Genomics Daily is an automated tool that retrieves and summarizes the latest genomics publications from major scientific journals. The script:

• Searches for publications based on predefined keywords listed in keywords.txt
• Filters publications from a curated list of journals listed in journals.txt
• Retrieves papers published within the last n days, where n is set to 1 by defaut
• Utilizes Claude AI by Anthropic to generate summaries of the most relevant papers

1. Clone the repository.

   git clone https://github.com/emmecola/genomics-daily.git
   cd genomics-daily
   

2. Install anthropic, pandas and requests libraries.

   pip install -r requirements.txt

3. Obtain an API key from Anthropic.

4. Set your Anthropic API key as an environment variable.

   export ANTHROPIC_API_KEY='your_api_key_here'

5. Run the script.

   python genomics-daily.py keywords.txt journals.txt [--days-back DAYS] [--mode {simple|advanced}]

   Optional arguments:

   • days-back: Number of days to look back for papers (default: 1). Example: --days-back 7 will search for papers published in the last week.
   • mode: Processing mode (default: simple)
     • simple: briefly summarize 3 relevant papers
     • advanced: generate a longer text including several papers, and highlighting their connections

6. Optionally, you can also post a short tweet about the generated summary. To do this:

   • Install the libraries specified in requirements_bot.txt

   • Set up your BSKY_USER, BSKY_PASSWORD, MASTODON_TOKEN and MASTODON_INSTANCE environment variables

   • Run the script

     python genomics-daily-bot.py summary.md

You can easily adjust the search parameters according to your needs:

• Edit keywords.txt to update search terms
• Edit journals.txt to change the list of targeted journals
• Consider a custom time interval (set days-back argument to a specific number of days)
• Generate an in-depth longer text (set mode to advanced)

This tool is for research purposes and relies on the Anthropic API for paper summaries and tweet generation.