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# 🎉 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://anaconda.org/conda-forge/ersilia) [](https://www.python.org/downloads/release/python-380/) [](https://github.com/psf/black)
[](https://zenodo.org/badge/latestdoi/277068989) [](https://ersilia.gitbook.io/ersilia-book/)
[](https://www.repostatus.org/#active)
## 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 for 🦠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:
- Published models from literature (with due third-party acknowledgement)
- Custom models developed by the Ersilia team or our valued contributors
You can read more about the project in the [Ersilia Book](https://ersilia.gitbook.io/ersilia-book/) and 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 following steps are a quick start guide to using Ersilia.
First, create a conda environment and activate it:
```bash
conda create -n ersilia python=3.10
conda activate ersilia
```
Then, clone this repository and install with `pip`:
```bash
git clone https://github.com/ersilia-os/ersilia.git
cd ersilia
pip install -e .
```
Alternatively, you can directly install from PyPi:
```bash
pip install ersilia
```
Once the Ersilia package 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 eos4e40
```
Note that you can use the model identifier (eos4e40) or its human-readable slug (antibiotic-activity).
Now you can serve the model:
```bash
ersilia serve eos4e40
```
To view some information of the model, type the following:
```bash
ersilia info
```
The simplest way to run a model is by passing a CSV file as input. If you don't have one, you can generate it easily. In this case, we take 5 molecules as an example:
```bash
ersilia example -n 5 -f my_input.csv
```
Now you can run the model:
```bash
ersilia run -i my_input.csv -o my_output.csv
```
To stop the service, you can simply close the model:
```bash
ersilia close
```
Finally, if you don't want to use the model anymore, delete it as follows:
```bash
ersilia delete eos4e40
```
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), an Ersilia 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!
### Authorship
Please note that Ersilia distinguises between software contributors and software authors. The Ersilia Model Hub Authorship guidelines can be found in the [Authorship file](https://github.com/ersilia-os/ersilia/blob/master/AUTHORSHIP.md) and current authors can be found in the Citation file. We acknowledge past authors of the software below:
- Carolina Caballero
### Cited by
The Ersilia Model Hub is used in a number of scientific projects. Read more about how we are implementing it in:
- [Turon, Hlozek et al, Nat Commun, 2023](https://www.nature.com/articles/s41467-023-41512-2)
- [Van Heerden et al, ACS Omega, 2023](https://pubs.acs.org/doi/10.1021/acsomega.3c05664)
- [Offensperger et al, Science, 2024](https://www.science.org/doi/10.1126/science.adk5864)
- [Turon et al, ACS Med Chem Lett, 2024](https://doi.org/10.1021/acsmedchemlett.4c00131)
## About Us
The [Ersilia Open Source Initiative](https://ersilia.io) is a Non Profit Organization 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!
### Funding
The Ersilia Model Hub is the flagship product of Ersilia. It has been funded thanks to a combination of funding sources. Full disclosure can be found in our [website](https://ersilia.io/supporters). Highlighted supporters include the Mozilla Builders Accelerator, Fast Forward, Splunk Pledge and the AI2050 Program by Schmidt Sciences.
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[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 for \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\n- Published models from literature (with due third-party acknowledgement)\n- Custom models developed by the Ersilia team or our valued contributors\n\nYou can read more about the project in the [Ersilia Book](https://ersilia.gitbook.io/ersilia-book/) and 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 following steps are a quick start guide to using Ersilia.\n\nFirst, create a conda environment and activate it:\n\n```bash\nconda create -n ersilia python=3.10\nconda activate ersilia\n```\n\nThen, clone this repository and install with `pip`:\n\n```bash\ngit clone https://github.com/ersilia-os/ersilia.git\ncd ersilia\npip install -e .\n```\n\nAlternatively, you can directly install from PyPi:\n```bash\npip install ersilia\n```\n\nOnce the Ersilia package 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\nersilia fetch eos4e40\n```\n\nNote that you can use the model identifier (eos4e40) or its human-readable slug (antibiotic-activity).\n\nNow you can serve the model:\n\n```bash\nersilia serve eos4e40\n```\n\nTo view some information of the model, type the following:\n\n```bash\nersilia info\n```\n\nThe simplest way to run a model is by passing a CSV file as input. If you don't have one, you can generate it easily. In this case, we take 5 molecules as an example:\n\n```bash\nersilia example -n 5 -f my_input.csv\n```\n\nNow you can run the model:\n\n```bash\nersilia run -i my_input.csv -o my_output.csv\n```\n\nTo stop the service, you can simply close the model:\n\n```bash\nersilia close\n```\n\nFinally, if you don't want to use the model anymore, delete it as follows:\n\n```bash\nersilia delete eos4e40\n```\n\nPlease see the [Ersilia Book](https://ersilia.gitbook.io/ersilia-book/) for more examples and detailed explanations.\n\n## Contribute\n\nThe 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:\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), an Ersilia 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### Authorship\n\nPlease note that Ersilia distinguises between software contributors and software authors. The Ersilia Model Hub Authorship guidelines can be found in the [Authorship file](https://github.com/ersilia-os/ersilia/blob/master/AUTHORSHIP.md) and current authors can be found in the Citation file. We acknowledge past authors of the software below:\n- Carolina Caballero\n\n### Cited by\n\nThe Ersilia Model Hub is used in a number of scientific projects. 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