The Ersilia Model Hub 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:
You can read more about the project in the Ersilia Book and browse available models in the Ersilia Model Hub.
Please check the package requirements in the Installation Guide. The following steps are a quick start guide to using Ersilia.
First, create a conda environment and activate it:
conda create -n ersilia python=3.10
conda activate ersilia
Then, clone this repository and install with pip:
git clone https://github.com/ersilia-os/ersilia.git
cd ersilia
pip install -e .
Alternatively, you can directly install from PyPi:
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 and fetch it:
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:
ersilia serve eos4e40
To view some information of the model, type the following:
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:
ersilia example -n 5 -f my_input.csv
Now you can run the model:
ersilia run -i my_input.csv -o my_output.csv
To stop the service, you can simply close the model:
ersilia close
Finally, if you don't want to use the model anymore, delete it as follows:
ersilia delete eos4e40
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:
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), 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 explaining the steps one-by-one.
This repository is open-sourced under the GPL-3 License. Please cite us if you use it!
Please note that Ersilia distinguises between software contributors and software authors. The Ersilia Model Hub Authorship guidelines can be found in the Authorship file and current authors can be found in the Citation file. We acknowledge past authors of the software below:
The Ersilia Model Hub is used in a number of scientific projects. Read more about how we are implementing it in:
The Ersilia Open Source Initiative 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 achieve our mission!
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. Highlighted supporters include the Mozilla Builders Accelerator, Fast Forward, Splunk Pledge and the AI2050 Program by Schmidt Sciences.
FAQs
A hub of AI/ML models for open source drug discovery and global health
We found that ersilia demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 1 open source maintainer collaborating on the project.
Did you know?
Socket for GitHub automatically highlights issues in each pull request and monitors the health of all your open source dependencies. Discover the contents of your packages and block harmful activity before you install or update your dependencies.
Security News
Fluent Assertions is facing backlash after dropping the Apache license for a commercial model, leaving users blindsided and questioning contributor rights.
Research
Security News
Socket researchers uncover the risks of a malicious Python package targeting Discord developers.
Security News
The UK is proposing a bold ban on ransomware payments by public entities to disrupt cybercrime, protect critical services, and lead global cybersecurity efforts.