Biocentral server

Flask-based python server using REST API that provides functionality for the biocentral frontend.

Features and modules

These are the currently provided modules:

Module	Features	Dependencies
protein_analysis	wip
embeddings	Embed protein sequences	biotrainer
ppi	Work with protein-protein interactions	hvi_toolkit
prediction_models	Train and evaluate models trained on embeddings	biotrainer
proteins	Work with protein data	taxoniq

Supported platforms

Biocentral and biocentral_server are designed to provide all common desktop operating systems (Windows, Linux, macOS). The following table gives an overview about the current test and packaging status:

OS	Tested	Packaging
Ubuntu 24.04	✅	.zip
Ubuntu 22.04	✅	.zip
Windows 10	✅	.zip
Windows 11	planned	tbd
macOS	planned	tbd

Installing and running

Make sure that you have Python 3.11 and poetry installed.

# [Ubuntu 24.04] 
# Install additional dependencies 
sudo apt-get install python3-tk
sudo apt-get install libcairo2-dev libxt-dev libgirepository1.0-dev
poetry install --extras linux

# [Windows 10/11]
poetry install
# Install torch with hardware settings for your system (see here: https://pytorch.org/get-started/locally/)
pip3 install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cu118

# Run with visual control panel
poetry run run-biocentral_server.py

# Run headless
poetry run run-biocentral_server.py --headless

Building

Building and bundling is done using pyinstaller and make.

On Windows, you can use winget to install make:

winget install ezwinports.make

Check that all build variables are correct:

make print-info

Then call build:

make build

To create a zip file with all required files for distribution:

make bundle

Note that this file only works on the operating system version you ran make build on!

Citation

Please cite the biocentral main repository if you are using biocentral_server in your scientific publication:

@Online{biocentral,
  accessed = {2024-09-10},
  author   = {Biocentral contributors},
  title    = {Biocentral - An open source bioinformatics application},
  url      = {https://github.com/biocentral/biocentral},
}