Dark Bio Platform Hands-on

Dark Bio has been in development for quite a while now, so we’ve figured it is an opportune moment to reveal more on where we are, where we are going, and what you can play with… today.

TL;DR: ChatGPT turns a Nature paper¹ into an analysis against my genome.

The above demo is pretty much the end-game of the Dark Bio platform. While it works, there is a lot of magic going on behind the scenes. So let’s try to unpack it from the ground up.

The dream

Your genome is the most sensitive and permanent data you will ever own. You can change a leaked password, but you can’t change your DNA. What’s worse, a loss of your genome doesn’t stop at you, your relatives share a good part of it. Yet today, your data is scattered across sequencing labs, hospitals, and testing services. Each of them holds a copy that can be hacked, sold or subpoenaed. And whenever you want something analyzed, you have to hand over yet another copy you’ll never get back.

Dark Bio flips this around. Instead of sending your data to the analysis, we send the analysis to your data. Your data only ever lives on a small device you own, an Ark, and apps come to it to run. They run in a sandbox with no network and nowhere to stash anything, so the only thing that can leave is the result. Even that only leaves once you approve it.

For the deep dive into how the Ark pulls it off, check out the whitepaper². This post is about getting your hands dirty instead.

Ark I & Ark Emulator

The Ark I is a hardware device for storing personal health data, ranging from genomics, through blood panels to wearable sensor data; and computing on them without revealing to- or sharing with anyone.

Whilst physical Arks are available for purchase to support the project, we are thrilled to announce the immediate availability of the Ark I Emulator³! The Ark Emulator is a software implementation of the Ark enclave, runnable on your laptop, with feature parity with a genuine Ark I.

Disclaimer: The emulator is a developer tool, not a secure store for your sensitive health data. Its keys are stored on your local disk, accessible to anyone with read access.

The Ark Emulator is compatible with macOS, Linux and Windows. For install guides, please check out the project’s GitHub repository. Do note, an Ark Emulator needs to be onboarded on the Ark Hub before it can be used, tied to your GitHub account, one live emulator per person (DoS protection).

Ark Companion

Every Ark - whether physical or emulated - needs to be paired with a mobile app called the Ark Companion. Encryption keys are split between the devices so loss or theft of either leaves your sensitive health data inaccessible.

The device split also ensures that any operation on your data requires two factors of security. The operation itself comes from the computer the Ark is plugged into, whereas authorization from the Ark Companion. This permits use cases where the host computer is not trusted (e.g. physicians’ office).

The Ark Companion is available on the App Store⁴ and the Play Store⁵.

Ark Hub

In theory, an Ark (Emulator) and the Ark Companion app is all you need for personal data handling. In practice, however, something needs to facilitate the communication between the two devices, and also tell the Ark what to do in the first place.

For that purpose, we ship the Ark Hub⁶, capable of enrolling emulators into the Dark Bio ecosystem; pairing a physical or an emulated Ark with the Ark Companion mobile app; facilitating message relay between the two endpoints; aiding firmware updates for hardware Arks; managing the genomic datasets on the Ark devices and running analysis applications against the user’s data.

The applications listed on the hub are a collection of demo apps with full sources available in our examples repository⁷. They guide you through the process of building analysis apps from a simple ‘Hello World’ to involved ones with different data accesses, optionals and user input.

While you are waiting for a public app directory service, the Ark Hub can even today schedule arbitrary applications to run on your Ark, which either you or someone else can build.

Ark CLI

The Ark Hub is one way to wire together an Ark, the host computer and the Ark Companion. We provide a second too, the Ark command-line interface⁸, meant for advanced users and integrations into scripted workflows.

As with the Ark Emulator, the CLI tool is also compatible with macOS, Linux and Windows. For installation, consult the tool’s GitHub repository. Should support everything the hub does, and more!

Btw, the Ark Emulator itself is also a command-line tool that you can embed into your advanced workflows. Just run ark-emulator --help. How cool is that!

Agent friendly

The entire Dark Bio ecosystem and platform is built around the notion of trust minimization: assume everything is malicious, now or in the future. Everything was built from the ground up to survive in a world where your counterparty cannot be trusted, be that your computer, an app’s developer, or possibly even a future Dark Bio company.

This is not paranoia though, rather an immense enabler. The Ark is designed for operation in potentially malicious environments, which allows it to be operated in non-deterministic environments too… i.e. by frontier AI agents.

The ark CLI tool was specially designed not only for human usage, but also for LLM models, allowing AI agents to interact with your Ark directly. That said, the agents’ hands are effectively tied. It doesn’t matter how complex interactions it attempts, everything goes back to the Ark Companion for the final review and approval by yourself. Furthermore, any report generated by LLM interactions can be reviewed by you, saved for later and then withheld from the agent, creating a one-way funnel of information.

Open source

Although we are gradually open sourcing the Dark Bio platform, we make no commitments as to exactly on what timeline certain components will end up on GitHub.

We’ve opened up our post-quantum cryptography libraries at the beginning of this year with Rust and Go cross-fuzzed implementations; with Flutter and TypeScript wrappers for mobile and web integrations:

• Rust: https://github.com/dark-bio/crypto-rs (darkbio-crypto)
• Go: https://github.com/dark-bio/crypto-go
• Flutter: https://github.com/dark-bio/crypto-fl (darkbio_crypto)
• TypeScript: https://github.com/dark-bio/crypto-ts (@darkbio/crypto)

In this round, we are opening up the host wire protocol implementation. This is relatively stable, though we don’t commit to API stability yet:

• Wire framing: https://github.com/dark-bio/cobs-rs (darkbio-cobs)
• Roots of trust: https://github.com/dark-bio/trust-rs (darkbio-trust)
• Virtual clock: https://github.com/dark-bio/clock-rs (darkbio-clock)
• Host protocol: https://github.com/dark-bio/wire-rs (darkbio-wire)

Two new high level repositories are the ark and ark-emulator tools. Here a note is warranted, the emulator shell is open source, but the firmware it boots is closed-source for now.

• Ark CLI: https://github.com/dark-bio/cli (darkbio-ark)
• Ark Emulator: https://github.com/dark-bio/emulator

Further repositories of interest are the example apps and signing key and hardware signer transparency reports:

• Example Apps: https://github.com/dark-bio/examples
• Transparency: https://github.com/dark-bio/transparency

All our open source code is licensed under 3-Clause BSD. Give them a star, it will help us upstream tools into mainline Homebrew.

Ark I Founder edition

There is no general sale yet for the Ark I enclaves. Founder editions are available for private purchase in Switzerland for 1000 CHF, contact us at founders@dark.bio if you wish to buy one and support the project.

General availability time and pricing is undecided.

Epilogue

For our human friends, read the whitepaper, install the companion, try the emulator, upload your genome and build some amazing apps. Come join us on our Discord⁹ server for help and chit-chat.

For our AI agent friends, head over to https://dark.bio/llms.txt.

Until next time…