BioVault Mobile App

A privacy-first genomic analysis app that serves as a gateway to the collaborative BioVault research network. Load your genetic data for local analysis, discover insights, and connect to the world of collaborative genomics.

Features

• 🧬 My DNA - Load and manage genetic data files locally on your device (23andMe, AncestryDNA, etc.)
• 🔍 Insights - Run ClinVar analysis and discover genetic insights
• 🌐 Research - Connect to the BioVault collaborative genomics network
• 📊 Web-Only Features - Enhanced analytics, network participants, biobanks, pipelines, and more

Development Setup

Prerequisites

• Node.js
• npm or yarn
• Expo CLI
• iOS Simulator (for iOS development)
• Android Studio/Emulator (for Android development)

Quickstart

Install NVM:

curl -o- https://raw.githubusercontent.com/nvm-sh/nvm/v0.40.3/install.sh | bash

brew install fastlane cocoapods

Get node 23:

nvm install 23.6.1
nvm alias default 23.6.1

Install packages:

npm install

Expo Doctor:

npx expo-doctor

iOS:

rm -rf ios
npm run cargo-ios -- ios
npm run prebuild
npm run device

Or this script:

./ios.sh

Installation

1. Clone and install dependencies:

   git clone <repository-url>
   cd biovault-app
   npm install

2. Start the development server:

   npm run start

Platform-Specific Setup

📱 iOS Development

Option 1: Physical Device (Recommended)

1. Install the BioVault Dev app from the Expo Dashboard
2. Open the BioVault Dev app on your iOS device
3. Scan the QR code generated by npm run start
4. Your device will connect to your development server

Option 2: iOS Simulator

• Use Radon Extension for VS Code/Cursor
• Or install Expo Orbit for easy simulator management
• Press i in the terminal after running npm run start

🤖 Android Development

Option 1: Physical Device (Recommended)

1. Download the latest BioVault APK from the Expo Dashboard
2. Install the APK on your Android device
3. Open the BioVault app
4. Scan the QR code generated by npm run start
5. Your device will connect to your development server

Option 2: Android Emulator

• Use Radon Extension for VS Code/Cursor
• Or install Expo Orbit for easy emulator management
• Press a in the terminal after running npm run start

🌐 Web Development

1. Run npm run start
2. Press w in the terminal, or
3. Open your browser to http://localhost:8081 (or the port shown in terminal)
4. The web version includes additional tabs not available on mobile

Rust Module Development

This app includes a native Rust module (modules/expo-biovault) for high-performance genome file parsing.

Prerequisites for Rust Development

• Rust toolchain: curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh
• iOS development: Xcode and iOS targets
• Android development: Android Studio, NDK, and Android targets

Setting Up Rust Targets

# iOS targets
rustup target add aarch64-apple-ios          # iOS device
rustup target add aarch64-apple-ios-sim      # iOS simulator

# Android targets
rustup target add aarch64-linux-android      # Android ARM64
cargo install cargo-ndk                      # Android NDK helper

Building Rust Libraries

For iOS Simulator (development):

npm run cargo-ios -- --target='ios-sim'

For iOS Device:

npm run cargo-ios -- --target='ios'

For Android:

npm run cargo-android

Android NDK Setup

The Android build requires NDK configuration. Install via Android Studio:

• Android Studio → SDK Manager → SDK Tools → NDK (Side by side)

The build scripts automatically configure the NDK toolchain.

Module Structure

modules/expo-biovault/
├── expo-module.config.json     # Module configuration
├── index.ts                    # JS exports
├── src/
│   └── ExpoBiovaultModule.ts    # TypeScript definitions
├── ios/
│   ├── ExpoBiovault.podspec     # iOS CocoaPods spec
│   ├── ExpoBiovaultModule.swift # iOS native implementation
│   └── rust/                   # iOS Rust libraries (auto-generated)
└── android/
    ├── build.gradle
    ├── src/main/
    │   ├── java/.../ExpoBiovaultModule.kt  # Android native implementation
    │   └── jniLibs/                        # Android Rust libraries (auto-generated)
    └── AndroidManifest.xml

Adding New Rust Functions

1. Add to Rust (biovault_rust_lib/src/lib.rs):

   #[unsafe(no_mangle)]
   pub extern "C" fn your_function(input: *const c_char) -> *mut c_char {
       // Your implementation
   }

2. Add iOS binding (modules/expo-biovault/ios/ExpoBiovaultModule.swift):

   @_silgen_name("your_function")
   func your_function(_ input: UnsafePointer<CChar>) -> UnsafeMutablePointer<CChar>?
   
   AsyncFunction("yourFunction") { (input: String) -> String in
       // Convert strings and call Rust function
   }

3. Add Android binding (modules/expo-biovault/android/.../ExpoBiovaultModule.kt):

   external fun yourFunction(input: String): String
   
   AsyncFunction("yourFunction") { input: String ->
       yourFunction(input)
   }

4. Export from module (modules/expo-biovault/index.ts):

   export async function yourFunction(input: string): Promise<string> {
   	return await ExpoBiovaultModule.yourFunction(input)
   }

5. Rebuild libraries:

   npm run cargo-ios -- --target='ios-sim'  # or 'ios' for device
   npm run cargo-android

Troubleshooting

"Cannot find native module" error:

• Run npx expo prebuild --clean to regenerate native projects
• For device testing, use npx expo run:ios --device (not Expo Dev Client)

iOS architecture mismatch:

• Use --target='ios-sim' for simulator
• Use --target='ios' for device
• The build scripts automatically copy the correct library

Android linking errors:

• Ensure NDK is installed via Android Studio
• Check that .so files are in android/src/main/jniLibs/arm64-v8a/

Development Tools

Recommended Extensions

• Radon Extension - Integrated simulator management for VS Code/Cursor
• Expo Orbit - Desktop app for managing simulators and builds

Testing the Rust via CLI

./cli parse --file /Users/madhavajay/dev/sequencing.com/23andme/genome_Madhava_Jay_v4_Full_20250611034825.zip --output madhava

Adding a new Rust method to the app

Add your FFI

// lib.rs
#[unsafe(no_mangle)]
pub unsafe extern "C" fn process_23andme_file(

// ExpoBioVaultModule.swift
@_silgen_name("process_23andme_file")

func process_23andme_file(_ inputPath: UnsafePointer<CChar>, _ customName: UnsafePointer<CChar>, _ outputDir: UnsafePointer<CChar>) -> UnsafeMutablePointer<CChar>?
///

public class ExpoBiovaultModule: Module {
  public func definition() -> ModuleDefinition {
    Name("ExpoBiovault")

    AsyncFunction("processGenomeFile") { (inputPath: String, customName: String, outputDir: String) -> String in
      let inputCString = inputPath.cString(using: .utf8)!
      let nameCString = customName.cString(using: .utf8)!
      let outputCString = outputDir.cString(using: .utf8)!
      
      guard let resultPtr = process_23andme_file(inputCString, nameCString, outputCString) else {
        throw Exception(name: "ProcessingError", description: "Failed to process genome file")
      }
      
      let result = String(cString: resultPtr)
      free_string(resultPtr)
      return result
    }
  }
}

TypeScript:

// ExpoBioVaultModule.ts
declare class ExpoBiovaultModule extends NativeModule {
	processGenomeFile(inputPath: string, customName: string, outputDir: string): Promise<string>
}

// index.ts
import ExpoBiovaultModule from './src/ExpoBiovaultModule'

export async function processGenomeFile(
	inputPath: string,
	customName: string,
	outputDir: string
): Promise<string> {
	return await ExpoBiovaultModule.processGenomeFile(inputPath, customName, outputDir)
}