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10_Security_and_Trust

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BioPro CI Bot edited this page May 16, 2026 · 1 revision

🛡️ BioPro Security & Trust Model

BioPro uses a hierarchical Trust Tree architecture to ensure that every analysis module you run is authentic, untampered, and verified by a recognized authority.

🏗️ The Trust Tree Structure

Unlike a simple "binary" lock, BioPro uses a chain of cryptographic proofs. This allows for institutional delegation (e.g., a University trusting a Lab, which in turn trusts a Researcher).

graph TD
    Root[🏛️ BioPro Core Authority] -->|Signs| Uni[🏫 University Anchor]
    Uni -->|Signs| Lab[🧪 Research Lab]
    Lab -->|Signs| Dev[👤 Developer Key]
    Dev -->|Signs| Plugin[📦 Analysis Plugin]

    subgraph "Local Trust Circle"
        User[👤 End User] -->|Manually Trusts| Indie[👤 Independent Dev]
    end
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1. The Root of Trust

The ultimate anchor is the BioPro Core Authority. Its public key is baked into the BioPro application. Every official plugin must eventually trace its heritage back to this root.

2. Verified Developers

When a developer is "Verified," it means an Authority (like BioPro or a registered University) has cryptographically signed their public key. This signature is stored in a delegation.json file on the developer's machine and bundled into every plugin they sign.

3. Organic Trust (Personal Anchors)

BioPro is an open ecosystem. If you want to run code from an independent researcher who isn't signed by a major authority:

  • The app will show a ⚠️ warning.
  • You can choose to "Trust this Developer" manually.
  • BioPro saves their ceremony to your local ~/.biopro/trusted_roots/ folder, effectively making them a "Verified Developer" on your machine only.

🔍 How Verification Works

Whenever you open a plugin, the TrustManager performs three strict checks:

  1. Integrity Check: It calculates a SHA-256 hash of every file in the plugin directory and compares it to the signed manifest. If even a single line of code is changed, the check fails.
  2. Signature Check: It verifies the digital signature of the manifest using the developer's public key.
  3. Chain Check: It recursively follows the trust_chain.json until it finds an "Anchor" (a key present in your local or hardcoded trusted roots).

🛠 For Developers: Signing your Work

To become part of the trust tree, you must:

  1. Initialize: Generate your keys using biopro-sign init.
  2. Request Delegation: Send your public.pub hex to an authority (like the BioPro team or your PI) to get a delegation.json.
  3. Sign: Run biopro-sign sign <folder> before distribution.

For technical details on the CLI, see the Developer Handbook.

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