Metadata-Version: 2.1
Name: ersilia
Version: 0.1.8
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
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Operating System :: OS Independent
Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
Requires-Python: >=3.7
Description-Content-Type: text/markdown
Requires-Dist: inputimeout
Requires-Dist: emoji
Requires-Dist: validators
Requires-Dist: h5py
Requires-Dist: loguru
Requires-Dist: pyairtable
Requires-Dist: PyYAML
Requires-Dist: dockerfile-parse
Requires-Dist: tqdm
Provides-Extra: docs
Requires-Dist: inputimeout ; extra == 'docs'
Requires-Dist: emoji ; extra == 'docs'
Requires-Dist: validators ; extra == 'docs'
Requires-Dist: h5py ; extra == 'docs'
Requires-Dist: loguru ; extra == 'docs'
Requires-Dist: pyairtable ; extra == 'docs'
Requires-Dist: PyYAML ; extra == 'docs'
Requires-Dist: dockerfile-parse ; extra == 'docs'
Requires-Dist: tqdm ; extra == 'docs'
Requires-Dist: sphinx ; extra == 'docs'
Requires-Dist: jinja2 ; extra == 'docs'
Provides-Extra: lake
Requires-Dist: inputimeout ; extra == 'lake'
Requires-Dist: emoji ; extra == 'lake'
Requires-Dist: validators ; extra == 'lake'
Requires-Dist: h5py ; extra == 'lake'
Requires-Dist: loguru ; extra == 'lake'
Requires-Dist: pyairtable ; extra == 'lake'
Requires-Dist: PyYAML ; extra == 'lake'
Requires-Dist: dockerfile-parse ; extra == 'lake'
Requires-Dist: tqdm ; extra == 'lake'
Requires-Dist: isaura (==0.1) ; extra == 'lake'
Provides-Extra: test
Requires-Dist: inputimeout ; extra == 'test'
Requires-Dist: emoji ; extra == 'test'
Requires-Dist: validators ; extra == 'test'
Requires-Dist: h5py ; extra == 'test'
Requires-Dist: loguru ; extra == 'test'
Requires-Dist: pyairtable ; extra == 'test'
Requires-Dist: PyYAML ; extra == 'test'
Requires-Dist: dockerfile-parse ; extra == 'test'
Requires-Dist: tqdm ; extra == 'test'
Requires-Dist: pytest ; extra == 'test'

<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) [![Gitpod Ready-to-Code](https://img.shields.io/badge/Gitpod-ready--to--code-blue?logo=gitpod)](https://gitpod.io/#https://github.com/ersilia-os/ersilia)

## 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, no-code solution to access AI/ML models to accelerate 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=3.7
    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 prediction **API**:

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

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

    ```bash
    ersilia close
    ```

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!


