BioChatter
| License |  |
Python |  |
| Package |    |
Build status |   |
| Tests |  |
Docker |   |
| Development |    |
Contributions |   |
Description
🤖 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.
🌟 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
🚀 Demo Applications and Utilities
-
BioChatter Light - Simple Python frontend (repo)
-
BioChatter Next - Advanced Next.js frontend (repo)
-
BioChatter Server - RESTful API server
📖 Learn more in our paper (self-archived here).
Installation
To use the package, install it from PyPI, for instance using pip (pip install biochatter) or Poetry (poetry add biochatter).
Extras
The package has some optional dependencies that can be installed using the
following extras (e.g. pip install biochatter[xinference]):
-
xinference: support for querying open-source LLMs through Xorbits Inference -
podcast: support for podcast text-to-speech (for the free Google TTS; the paid OpenAI TTS can be used without this extra) -
streamlit: support for streamlit UI functions (used in BioChatter Light)
Usage
Check out the documentation for examples, use cases,
and more information. Many common functionalities covered by BioChatter can be
seen in use in the BioChatter
Light code base.
🤝 Getting involved
We are very happy about contributions from the community, large and small! If you would like to contribute to BioCypher development, please refer to our contribution guidelines and the developer docs. :)
If you want to ask informal questions, talk about dev things, or just chat, please join our community at https://biocypher.zulipchat.com!
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.
This disclaimer was adapted from the Pooch project.
Git LFS Configuration
This 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:
- Disable Git LFS smudge globally (set once for all repositories):
git lfs install --skip-smudge
git clone https://github.com/biocypher/biochatter.git
- Skip LFS files for a one-time clone:
GIT_LFS_SKIP_SMUDGE=1 git clone https://github.com/biocypher/biochatter.git
Both options will prevent Git LFS from downloading the large files while still allowing you to work with the repository normally.
Citation
If you use BioChatter in your work, please cite our paper.
1 maintainer
Metadata
1 maintainer
Release files for biochatter 0.14.2
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| biochatter-0.14.2.tar.gz | 94.8 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| biochatter-0.14.2-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 219.0 kB
Release files / biochatter-0.14.2.tar.gz
| Download URL | biochatter-0.14.2.tar.gz |
|---|---|
| Size | 94.8 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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| Upload date | |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
poetry/2.2.1 CPython/3.12.10 Darwin/24.6.0
|
Release files / biochatter-0.14.2-py3-none-any.whl
| Download URL | biochatter-0.14.2-py3-none-any.whl |
|---|---|
| Size | 124.2 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
poetry/2.2.1 CPython/3.12.10 Darwin/24.6.0
|
