vianu

Together we are building an Open Source Community for Life Sciences.

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Vianu is a Python package designed for developers working in the life sciences and healthcare sectors. It provides access to a variety of tools and workflows, allowing users to quickly build, validate, and deploy data-driven applications.

Available Tools

• Lasa: A tool for phonetic comparison of novel drug names with authorized ones from different locations.
• FraudCrawler: A data ingestion and transformation pipeline for real-world healthcare data.
• SpoCK: A tool to search public websites for spotting adverse drug reactions
• DrugSafetyCompare: A tool to search for published drug labels and compare their safety profiles. See in action

Installation

To install Vianu, use the following command:

bash pip install vianu

Alternatively, you can install vianu from source:

bash git clone https://github.com/smc40/vianu.git cd vianu poetry install poetry shell

Usage

Lasa

TBD

Launch a Demo App

Launch a Demo Pipeline

bash cd vianu/lasa poetry install poetry shell python -m vianu.tools.tici.launch_demo_pipeline

FraudCrawler

Launch a Demo App

bash python vianu/fraudcrawler/launch_demo_app.py

Launch a Demo Pipeline

bash python -m vianu.fraudcrawler.launch_demo_pipeline

DrugSafetyCompare

DrugSafetyCompare is a tool designed to help users search for drugs, retrieve product information from Germany and Switzerland, extract adverse events, and compare side effects using SOC (System Organ Class) classification. Leveraging OpenAI's GPT-4 and interactive visualization tools, DrugSafetyCompare provides a comprehensive overview of drug safety profiles.

Launch a Demo App

To lauch the demo app do the following:

bash poetry install poetry shell python vianu/tools/drugsafetycompare/launch_demo_app_count.py Or simply launch the starter-script: ```bash vianudrugsafetycompareapp

```

Launch a Demo Pipeline

bash poetry install poetry shell python -m vianu.drugsafetycompare.launch_demo_pipeline

SpoCK

Launch a Demo App

bash python vianu/spock/launch_demo_app.py

Launch a Demo Pipeline

bash python -m vianu.spock.launch_demo_pipeline

Run tests

To run all tests with a covarage report run: bash pytest --cov-report=html tests/tests-*/* -s

Contributing

We welcome contributions from the community! Please read the CONTRIBUTING.md for guidelines on how to get started.

Code of Conduct

We strive to create a welcoming environment for everyone. Please read our Code of Conduct for more details.

License

This project is licensed under the MIT License.

Feedback and Support

For any issues or feature requests, please use the GitHub Issues page.

Acknowledgments

We thank all contributors and the broader open-source community for their support and feedback.