Ersilia Book
  • 🤗Welcome to Ersilia!
    • The Ersilia Open Source Initiative
    • Ten principles
    • Ersilia's ecosystem
  • 🚀Ersilia Model Hub
    • Getting started
    • Online inference
    • Local inference
    • Model contribution
      • Model template
      • Model incorporation workflow
      • Troubleshooting models
      • BioModels annotation
    • For developers
      • Command line interface
      • CI/CD workflows
      • Test command
      • Testing playground
      • Model packaging
      • Inputs
      • Codebase quality and consistency
      • Results caching
  • 💊Chemistry tools
    • Automated activity prediction models
      • Light-weight AutoML with LazyQSAR
      • Accurate AutoML with ZairaChem
      • Model distillation with Olinda
    • Sampling the chemical space
    • Encryption of AI/ML models
  • AMR chemical collections
  • 🙌Contributors
    • Communication channels
    • Tech stack
    • Internships
      • Outreachy Summer 2025
      • Outreachy Winter 2024
      • Outreachy Summer 2024
      • Outreachy Winter 2023
      • Outreachy Summer 2023
      • Outreachy Winter 2022
      • Outreachy Summer 2022
  • 📑Training materials
    • AI2050 intro workshop
    • AI2050 AI for Drug Discovery
    • Introduction to ML for Drug Discovery
    • Python 101
    • External resources
  • 🎨Styles
    • Brand guidelines
    • Slide and document templates
    • Scientific figures with Stylia
    • Coding style
  • 🌍About Us
    • Where to find us?
    • Diversity and inclusion statement
    • Code of conduct
    • Open standards and best practices
    • Ersilia privacy notice
    • Strategic Plan 2025-2027
    • Ersilia, the Invisible City
Powered by GitBook

2025, Ersilia Open Source Initiative

On this page
  • The Ersilia CLI
  • Working with models as Docker containers
  • Working with models from source
  • CI/CD workflows and testing
  • Model packaging

Was this helpful?

  1. Ersilia Model Hub

For developers

In-depth documentation of the Ersilia Model Hub to help developers contribute to our open source platform.

PreviousBioModels annotationNextCommand line interface

Last updated 1 month ago

Was this helpful?

This chapter is mainly intended to developers who want to contribute to Ersilia's infrastructure. If you intend to contribute AI/ML models, please refer to the chapter.

The Ersilia CLI

The main codebase of Ersilia is the . For a full reference of all commands available, please visit . A detailed reference of the Ersilia API can be accessed .

To start contributing to Ersilia, please and work on it locally. We recommend installing Ersilia in editable mode inside a Conda environment:

conda create -n ersilia python=3.12
conda activate ersilia
git clone https://github.com/your_username/ersilia
cd ersilia
pip install -e . 

Working with models as Docker containers

All models incorporated in Ersilia are for easy deployment. While the dockerization step happens as part of our , it is recommended to install Docker for model testing purposes.

Running models as Docker container is the recommended way since it maximizes interoperability across systems and persistency.

Working with models from source

Ersilia models can also be packaged from source. The source code and parameters for a given model are available in its corresponding GitHub repository. Some model checkpoints are too large (>100MB) for GitHub storage. If you want to work with models from source, please make sure that is installed and active in your system to push large files to the model repository.

Working with models from source is often recommendable to quickly explore potential issues with the model. Typically, a dedicated Conda environment will be created by Ersilia automatically at fetch time.

CI/CD workflows and testing

Ersilia relies heavily on GitHub Actions workflows for automation and testing. Visit the corresponding sections to learn more about:

Model packaging

An important part of the Ersilia infrastructure is the packaging of models with . Please see the for more information.

The legacy method for packaging models was strongly based on . This is progressively being deprecated in favor our Ersilia Pack, which is built on top of .

🚀
Model contribution
Ersilia CLI
this page
here
fork our master branch
dockerized
CI/CD workflows
git-lfs
The model testing command
A fully-featured testing playground for the Ersilia CLI
Styling and guidelines to ensure code quality in an automater manner
BentoML
FastAPI
Basic concepts of CI/CD at Ersilia
Ersilia Pack
Ersilia Pack documentation