The Ersilia Model Hub is the main project of the Ersilia Open Source Initiative. The aim is to provide a platform for a user-friendly deployment of AI/ML models, where scientists can browse through the assets, identify those which is relevant to their research and obtain predictions without the need of coding expertise. Currently, most of the tools developed, even when published and fully open-sourced, remain unusable by a large majority of the scientific community who does not have the necessary expertise. This gap becomes even larger in Low and Middle Income Country institutions where access to bioinformatic facilities or data science experts are scarce. With this project, we hope to democratize access to this expertise and support research into neglected and infectious diseases.
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. All assets are open source, but please do check the Licenses of each model before using them.
- Read more about the project better at the Ersilia Book
- Available models can be checked at Ersilia Model Hub
Follow the installation instructions from the Ersilia Book.
Once Ersilia is installed, you can browse models in the Ersilia Model Hub.
Select one model. For example chemprop-antibiotic. You can fetch your model with the Ersilia CLI:
ersilia fetch chemprop-antibiotic
Generate a few (5) example molecules, to be used as input. Molecules are typically expressed in SMILES format.
ersilia example chemprop-antibiotic -n 5 -f my_molecules.csv
Then, serve your model:
ersilia serve chemprop-antibiotic
And run the prediction API:
ersilia api -i my_molecules.csv -o my_predictions.csv
Finally, close the service when you are done.
ersilia close
Please see the Ersilia Book for more examples and detailed explanations.
The Ersilia Model Hub is developed and maintained by a small team of Ersilia employees and volunteers, and any contribution is highly valued! There are several ways in which you can contribute to the project:
- If you are a developer, check the issues and help us to improve the tool
- If you have developed a model and would like to include it in the Hub to increase its visibility and usability, please contact us or open an issue. We are currently working on an automated contribution tool to facilitate the process.
- If you are a scientist with a cool dataset, also contact us or open an issue as we might be interested in developing a model based on the data!
- If there is a third-party model you have identified and would like to see it in the Hub, open an issue with the relevant information and we will get back to you as soon as possible.
The Ersilia Open Source Initiative adheres to the Contributor Covenant guidelines.
We are working to grow the Hub organically and responding to our users needs. Here are the details of the next features to come, stay tuned!
- Deployment for Windows System (expected: February 2022)
- Automated third-party model contributions (expected: March 2022)
- Possibility to run lite models online (expected: May 2022)
This repository is open-sourced under the MIT License. Please cite us if you use it.
The Ersilia Open Source Initiative is a Non Profit Organization incorporated with the Charity Commission for England and Wales (number 1192266). Our mission is to reduce the imbalance in biomedical research productivity between countries by supporting research in underfunded settings.
You can support us via Open Collective.