Metadata-Version: 2.1
Name: ersilia
Version: 0.1.24
Summary: A hub of AI/ML models for open source drug discovery and global health
Home-page: https://github.com/ersilia-os/ersilia
Author: Ersilia Open Source Initiative
Author-email: hello@ersilia.io
License: GPLv3
Project-URL: Landing page, https://ersilia.io
Project-URL: Models, https://ersilia.io/model-hub
Project-URL: Source Code, https://github.com/ersilia-os/ersilia/
Keywords: drug-discovery machine-learning ersilia open-science global-health model-hub infectious-diseases
Platform: UNKNOWN
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Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
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Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
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<div id="top"></div>
<img src="https://github.com/ersilia-os/ersilia/blob/master/assets/Ersilia_Plum.png" height="70">

# Welcome to the Ersilia Model Hub

[![Donate](https://img.shields.io/badge/Donate-PayPal-green.svg)](https://www.paypal.com/uk/fundraiser/charity/4145012) [![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-v2.0%20adopted-ff69b4.svg)](CODE_OF_CONDUCT.md) [![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-yellow.svg)](https://www.gnu.org/licenses/agpl-3.0) [![DOI](https://zenodo.org/badge/277068989.svg)](https://zenodo.org/badge/latestdoi/277068989)

[![documentation](https://img.shields.io/badge/-Documentation-purple?logo=read-the-docs&logoColor=white)](https://ersilia.gitbook.io/ersilia-book/) [![PyPI version fury.io](https://badge.fury.io/py/ersilia.svg)](https://pypi.python.org/pypi/ersilia/) [![Python 3.7](https://img.shields.io/badge/python-3.7-blue.svg)](https://www.python.org/downloads/release/python-370/) [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg?logo=Python&logoColor=white)](https://github.com/psf/black)

## Table of Contents

1. [Project Description](https://github.com/ersilia-os/ersilia#project-description)
2. [Quick start guide](https://github.com/ersilia-os/ersilia#quick-start-guide)
3. [Contribute](https://github.com/ersilia-os/ersilia#contribute)
4. [License and citation](https://github.com/ersilia-os/ersilia#license-and-citation)
5. [About us](https://github.com/ersilia-os/ersilia#about-us)

## Project Description

The Ersilia Model Hub is a unified platform of pre-trained AI/ML models for infectious and neglected disease research. The end goal is to provide an open-source, low-code solution to access AI/ML models for **drug discovery**. The models embedded in the hub include both models published in the literature (with appropriate third party acknowledgement) and models developed by the Ersilia team or contributors.

* Read more about the project in the [Ersilia Book](https://ersilia.gitbook.io/ersilia-book/)
* Browse available models in the [Ersilia Model Hub](https://ersilia.io/model-hub/)

## Quick Start Guide

Please check the package requirements in the [Installation Guide](https://ersilia.gitbook.io/ersilia-book/quick-start/installation). The next steps are a quickstart guide to installing Ersilia.

1. Create a conda environment and activate it

    ```bash
    conda create -n ersilia python=3.10
    conda activate ersilia
    ```

1. Clone this repository and install with pip

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

1. Once the Ersilia Model Hub is installed, you can use the CLI to run predictions. First, select a model from the [Ersilia Model Hub](https://ersilia.io/model-hub/) and **fetch** it:

    ```bash
    ersilia fetch retrosynthetic-accessibility
    ```

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

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

1. Then, **serve** your model:

    ```bash
    ersilia serve retrosynthetic-accessibility
    ```

1. And **run** the model:

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

1. Finally, **close** the service when you are done.

    ```bash
    ersilia close
    ```

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

```bash
ersilia delete retrosynthetic-accessibility
```


Please see the [Ersilia Book](https://ersilia.gitbook.io/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](https://github.com/ersilia-os/ersilia/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](https://github.com/ersilia-os/ersilia/discussions) for the project
* Check our [Contributing Guide](https://github.com/ersilia-os/ersilia/blob/master/CONTRIBUTING.md) for more details

The Ersilia Open Source Initiative adheres to the [Contributor Covenant](https://ersilia.gitbook.io/ersilia-wiki/code-of-conduct) 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](https://github.com/ersilia-os/ersilia/issues/new?assignees=&labels=new-model&template=model_request.yml&title=%F0%9F%A6%A0+Model+Request%3A+%3Cname%3E) or contact us using the following [form](https://www.ersilia.io/request-model).

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](https://github.com/ersilia-os/eos-demo) explaining the steps one-by-one.

## License and Citation

This repository is open-sourced under the [GPL-3 License](https://github.com/ersilia-os/ersilia/blob/master/LICENSE).
Please [cite us](https://github.com/ersilia-os/ersilia/blob/master/CITATION.cff) if you use it!

## About Us

The [Ersilia Open Source Initiative](https://ersilia.io) is a Non Profit Organization ([1192266](https://register-of-charities.charitycommission.gov.uk/charity-search/-/charity-details/5170657/full-print)) with the mission is to equip labs, universities and clinics in LMIC with AI/ML tools for infectious disease research.

[Help us](https://www.ersilia.io/donate) achieve our mission or [volunteer](https://www.ersilia.io/volunteer) with us!


