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ivybiosciences/README.md

Ivy Biosciences

AI-Powered Drug Discovery Platform

License Status Node.js Python Go

Democratizing computational biology through natural language


Overview

Ivy Biosciences is a comprehensive drug discovery platform integrating 36+ AI models for molecular design, protein analysis, and biomedical research. Researchers can interact through natural language queries like "Fold this protein and dock it with aspirin" without requiring deep computational expertise.

Core Capabilities

Category Models & Tools
Protein Analysis ESMFold, binding site detection, BLAST, HMMER
Molecular Docking DiffDock, AutoDock Vina, scoring functions
Drug Design REINVENT4, fragment libraries, scaffold hopping
ADMET Profiling ADMETLab3, ProTox3, drug-likeness
Synthesis Planning AiZynthFinder, retrosynthetic routes
Literature Mining BioBERT, PubMed analysis
Genomics Scanpy, scVI for single-cell analysis

Platform Architecture

┌─────────────────────────────────────────────────────────────────────┐
│                                                                     │
│  ┌─────────────┐         ┌─────────────────┐         ┌───────────┐ │
│  │ ivybloom-cli│         │ ivybiosciences- │         │ ivylaunch │ │
│  │    (Go)     │────────▶│      next       │         │ (Remotion)│ │
│  │  CLI + TUI  │         │  (Next.js Web)  │         │  Videos   │ │
│  └─────────────┘         └────────┬────────┘         └───────────┘ │
│                                   │                                 │
│                                   ▼                                 │
│                     ┌─────────────────────────┐                    │
│                     │  ivybiosciences-modal   │                    │
│                     │   (Python + Modal.com)  │                    │
│                     │   36+ AI Models on GPU  │                    │
│                     └─────────────────────────┘                    │
│                                                                     │
└─────────────────────────────────────────────────────────────────────┘

Repositories

Next.js Web Application & API Gateway

The primary web interface featuring natural language orchestration, 3D molecular visualization (Mol*), real-time job monitoring, and comprehensive export capabilities.

Stack
Frontend Next.js 14, React 18, TypeScript 5.9+, Tailwind CSS v4, MUI v7
Database Supabase (PostgreSQL + RLS)
Auth Clerk (SSO, MFA)
State Zustand + React Query v5
Hosting Vercel
cd ~/ivybiosciences-next
npm run dev    # Start development server

Serverless GPU Compute Backend

Python-based backend running on Modal.com infrastructure with auto-scaling GPU resources (A100, A10G, T4) for computationally intensive scientific workflows.

Stack
Compute Modal.com (serverless GPU)
API FastAPI
Database PostgreSQL (async SQLAlchemy)
Cache Upstash Redis
cd ~/ivybiosciences-modal
modal deploy ivyai/server_app_modal_refactor/main.py

Terminal Interface

Production-ready Go CLI with an interactive TUI dashboard for power users, batch processing, and CI/CD integration.

Stack
Language Go 1.24+
CLI Cobra
TUI Charmbracelet (Bubbletea, Lipgloss)
Auth Browser OAuth, API keys, device flow
# Installation
brew install ivybiosciences/tap/ivybloom
# or
npm install -g ivybloom
# or
curl -fsSL https://raw.githubusercontent.com/ivybiosciences/ivybloom-cli/main/install.sh | bash

# Usage
ivybloom auth login
ivybloom run esmfold protein_sequence=MKLLVLGLVGFGVG
ivybloom tui  # Interactive dashboard

Video Generation

Remotion-based video generation for marketing and launch campaigns. Produces multiple compositions from 45s teasers to 2.5min showcases.

Stack
Framework Remotion 4.0
Frontend React 19, TypeScript
Output 1920x1080 @ 30fps MP4
cd ~/ivylaunch
npm start           # Remotion Studio
npm run build:all   # Render all compositions

Tech Stack Overview

Languages

TypeScript Python Go

Frontend

React Next.js Tailwind

Backend & Infrastructure

PostgreSQL Supabase Redis Modal Vercel

Scientific Computing

Mol* RDKit BioBERT


Key Features

  • Natural Language Interface - Query AI models conversationally
  • 36+ Integrated AI Models - ESMFold, DiffDock, REINVENT4, ADMET, and more
  • 3D Molecular Visualization - Mol* viewer for proteins and molecules
  • Real-time Job Monitoring - WebSocket-based progress tracking
  • Multi-format Export - PDF, XLSX, PPTX, SVG, PDB, SDF
  • Guest Mode - Try without account (rate-limited)
  • CLI + TUI - Full terminal interface with batch processing
  • Auto-scaling GPU - A100, A10G, T4 via Modal.com

Security

  • Clerk Authentication - SSO, MFA, session management
  • Row-Level Security - Supabase RLS policies
  • CSRF Protection - Token validation
  • Rate Limiting - Upstash-based throttling
  • Audit Logging - Comprehensive activity tracking
  • API Protection - Tiered access control

License

All public repositories use FSL-1.1-Apache-2.0 (Functional Source License).

  • Allowed: Self-hosting, internal use, building integrations
  • Not Allowed: Offering as competing SaaS (until Apache conversion in 2 years)

Documentation & Resources


Support


Advancing biotechnology through innovative and disruptive approaches

Node.js Version TypeScript Next.js GitHub followers Twitter Follow

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