Protocol Labs Ecosystem Integration

Bio-DID-Seq leverages the cutting-edge decentralized infrastructure from Protocol Labs to provide a robust, scalable, and future-proof platform for research data management.

Overview

Protocol Labs has built the foundational infrastructure for the decentralized web. Bio-DID-Seq integrates multiple Protocol Labs projects:

Technology	Purpose in Bio-DID-Seq
IPFS	Content-addressed storage for research data
Filecoin	Long-term verifiable storage with cryptographic proofs
libp2p	Peer-to-peer networking for decentralized communication
IPLD	Interoperable data model for linked data structures
UCAN	User-controlled authorization for capability-based security
Storacha	Hot storage layer for fast retrieval
Saturn CDN	Global content delivery network for IPFS
FVM	Smart contracts for programmable storage deals
drand	Distributed randomness for cryptographic operations

IPFS Integration

Content-Addressed Storage

Every piece of research data is stored using content addressing:

typescript

interface IPFSContent {
  cid: string;           // Content Identifier (cryptographic hash)
  size: number;          // File size in bytes
  links: IPFSLink[];     // DAG links to other content
  metadata: {
    did: string;         // Associated DID
    timestamp: number;   // Upload timestamp
    version: number;     // Content version
  };
}

async function uploadResearchData(file: Blob, token: string) {
  const body = new FormData();
  body.append('file', file);

  const res = await fetch('https://api.ekayana.com/api/upload', {
    method: 'POST',
    headers: { Authorization: `Bearer ${token}` },
    body,
  });

  const result = await res.json();

  return {
    cid: result.cid,
    gatewayUrl: `https://gateway.ekayana.com/ipfs/${result.cid}`,
  };
}

Uploads are pinned as part of the write, so no separate pin step is required.

Filecoin Integration

Verifiable Long-Term Storage

Filecoin provides cryptographic proofs that your research data is being stored correctly:

typescript

interface FilecoinDeal {
  dealId: string;
  cid: string;
  provider: string;
  startEpoch: number;
  endEpoch: number;
  verified: boolean;
  proofType: 'PoRep' | 'PoSt';
}

async function createStorageDeal(cid: string, duration: number) {
  const deal = await filecoinClient.createDeal({
    cid,
    duration: duration,
    replication: 3,
    verified: true,
    fastRetrieval: true
  });
  
  return deal;
}

Filecoin Virtual Machine (FVM)

Bio-DID-Seq leverages FVM for programmable storage and data DAOs, enabling decentralized governance for research data funding and access control.

libp2p Networking

Peer-to-Peer Communication

libp2p provides the networking layer for Bio-DID-Seq's decentralized architecture:

typescript

import { createLibp2p } from 'libp2p';
import { noise } from '@chainsafe/libp2p-noise';
import { kadDHT } from '@libp2p/kad-dht';
import { gossipsub } from '@chainsafe/libp2p-gossipsub';

const node = await createLibp2p({
  transports: [tcp(), webSockets()],
  connectionEncryption: [noise()],
  services: {
    dht: kadDHT({ clientMode: false }),
    pubsub: gossipsub({ allowPublishToZeroTopicPeers: true })
  }
});

// Subscribe to research data updates
await node.services.pubsub.subscribe('bio-did-seq/updates');

IPLD Data Model

Linked Data Structures

IPLD provides the data model for Bio-DID-Seq's knowledge graphs:

typescript

interface ResearchPaperDAG {
  '@context': string[];
  did: string;
  title: string;
  authors: CID[];        // Links to author DIDs
  content: CID;          // Link to full content
  references: CID[];     // Links to referenced papers
  knowledgeGraph: CID;   // Link to extracted knowledge
}

Storacha (web3.storage) Integration

Hot Storage Layer

Storacha provides the hot storage layer for fast data retrieval:

typescript

import { create } from '@web3-storage/w3up-client';

const client = await create();

async function uploadToStoracha(file: File, metadata: ResearchMetadata) {
  const space = await client.createSpace('research-project');
  await client.setCurrentSpace(space.did());
  
  const cid = await client.uploadFile(file);
  
  return {
    dataCid: cid.toString(),
    space: space.did()
  };
}

Saturn CDN

Global Content Delivery

Saturn provides a Web3 CDN for fast, verifiable content delivery:

typescript

async function retrieveViaSaturn(cid: string) {
  const response = await fetch(`https://strn.pl/ipfs/${cid}`);
  const data = await response.arrayBuffer();
  
  // Verify content hash matches CID
  const verified = await verifyCID(cid, new Uint8Array(data));
  
  return { data, verified };
}

drand Integration

Distributed Randomness

drand provides unbiased, verifiable randomness for cryptographic operations:

typescript

import { HttpChainClient, fetchBeacon } from 'drand-client';

async function getVerifiableRandomness() {
  const chain = new HttpChainClient('https://api.drand.sh');
  const beacon = await fetchBeacon(chain);
  
  return {
    round: beacon.round,
    randomness: beacon.randomness,
    signature: beacon.signature
  };
}

// Use for fair reviewer selection
async function selectReviewers(candidates: string[], numReviewers: number) {
  const beacon = await getVerifiableRandomness();
  const shuffled = deterministicShuffle(candidates, beacon.randomness);
  return shuffled.slice(0, numReviewers);
}

Architecture Diagram

┌─────────────────────────────────────────────────────────────────┐
│                    Bio-DID-Seq Platform                         │
├─────────────────────────────────────────────────────────────────┤
│  ┌──────────┐  ┌──────────┐  ┌──────────┐  ┌──────────┐         │
│  │ BioAgents│  │ Knowledge│  │   DID    │  │   UCAN   │         │
│  │  (AI/ML) │  │   Graph  │  │Management│  │   Auth   │         │
│  └────┬─────┘  └────┬─────┘  └────┬─────┘  └────┬─────┘         │
│       └─────────────┴─────────────┴─────────────┘               │
│                          │                                      │
│  ┌───────────────────────┴────────────────────────────────────┐ │
│  │                Protocol Labs Stack                         │ │
│  │  ┌─────┐ ┌────────┐ ┌──────┐ ┌────┐ ┌────┐ ┌──────┐ ┌─────┐│ │
│  │  │IPFS │ │Filecoin│ │libp2p│ │IPLD│ │UCAN│ │Saturn│ │drand││ │
│  │  └─────┘ └────────┘ └──────┘ └────┘ └────┘ └──────┘ └─────┘│ │
│  └────────────────────────────────────────────────────────────┘ │
└─────────────────────────────────────────────────────────────────┘

Resources

Solana Registry Program Dataverse Integration