Literature Assistant

Automated AI-powered assistant to scan microbiome literature, summarize new papers, and deliver updates via email.

Project Structure

lit-assistant/
├── config/ # Configurations (ignored by git)
├── data/ # Paper data & summaries (ignored by git)
├── logs/ # Logs for debugging (ignored by git)
├── src/ # Python scripts for workflow
│ ├── fetch_papers.py
│ ├── summarize.py
│ ├── send_email.py
│ └── daily_lit_summary.py
├── environment.yml # Conda environment file
└── run_daily.sh # Cron script for daily execution

Setup Instructions

• Clone repository
• Create conda environment from environment.yml
• Populate config/config.ini
• Run run_daily.sh via cron job

Usage

Automated via cron. Outputs emailed daily.

Security

Never commit your config files (config.ini) or sensitive credentials.