https://github.com/biocentral/biocentral_server
Compute functionality for biocentral.
https://github.com/biocentral/biocentral_server
embeddings fastapi models openapi protein protein-language-model protein-protein-interaction python
Last synced: 9 days ago
JSON representation
Compute functionality for biocentral.
- Host: GitHub
- URL: https://github.com/biocentral/biocentral_server
- Owner: biocentral
- License: gpl-3.0
- Created: 2024-07-22T14:37:20.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2025-12-17T17:28:24.000Z (about 2 months ago)
- Last Synced: 2025-12-21T05:07:23.724Z (about 1 month ago)
- Topics: embeddings, fastapi, models, openapi, protein, protein-language-model, protein-protein-interaction, python
- Language: Python
- Homepage: https://biocentral.cloud
- Size: 3.82 MB
- Stars: 3
- Watchers: 1
- Forks: 3
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: Changelog.md
- Contributing: Contributing.md
- License: LICENSE
Awesome Lists containing this project
README
# biocentral_server
Compute functionality for biocentral. Provided via a dockerized FastAPI server.
## Features and modules
These are the currently provided modules:
| Module | Features | External Dependencies |
|---------------|:-----------------------------------------------:|:---------------------:|
| embeddings | Embed protein sequences | [biotrainer] |
| ppi | Work with protein-protein interactions | [hvi_toolkit] |
| predict | Create predictions from pre-trained models | [TMbed], [VespaG] |
| custom_models | Train and evaluate models trained on embeddings | [biotrainer] |
| proteins | Work with protein data | [taxoniq] |
| plm_eval | Automatically evaluate protein language models | [biotrainer], [PBC] |
[biotrainer]: https://github.com/sacdallago/biotrainer
[hvi_toolkit]: https://github.com/SebieF/hvi_toolkit
[taxoniq]: https://github.com/taxoniq/taxoniq
[PBC]: https://github.com/Rostlab/pbc
[TMbed]: https://github.com/BernhoferM/TMbed
[VespaG]: https://github.com/JSchlensok/VespaG/
## Installing and running
See the docs on [how to get started](/docs/getting_started.md) with biocentral_server.
For development, see the [development guide](/docs/Contributing/development_setup.md).
## Citation
Please cite the [biocentral main repository](https://github.com/biocentral/biocentral) if you are using
biocentral_server in your scientific publication:
```text
@Online{biocentral,
accessed = {2024-09-10},
author = {Biocentral contributors},
title = {Biocentral - An open source bioinformatics application},
url = {https://github.com/biocentral/biocentral},
}
```