Bio x AI Hackathon
  • Welcome to the Bio x AI Hackathon
  • Getting Started
    • Quickstart
    • Important Links
  • Developers
    • BioAgents
    • CoreAgents
    • Eliza Agent Framework
    • Knowledge Graphs
    • .cursorrules
    • Starter-repos
    • Plugin Guide
  • Vision and Mission
    • Bio x AI Hackathon
    • The Problems in Science
    • TechBio
    • Guidance from the Judges
      • Important Datasets and Code Repositories
      • Reading List
      • Common Mistakes for Developers new to Academia
    • Hackathon Ideas
      • Full Projects
        • The Complexity Slider - Finding Hypotheses at the Limits of Human Knowledge
        • [Hard Mode] Metadata Generation on datasets with No Manuscript or Code Associated
        • Inverse Reproducibility - Given Manuscript and Data, Make the Code
        • Atlas of Research Methods Formatted for Agentic Reuse
        • Utilizing Knowledge Graphs for the Detection of Potential Null Results
        • Creating an Iterative Publication Stack by Linking Together Existing Tooling
        • Longevity Atlas: Building a Decentralized Knowledge Network with Agentic Research Hypothesis Engine
        • CoreAgent Track - Opportunities to work with BioDAOs
        • SpineDAO Chronos Project Spec
      • Individual Plugins
        • Plug-ins for every piece of research tooling known to humankind
        • Reproducibility Assistant - Code Cleaning, Dockerization, etc
        • Finding and Differentiating Cardinal vs Supporting Assertions
        • [Easier Mode] Metadata Generation on Datasets Given the Manuscript and Code Repository
        • Sentiment Analysis on Existing Citations, Dissenting vs Confirming
        • Agentic Metadata Template Creation for Standard Lab Equipment
  • Ops
    • Calendar
      • Key Dates
      • Office Hours
    • Judges and Mentors
      • Communicating to Judges and Mentors
      • BioAgent Judging Panel
      • CoreAgent Judging Panel
      • Mentors
    • Prize Tracks
    • Hackathon Rules
    • Kickoff Speakers
    • FAQ
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  1. Getting Started

Quickstart

Start up a BioAgent locally to build on

PreviousWelcome to the Bio x AI HackathonNextImportant Links

Last updated 1 month ago

Local Development Setup

Prerequisites

  • Docker installed

  • pnpm installed

  • Node.js installed

Setup Steps

  1. Follow the setup instructions in

  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 .

  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:

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

Uncomment line 25 and 27 in

SETUP.md
here
index.ts