> For the complete documentation index, see [llms.txt](https://ersilia.gitbook.io/ersilia-book/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://ersilia.gitbook.io/ersilia-book/about-us/open-standards-and-best-practices.md). # Open standards and best practices {% hint style="info" %} Ersilia is [recognized as a Digital Public Good](https://medium.com/ersiliaio/ersilia-becomes-a-digital-public-good-64fb2e8bb72c) by the Digital Public Goods Alliance. {% endhint %} ## Open standards We follow [DPG Alliance tips for Open Standards](https://github.com/DPGAlliance/publicgoods-candidates/blob/main/help-center/open-standards.md). 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. | See our [GitHub profile](https://github.com/ersilia-os) for more information. A summary of our GitHub security usage can be found [here](https://github.com/ersilia-os/ersilia/security). | | Internationalization | UTF-8 encodings is used in our scripts, most of them written in Python. Code is formatted with Black. | You can see our main codebase [here](https://github.com/ersilia-os/ersilia). | | Application Programming Interfaces (APIs) | OpenAPI, especially via Swagger UI as facilitated by BentoML. | Check one of our deployed models [here](https://eos80ch-m365k.ondigitalocean.app/). | | Data Exchange and Configuration Formats | We primarily use YAML, JSON, CSV and TOML formats. | [Setup file](https://github.com/ersilia-os/ersilia/blob/master/pyproject.toml) in TOML format. [Metadata file](https://github.com/ersilia-os/eos3b5e/blob/main/metadata.json) in JSON. [Workflow file](https://github.com/ersilia-os/ersilia/blob/master/.github/workflows/pr_check.yml) in YAML. [Data file](https://github.com/ersilia-os/pharmacogx-embeddings/blob/main/data/chemical_descriptors/drug_molecules.csv) in CSV. | | Standard Content Formats and Multimedia | Content and multimedia are not our main assets. Internally, we store documents and media files with standard formats. | An example of a one-pager in PDF format can be found [here](https://drive.google.com/file/d/1Xxgpjh3gCQdD_MqEDxweJIPY_1JGKSIN/view?usp=sharing). We store videos in MP4 format, and upload them to [Youtube](https://www.youtube.com/channel/UCeioZf4Qj4hWi3O5Ta2k-xQ). | ## Best practices and principles We follow [DPG Alliance tips for Best Practices and Principles](https://github.com/DPGAlliance/publicgoods-candidates/blob/main/help-center/best-practices.md). Below is a summary and proof of adherence to these principles. | Concept | Comment | Proof of Adherence | | ------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | ICT4D | We endorse the [Principles for Digital Development](https://digitalprinciples.org). | Signed proof of endorsement available [here](https://github.com/ersilia-os/ersilia/security). | | 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. | Ersilia stories in [Medium](https://medium.com/ersiliaio). Activity in [GitHub Issues](https://github.com/ersilia-os/ersilia/issues). Other stories by the community: [GDI example](https://www.gooddatainstitute.com/post/pipeline-dreams-smiles-all-around-as-mlops-boosts-drug-discovery). | | Change management and version control | We use all version control functionalities of GitHub. | [Commit history](https://github.com/ersilia-os/ersilia/commits/master/) of our main repository. | | Test driven development using automated tests | Extensive and customized tests are performed, both for the main code and the models. | [Testing module](https://github.com/ersilia-os/ersilia/tree/master/test) in the Ersilia CLI. Test [workflow](https://github.com/ersilia-os/ersilia/actions/workflows/pr_check.yml). | | CI/CD | We use GitHub Actions for our CI/CD workflows, especially for model incorporation. | A subset of GitHub Actions can be found [here](https://github.com/ersilia-os/ersilia/actions/workflows/pr_check.yml). | | Code review | We operate via pull requests and code reviewing is necessary previous to approval. | As an example, a video showing our model incorporation and reviewing process if found [here](https://youtu.be/I7dYI4ZF7Q0?si=3Ugo8zeqgBd5gQU-). | | Agile development | We use GitHub projects following the "Epic", "Sprint", etc. logic. | [Agile template](https://github.com/ersilia-os/ersilia/blob/master/.github/ISSUE_TEMPLATE/project-issue.yml) for defining projects. | | 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. | [DockerHub](https://hub.docker.com/u/ersiliaos) model registry of Ersilia. | | Component based architecture | By design, our architecture is component based. | Find a high-level diagram [here](https://ersilia.gitbook.io/ersilia-book/ersilia-model-hub/introduction). | | Cloud Computing | We have infrastructure as service scripts for AWS. However, the Ersilia Model Hub is designed to be cloud-agnostic. | Example of AWS integration [scripts](https://github.com/ersilia-os/model-inference-pipeline) for the Ersilia Model Hub. | | AI/ML | We use ONNX format for interoperability as much as possible in our assets. | This in-house library ([olinda](https://github.com/ersilia-os/olinda)) is specifically dedicated to distilling and converting models to ONNX. | | Data Principles | We follow FAIR data principles in all our projects. Most of our projects are collaborative. | As an example, see our data sharing efforts as part of the [Ligand Discovery](https://github.com/ligand-discovery) project. These efforts were led by Ersilia. | | User Interface and User Experience (UI/UX) | Graphical user interfaces and a simple command-line interface are available. | [Ersilia CLI](https://github.com/ersilia-os/ersilia) is our primary tool. For some selected models, we offer online deployment with a [GUI](https://github.com/ersilia-os/ersilia-gui). | | Coding Styles and Standards | We follow PEP 8 and format with Black. | Black label in our [README file](https://github.com/ersilia-os/ersilia?tab=readme-ov-file). | | Open Source | We are a fully open source project and are part of several open source communities. | Software Sustainability Institute [cohort](https://www.software.ac.uk/blog/ersilia-ai-tool-drug-discovery-africa). Code for Science and Society [cohort](https://www.codeforsociety.org/eventfund/grantees/bringing-data-science-and-ai-ml-tools-to-infectious-disease-research-a-hands-on-workshop). |