
-struct UserInfo {
-    id: String,
-    email: String,
-    full_name: String,
-    role: String,
-}
-
-async fn login(
-    Extension(pool): Extension<PgPool>,
-    Json(payload): Json<LoginRequest>,
-) -> Result<Json<LoginResponse>, error::ApiError> {
-    // Query user from database
-    let user = sqlx::query!(
-        "SELECT id, email, full_name, password_hash, role FROM users WHERE email = $1",
-        payload.email
-    )
-    .fetch_optional(&pool)
-    .await?
-    .ok_or(error::ApiError::Unauthorized("Invalid credentials".to_string()))?;
-
-    // Verify password
-    let password_valid = verify(&payload.password, &user.password_hash)?;
-    if !password_valid {
-        return Err(error::ApiError::Unauthorized("Invalid credentials".to_string()));
-    }
-
-    // Generate JWT token
-    let claims = Claims {
-        sub: user.id.to_string(),
-        email: user.email.clone(),
-        role: user.role.clone(),
-        exp: (chrono::Utc::now() + chrono::Duration::hours(24)).timestamp() as usize,
-    };
-
-    let token = encode(
-        &Header::default(),
-        &claims,
-        &EncodingKey::from_secret(std::env::var("JWT_SECRET").unwrap().as_bytes()),
-    )?;
-
-    // Generate refresh token (valid for 7 days)
-    let refresh_claims = Claims {
-        sub: user.id.to_string(),
-        email: user.email.clone(),
-        role: user.role.clone(),
-        exp: (chrono::Utc::now() + chrono::Duration::days(7)).timestamp() as usize,
-    };
-
-    let refresh_token = encode(
-        &Header::default(),
-        &refresh_claims,
-        &EncodingKey::from_secret(std::env::var("JWT_SECRET").unwrap().as_bytes()),
-    )?;
-
-    // Log audit event
-    sqlx::query!(
-        "INSERT INTO audit_log (user_id, action, ip_address) VALUES ($1, $2, $3)",
-        user.id,
-        "login",
-        // Extract IP from request context
-    )
-    .execute(&pool)
-    .await?;
-
-    Ok(Json(LoginResponse {
-        token,
-        refresh_token,
-        user: UserInfo {
-            id: user.id.to_string(),
-            email: user.email,
-            full_name: user.full_name,
-            role: user.role,
-        },
-    }))
-}
-
-#[derive(Serialize, Deserialize)]
-struct Claims {
-    sub: String,  // user ID
-    email: String,
-    role: String,
-    exp: usize,   // expiration timestamp
-}
-
-async fn refresh_token(
-    // Implementation for refreshing JWT tokens
-) -> Result<Json<LoginResponse>, error::ApiError> {
-    // ... (similar to login, but validates refresh token)
-    todo!()
-}
-```
-
-**Job Submission Route** (src/routes/jobs.rs):
-```rust
-use axum::{Router, Json, routing::{post, get}, Extension};
-use serde::{Deserialize, Serialize};
-use sqlx::PgPool;
-use rdkafka::producer::FutureProducer;
-use uuid::Uuid;
-
-pub fn routes() -> Router {
-    Router::new()
-        .route("/", post(submit_job))
-        .route("/:job_id", get(get_job_status))
-}
-
-#[derive(Deserialize)]
-struct SubmitJobRequest {
-    experiment_id: String,
-    job_type: String,  // alignment, off_target, diff_expr
-    parameters: serde_json::Value,
-}
-
-#[derive(Serialize)]
-struct SubmitJobResponse {
-    job_id: String,
-    status: String,
-    message: String,
-}
-
-async fn submit_job(
-    Extension(pool): Extension<PgPool>,
-    Extension(producer): Extension<FutureProducer>,
-    // Extract authenticated user from middleware
-    Json(payload): Json<SubmitJobRequest>,
-) -> Result<Json<SubmitJobResponse>, error::ApiError> {
-    let job_id = Uuid::new_v4();
-
-    // Insert job record into database
-    sqlx::query!(
-        "INSERT INTO analysis_jobs (id, experiment_id, job_type, status) VALUES ($1, $2, $3, $4)",
-        job_id,
-        Uuid::parse_str(&payload.experiment_id)?,
-        payload.job_type,
-        "queued"
-    )
-    .execute(&pool)
-    .await?;
-
-    // Publish job to Kafka
-    let topic = match payload.job_type.as_str() {
-        "alignment" => "jobs.alignment",
-        "off_target" => "jobs.off_target",
-        "diff_expr" => "jobs.diff_expr",
-        _ => return Err(error::ApiError::BadRequest("Invalid job type".to_string())),
-    };
-
-    let job_message = serde_json::json!({
-        "job_id": job_id.to_string(),
-        "experiment_id": payload.experiment_id,
-        "parameters": payload.parameters,
-    });
-
-    producer
-        .send(
-            FutureRecord::to(topic)
-                .payload(&serde_json::to_string(&job_message)?)
-                .key(&job_id.to_string()),
-            Duration::from_secs(5),
-        )
-        .await
-        .map_err(|e| error::ApiError::Internal(format!("Kafka error: {:?}", e)))?;
-
-    Ok(Json(SubmitJobResponse {
-        job_id: job_id.to_string(),
-        status: "queued".to_string(),
-        message: format!("Job {} submitted successfully", job_id),
-    }))
-}
-
-async fn get_job_status(
-    Extension(pool): Extension<PgPool>,
-    axum::extract::Path(job_id): axum::extract::Path<String>,
-) -> Result<Json<JobStatus>, error::ApiError> {
-    let job = sqlx::query_as!(
-        JobStatus,
-        "SELECT id, status, started_at, completed_at, error_message FROM analysis_jobs WHERE id = $1",
-        Uuid::parse_str(&job_id)?
-    )
-    .fetch_optional(&pool)
-    .await?
-    .ok_or(error::ApiError::NotFound("Job not found".to_string()))?;
-
-    Ok(Json(job))
-}
-
-#[derive(Serialize)]
-struct JobStatus {
-    id: Uuid,
-    status: String,
-    started_at: Option<chrono::DateTime<chrono::Utc>>,
-    completed_at: Option<chrono::DateTime<chrono::Utc>>,
-    error_message: Option<String>,
-}
-```
-
----
-
-### 5.2 API Versioning Strategy
-
-**Approach**: URL path versioning (`/api/v1`, `/api/v2`)
-
-**Version Support Policy**:
-- **v1**: Current stable version (launched 2025-Q1)
-- **v2**: Next major version (planned 2025-Q3)
-- **Deprecation**: v1 will be deprecated 12 months after v2 launch
-- **Sunset**: v1 will be removed 6 months after deprecation notice
-
-**Backward Compatibility**:
-- Additive changes only (new fields, new endpoints)
-- Breaking changes trigger new major version
-- Clients specify version in `Accept` header: `application/vnd.crispr.v1+json`
-
----
-
-### 5.3 Rate Limiting
-
-**Implementation**: Redis sliding window algorithm
-
-```rust
-// src/middleware/rate_limit.rs
-use axum::{middleware::Next, http::{Request, StatusCode}, response::Response};
-use redis::AsyncCommands;
-
-pub async fn rate_limit_middleware<B>(
-    Extension(redis): Extension<redis::Client>,
-    request: Request<B>,
-    next: Next<B>,
-) -> Result<Response, StatusCode> {
-    let user_id = extract_user_id(&request)?;  // From JWT
-    let key = format!("rate_limit:{}:{}", user_id, get_current_minute());
-
-    let mut conn = redis.get_async_connection().await
-        .map_err(|_| StatusCode::INTERNAL_SERVER_ERROR)?;
-
-    // Increment request count
-    let count: u32 = conn.incr(&key, 1).await
-        .map_err(|_| StatusCode::INTERNAL_SERVER_ERROR)?;
-
-    // Set expiry on first request
-    if count == 1 {
-        conn.expire(&key, 60).await
-            .map_err(|_| StatusCode::INTERNAL_SERVER_ERROR)?;
-    }
-
-    // Check limit (100 requests per minute for standard users)
-    let limit = get_user_rate_limit(&user_id);
-    if count > limit {
-        return Err(StatusCode::TOO_MANY_REQUESTS);
-    }
-
-    Ok(next.run(request).await)
-}
-
-fn get_user_rate_limit(user_id: &str) -> u32 {
-    // Query user role from database/cache
-    // admin: 1000, researcher: 100, guest: 10
-    100
-}
-```
-
-**Rate Limits**:
-- **Admin**: 1000 requests/minute
-- **Researcher**: 100 requests/minute
-- **Guest**: 10 requests/minute
-
----
-
-### 5.4 WebSocket Support (Real-Time Updates)
-
-**Purpose**: Push job progress updates to UI in real-time
-
-**Implementation** (using `axum::extract::ws`):
-
-```rust
-use axum::{
-    extract::ws::{WebSocket, WebSocketUpgrade, Message},
-    response::Response,
-    Extension,
-};
-use tokio::sync::broadcast;
-
-pub async fn websocket_handler(
-    ws: WebSocketUpgrade,
-    Extension(tx): Extension<broadcast::Sender<String>>,
-) -> Response {
-    ws.on_upgrade(|socket| handle_socket(socket, tx))
-}
-
-async fn handle_socket(mut socket: WebSocket, tx: broadcast::Sender<String>) {
-    let mut rx = tx.subscribe();
-
-    loop {
-        tokio::select! {
-            // Receive messages from client (e.g., subscribe to specific job)
-            Some(msg) = socket.recv() => {
-                if let Ok(Message::Text(text)) = msg {
-                    // Handle subscription requests
-                    tracing::info!("Received: {}", text);
-                }
-            }
-
-            // Broadcast job updates to client
-            Ok(update) = rx.recv() => {
-                if socket.send(Message::Text(update)).await.is_err() {
-                    break;  // Client disconnected
-                }
-            }
-        }
-    }
-}
-```
-
-**Kafka Consumer** (publishes to WebSocket broadcast channel):
-```rust
-async fn consume_job_updates(tx: broadcast::Sender<String>) {
-    let consumer: StreamConsumer = ClientConfig::new()
-        .set("group.id", "websocket-broadcaster")
-        .set("bootstrap.servers", "kafka:9092")
-        .create()
-        .expect("Consumer creation failed");
-
-    consumer.subscribe(&["jobs.progress"]).unwrap();
-
-    loop {
-        match consumer.recv().await {
-            Ok(message) => {
-                if let Some(payload) = message.payload() {
-                    let update = String::from_utf8_lossy(payload).to_string();
-                    let _ = tx.send(update);  // Broadcast to all WebSocket clients
-                }
-            }
-            Err(e) => tracing::error!("Kafka error: {:?}", e),
-        }
-    }
-}
-```
-
----
-
-## 6. UI Layer
-
-### 6.1 React TypeScript Frontend
-
-**Technology Stack**:
-- **Framework**: React 18 with TypeScript 5.3
-- **Build Tool**: Vite 5.0 (fast HMR, optimized production builds)
-- **State Management**: Zustand (lightweight, <1KB)
-- **Routing**: React Router v6
-- **UI Components**: Shadcn/ui (Radix UI + Tailwind CSS)
-- **Data Fetching**: TanStack Query (React Query) for caching
-- **Visualization**: D3.js, Plotly.js, IGV.js (genomic browser)
-- **Testing**: Vitest, React Testing Library
-
-**Project Structure**:
-```
-frontend/
-├── src/
-│   ├── App.tsx                     # Root component
-│   ├── main.tsx                    # Entry point
-│   ├── pages/
-│   │   ├── Dashboard.tsx           # Overview, recent experiments
-│   │   ├── ExperimentWizard.tsx    # Step-by-step experiment setup
-│   │   ├── ExperimentDetail.tsx    # View experiment results
-│   │   ├── JobMonitor.tsx          # Real-time job tracking
-│   │   └── Visualizations.tsx      # Interactive plots
-│   ├── components/
-│   │   ├── Layout/
-│   │   │   ├── Header.tsx
-│   │   │   ├── Sidebar.tsx
-│   │   │   └── Footer.tsx
-│   │   ├── Experiments/
-│   │   │   ├── ExperimentCard.tsx
-│   │   │   ├── ExperimentForm.tsx
-│   │   │   └── SampleUploader.tsx
-│   │   ├── Jobs/
-│   │   │   ├── JobCard.tsx
-│   │   │   ├── JobProgressBar.tsx
-│   │   │   └── JobTimeline.tsx
-│   │   └── Visualizations/
-│   │       ├── VolcanoPlot.tsx     # D3.js volcano plot
-│   │       ├── MAPlot.tsx          # M-A plot for diff expr
-│   │       ├── Heatmap.tsx         # Gene expression heatmap
-│   │       └── GenomeBrowser.tsx   # IGV.js integration
-│   ├── hooks/
-│   │   ├── useExperiments.ts       # React Query hooks
-│   │   ├── useJobs.ts
-│   │   ├── useWebSocket.ts         # WebSocket connection
-│   │   └── useAuth.ts              # Authentication state
-│   ├── stores/
-│   │   ├── authStore.ts            # Zustand auth store
-│   │   └── uiStore.ts              # UI preferences
-│   ├── api/
-│   │   └── client.ts               # Axios API client
-│   └── utils/
-│       ├── formatters.ts
-│       └── validators.ts
-├── public/
-├── index.html
-├── package.json
-├── vite.config.ts
-└── tsconfig.json
-```
-
----
-
-### 6.2 Component Hierarchy
-
-```
-App
-├── AuthProvider
-│   ├── LoginPage
-│   └── ProtectedRoutes
-│       ├── Layout
-│       │   ├── Header
-│       │   ├── Sidebar
-│       │   └── Main
-│       │       ├── Dashboard
-│       │       │   ├── ExperimentCard[]
-│       │       │   ├── JobCard[]
-│       │       │   └── QuickStats
-│       │       ├── ExperimentWizard
-│       │       │   ├── Step1_BasicInfo
-│       │       │   ├── Step2_GuideRNA
-│       │       │   ├── Step3_Samples
-│       │       │   └── Step4_Analysis
-│       │       ├── ExperimentDetail
-│       │       │   ├── ExperimentHeader
-│       │       │   ├── SampleTable
-│       │       │   ├── JobTimeline
-│       │       │   └── ResultsTabs
-│       │       │       ├── OffTargetsTab
-│       │       │       │   └── OffTargetTable
-│       │       │       ├── DiffExprTab
-│       │       │       │   ├── VolcanoPlot
-│       │       │       │   ├── MAPlot
-│       │       │       │   └── GeneTable
-│       │       │       └── ImmuneResponseTab
-│       │       │           ├── SignatureEnrichment
-│       │       │           └── PathwayHeatmap
-│       │       └── JobMonitor
-│       │           ├── JobList
-│       │           └── JobDetails
-│       │               ├── JobProgressBar
-│       │               ├── JobLogs
-│       │               └── ResourceUsage
-└── Footer
-```
-
----
-
-### 6.3 Key Components
-
-#### 6.3.1 Experiment Wizard
-
-**Multi-step form for creating new experiments**:
-
-```tsx
-// src/pages/ExperimentWizard.tsx
-import { useState } from 'react';
-import { useMutation } from '@tanstack/react-query';
-import { api } from '@/api/client';
-
-interface ExperimentForm {
-  name: string;
-  description: string;
-  organism: string;
-  targetGene: string;
-  cas13Variant: 'Cas13a' | 'Cas13b' | 'Cas13d';
-  guideRNASequence: string;
-  samples: Sample[];
-}
-
-interface Sample {
-  name: string;
-  type: string;
-  fastqR1: File;
-  fastqR2?: File;
-}
-
-export function ExperimentWizard() {
-  const [step, setStep] = useState(1);
-  const [formData, setFormData] = useState<Partial<ExperimentForm>>({});
-
-  const createExperiment = useMutation({
-    mutationFn: async (data: ExperimentForm) => {
-      // Upload FASTQ files to MinIO
-      const uploadedSamples = await Promise.all(
-        data.samples.map(async (sample) => {
-          const formData = new FormData();
-          formData.append('file', sample.fastqR1);
-          if (sample.fastqR2) formData.append('file', sample.fastqR2);
-
-          const response = await api.post('/api/v1/samples/upload', formData);
-          return { ...sample, ...response.data };
-        })
-      );
-
-      // Create experiment
-      return api.post('/api/v1/experiments', {
-        ...data,
-        samples: uploadedSamples,
-      });
-    },
-    onSuccess: (data) => {
-      // Redirect to experiment detail page
-      navigate(`/experiments/${data.data.id}`);
-    },
-  });
-
-  const handleNext = () => {
-    if (step < 4) setStep(step + 1);
-    else createExperiment.mutate(formData as ExperimentForm);
-  };
-
-  return (
-    <div className="max-w-4xl mx-auto p-6">
-      <h1 className="text-3xl font-bold mb-8">Create New Experiment</h1>
-
-      <div className="mb-8">
-        <StepIndicator currentStep={step} />
-      </div>
-
-      {step === 1 && <BasicInfoStep data={formData} onChange={setFormData} />}
-      {step === 2 && <GuideRNAStep data={formData} onChange={setFormData} />}
-      {step === 3 && <SamplesStep data={formData} onChange={setFormData} />}
-      {step === 4 && <AnalysisStep data={formData} onChange={setFormData} />}
-
-      <div className="mt-8 flex justify-between">
-        <button onClick={() => setStep(step - 1)} disabled={step === 1}>
-          Previous
-        </button>
-        <button onClick={handleNext} disabled={!isStepValid(step, formData)}>
-          {step === 4 ? 'Submit' : 'Next'}
-        </button>
-      </div>
-    </div>
-  );
-}
-```
-
----
-
-#### 6.3.2 Real-Time Job Monitor
-
-**WebSocket-powered live job tracking**:
-
-```tsx
-// src/hooks/useWebSocket.ts
-import { useEffect, useState } from 'react';
-
-export function useWebSocket(url: string) {
-  const [messages, setMessages] = useState<string[]>([]);
-  const [socket, setSocket] = useState<WebSocket | null>(null);
-
-  useEffect(() => {
-    const ws = new WebSocket(url);
-
-    ws.onopen = () => {
-      console.log('WebSocket connected');
-    };
-
-    ws.onmessage = (event) => {
-      const update = JSON.parse(event.data);
-      setMessages((prev) => [...prev, update]);
-    };
-
-    ws.onerror = (error) => {
-      console.error('WebSocket error:', error);
-    };
-
-    ws.onclose = () => {
-      console.log('WebSocket disconnected');
-    };
-
-    setSocket(ws);
-
-    return () => {
-      ws.close();
-    };
-  }, [url]);
-
-  const sendMessage = (message: string) => {
-    if (socket && socket.readyState === WebSocket.OPEN) {
-      socket.send(message);
-    }
-  };
-
-  return { messages, sendMessage };
-}
-```
-
-```tsx
-// src/pages/JobMonitor.tsx
-import { useWebSocket } from '@/hooks/useWebSocket';
-import { useQuery } from '@tanstack/react-query';
-
-export function JobMonitor() {
-  const { data: jobs } = useQuery({
-    queryKey: ['jobs'],
-    queryFn: () => api.get('/api/v1/jobs'),
-    refetchInterval: 5000,  // Fallback polling
-  });
-
-  const { messages } = useWebSocket('wss://api.crispr.example.com/ws');
-
-  // Merge WebSocket updates with initial job data
-  const [liveJobs, setLiveJobs] = useState(jobs || []);
-
-  useEffect(() => {
-    messages.forEach((update) => {
-      setLiveJobs((prev) =>
-        prev.map((job) =>
-          job.id === update.job_id ? { ...job, ...update } : job
-        )
-      );
-    });
-  }, [messages]);
-
-  return (
-    <div>
-      <h1>Job Monitor</h1>
-      <div className="grid grid-cols-1 md:grid-cols-2 lg:grid-cols-3 gap-4">
-        {liveJobs.map((job) => (
-          <JobCard key={job.id} job={job} />
-        ))}
-      </div>
-    </div>
-  );
-}
-
-function JobCard({ job }: { job: Job }) {
-  const statusColor = {
-    queued: 'bg-gray-500',
-    running: 'bg-blue-500',
-    completed: 'bg-green-500',
-    failed: 'bg-red-500',
-  }[job.status];
-
-  return (
-    <div className="border rounded-lg p-4">
-      <div className="flex items-center justify-between mb-2">
-        <h3 className="font-bold">{job.job_type}</h3>
-        <span className={`px-2 py-1 rounded text-white text-sm ${statusColor}`}>
-          {job.status}
-        </span>
-      </div>
-
-      {job.status === 'running' && (
-        <div className="w-full bg-gray-200 rounded-full h-2">
-          <div
-            className="bg-blue-600 h-2 rounded-full transition-all duration-300"
-            style={{ width: `${job.progress || 0}%` }}
-          />
-        </div>
-      )}
-
-      <div className="text-sm text-gray-600 mt-2">
-        Started: {new Date(job.started_at).toLocaleString()}
-      </div>
-    </div>
-  );
-}
-```
-
----
-
-#### 6.3.3 Interactive Visualizations
-
-**Volcano Plot with D3.js**:
-
-```tsx
-// src/components/Visualizations/VolcanoPlot.tsx
-import { useEffect, useRef } from 'react';
-import * as d3 from 'd3';
-
-interface Gene {
-  gene_symbol: string;
-  log2_fold_change: number;
-  padj: number;
-}
-
-export function VolcanoPlot({ data }: { data: Gene[] }) {
-  const svgRef = useRef<SVGSVGElement>(null);
-
-  useEffect(() => {
-    if (!svgRef.current || !data.length) return;
-
-    const width = 800;
-    const height = 600;
-    const margin = { top: 20, right: 20, bottom: 50, left: 60 };
-
-    // Clear previous plot
-    d3.select(svgRef.current).selectAll('*').remove();
-
-    const svg = d3.select(svgRef.current)
-      .attr('width', width)
-      .attr('height', height);
-
-    // Transform data
-    const plotData = data.map((gene) => ({
-      ...gene,
-      neg_log10_padj: -Math.log10(gene.padj),
-      significant: gene.padj < 0.05 && Math.abs(gene.log2_fold_change) > 1,
-    }));
-
-    // Scales
-    const xScale = d3.scaleLinear()
-      .domain(d3.extent(plotData, (d) => d.log2_fold_change) as [number, number])
-      .range([margin.left, width - margin.right]);
-
-    const yScale = d3.scaleLinear()
-      .domain([0, d3.max(plotData, (d) => d.neg_log10_padj) as number])
-      .range([height - margin.bottom, margin.top]);
-
-    // Axes
-    svg.append('g')
-      .attr('transform', `translate(0, ${height - margin.bottom})`)
-      .call(d3.axisBottom(xScale));
-
-    svg.append('g')
-      .attr('transform', `translate(${margin.left}, 0)`)
-      .call(d3.axisLeft(yScale));
-
-    // Points
-    svg.selectAll('circle')
-      .data(plotData)
-      .join('circle')
-      .attr('cx', (d) => xScale(d.log2_fold_change))
-      .attr('cy', (d) => yScale(d.neg_log10_padj))
-      .attr('r', 3)
-      .attr('fill', (d) => (d.significant ? '#e74c3c' : '#95a5a6'))
-      .attr('opacity', 0.6)
-      .on('mouseover', function (event, d) {
-        d3.select(this).attr('r', 6).attr('opacity', 1);
-
-        // Show tooltip
-        tooltip
-          .style('opacity', 1)
-          .html(`<strong>${d.gene_symbol}</strong><br/>
-                 Log2FC: ${d.log2_fold_change.toFixed(2)}<br/>
-                 Adj. p-value: ${d.padj.toExponential(2)}`)
-          .style('left', `${event.pageX + 10}px`)
-          .style('top', `${event.pageY - 20}px`);
-      })
-      .on('mouseout', function () {
-        d3.select(this).attr('r', 3).attr('opacity', 0.6);
-        tooltip.style('opacity', 0);
-      });
-
-    // Tooltip
-    const tooltip = d3.select('body')
-      .append('div')
-      .attr('class', 'tooltip')
-      .style('position', 'absolute')
-      .style('background', 'white')
-      .style('border', '1px solid #ccc')
-      .style('padding', '10px')
-      .style('border-radius', '5px')
-      .style('opacity', 0);
-
-    // Threshold lines
-    svg.append('line')
-      .attr('x1', xScale(-1))
-      .attr('x2', xScale(-1))
-      .attr('y1', margin.top)
-      .attr('y2', height - margin.bottom)
-      .attr('stroke', 'gray')
-      .attr('stroke-dasharray', '4');
-
-    svg.append('line')
-      .attr('x1', xScale(1))
-      .attr('x2', xScale(1))
-      .attr('y1', margin.top)
-      .attr('y2', height - margin.bottom)
-      .attr('stroke', 'gray')
-      .attr('stroke-dasharray', '4');
-
-    svg.append('line')
-      .attr('x1', margin.left)
-      .attr('x2', width - margin.right)
-      .attr('y1', yScale(-Math.log10(0.05)))
-      .attr('y2', yScale(-Math.log10(0.05)))
-      .attr('stroke', 'gray')
-      .attr('stroke-dasharray', '4');
-  }, [data]);
-
-  return <svg ref={svgRef} />;
-}
-```
-
-**Genomic Browser with IGV.js**:
-
-```tsx
-// src/components/Visualizations/GenomeBrowser.tsx
-import { useEffect, useRef } from 'react';
-import igv from 'igv';
-
-export function GenomeBrowser({ bam_url, region }: { bam_url: string; region: string }) {
-  const containerRef = useRef<HTMLDivElement>(null);
-
-  useEffect(() => {
-    if (!containerRef.current) return;
-
-    const options = {
-      genome: 'macFas5',  // Rhesus macaque genome
-      locus: region,      // e.g., "chr1:1000000-2000000"
-      tracks: [
-        {
-          name: 'Genes',
-          type: 'annotation',
-          format: 'refGene',
-          url: 'https://api.genome.ucsc.edu/getData/track?genome=macFas5&track=refGene',
-        },
-        {
-          name: 'Aligned Reads',
-          type: 'alignment',
-          format: 'bam',
-          url: bam_url,
-          indexURL: `${bam_url}.bai`,
-          height: 500,
-        },
-      ],
-    };
-
-    igv.createBrowser(containerRef.current, options);
-  }, [bam_url, region]);
-
-  return <div ref={containerRef} style={{ height: '800px' }} />;
-}
-```
-
----
-
-## 7. Security & Authentication
-
-### 7.1 OAuth2 Authentication Flow
-
-**Architecture**:
-
-```
-┌────────────┐                                       ┌────────────┐
-│   Client   │                                       │    API     │
-│  (React)   │                                       │  Gateway   │
-└─────┬──────┘                                       └─────┬──────┘
-      │                                                      │
-      │ 1. POST /api/v1/auth/login                         │
-      │    { email, password }                             │
-      ├────────────────────────────────────────────────────>│
-      │                                                      │ 2. Validate credentials
-      │                                                      │    (PostgreSQL)
-      │                                                      │
-      │ 3. Response                                         │
-      │    { token, refresh_token, user }                  │
-      │<────────────────────────────────────────────────────┤
-      │                                                      │
-      │ 4. Store tokens in localStorage                    │
-      │                                                      │
-      │ 5. API Request with Authorization header           │
-      │    Authorization: Bearer <JWT>                     │
-      ├────────────────────────────────────────────────────>│
-      │                                                      │ 6. Validate JWT
-      │                                                      │    (check signature, expiry)
-      │                                                      │
-      │                                                      │ 7. Check permissions
-      │                                                      │    (RBAC from JWT claims)
-      │                                                      │
-      │ 8. Response                                         │
-      │<────────────────────────────────────────────────────┤
-      │                                                      │
-      │ 9. Token expired (401)                             │
-      │<────────────────────────────────────────────────────┤
-      │                                                      │
-      │ 10. POST /api/v1/auth/refresh                      │
-      │     { refresh_token }                              │
-      ├────────────────────────────────────────────────────>│
-      │                                                      │ 11. Validate refresh token
-      │                                                      │
-      │ 12. New tokens                                      │
-      │     { token, refresh_token }                       │
-      │<────────────────────────────────────────────────────┤
-      │                                                      │
-```
-
-**JWT Token Structure**:
-
-```json
-{
-  "header": {
-    "alg": "RS256",
-    "typ": "JWT"
-  },
-  "payload": {
-    "sub": "550e8400-e29b-41d4-a716-446655440000",  // user ID
-    "email": "researcher@example.com",
-    "role": "researcher",
-    "permissions": [
-      "experiments:read",
-      "experiments:create",
-      "jobs:submit",
-      "results:read"
-    ],
-    "iat": 1705401600,  // issued at (Unix timestamp)
-    "exp": 1705488000   // expires at (24 hours later)
-  },
-  "signature": "..."
-}
-```
-
-**Token Storage** (Frontend):
-- **Access Token**: `localStorage.setItem('access_token', token)`
-- **Refresh Token**: `httpOnly` cookie (more secure, prevents XSS)
-- **Auto-refresh**: Axios interceptor detects 401, refreshes token, retries request
-
----
-
-### 7.2 Role-Based Access Control (RBAC)
-
-**Roles**:
-
-| Role | Permissions | Description |
-|------|-------------|-------------|
-| **Guest** | `experiments:read`, `results:read` | Read-only access to public experiments |
-| **Researcher** | `experiments:*`, `jobs:submit`, `results:*` | Create experiments, submit jobs, view results |
-| **Bioinformatician** | All researcher permissions + `pipelines:configure`, `data:export` | Configure analysis pipelines, export raw data |
-| **Admin** | `*:*` | Full system access, user management |
-
-**Permission Enforcement** (Middleware):
-
-```rust
-// src/middleware/auth.rs
-use axum::{http::{Request, StatusCode}, middleware::Next, response::Response};
-use jsonwebtoken::{decode, DecodingKey, Validation};
-
-pub async fn auth_middleware<B>(
-    request: Request<B>,
-    next: Next<B>,
-) -> Result<Response, StatusCode> {
-    // Extract Authorization header
-    let auth_header = request
-        .headers()
-        .get("Authorization")
-        .and_then(|h| h.to_str().ok())
-        .ok_or(StatusCode::UNAUTHORIZED)?;
-
-    // Parse Bearer token
-    let token = auth_header
-        .strip_prefix("Bearer ")
-        .ok_or(StatusCode::UNAUTHORIZED)?;
-
-    // Decode and validate JWT
-    let key = DecodingKey::from_secret(std::env::var("JWT_SECRET").unwrap().as_bytes());
-    let validation = Validation::default();
-
-    let token_data = decode::<Claims>(token, &key, &validation)
-        .map_err(|_| StatusCode::UNAUTHORIZED)?;
-
-    // Check required permission (extract from route metadata)
-    let required_permission = extract_required_permission(&request);
-    if !has_permission(&token_data.claims, required_permission) {
-        return Err(StatusCode::FORBIDDEN);
-    }
-
-    // Inject user claims into request extensions
-    request.extensions_mut().insert(token_data.claims);
-
-    Ok(next.run(request).await)
-}
-
-fn has_permission(claims: &Claims, required: &str) -> bool {
-    claims.permissions.iter().any(|p| p == required || p == "*:*")
-}
-```
-
-**Route-Level Permissions** (declarative):
-
-```rust
-Router::new()
-    .route("/api/v1/experiments", post(create_experiment))
-    .layer(require_permission("experiments:create"))
-
-    .route("/api/v1/admin/users", get(list_users))
-    .layer(require_permission("admin:users:read"))
-```
-
----
-
-### 7.3 Data Encryption
-
-**At Rest**:
-- **PostgreSQL**: Transparent Data Encryption (TDE) with AES-256
-- **MongoDB**: Encrypted storage engine with key rotation
-- **MinIO**: Server-side encryption (SSE-S3) with AWS KMS
-
-**In Transit**:
-- **External**: TLS 1.3 with certificate pinning
-- **Internal (service-to-service)**: Mutual TLS (mTLS) with Istio service mesh
-
-**Secrets Management**:
-- **Kubernetes Secrets**: Base64-encoded (encrypted at rest by etcd)
-- **External Secrets Operator**: Sync from AWS Secrets Manager / HashiCorp Vault
-- **Rotation Policy**: Database credentials rotated every 90 days
-
----
-
-### 7.4 Security Best Practices
-
-1. **Input Validation**: All user inputs sanitized to prevent SQL injection, XSS
-2. **Rate Limiting**: Prevent brute-force attacks and API abuse
-3. **Audit Logging**: All sensitive operations logged (login, data access, exports)
-4. **Least Privilege**: Services run with minimal permissions
-5. **Vulnerability Scanning**: Automated container scanning (Trivy, Snyk)
-6. **Penetration Testing**: Annual third-party security audits
-7. **HIPAA Compliance**: Encrypted data, access logs, BAAs with cloud providers
-
----
-
-## 8. Monitoring & Observability
-
-### 8.1 Prometheus Metrics Collection
-
-**Metrics Exposed by Each Service**:
-
-```rust
-// Example: Axum API metrics
-use prometheus::{Encoder, TextEncoder, Counter, Histogram, register_counter, register_histogram};
-
-lazy_static! {
-    static ref HTTP_REQUESTS_TOTAL: Counter = register_counter!(
-        "http_requests_total",
-        "Total HTTP requests"
-    ).unwrap();
-
-    static ref HTTP_REQUEST_DURATION: Histogram = register_histogram!(
-        "http_request_duration_seconds",
-        "HTTP request latency"
-    ).unwrap();
-
-    static ref JOBS_SUBMITTED_TOTAL: Counter = register_counter!(
-        "jobs_submitted_total",
-        "Total jobs submitted"
-    ).unwrap();
-
-    static ref JOBS_COMPLETED_TOTAL: Counter = register_counter!(
-        "jobs_completed_total",
-        "Total jobs completed"
-    ).unwrap();
-}
-
-async fn metrics_handler() -> String {
-    let encoder = TextEncoder::new();
-    let metric_families = prometheus::gather();
-    let mut buffer = vec![];
-    encoder.encode(&metric_families, &mut buffer).unwrap();
-    String::from_utf8(buffer).unwrap()
-}
-```
-
-**Prometheus Scrape Configuration** (see `monitoring/prometheus.yml`):
-
-```yaml
-global:
-  scrape_interval: 15s
-  evaluation_interval: 15s
-
-scrape_configs:
-  - job_name: 'api-gateway'
-    kubernetes_sd_configs:
-      - role: pod
-        namespaces:
-          names:
-            - crispr-production
-    relabel_configs:
-      - source_labels: [__meta_kubernetes_pod_label_app]
-        regex: api-gateway
-        action: keep
-    metrics_path: /metrics
-
-  - job_name: 'alignment-service'
-    kubernetes_sd_configs:
-      - role: pod
-        namespaces:
-          names:
-            - crispr-production
-    relabel_configs:
-      - source_labels: [__meta_kubernetes_pod_label_app]
-        regex: alignment-service
-        action: keep
-    metrics_path: /metrics
-
-  - job_name: 'postgresql'
-    static_configs:
-      - targets: ['postgres-exporter:9187']
-
-  - job_name: 'kafka'
-    static_configs:
-      - targets: ['kafka-exporter:9308']
-
-  - job_name: 'kubernetes-nodes'
-    kubernetes_sd_configs:
-      - role: node
-```
-
----
-
-### 8.2 Grafana Dashboards
-
-**Dashboard 1: System Overview**
-
-- **Total Experiments**: Gauge (current count)
-- **Jobs Submitted Today**: Counter
-- **Jobs Completed/Failed**: Pie chart
-- **API Request Rate**: Line graph (requests/sec)
-- **API P95 Latency**: Line graph
-- **Database Connection Pool Usage**: Gauge
-- **Kafka Consumer Lag**: Line graph per topic
-
-**Dashboard 2: Processing Pipeline**
-
-- **Active Jobs by Type**: Bar chart (alignment, off-target, diff-expr)
-- **Average Job Duration**: Line graph per job type
-- **Worker CPU/Memory Usage**: Heatmap per pod
-- **Queue Depth**: Line graph per Kafka topic
-- **Success Rate**: Gauge (completed / total)
-
-**Dashboard 3: Resource Utilization**
-
-- **Kubernetes Cluster CPU/Memory**: Line graph
-- **Node CPU/Memory per Node**: Heatmap
-- **Storage Usage** (PostgreSQL, MongoDB, MinIO): Gauge
-- **Network Throughput**: Line graph (ingress/egress)
-
-**Grafana Configuration** (see `monitoring/grafana-dashboard.json`):
-
-```json
-{
-  "dashboard": {
-    "title": "CRISPR-Cas13 Pipeline - System Overview",
-    "panels": [
-      {
-        "id": 1,
-        "title": "API Request Rate",
-        "targets": [
-          {
-            "expr": "rate(http_requests_total[5m])",
-            "legendFormat": "{{method}} {{path}}"
-          }
-        ],
-        "type": "graph"
-      },
-      {
-        "id": 2,
-        "title": "Jobs Submitted Today",
-        "targets": [
-          {
-            "expr": "increase(jobs_submitted_total[1d])"
-          }
-        ],
-        "type": "singlestat"
-      }
-    ]
-  }
-}
-```
-
----
-
-### 8.3 Distributed Tracing (Jaeger)
-
-**Why Distributed Tracing?**
-- Visualize request flow across microservices
-- Identify performance bottlenecks
-- Debug complex failures in distributed systems
-
-**OpenTelemetry Integration** (Rust):
-
-```rust
-use opentelemetry::{global, sdk::trace::Tracer};
-use opentelemetry_jaeger::JaegerPipeline;
-use tracing_subscriber::layer::SubscriberExt;
-
-fn init_tracing() {
-    let tracer: Tracer = JaegerPipeline::default()
-        .with_service_name("api-gateway")
-        .with_agent_endpoint("jaeger-agent:6831")
-        .install_batch(opentelemetry::runtime::Tokio)
-        .expect("Failed to install Jaeger tracer");
-
-    let telemetry = tracing_opentelemetry::layer().with_tracer(tracer);
-    let subscriber = tracing_subscriber::Registry::default().with(telemetry);
-
-    tracing::subscriber::set_global_default(subscriber)
-        .expect("Failed to set subscriber");
-}
-
-#[tracing::instrument]
-async fn submit_job(job: Job) -> Result<String, ApiError> {
-    // This function will automatically create a span in Jaeger
-    // with function name, arguments, and return value
-
-    let span = tracing::info_span!("submit_job", job_id = %job.id);
-    let _enter = span.enter();
-
-    // ... implementation
-}
-```
-
-**Trace Visualization** (example span hierarchy):
-```
-POST /api/v1/jobs (200ms)
-├── validate_request (5ms)
-├── query_database (50ms)
-│   └── SELECT * FROM experiments (45ms)
-├── publish_to_kafka (100ms)
-│   ├── serialize_message (10ms)
-│   └── kafka_send (90ms)
-└── update_cache (45ms)
-    └── redis_set (40ms)
-```
-
----
-
-### 8.4 Alerting Rules
-
-**Prometheus Alerting Rules** (see `monitoring/alerts.yml`):
-
-```yaml
-groups:
-  - name: crispr_pipeline_alerts
-    interval: 30s
-    rules:
-      # High API error rate
-      - alert: HighAPIErrorRate
-        expr: rate(http_requests_total{status=~"5.."}[5m]) > 0.05
-        for: 5m
-        labels:
-          severity: critical
-        annotations:
-          summary: "High API error rate detected"
-          description: "API error rate is {{ $value | humanizePercentage }} (threshold: 5%)"
-
-      # High Kafka consumer lag
-      - alert: HighKafkaConsumerLag
-        expr: kafka_consumer_lag > 1000
-        for: 10m
-        labels:
-          severity: warning
-        annotations:
-          summary: "Kafka consumer lag is high"
-          description: "Topic {{ $labels.topic }} has {{ $value }} messages in lag"
-
-      # Database connection pool exhaustion
-      - alert: DatabaseConnectionPoolExhausted
-        expr: database_connection_pool_active / database_connection_pool_max > 0.9
-        for: 5m
-        labels:
-          severity: critical
-        annotations:
-          summary: "Database connection pool nearly exhausted"
-          description: "{{ $value | humanizePercentage }} of connections are in use"
-
-      # Long-running jobs
-      - alert: JobRunningTooLong
-        expr: time() - job_started_timestamp > 3600 * 6  # 6 hours
-        for: 0m
-        labels:
-          severity: warning
-        annotations:
-          summary: "Job {{ $labels.job_id }} has been running for over 6 hours"
-
-      # Disk space low
-      - alert: DiskSpaceLow
-        expr: node_filesystem_avail_bytes / node_filesystem_size_bytes < 0.1
-        for: 5m
-        labels:
-          severity: critical
-        annotations:
-          summary: "Disk space below 10% on {{ $labels.instance }}"
-```
-
-**Alert Routing** (Alertmanager):
-- **Critical**: PagerDuty (24/7 on-call)
-- **Warning**: Slack #crispr-alerts channel
-- **Info**: Email to dev team
-
----
-
-## 9. Deployment Strategy
-
-### 9.1 Kubernetes Deployment Manifests
-
-**Namespace** (deployment/namespace.yaml):
-```yaml
-apiVersion: v1
-kind: Namespace
-metadata:
-  name: crispr-production
-  labels:
-    name: crispr-production
-```
-
-**API Gateway Deployment** (deployment/api-gateway.yaml):
-```yaml
-apiVersion: apps/v1
-kind: Deployment
-metadata:
-  name: api-gateway
-  namespace: crispr-production
-spec:
-  replicas: 3
-  selector:
-    matchLabels:
-      app: api-gateway
-  template:
-    metadata:
-      labels:
-        app: api-gateway
-    spec:
-      containers:
-      - name: api-gateway
-        image: crispr-registry.io/api-gateway:v1.0.0
-        ports:
-        - containerPort: 3000
-        env:
-        - name: DATABASE_URL
-          valueFrom:
-            secretKeyRef:
-              name: database-credentials
-              key: url
-        - name: REDIS_URL
-          valueFrom:
-            secretKeyRef:
-              name: redis-credentials
-              key: url
-        - name: KAFKA_BROKERS
-          value: "kafka-0.kafka:9092,kafka-1.kafka:9092,kafka-2.kafka:9092"
-        - name: JWT_SECRET
-          valueFrom:
-            secretKeyRef:
-              name: jwt-secret
-              key: secret
-        resources:
-          requests:
-            cpu: "500m"
-            memory: "1Gi"
-          limits:
-            cpu: "2"
-            memory: "4Gi"
-        livenessProbe:
-          httpGet:
-            path: /health
-            port: 3000
-          initialDelaySeconds: 30
-          periodSeconds: 10
-        readinessProbe:
-          httpGet:
-            path: /ready
-            port: 3000
-          initialDelaySeconds: 5
-          periodSeconds: 5
----
-apiVersion: v1
-kind: Service
-metadata:
-  name: api-gateway
-  namespace: crispr-production
-spec:
-  selector:
-    app: api-gateway
-  ports:
-  - protocol: TCP
-    port: 80
-    targetPort: 3000
-  type: ClusterIP
----
-apiVersion: networking.k8s.io/v1
-kind: Ingress
-metadata:
-  name: api-gateway-ingress
-  namespace: crispr-production
-  annotations:
-    cert-manager.io/cluster-issuer: letsencrypt-prod
-    nginx.ingress.kubernetes.io/ssl-redirect: "true"
-spec:
-  ingressClassName: nginx
-  tls:
-  - hosts:
-    - api.crispr.example.com
-    secretName: api-gateway-tls
-  rules:
-  - host: api.crispr.example.com
-    http:
-      paths:
-      - path: /
-        pathType: Prefix
-        backend:
-          service:
-            name: api-gateway
-            port:
-              number: 80
-```
-
-**Alignment Service Deployment** (deployment/alignment-service.yaml):
-```yaml
-apiVersion: apps/v1
-kind: Deployment
-metadata:
-  name: alignment-service
-  namespace: crispr-production
-spec:
-  replicas: 5
-  selector:
-    matchLabels:
-      app: alignment-service
-  template:
-    metadata:
-      labels:
-        app: alignment-service
-    spec:
-      affinity:
-        nodeAffinity:
-          requiredDuringSchedulingIgnoredDuringExecution:
-            nodeSelectorTerms:
-            - matchExpressions:
-              - key: node-role
-                operator: In
-                values:
-                - compute-intensive
-      containers:
-      - name: alignment-worker
-        image: crispr-registry.io/alignment-service:v1.0.0
-        env:
-        - name: KAFKA_BROKERS
-          value: "kafka-0.kafka:9092,kafka-1.kafka:9092,kafka-2.kafka:9092"
-        - name: MINIO_ENDPOINT
-          value: "http://minio:9000"
-        - name: MINIO_ACCESS_KEY
-          valueFrom:
-            secretKeyRef:
-              name: minio-credentials
-              key: access_key
-        - name: MINIO_SECRET_KEY
-          valueFrom:
-            secretKeyRef:
-              name: minio-credentials
-              key: secret_key
-        resources:
-          requests:
-            cpu: "4"
-            memory: "16Gi"
-          limits:
-            cpu: "8"
-            memory: "32Gi"
-```
-
----
-
-### 9.2 CI/CD Pipeline
-
-**GitHub Actions Workflow** (.github/workflows/deploy.yml):
-
-```yaml
-name: Deploy to Production
-
-on:
-  push:
-    branches:
-      - main
-
-jobs:
-  test:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3
-
-      - name: Run tests
-        run: |
-          cd api && cargo test
-          cd ../frontend && npm test
-
-  build:
-    needs: test
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3
-
-      - name: Build Docker images
-        run: |
-          docker build -t crispr-registry.io/api-gateway:${{ github.sha }} api/
-          docker build -t crispr-registry.io/alignment-service:${{ github.sha }} docker/alignment-service/
-          docker build -t crispr-registry.io/off-target-service:${{ github.sha }} docker/off-target-service/
-          docker build -t crispr-registry.io/diff-expr-service:${{ github.sha }} docker/diff-expr-service/
-
-      - name: Push to registry
-        run: |
-          echo ${{ secrets.REGISTRY_PASSWORD }} | docker login -u ${{ secrets.REGISTRY_USERNAME }} --password-stdin crispr-registry.io
-          docker push crispr-registry.io/api-gateway:${{ github.sha }}
-          docker push crispr-registry.io/alignment-service:${{ github.sha }}
-          docker push crispr-registry.io/off-target-service:${{ github.sha }}
-          docker push crispr-registry.io/diff-expr-service:${{ github.sha }}
-
-  deploy:
-    needs: build
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3
-
-      - name: Deploy to Kubernetes
-        run: |
-          kubectl set image deployment/api-gateway api-gateway=crispr-registry.io/api-gateway:${{ github.sha }} -n crispr-production
-          kubectl set image deployment/alignment-service alignment-worker=crispr-registry.io/alignment-service:${{ github.sha }} -n crispr-production
-          kubectl rollout status deployment/api-gateway -n crispr-production
-          kubectl rollout status deployment/alignment-service -n crispr-production
-```
-
----
-
-### 9.3 Blue-Green Deployment
-
-**Strategy**: Maintain two identical production environments (blue/green), switch traffic atomically
-
-```yaml
-# Blue deployment (current production)
-apiVersion: apps/v1
-kind: Deployment
-metadata:
-  name: api-gateway-blue
-  namespace: crispr-production
-spec:
-  replicas: 3
-  selector:
-    matchLabels:
-      app: api-gateway
-      version: blue
-
-# Green deployment (new version)
-apiVersion: apps/v1
-kind: Deployment
-metadata:
-  name: api-gateway-green
-  namespace: crispr-production
-spec:
-  replicas: 3
-  selector:
-    matchLabels:
-      app: api-gateway
-      version: green
-
-# Service (switch between blue/green by updating selector)
-apiVersion: v1
-kind: Service
-metadata:
-  name: api-gateway
-  namespace: crispr-production
-spec:
-  selector:
-    app: api-gateway
-    version: blue  # Change to "green" to switch traffic
-  ports:
-  - port: 80
-    targetPort: 3000
-```
-
-**Deployment Process**:
-1. Deploy green version (new code)
-2. Run smoke tests on green
-3. Update Service selector to `version: green`
-4. Monitor for 30 minutes (watch error rates, latencies)
-5. If successful, delete blue deployment
-6. If failed, rollback by switching Service selector back to `version: blue`
-
----
-
-## 10. Technology Stack
-
-### 10.1 Core Technologies
-
-| Layer | Technology | Version | Justification |
-|-------|-----------|---------|---------------|
-| **API Layer** | Axum (Rust) | 0.7 | High performance, memory safety, strong typing |
-| | Tower (middleware) | 0.4 | Composable HTTP middleware |
-| | Tokio (async runtime) | 1.35 | Efficient async I/O |
-| **Processing Layer** | Python | 3.11 | Rich bioinformatics ecosystem (Biopython, NumPy) |
-| | R (Bioconductor) | 4.3 | Industry standard for genomics (DESeq2, edgeR) |
-| | Bowtie2 | 2.5.1 | Fast, memory-efficient short read aligner |
-| **Frontend** | React | 18 | Component-based UI, large ecosystem |
-| | TypeScript | 5.3 | Type safety, better developer experience |
-| | Vite | 5.0 | Fast builds, HMR |
-| | D3.js | 7.8 | Flexible data visualizations |
-| | IGV.js | 2.15 | Interactive genomic browser |
-| **Databases** | PostgreSQL | 16 | ACID compliance, complex queries, JSON support |
-| | MongoDB | 7.0 | Flexible schema for genomic annotations |
-| | Redis | 7.2 | High-performance caching, session storage |
-| | MinIO | RELEASE.2024-01 | S3-compatible object storage |
-| **Message Queue** | Apache Kafka | 3.6 | Fault-tolerant, high-throughput message queue |
-| **Orchestration** | Kubernetes | 1.28 | Container orchestration, auto-scaling |
-| | Helm | 3.13 | Kubernetes package manager |
-| **Monitoring** | Prometheus | 2.48 | Metrics collection, alerting |
-| | Grafana | 10.2 | Visualization, dashboards |
-| | Jaeger | 1.52 | Distributed tracing |
-| **CI/CD** | GitHub Actions | N/A | Automated testing, building, deployment |
-| | Docker | 24.0 | Container packaging |
-
----
-
-### 10.2 Bioinformatics Tools
-
-| Tool | Version | Purpose |
-|------|---------|---------|
-| Bowtie2 | 2.5.1 | Read alignment to reference genome |
-| Samtools | 1.17 | BAM file manipulation |
-| FastQC | 0.12.1 | Quality control of sequencing data |
-| MultiQC | 1.16 | Aggregate QC reports |
-| featureCounts | 2.0.3 | Count reads per gene (from Subread package) |
-| DESeq2 | 1.42 | Differential gene expression analysis |
-| edgeR | 3.44 | Alternative differential expression tool |
-| Biopython | 1.81 | Python library for sequence analysis |
-| PyTorch | 2.1 | Machine learning for off-target prediction |
-
----
-
-## 11. Scalability & Performance
-
-### 11.1 Performance Targets
-
-| Metric | Target | Measurement |
-|--------|--------|-------------|
-| **API Latency** | P50 < 50ms, P95 < 200ms, P99 < 500ms | Prometheus histogram |
-| **Throughput** | 50-100 samples/day (200GB-1TB) | Job completion rate |
-| **Database Queries** | P95 < 100ms | PostgreSQL `pg_stat_statements` |
-| **Job Queue Latency** | Kafka consumer lag < 100 messages | Kafka exporter |
-| **Frontend Load Time** | First Contentful Paint < 1.5s | Lighthouse CI |
-| **Uptime** | 99.9% (8.7 hours downtime/year) | Prometheus uptime probe |
-
----
-
-### 11.2 Scalability Strategies
-
-#### 11.2.1 Horizontal Scaling
-
-- **API Gateway**: 2-20 replicas (CPU-based HPA)
-- **Processing Workers**: 1-50 pods (queue-depth based HPA)
-- **Database Read Replicas**: 3 PostgreSQL replicas for read-heavy queries
-- **Kafka Partitions**: 10 partitions per topic (allows 10 parallel consumers)
-
-#### 11.2.2 Caching Strategy
-
-**Multi-layer caching**:
-
-1. **CDN** (CloudFlare): Static assets (JS, CSS, images)
-2. **Browser**: HTTP cache headers for API responses
-3. **Redis**: Hot data (user sessions, recent experiments, job statuses)
-4. **Database Query Cache**: PostgreSQL `pg_prewarm` for frequently accessed tables
-
-**Cache Invalidation**:
-- **TTL-based**: Most caches expire after 5-10 minutes
-- **Event-driven**: Kafka events trigger cache invalidation (e.g., job completion → invalidate job status cache)
-
-#### 11.2.3 Database Optimization
-
-**PostgreSQL**:
-- **Indexes**: Create indexes on frequently queried columns (user_id, experiment_id, status)
-- **Partitioning**: Partition `audit_log` table by month (improves query performance)
-- **Connection Pooling**: PgBouncer with 100 max connections
-- **VACUUM**: Automated weekly VACUUM ANALYZE to reclaim space
-
-**MongoDB**:
-- **Sharding**: Shard `genes` collection by chromosome (24 shards)
-- **Indexes**: Compound indexes on `{gene_symbol: 1, chromosome: 1}`
-- **Aggregation Pipeline**: Use MongoDB aggregation for complex genomic queries
-
----
-
-## 12. Trade-off Analysis
-
-### 12.1 Architectural Decisions
-
-| Decision | Alternatives Considered | Trade-offs | Rationale |
-|----------|-------------------------|------------|-----------|
-| **Rust for API** | Node.js, Go, Python | **Pro**: 10x performance, memory safety<br/>**Con**: Steeper learning curve, longer compile times | Performance critical for high-throughput API |
-| **Microservices** | Monolith | **Pro**: Independent scaling, fault isolation<br/>**Con**: Operational complexity, network overhead | Flexibility to scale each component independently |
-| **Kafka vs RabbitMQ** | RabbitMQ, AWS SQS | **Pro**: High throughput, log-based architecture<br/>**Con**: More complex setup | Kafka's replay capability useful for debugging |
-| **PostgreSQL + MongoDB** | PostgreSQL only | **Pro**: Best tool for each data type<br/>**Con**: Two databases to maintain | Flexible schema needed for genomic annotations |
-| **Kubernetes** | Docker Swarm, ECS | **Pro**: Industry standard, rich ecosystem<br/>**Con**: Steeper learning curve | Better auto-scaling, service mesh support |
-| **React** | Vue, Svelte | **Pro**: Largest ecosystem, more developers<br/>**Con**: Slightly larger bundle size | Better component library availability |
-
----
-
-### 12.2 Cost-Performance Trade-offs
-
-**Scenario**: Processing 100 samples/day
-
-| Component | Configuration | Monthly Cost | Performance | Scalability |
-|-----------|---------------|--------------|-------------|-------------|
-| **Kubernetes Cluster** | 20 nodes (c5.4xlarge) | $8,000 | High | Excellent |
-| **PostgreSQL RDS** | db.r5.2xlarge (3 replicas) | $2,500 | High | Good |
-| **MongoDB Atlas** | M30 (3 shards) | $1,800 | High | Excellent |
-| **Redis ElastiCache** | cache.r5.xlarge (3 nodes) | $900 | High | Good |
-| **MinIO (S3)** | 50TB storage + transfer | $1,200 | High | Excellent |
-| **Kafka MSK** | kafka.m5.large (3 brokers) | $1,400 | High | Excellent |
-| **Total** | | **$15,800/month** | | |
-
-**Cost Optimization Opportunities**:
-1. **Spot Instances**: Use spot instances for batch processing workers (50-70% cost savings)
-2. **S3 Lifecycle Policies**: Archive old data to Glacier (90% storage cost reduction)
-3. **Reserved Instances**: Commit to 1-year reserved instances for baseline capacity (30% discount)
-4. **Right-sizing**: Monitor resource usage, downsize over-provisioned services
-
----
-
-## Conclusion
-
-This architecture provides a **scalable, fault-tolerant, and secure** foundation for the CRISPR-Cas13 bioinformatics pipeline. Key highlights:
-
-✅ **Microservices Architecture**: Independent scaling, fault isolation
-✅ **Multi-layer Data Strategy**: PostgreSQL (relational), MongoDB (genomic), Redis (cache), MinIO (objects)
-✅ **Kafka-based Job Orchestration**: Decoupled, fault-tolerant processing
-✅ **Rust API Layer**: High performance, memory safety
-✅ **React Frontend**: Modern, interactive UI with real-time updates
-✅ **Comprehensive Monitoring**: Prometheus, Grafana, Jaeger for observability
-✅ **Security-first Design**: OAuth2, RBAC, encryption at rest and in transit
-✅ **Cloud-native**: Kubernetes for orchestration, auto-scaling policies
-
-**Next Steps** (SPARC Phase 4 - Refinement):
-1. Implement Test-Driven Development (TDD) for each component
-2. Create integration tests for end-to-end workflows
-3. Conduct load testing (Apache JMeter, k6) to validate performance targets
-4. Security audit and penetration testing
-5. Documentation: API reference, deployment guide, operational runbook
-
----
-
-**Document Version**: 1.0
-**Last Updated**: 2025-10-12
-**Author**: Architecture Agent (SPARC Phase 3)
-**Review Status**: Ready for Technical Review