biorecap: an R package for summarizing bioRxiv preprints with a local LLM

TL;DR

biorecap is an R package that enables researchers to efficiently retrieve and summarize bioRxiv preprints using local large language models, helping manage information overload in life sciences research.

Contribution

It introduces a novel R package that integrates local LLMs with bioRxiv preprint summarization, emphasizing security, flexibility, and user-friendly design.

Findings

Allows local LLM-based summarization of bioRxiv preprints

Generates timestamped CSV and HTML reports for recent preprints

Facilitates efficient updates in life sciences research workflows

Abstract

The establishment of bioRxiv facilitated the rapid adoption of preprints in the life sciences, accelerating the dissemination of new research findings. However, the sheer volume of preprints published daily can be overwhelming, making it challenging for researchers to stay updated on the latest developments. Here, I introduce biorecap, an R package that retrieves and summarizes bioRxiv preprints using a large language model (LLM) running locally on nearly any commodity laptop. biorecap leverages the ollamar package to interface with the Ollama server and API endpoints, allowing users to prompt any local LLM available through Ollama. The package follows tidyverse conventions, enabling users to pipe the output of one function as input to another. Additionally, biorecap provides a single wrapper function that generates a timestamped CSV file and HTML report containing short summaries of recent preprints published in user-configurable subject areas. By combining the strengths of LLMs with the flexibility and security of local execution, biorecap represents an advancement in the tools available for managing the information overload in modern scientific research. The biorecap R package is available on GitHub at https://github.com/stephenturner/biorecap under an open-source (MIT) license.