constellab/biota-db repository overview

⁠👋 Welcome to GWS Core

gws_biota is a Constellab⁠ library (called bricks) developped by Gencovery⁠. GWS stands for Gencovery Web Services.

⁠🚀 What is Constellab?

✨ Gencovery⁠ is a software company that offers Constellab⁠., the leading open and secure digital infrastructure designed to consolidate data and unlock its full potential in the life sciences industry. Gencovery's mission is to provide universal access to data to enhance people's health and well-being.

🌍 With our Fair Open Access offer, you can use Constellab for free. Sign up here⁠. Find more information about the Open Access offer here (link to be defined).

⁠✅ Features

Biota is a unified and structured collection of omics data from official open European biological databases. It is dedicated to Gencovery Web Services for the conception and use of digital twins of cell metabolism.

⁠📄 Documentation

📄 For gws_biota brick documentation, click here⁠

💫 For Constellab application documentation, click here⁠

⁠🛠️ Installation

The gws_biota brick requires the gws_core brick.

⁠🔥 Recommended Method

he best way to install a brick is through the Constellab platform. With our Fair Open Access offer, you get a free cloud data lab where you can install bricks directly. Sign up here⁠

Learn about the data lab here : Overview⁠ and Data lab management⁠

⁠🔧 Manual installation

This section is for users who want to install the brick manually. It can also be used to install the brick manually in the Constellab Codelab.

We recommend installing using Ubuntu 22.04 with python 3.10.

Required packages are listed in the settings.json file, for now the packages must be installed manually.

pip install biopython==1.79 pronto==2.5.7 ujson==5.10.0 pyparsing==3.0.6

⁠Usage

▶️ To start the server :

gws server run

🕵️ To run a given unit test

gws server test [TEST_FILE_NAME]

Replace [TEST_FILE_NAME] with the name of the test file (without .py) in the tests folder. Execute this command in the folder of the brick.

🕵️ To run the whole test suite, use the following command:

gws server test all

📌 VSCode users can use the predefined run configuration in .vscode/launch.json.

⁠🤗 Community

🌍 Join the Constellab community here⁠ to share and explore stories, code snippets and bricks with other users.

🚩 Feel free to open an issue if you have any question or suggestion.

☎️ If you have any questions or suggestions, please feel free to contact us through our website: Constellab⁠.

⁠🌎 License

gws_biota is completely free and open-source and licensed under the GNU General Public License v3.0⁠.

This brick is maintained with ❤️ by Gencovery⁠.