# Ersilia Book

## Ersilia Book

- [The Ersilia Open Source Initiative](https://ersilia.gitbook.io/ersilia-book/welcome-to-ersilia/readme.md): We equip laboratories in the Global South with data science tools for infectious disease research
- [Ten principles](https://ersilia.gitbook.io/ersilia-book/welcome-to-ersilia/ten-principles.md): Ersilia’s 10 Principles guide our decision-making and roadmap
- [Ersilia's ecosystem](https://ersilia.gitbook.io/ersilia-book/welcome-to-ersilia/ersilias-ecosystem.md): Learn about the work of Ersilia and where to start using/contributing to our tools
- [Getting started](https://ersilia.gitbook.io/ersilia-book/ersilia-model-hub/getting-started.md)
- [Online inference](https://ersilia.gitbook.io/ersilia-book/ersilia-model-hub/online-inference.md): Documentation to run Ersilia models online
- [Local inference](https://ersilia.gitbook.io/ersilia-book/ersilia-model-hub/local-inference.md): Documentation to run models on-premises
- [Model contribution](https://ersilia.gitbook.io/ersilia-book/ersilia-model-hub/model-contribution.md): Documentation for those who want to contribute new models to the Hub
- [Model template](https://ersilia.gitbook.io/ersilia-book/ersilia-model-hub/model-contribution/model-template.md): This pages provides a deep dive into the structure of the model template for new model incorporation.
- [Model incorporation workflow](https://ersilia.gitbook.io/ersilia-book/ersilia-model-hub/model-contribution/example-of-the-model-incorporation-workflow.md): Example of an end-to-end model incorporation workflow
- [Troubleshooting models](https://ersilia.gitbook.io/ersilia-book/ersilia-model-hub/model-contribution/troubleshooting-models.md): This page describes a few steps you can take when a Ersilia model is not working.
- [BioModels annotation](https://ersilia.gitbook.io/ersilia-book/ersilia-model-hub/model-contribution/biomodels-annotation.md): This page describes how to annotate Ersilia models in the BioModels Tool contributing towards FAIRness.
- [For developers](https://ersilia.gitbook.io/ersilia-book/ersilia-model-hub/developer-docs.md): In-depth documentation of the Ersilia Model Hub to help developers contribute to our open source platform.
- [Command line interface](https://ersilia.gitbook.io/ersilia-book/ersilia-model-hub/developer-docs/command-line-interface.md): Command Line Interface to interact with the Ersilia Model Hub
- [Python API](https://ersilia.gitbook.io/ersilia-book/ersilia-model-hub/developer-docs/python-api.md)
- [CI/CD workflows](https://ersilia.gitbook.io/ersilia-book/ersilia-model-hub/developer-docs/ci-cd-workflows.md): Ersilia relies on GitHub Actions for CI/CD. Here is a high-level summary of workflows involved in maintaining the Ersilia CLI and code-bases from all the models available via the Hub.
- [Model Testing](https://ersilia.gitbook.io/ersilia-book/ersilia-model-hub/developer-docs/model-testing.md)
- [CLI Testing](https://ersilia.gitbook.io/ersilia-book/ersilia-model-hub/developer-docs/cli-testing.md): The Testing Playground is a new testing system added to the Ersilia testing pipeline. It aims to advance the testing pipeline using the ersilia CLI commands. It provides a flexible and robust frame.
- [Results caching](https://ersilia.gitbook.io/ersilia-book/ersilia-model-hub/developer-docs/results-caching.md)
- [Best code practices](https://ersilia.gitbook.io/ersilia-book/ersilia-model-hub/developer-docs/developer-guide-for-codebase-quality-and-consistency.md): This guide outlines the rules and tools used to ensure quality and consistency in Ersilia's codebase. By adhering to these practices, we aim to maintain a high standard of code readability, maintainab
- [Precalculation Store](https://ersilia.gitbook.io/ersilia-book/ersilia-model-hub/developer-docs/precalculation-store.md)
- [Ersilia Version Control (EOSVC)](https://ersilia.gitbook.io/ersilia-book/ersilia-model-hub/developer-docs/ersilia-version-control-eosvc.md): CLI for syncing large artifacts to S3
- [Model Hub maintenance](https://ersilia.gitbook.io/ersilia-book/ersilia-model-hub/model-hub-maintenance.md): The Ersilia Model Hub is maintained through a dedicated maintenance repository. It describes the automated workflows, reports and processes used to track model health, testing and maintenance actions.
- [Automated activity prediction models](https://ersilia.gitbook.io/ersilia-book/chemistry-tools/automated-activity-prediction-models.md): We are developing AutoML tools for chemistry data to facilitate adoption of AI/ML
- [Light-weight AutoML with LazyQSAR](https://ersilia.gitbook.io/ersilia-book/chemistry-tools/automated-activity-prediction-models/light-weight-automl-with-lazyqsar.md): Here we describe LazyQSAR, our library for baseline modeling of QSAR tasks
- [ZairaChem](https://ersilia.gitbook.io/ersilia-book/chemistry-tools/automated-activity-prediction-models/zairachem.md)
- [Model distillation with Olinda](https://ersilia.gitbook.io/ersilia-book/chemistry-tools/automated-activity-prediction-models/model-distillation-with-olinda.md): Olinda is a model distillation tool for chemistry data
- [Sampling the chemical space](https://ersilia.gitbook.io/ersilia-book/chemistry-tools/sampling-the-chemical-space.md): We present ChemSampler, a simple tool to sample molecules in a given region of the chemical space
- [Encryption of AI/ML models](https://ersilia.gitbook.io/ersilia-book/chemistry-tools/encryption-of-ai-ml-models.md): This page describes our ChemXor library, a tool to build privacy-preserving machine learning models for drug discovery. We believe that encrypted assets can foster collaboration
- [AMR chemical collections](https://ersilia.gitbook.io/ersilia-book/chemistry-tools/amr-chemical-collections.md): This page outlines our goal to create the reference database of purchasable compound collections with potential interest to the field of AMR
- [Internships](https://ersilia.gitbook.io/ersilia-book/contributors/internships.md)
- [Outreachy Summer 2025](https://ersilia.gitbook.io/ersilia-book/contributors/internships/outreachy-summer-2025.md): Please find here the guidelines for the Outreachy contribution period running from 17th March to the 15th April 2025
- [Outreachy Winter 2024](https://ersilia.gitbook.io/ersilia-book/contributors/internships/outreachy-winter-2024.md): Please find here the guidelines for the Outreachy contribution period running from 1st to 29th October
- [Outreachy Summer 2024](https://ersilia.gitbook.io/ersilia-book/contributors/internships/outreachy-summer-2024.md): Please find here the guidelines for the Outreachy contribution period running from 4th March to 2nd April 2024.
- [Outreachy Winter 2023](https://ersilia.gitbook.io/ersilia-book/contributors/internships/outreachy-winter-2023.md): Please find here the guidelines for the Outreachy contribution period running from 2nd October 2023 to 27th October 2023
- [Outreachy Summer 2023](https://ersilia.gitbook.io/ersilia-book/contributors/internships/outreachy-summer-2023.md): This page describes the contribution guidelines for the interns interested in participating in the Outreachy round from May 2023 to August 2023
- [Outreachy Winter 2022](https://ersilia.gitbook.io/ersilia-book/contributors/internships/outreachy-winter-2022.md): This page describes the contribution guidelines for the interns interested in participating in the Outreachy round from December 2022 to March 2023
- [Outreachy Summer 2022](https://ersilia.gitbook.io/ersilia-book/contributors/internships/outreachy-summer-2022.md): Specific instructions for the summer Ersilia interns (June 2022 - September 2022)
- [Brand guidelines](https://ersilia.gitbook.io/ersilia-book/styles/brand-guidelines.md): Brand guidelines for Ersilia digital assets
- [Slide and document templates](https://ersilia.gitbook.io/ersilia-book/styles/slide-and-document-templates.md): Templates for presentations, documents and code
- [Scientific figures with Stylia](https://ersilia.gitbook.io/ersilia-book/styles/scientific-figures.md): Sytlia is a small Python library for styling plots
- [Claude 101](https://ersilia.gitbook.io/ersilia-book/agentic-ai/claude-101.md): Set up instructions for Claude usage with Ersilia's organisation
- [Ersilia Skills](https://ersilia.gitbook.io/ersilia-book/agentic-ai/ersilia-skills.md): A guide to Ersilia's Claude Code skills repository: what it contains, how to install it, and how to contribute new skills.
- [Where to find us?](https://ersilia.gitbook.io/ersilia-book/about-us/where-to-find-us.md): Ersilia is active in social media and in the open science space.
- [Strategic Plan 2025-2027](https://ersilia.gitbook.io/ersilia-book/about-us/strategic-plan-2025-2027.md)
- [Ersilia, the Invisible City](https://ersilia.gitbook.io/ersilia-book/about-us/ersilia-the-invisible-city.md): Ersilia is a city imagined by Cuban-Italian writer Italo Calvino in his book 'Invisible Cities'. Calvino's vivid description of the city is a perfect metaphore for our mission.
- [Diversity and inclusion statement](https://ersilia.gitbook.io/ersilia-book/about-us/diversity-and-inclusion-statement.md): Diversity and inclusion are core principles of Ersilia.
- [Gender Equality Plan](https://ersilia.gitbook.io/ersilia-book/about-us/gender-equality-plan.md): This Gender Equality Plan is officially approved by the Board and reviewed yearly
- [Code of conduct](https://ersilia.gitbook.io/ersilia-book/about-us/code-of-conduct.md): Contributor covenant of the Ersilia Open Source Initiative
- [Open standards and best practices](https://ersilia.gitbook.io/ersilia-book/about-us/open-standards-and-best-practices.md): This page describes Ersilia's open standards and best practices principles
- [AI Policy](https://ersilia.gitbook.io/ersilia-book/about-us/ai-policy.md): This policy has been developed with the support of the Non Profit AI Policy Builder from Fast Forward
- [Ersilia privacy notice](https://ersilia.gitbook.io/ersilia-book/about-us/ersilia-privacy-notice.md): Privacy notice for the Ersilia Open source Initiative