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  • 🤗Welcome to Ersilia!
    • The Ersilia Open Source Initiative
    • Ten principles
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  • 🌍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
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2025, Ersilia Open Source Initiative

On this page
  • Open standards
  • Best practices and principles

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  1. About Us

Open standards and best practices

This page describes Ersilia's open standards and best practices principles

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Last updated 6 months ago

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Ersilia is by the Digital Public Goods Alliance.

Open standards

We follow . Below is a summary and proof of adherence to these standards.

Concept
Comment
Proof of Adherence

Accessibility, Security, Authentication and Authorization

Ersilia uses GitHub primarily. Accessibility, security and authentication/authorization is therefore reliant on GitHub solutions. We use DependaBot to monitor package dependencies and identify security liabilities. GitHub Secrets are used intensively in our workflows.

Internationalization

UTF-8 encodings is used in our scripts, most of them written in Python. Code is formatted with Black.

Application Programming Interfaces (APIs)

OpenAPI, especially via Swagger UI as facilitated by BentoML.

Data Exchange and Configuration Formats

We primarily use YAML, JSON, CSV and TOML formats.

Standard Content Formats and Multimedia

Content and multimedia are not our main assets. Internally, we store documents and media files with standard formats.

Best practices and principles

We follow . Below is a summary and proof of adherence to these principles.

Concept
Comment
Proof of Adherence

ICT4D

User stories

We share community stories via our blog publication. We are active on social media and use GitHub Issues for the more technical aspects.

Change management and version control

We use all version control functionalities of GitHub.

Test driven development using automated tests

Extensive and customized tests are performed, both for the main code and the models.

CI/CD

We use GitHub Actions for our CI/CD workflows, especially for model incorporation.

Code review

We operate via pull requests and code reviewing is necessary previous to approval.

Agile development

We use GitHub projects following the "Epic", "Sprint", etc. logic.

Modularity and Maintainability, Reusability and extensibility

The Ersilia Model Hub is highly modular, with each model corresponding to one artifact stored in an isolated environment.

Component based architecture

By design, our architecture is component based.

Cloud Computing

We have infrastructure as service scripts for AWS. However, the Ersilia Model Hub is designed to be cloud-agnostic.

AI/ML

We use ONNX format for interoperability as much as possible in our assets.

Data Principles

We follow FAIR data principles in all our projects. Most of our projects are collaborative.

User Interface and User Experience (UI/UX)

Graphical user interfaces and a simple command-line interface are available.

Coding Styles and Standards

We follow PEP 8 and format with Black.

Open Source

We are a fully open source project and are part of several open source communities.

See our for more information. A summary of our GitHub security usage can be found .

You can see our main codebase .

Check one of our deployed models .

in TOML format. in JSON. in YAML. in CSV.

An example of a one-pager in PDF format can be found . We store videos in MP4 format, and upload them to .

We endorse the .

Signed proof of endorsement available .

Ersilia stories in . Activity in . Other stories by the community: .

of our main repository.

in the Ersilia CLI. Test .

A subset of GitHub Actions can be found .

As an example, a video showing our model incorporation and reviewing process if found .

for defining projects.

model registry of Ersilia.

Find a high-level diagram .

Example of AWS integration for the Ersilia Model Hub.

This in-house library () is specifically dedicated to distilling and converting models to ONNX.

As an example, see our data sharing efforts as part of the project. These efforts were led by Ersilia.

is our primary tool. For some selected models, we offer online deployment with a .

Black label in our .

Software Sustainability Institute . Code for Science and Society .

🌍
recognised as a Digital Public Good
DPG Alliance tips for Open Standards
DPG Alliance tips for Best Practices and Principles
GitHub profile
here
here
here
Setup file
Metadata file
Workflow file
Data file
here
Youtube
Principles for Digital Development
here
Medium
GitHub Issues
GDI example
Commit history
Testing module
workflow
here
here
Agile template
DockerHub
here
scripts
olinda
Ligand Discovery
Ersilia CLI
GUI
README file
cohort
cohort