Quickstart

Start up a BioAgent locally to build on

Local Development Setup

Quickstart

Prerequisites

• Docker installed

• pnpm installed

• Node.js installed

Setup Steps

1. Follow the setup instructions in SETUP.md

2. Start the Oxigraph server: (Or use OriginTrail's DKG)

docker run --rm -v $PWD/oxigraph:/data -p 7878:7878 ghcr.io/oxigraph/oxigraph serve --location /data --bind 0.0.0.0:7878

Now your local oxigraph instance is ready to load the processed scientific papers from the sampleJsonLds folder. More info here.

1. Load JSON-LD data into Oxigraph/OriginTrail's DKG:

pnpm run script scripts/jsonldToTriple.ts

Now your oxigraph has the triples loaded!

1. (Optional) Start PostgreSQL with vector support:

docker run --name BioAgents-db -e POSTGRES_PASSWORD=123 -p 5432:5432 -d ankane/pgvector

Alternatively, you can use pglite instead of PostgreSQL (Eliza will give you that option when starting for the 1st time)

1. Start the development server:

pnpm run dev

1. Enable the hypothesis generation service:

2. Uncomment line 25 and 27 in index.ts

Local Development

Prerequisites

• Node.js 23.3.0 or later

• pnpm 9.15.4

• Git

• Python 3

• FFmpeg

• Ghostscript

• GraphicsMagick

• PostgreSQL

System Dependencies

Ubuntu/Debian

sudo apt-get update && sudo apt-get install -y \
    git \
    python3 \
    python3-pip \
    curl \
    node-gyp \
    ffmpeg \
    libtool-bin \
    autoconf \
    automake \
    libopus-dev \
    make \
    g++ \
    build-essential \
    libcairo2-dev \
    libjpeg-dev \
    libpango1.0-dev \
    libgif-dev \
    openssl \
    libssl-dev \
    libsecret-1-dev \
    ghostscript \
    graphicsmagick

macOS

brew install \
    git \
    python3 \
    ffmpeg \
    ghostscript \
    graphicsmagick \
    libtool \
    autoconf \
    automake \
    opus \
    cairo \
    pango \
    libgif \
    openssl

Project Setup

1. Clone the repository:

git clone https://github.com/bio-xyz/BioAgents.git
cd BioAgents

1. Install pnpm:

npm install -g pnpm@9.15.4

1. Install dependencies (Ingnore the bun.lock file for now):

pnpm install

1. Set up environment variables:

cp .env.example .env

For basic working just add OPENAI_API_KEY= and ANTHROPIC_API_KEY= and remove the rest (important)

Edit .env with your configuration values.

1. Start the development server:

pnpm run dev

Database Setup (OPTIONAL)

1. Install and start PostgreSQL (docker preferred)

2. Create a database

3. Update POSTGRES_URL in your .env file with your database credentials