NBDR Protocol

# FASTQ files for biosample 55052008714000
biocid://v1/story/IPA/0x19A615224D03487AaDdC43e4520F9D83923d9512/55052008714000/R1.fastq.gz

# VCF file on Story Protocol
biocid://v1/story/0x5021F7438ea502b0c346cB59F8E92B749Ecd74B5/41221040804049/genome.vcf

# SQLite annotation database
biocid://v1/story/IPA/0xB8d03f2E1C02e4cC5b5fe1613c575c01BDD12269/55052008714000/annotation.sqlite

# Install dependencies
sudo apt-get install -y build-essential meson ninja-build \
                        libfuse3-dev libcurl4-openssl-dev \
                        libjansson-dev autoconf automake libtool

# Build libsecp256k1 (ECDSA signature verification)
git clone https://github.com/bitcoin-core/secp256k1.git
cd secp256k1
./autogen.sh && ./configure --enable-module-recovery
make && sudo make install && sudo ldconfig

# Build web3fuse
git clone https://github.com/Genobank/web3fuse.git
cd web3fuse
make

# Run tests
make test

# Set user signature for authentication
export USER_SIGNATURE="0xa5141ae955bba91ad46a940aefc3b05120489b8b..."

# Mount FASTQ files via BioCID
biofs --mount /mnt/genomics \
      --uri "biocid://v1/story/IPA/0x19A615224D03487AaDdC43e4520F9D83923d9512/55052008714000"

# Access files (NFT ownership verified on-chain)
ls /mnt/genomics/
head /mnt/genomics/55052008714000_R1.fastq.gz

# Unmount
fusermount -u /mnt/genomics

# Install via pip
pip install biofs-sdk

# Or install from source
git clone https://github.com/Genobank/biofs-sdk.git
cd biofs-sdk
pip install -e .

from biofs import BioCIDClient

# Initialize client with Web3 signature
client = BioCIDClient(wallet_signature="0xa5141ae955bba91ad46a940aefc3b05120489b8b...")

# Verify access to BioCID (NFT ownership check)
biocid_url = "biocid://v1/story/IPA/0x19A615224D03487AaDdC43e4520F9D83923d9512/55052008714000/genome.vcf"
if client.verify_access(biocid_url):
    print("✅ Access granted")

# Download file to local path
client.download(biocid_url, output_path="./genome.vcf")

# Stream large files (memory-efficient)
for chunk in client.stream(biocid_url, chunk_size=8192):
    process_chunk(chunk)

# Get metadata without downloading
info = client.info(biocid_url)
print(f"File size: {info['size']} bytes")

from biofs import BioCIDClient
import pysam
import pandas as pd
import os

# Initialize client
client = BioCIDClient(wallet_signature=os.environ['USER_SIGNATURE'])

# BioCID URLs for biosample files
biosample_id = "55052008714000"
vcf_biocid = f"biocid://v1/story/IPA/0x19A6.../{biosample_id}/genome.vcf"

# Verify access before processing
if not client.verify_access(vcf_biocid):
    raise PermissionError("You do not have access to this genomic data")

# Download VCF file
vcf_path = "./genome.vcf"
client.download(vcf_biocid, output_path=vcf_path)

# Analyze with pysam
vcf = pysam.VariantFile(vcf_path)

pathogenic_variants = []
for variant in vcf:
    if variant.info.get('CLNSIG') == 'Pathogenic':
        pathogenic_variants.append({
            'chrom': variant.contig,
            'pos': variant.pos,
            'ref': variant.ref,
            'alt': variant.alts[0]
        })

# Generate report
df = pd.DataFrame(pathogenic_variants)
print(f"Found {len(df)} pathogenic variants")

# Get file metadata and provenance
info = client.info(vcf_biocid)
print(f"Owner: {info['owner']}")
print(f"IP Asset: {info['ipId']}")

# Install via npm (recommended)
npx @genobank/biofs@latest --version

# Or install globally
npm install -g @genobank/biofs@latest

# Verify installation
biofs --version
# Output: 1.6.2

# Normal tokenization - no debug messages
biofs tokenize genome.vcf --network mainnet --title "Patient Genome"

# Output:
✅ Step 1/6: ✓ File validated: genome.vcf (5.2 GB)
✅ Step 2/6: ✓ AI Classification: VCF Germline Variants
✅ Step 3/6: ✓ Uploaded to encrypted S3 vault
✅ Step 4/6: ✓ Registered in MongoDB
✅ Step 5/6: ✓ Minting IP Asset NFT on Story Protocol mainnet...
✅ Step 6/6: ✓ BioIP Tokenization Complete!

📦 IP Asset ID:     0x1234567890abcdef...
🔗 BioCID:          biocid://v1/story/IPA/0x5021F7.../55052008714000
🏛️  PIL License:     Non-Commercial Research

# Same command with --debug flag
biofs tokenize genome.vcf --network mainnet --title "Patient Genome" --debug

# Output: (includes internal operations)
🔍 Calling get_my_granted_bioips...
🔍 Signature preview: 0xa5141ae955bba91ad46a940aef...
🔍 API Response status: Success
🔍 Full response: {
  "status": "Success",
  "status_details": {
    "granted_bioips": [...],
    "total_count": 3
  }
}
🔍 Parsed granted BioIPs count: 3
🔍 First granted file: {
  "ip_id": "0x789...",
  "filename": "reference_genome.vcf",
  "license_type": "non-commercial"
}

✅ Step 1/6: ✓ File validated: genome.vcf (5.2 GB)

🔍 Detected IP Asset ID: 0x1234567890abcdef...
🔍 Calling getBioIPDownloadURL API...
🔍 API Response: {
  "access_granted": true,
  "presigned_url": "https://s3.amazonaws.com/...",
  "license_type": "non-commercial"
}
🔍 Access granted! Filename: genome.vcf

✅ Step 2/6: ✓ AI Classification: VCF Germline Variants

🔍 Response status: Success
🔍 Full response: {
  "status": "Success",
  "bioip_id": "12345",
  "s3_path": "/biowallet/0x5f5a60.../genome.vcf",
  "mongodb_id": "67890"
}

✅ Step 3/6: ✓ Uploaded to encrypted S3 vault
✅ Step 4/6: ✓ Registered in MongoDB
✅ Step 5/6: ✓ Minting IP Asset NFT on Story Protocol mainnet...
✅ Step 6/6: ✓ BioIP Tokenization Complete!

📦 IP Asset ID:     0x1234567890abcdef...
🔗 BioCID:          biocid://v1/story/IPA/0x5021F7.../55052008714000
🏛️  PIL License:     Non-Commercial Research

# Set DEBUG environment variable (persists for session)
export DEBUG=1

# All subsequent commands will show debug output
biofs tokenize genome.vcf --network mainnet
biofs files
biofs download biocid://v1/story/IPA/0x123.../genome.vcf

# Disable debug mode
unset DEBUG

// src/lib/utils/logger.ts
export class Logger {
  static debug(message: string): void {
    if (process.env.DEBUG) {
      console.log(chalk.gray(`🔍 ${message}`));
    }
  }

  static info(message: string): void {
    console.log(chalk.blue(`ℹ️  ${message}`));
  }

  static success(message: string): void {
    console.log(chalk.green(`✅ ${message}`));
  }

  static error(message: string): void {
    console.log(chalk.red(`❌ ${message}`));
  }
}

// Global debug flag set by CLI
program
  .option('--debug', 'Enable debug output')
  .hook('preAction', (thisCommand) => {
    const opts = thisCommand.opts();
    if (opts.debug) {
      process.env.DEBUG = '1';
    }
  });

# Install BioFS CLI v1.6.2+
npm install -g @genobank/biofs@latest

# Verify node command is available
biofs node --help

# Generate configuration template
biofs node init --type lab --name "AUGenomics Lab"

# Edit lab-config.yaml with your settings:
# - node.wallet: Your lab's Ethereum wallet
# - storage.bucket: Your S3 bucket name
# - database.url: PostgreSQL connection string
# - services.anthropic_api_key: Claude API key (optional)
# - services.story_executor_key: Story Protocol executor (optional)

# Start node with configuration
biofs node start --config lab-config.yaml

# Output:
✅ Lab registry started
✅ S3 File Manager started (bucket: s3://augenomics-genomics)
✅ IPFS Pinning Service started
✅ Anthropic Proxy enabled (quota: 1M tokens/month)
✅ Story Protocol Proxy enabled (quota: 100 transactions/month)
✅ API server started on port 8080
🏗️  Lab Node running at https://biofs.augenomics.org

# View current usage and limits
biofs node quota --service anthropic

# Output:
📊 Anthropic Quota Status
   Monthly Limit:    1,000,000 tokens
   Used This Month:    450,230 tokens (45%)
   Remaining:          549,770 tokens
   Reset Date:         2025-11-01

# View Story Protocol gas usage
biofs node quota --service story

# Output:
⛽ Story Protocol Gas Quota
   Monthly Limit:    100 transactions
   Used This Month:  37 transactions (37%)
   Remaining:        63 transactions
   Reset Date:       2025-11-01

# In lab-config.yaml
replication:
  enabled: true
  interval_hours: 24
  replica_bucket: backup.augenomics.org
  replica_region: us-east-1  # Different from primary region

# Check replication status
curl http://localhost:8080/api/v1/replication/health

# Output:
{
  "success": true,
  "health": {
    "replication_enabled": true,
    "primary_bucket": "augenomics-genomics",
    "replica_bucket": "backup.augenomics.org",
    "interval_hours": 24,
    "last_run": "2025-10-24T17:00:00Z"
  }
}

{
  "name": "Biosample 55052008714000 - FASTQ Files",
  "description": "Whole Genome Sequencing FASTQ files",
  "image": "ipfs://QmXYZ.../thumbnail.png",

  // Storage location (public)
  "storage": {
    "type": "s3",
    "region": "us-east-1",
    "bucket": "test.vault.genoverse.io",
    "path": "/biowallet/0x5f5a60.../55052008714000/"
  },

  // Encrypted credentials (only decryptable by NFT owner)
  "credentials": {
    "encrypted": "0xABC123...",  // Encrypted with owner's public key
    "algorithm": "ECIES",
    "expires_at": 1735689600  // Unix timestamp
  },

  // Story Protocol IP asset reference
  "ipAsset": {
    "ipId": "0x789...",
    "parentIpId": "0x456...",  // Biosample tube NFT
    "licenseTerms": "0xDEF..."
  }
}

{
  "license_type": "PIL",
  "commercial_use": true,           // Can be used commercially
  "derivatives_allowed": true,       // Can create derivative works (VCF, etc.)
  "attribution_required": true,      // Must credit original owner
  "commercial_revenue_share": 15,    // Programmable % royalty to original owner
  "allowed_territories": ["*"],      // Global access
  "expiration": null,                // No expiration
  "revocable": true                  // Owner can revoke consent
}

// web3fuse/src/pil_verifier.c
int check_pil_license(const char *biocid,
                      const char *user_wallet,
                      const char *operation) {

    // 1. Query Story Protocol for IP asset license
    pil_terms_t terms = query_story_protocol(biocid);

    // 2. Check operation against terms
    if (strcmp(operation, "derive") == 0 && !terms.derivatives_allowed) {
        return -EACCES;  // Permission denied
    }

    // 3. Check if commercial context
    bool is_commercial = is_commercial_entity(user_wallet);
    if (is_commercial && !terms.commercial_use) {
        return -EACCES;  // Commercial use not allowed
    }

    // 4. Log access for royalty tracking
    log_access_for_royalty(biocid, user_wallet, operation);

    return 0;  // Access granted
}