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2.0](https://img.shields.io/badge/license-Apache%202-blue)](https://opensource.org/license/apache-2-0) | __Python__ | [![Python](https://img.shields.io/pypi/pyversions/biochatter)](https://www.python.org) |\n| __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) |\n| __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) |\n| __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) |\n\n## Description\n\n🤖 BioChatter is a community-driven Python library that connects biomedical\napplications to conversational AI, making it easy to leverage generative AI\nmodels in the biomedical domain.\n\n### 🌟 Key Features\n- Generic backend for biomedical AI applications\n- Seamless integration with multiple LLM providers\n- Native connection to BioCypher knowledge graphs\n- Extensive testing and evaluation framework\n- Living benchmark of specific biomedical applications\n\n### 🚀 Demo Applications and Utilities\n\n- [BioChatter Light](https://light.biochatter.org) - Simple Python frontend\n([repo](https://github.com/biocypher/biochatter-light))\n\n- [BioChatter Next](https://next.biochatter.org) - Advanced Next.js frontend\n([repo](https://github.com/biocypher/biochatter-next))\n\n- [BioChatter Server](https://github.com/biocypher/biochatter-server) - RESTful\nAPI server\n\n📖 Learn more in our [paper](https://www.nature.com/articles/s41587-024-02534-3)\n(self-archived [here](https://zenodo.org/records/15684945)).\n\n## Installation\n\nTo use the package, install it from PyPI, for instance using pip (`pip install\nbiochatter`) or Poetry (`poetry add biochatter`).\n\n### Extras\n\nThe package has some optional dependencies that can be installed using the\nfollowing extras (e.g. `pip install biochatter[xinference]`):\n\n- `xinference`: support for querying open-source LLMs through Xorbits Inference\n\n- `podcast`: support for podcast text-to-speech (for the free Google TTS; the\npaid OpenAI TTS can be used without this extra)\n\n- `streamlit`: support for streamlit UI functions (used in BioChatter Light)\n\n## Usage\n\nCheck out the [documentation](https://biochatter.org/) for examples, use cases,\nand more information. Many common functionalities covered by BioChatter can be\nseen in use in the [BioChatter\nLight](https://github.com/biocypher/biochatter-light) code base.  [![Built with\nMaterial for\nMkDocs](https://img.shields.io/badge/Material_for_MkDocs-526CFE?style=for-the-badge\u0026logo=MaterialForMkDocs\u0026logoColor=white)](https://squidfunk.github.io/mkdocs-material/)\n\n## 🤝 Getting involved\n\nWe are very happy about contributions from the community, large and small!\nIf you would like to contribute to BioCypher development, please refer to\nour [contribution guidelines](CONTRIBUTING.md) and the [developer\ndocs](DEVELOPER.md). :)\n\nIf you want to ask informal questions, talk about dev things, or just chat,\nplease join our community at https://biocypher.zulipchat.com!\n\n\u003e **Imposter syndrome disclaimer:** We want your help. No, really. There may be a little voice inside your head that is telling you that you're not ready, that you aren't skilled enough to contribute. We assure you that the little voice in your head is wrong. Most importantly, there are many valuable ways to contribute besides writing code.\n\u003e\n\u003e This disclaimer was adapted from the [Pooch](https://github.com/fatiando/pooch) project.\n\n## Git LFS Configuration\n\nThis repository uses Git LFS for some large files. If you're a developer and don't need to work with these files, you have two options:\n\n1. Disable Git LFS smudge globally (set once for all repositories):\n```bash\ngit lfs install --skip-smudge\ngit clone https://github.com/biocypher/biochatter.git\n```\n\n2. Skip LFS files for a one-time clone:\n```bash\nGIT_LFS_SKIP_SMUDGE=1 git clone https://github.com/biocypher/biochatter.git\n```\n\nBoth options will prevent Git LFS from downloading the large files while still allowing you to work with the repository normally.\n\n## Citation\n\nIf you use BioChatter in your work, please cite our\n[paper](https://www.nature.com/articles/s41587-024-02534-3).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiocypher%2Fbiochatter","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbiocypher%2Fbiochatter","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiocypher%2Fbiochatter/lists"}