<div id="top"></div>
<img src="https://raw.githubusercontent.com/ersilia-os/ersilia/master/assets/Ersilia_Plum.png" height="70">
# 🎉 Welcome to the Ersilia Model Hub 🌟
[](https://www.paypal.com/uk/fundraiser/charity/4145012) [](CODE_OF_CONDUCT.md) [](https://www.gnu.org/licenses/agpl-3.0)
[](https://pypi.python.org/pypi/ersilia/) [](https://www.python.org/downloads/release/python-370/) [](https://github.com/psf/black)
[](https://zenodo.org/badge/latestdoi/277068989) [](https://ersilia.gitbook.io/ersilia-book/)
## 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](https://ersilia.io) 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](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!
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"description": "<div id=\"top\"></div>\n<img src=\"https://raw.githubusercontent.com/ersilia-os/ersilia/master/assets/Ersilia_Plum.png\" height=\"70\">\n\n# \ud83c\udf89 Welcome to the Ersilia Model Hub \ud83c\udf1f\n\n[](https://www.paypal.com/uk/fundraiser/charity/4145012) [](CODE_OF_CONDUCT.md) [](https://www.gnu.org/licenses/agpl-3.0)\n[](https://pypi.python.org/pypi/ersilia/) [](https://www.python.org/downloads/release/python-370/) [](https://github.com/psf/black)\n[](https://zenodo.org/badge/latestdoi/277068989) [](https://ersilia.gitbook.io/ersilia-book/)\n\n## Table of Contents\n\n1. [Project Description](https://github.com/ersilia-os/ersilia#project-description)\n2. [Quick start guide](https://github.com/ersilia-os/ersilia#quick-start-guide)\n3. [Contribute](https://github.com/ersilia-os/ersilia#contribute)\n4. [License and citation](https://github.com/ersilia-os/ersilia#license-and-citation)\n5. [About us](https://github.com/ersilia-os/ersilia#about-us)\n\n## Project Description\n\nThe [Ersilia Model Hub](https://ersilia.io) is a unified platform of pre-trained AI/ML models dedicated to \ud83e\udda0 infectious and neglected disease research. Our mission is to offer an open-source, \ud83d\udee0 low-code solution that provides seamless access to AI/ML models for \ud83d\udc8a drug discovery. Models housed in our hub come from two sources:\n\n1. \ud83d\udcda Published models from literature (with due third-party acknowledgement)\n2. \ud83d\udee0 Custom models developed by the **Ersilia team** or our valued contributors.\n\n* Read more about the project in the [Ersilia Book](https://ersilia.gitbook.io/ersilia-book/)\n* Browse available models in the [Ersilia Model Hub](https://ersilia.io/model-hub/)\n\n## Quick Start Guide\n\nPlease 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.\n\n1. Create a conda environment and activate it\n\n ```bash\n conda create -n ersilia python=3.10\n conda activate ersilia\n ```\n\n1. Clone this repository and install with pip\n\n ```bash\n git clone https://github.com/ersilia-os/ersilia.git\n cd ersilia\n pip install -e .\n ```\n\n1. 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:\n\n ```bash\n ersilia fetch retrosynthetic-accessibility\n ```\n\n1. Generate a few (5) example molecules, to be used as input. The **example** command will generate the adequate input for the model in use\n\n ```bash\n ersilia example retrosynthetic-accessibility -n 5 -f my_molecules.csv\n ```\n\n1. Then, **serve** your model:\n\n ```bash\n ersilia serve retrosynthetic-accessibility\n ```\n\n1. 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There are several ways in which you can contribute to the project:\n\n* A good place to start is checking open [issues](https://github.com/ersilia-os/ersilia/issues).\n* If you have identified a bug in the code, please open a new issue using the bug template.\n* Share any feedback with the community using [GitHub Discussions](https://github.com/ersilia-os/ersilia/discussions) for the project\n* Check our [Contributing Guide](https://github.com/ersilia-os/ersilia/blob/master/CONTRIBUTING.md) for more details\n\nThe Ersilia Open Source Initiative adheres to the [Contributor Covenant](https://ersilia.gitbook.io/ersilia-wiki/code-of-conduct) code of conduct.\n\n### Submit a New Model\n\nIf 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).\n\nAfter 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.\n\n## License and Citation\n\nThis repository is open-sourced under the [GPL-3 License](https://github.com/ersilia-os/ersilia/blob/master/LICENSE).\nPlease [cite us](https://github.com/ersilia-os/ersilia/blob/master/CITATION.cff) if you use it!\n\n## About Us\n\nThe [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.\n\n[Help us](https://www.ersilia.io/donate) achieve our mission or [volunteer](https://www.ersilia.io/volunteer) with us!\n",
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