dhanshreea/ersilia

The Ersilia Model Hub, a repository of AI/ML models for infectious and neglected disease research.

🎉 Welcome to the Ersilia Model Hub 🌟

Table of Contents

1. Project Description
2. Quick start guide
3. Contribute
4. License and citation
5. About us

Project Description

The Ersilia Model Hub is a unified platform of pre-trained AI/ML models dedicated to 🦠 infectious and neglected disease research. Our mission is to offer an open-source, 🛠 low-code solution that provides seamless access to AI/ML models for 💊 drug discovery. Models housed in our hub come from two sources:

1. 📚 Published models from literature (with due third-party acknowledgement)
2. 🛠 Custom models developed by the Ersilia team or our valued contributors.

• Read more about the project in the Ersilia Book
• Browse available models in the Ersilia Model Hub

Quick Start Guide

Please check the package requirements in the Installation Guide. The next steps are a quickstart guide to installing Ersilia.

1. Create a conda environment and activate it

   conda create -n ersilia python=3.10
   conda activate ersilia

2. Clone this repository and install with pip

   git clone https://github.com/ersilia-os/ersilia.git
   cd ersilia
   pip install -e .

3. Once the Ersilia Model Hub is installed, you can use the CLI to run predictions. First, select a model from the Ersilia Model Hub and fetch it:

   ersilia fetch retrosynthetic-accessibility

4. Generate a few (5) example molecules, to be used as input. The example command will generate the adequate input for the model in use

   ersilia example retrosynthetic-accessibility -n 5 -f my_molecules.csv

5. Then, serve your model:

   ersilia serve retrosynthetic-accessibility

6. And run the model:

   ersilia run -i my_molecules.csv -o my_predictions.csv

7. Finally, close the service when you are done.

   ersilia close

8. If you no longer want to use the model, you can delete it.

   ersilia delete retrosynthetic-accessibility

Please see the Ersilia Book for more examples and detailed explanations.

Contribute

The Ersilia Model Hub is a Free, Open Source Software and we highly value new contributors. There are several ways in which you can contribute to the project:

• A good place to start is checking open issues.
• If you have identified a bug in the code, please open a new issue using the bug template.
• Share any feedback with the community using GitHub Discussions for the project
• Check our Contributing Guide for more details

The Ersilia Open Source Initiative adheres to the Contributor Covenant code of conduct.

Submit a New Model

If you want to incorporate a new model in the platform, open a new issue using the model request template or contact us using the following form.

After submitting your model request via an issue (suggested), a maintainer will review your request. If they /approve your request, a new model respository will be created for you to fork and use! There is a demo repository explaining the steps one-by-one.

License and Citation

This repository is open-sourced under the GPL-3 License. Please cite us if you use it!

About Us

The Ersilia Open Source Initiative is a Non Profit Organization (1192266) with the mission is to equip labs, universities and clinics in LMIC with AI/ML tools for infectious disease research.

Help us achieve our mission or volunteer with us!