diff --git a/README.md b/README.md index aec45b96..cbf69c22 100644 --- a/README.md +++ b/README.md @@ -5,35 +5,33 @@ | __License__ | [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT) | __Python__ | [![Python](https://img.shields.io/pypi/pyversions/biochatter)](https://www.python.org) | | __Package__ | [![PyPI version](https://img.shields.io/pypi/v/biochatter)](https://pypi.org/project/biochatter/) [![Downloads](https://static.pepy.tech/badge/biochatter)](https://pepy.tech/project/biochatter) [![DOI](https://zenodo.org/badge/650181006.svg)](https://zenodo.org/doi/10.5281/zenodo.10777945) | __Build status__ | [![CI](https://github.com/biocypher/biochatter/actions/workflows/ci.yaml/badge.svg)](https://github.com/biocypher/biochatter/actions/workflows/ci.yaml) [![Docs](https://github.com/biocypher/biochatter/actions/workflows/docs.yaml/badge.svg)](https://github.com/biocypher/biochatter/actions/workflows/docs.yaml) | | __Tests__ | [![Coverage](https://raw.githubusercontent.com/biocypher/biochatter/coverage/coverage.svg)](https://github.com/biocypher/biochatter/actions/workflows/ci.yaml) | __Docker__ | [![Latest image](https://img.shields.io/docker/v/biocypher/chatgse)](https://hub.docker.com/repository/docker/biocypher/chatgse/general) [![Image size](https://img.shields.io/docker/image-size/biocypher/chatgse/latest)](https://hub.docker.com/repository/docker/biocypher/chatgse/general) | -| __Development__ | [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) [![Code style](https://img.shields.io/badge/code%20style-black-000000.svg)](https://black.readthedocs.io/en/stable/) | __Contributions__ | [![PRs Welcome](https://img.shields.io/badge/PRs-welcome-brightgreen.svg?style=flat-square)](http://makeapullrequest.com) [![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg)](CONTRIBUTING.md) | +| __Development__ | [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) [![Code style](https://img.shields.io/badge/code%20style-black-000000.svg)](https://black.readthedocs.io/en/stable/) [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff) | __Contributions__ | [![PRs Welcome](https://img.shields.io/badge/PRs-welcome-brightgreen.svg?style=flat-square)](http://makeapullrequest.com) [![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg)](CONTRIBUTING.md) | ## Description -Generative AI models have shown tremendous usefulness in increasing -accessibility and automation of a wide range of tasks. Yet, their application to -the biomedical domain is still limited, in part due to the lack of a common -framework for deploying, testing, and evaluating the diverse models and -auxiliary technologies that are needed. This repository contains the -`biochatter` Python package, a generic backend library for the connection of -biomedical applications to conversational AI. +🤖 BioChatter is a community-driven Python library that connects biomedical +applications to conversational AI, making it easy to leverage generative AI +models in the biomedical domain. -The library is described in [this preprint](https://arxiv.org/abs/2305.06488) and -used in various demo applications for showcasing its use: +### 🌟 Key Features +- Generic backend for biomedical AI applications +- Seamless integration with multiple LLM providers +- Native connection to BioCypher knowledge graphs +- Extensive testing and evaluation framework +- Living benchmark of specific biomedical applications -- a simple Python-based frontend called [BioChatter -Light](https://light.biochatter.org), which we develop at -https://github.com/biocypher/biochatter-light; +### 🚀 Demo Applications and Utilities -- an advanced Next.js-based frontend called [BioChatter -Next](https://next.biochatter.org), which we develop at -https://github.com/biocypher/biochatter-next; +- [BioChatter Light](https://light.biochatter.org) - Simple Python frontend +([repo](https://github.com/biocypher/biochatter-light)) -- a RESTful API server for use by the Next frontend (and any other REST-based -application) at https://github.com/biocypher/biochatter-server. +- [BioChatter Next](https://next.biochatter.org) - Advanced Next.js frontend +([repo](https://github.com/biocypher/biochatter-next)) -BioChatter is part of the [BioCypher](https://github.com/biocypher) ecosystem, -connecting natively to BioCypher knowledge graphs. The BioChatter paper is -being written [here](https://github.com/biocypher/biochatter-paper). +- [BioChatter Server](https://github.com/biocypher/biochatter-server) - RESTful +API server + +📖 Learn more in our [paper](https://www.nature.com/articles/s41587-024-02534-3). ## Installation @@ -80,16 +78,7 @@ please join our community at https://biocypher.zulipchat.com! Check out [this repository](https://github.com/csbl-br/awesome-compbio-chatgpt) for more info on computational biology usage of large language models. -## Troubleshooting - -If you're on Apple Silicon, you may encounter issues with the `grpcio` -dependency (`grpc` library, which is used in `pymilvus`). If so, try to install -the binary from source after removing the installed package from the virtual -environment from -[here](https://stackoverflow.com/questions/72620996/apple-m1-symbol-not-found-cfrelease-while-running-python-app): +## Citation -```bash -pip uninstall grpcio -export GRPC_PYTHON_LDFLAGS=" -framework CoreFoundation" -pip install grpcio==1.53.0 --no-binary :all: -``` +If you use BioChatter in your work, please cite our +[paper](https://www.nature.com/articles/s41587-024-02534-3).