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:
- 📚 Published models from literature (with due third-party acknowledgement)
- 🛠 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
Please check the package requirements in the Installation Guide. The next steps are a quickstart guide to installing Ersilia.
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Create a conda environment and activate it
conda create -n ersilia python=3.10 conda activate ersilia
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Clone this repository and install with pip
git clone https://github.com/ersilia-os/ersilia.git cd ersilia pip install -e .
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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
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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
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Then, serve your model:
ersilia serve retrosynthetic-accessibility
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And run the model:
ersilia run -i my_molecules.csv -o my_predictions.csv
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Finally, close the service when you are done.
ersilia close
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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.
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.
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.
This repository is open-sourced under the GPL-3 License. Please cite us if you use it!
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.