Automation in Biology

The community curates papers, software, datasets, protocols, book chapters, technical reports, hardware designs, presentations, and other scholarly outputs related to automation in biological research. Zenodo remains the authoritative location for deposited files, metadata, licences, versions, DOIs, and community membership. This GitHub repository provides structured submission issues, transparent curation status, validation, and the general accepted-software registry. Accepted R packages are additionally indexed through the separate Automation in Biology R-universe registry, which publishes packages at biologyautomation.r-universe.dev. Non-R software and other accepted software repositories remain represented through this main community repository and its accepted-software registry.

Submit a research output

Research outputs are deposited through Zenodo. This GitHub repository does not host submitted research files.

Submission process

1. Sign in to Zenodo.
2. Create a new upload or open an existing published Zenodo record.
3. Submit the record to the Automation in Biology community.
4. Open a submission issue in this GitHub repository.
5. Include the Zenodo record URL and requested metadata.
6. Respond to any curator questions or requested changes.
7. After review, a maintainer applies the zenodo-approve label.
8. A protected GitHub Actions workflow accepts the pending Zenodo community-inclusion request, verifies public community membership, and applies the accepted label.
9. The accepted-registry workflow independently verifies membership and updates the public software registry in this repository.
10. If the accepted software is a valid R package, it may also be indexed in the separate Automation in Biology R-universe registry.

Open a GitHub submission issue

Automated Zenodo curation

The repository includes a protected workflow for accepting reviewed Zenodo submissions:

.github/workflows/accept-zenodo-community-request.yml

The workflow runs only when the repository owner applies the zenodo-approve label to an open submission issue. It:

1. Extracts exactly one Zenodo record URL from the issue.
2. Confirms the record is a published software output.
3. Confirms that the issue includes an external GitHub software repository.
4. Finds the open Zenodo community-inclusion request for the biologyautomation community.
5. Accepts the request using the protected zenodo-production environment.
6. Verifies that the record is publicly visible in the community.
7. Removes zenodo-approve and applies accepted.
8. Triggers the accepted-repository registry workflow.

The Zenodo API token is stored only as the ZENODO_API_TOKEN secret in the protected zenodo-production environment. Contributors must never provide API tokens, passwords, or private credentials to curators.

If automated acceptance is unavailable, a curator may accept the request manually in Zenodo. The accepted label must not be applied until public community membership has been verified.

Submit software directly from GitHub

Software authors can use the native GitHub–Zenodo integration to archive a versioned GitHub release and request inclusion in the Automation in Biology community.

The integration must be configured in the repository containing the software, not in this community-administration repository.

Step 1: Add .zenodo.json

Create a file named .zenodo.json in the root of the software repository.

At minimum, include the software creators, title, description, licence, keywords, and the Automation in Biology community identifier:

{
  "title": "Name of the software",
  "description": "A clear description of the software and its role in automating biological research.",
  "upload_type": "software",
  "creators": [
    {
      "name": "Family name, Given name",
      "affiliation": "Institution name",
      "orcid": "0000-0000-0000-0000"
    }
  ],
  "license": "MIT",
  "keywords": [
    "automation in biology",
    "laboratory automation",
    "research software"
  ],
  "communities": [
    {
      "identifier": "biologyautomation"
    }
  ]
}

Replace all example metadata with accurate information for the software. The community identifier must remain:

{
  "identifier": "biologyautomation"
}

Step 2: Connect GitHub to Zenodo

The software repository owner must:

1. Sign in to Zenodo.
2. Link their GitHub account to Zenodo.
3. Open the GitHub section from their Zenodo profile menu.
4. Select Sync now.
5. Find the software repository.
6. Enable the repository using the toggle.

This must be configured by someone with the necessary access to the software repository and its Zenodo integration.

Step 3: Create a GitHub release

After committing .zenodo.json, create a versioned GitHub release, for example:

v1.0.0

Zenodo will detect the new release, archive the released source code, create a software record, and mint a DOI.

Creating commits or pushing ordinary branches is not sufficient. A published GitHub release is required.

Step 4: Submit the record to the community

After Zenodo creates the record, submit the published record to the Automation in Biology community. This creates a pending Zenodo community-inclusion request for curator review.

The request is not automatically approved merely because .zenodo.json names the community. A curator may accept it, request metadata changes, or decline it if it is outside the community scope.

Step 5: Open a tracking issue

Open a submission issue in this repository and provide:

• The Zenodo record URL
• The software repository URL
• The release version
• A description of its relevance to automation in biology

Open a software submission issue

Important limitations

The GitHub–Zenodo integration is intended primarily for software releases.

Use a normal Zenodo deposit for outputs such as:

• Papers
• Book chapters
• Datasets not distributed as software releases
• Posters
• Presentations
• Experimental protocols
• Hardware documentation requiring separately packaged files

Each contributor should enable the integration using their own GitHub and Zenodo accounts.

Contributors must never send Zenodo API tokens, GitHub credentials, passwords, or private access tokens to community curators.

Eligible outputs

The community considers:

• Research papers and preprints
• Software and source code
• Research datasets
• Experimental protocols and workflows
• Book chapters
• Technical reports
• Posters and presentations
• Hardware designs and documentation
• Educational and training materials

Submissions must have a clear and substantial connection to automation in biological research.

Relevant topics include:

• Laboratory automation
• Robotic experimentation
• Automated sample preparation
• High-throughput experimentation
• Autonomous and self-driving laboratories
• Biofoundries
• Automated microscopy and phenotyping
• Automated biological data analysis
• Workflow-management systems
• Laboratory-information systems
• Scientific software and instrumentation
• Standards and interoperability
• Reproducible automated protocols
• Machine learning integrated with experimental workflows

Important submission rules

• Submitters must deposit their own files through their own Zenodo account.
• Do not upload confidential, sensitive, personal, restricted, or unpublished research files to GitHub.
• A GitHub issue does not constitute acceptance into the Zenodo community.
• Applying zenodo-approve authorises the protected acceptance workflow; it is a curator-only action.
• Community inclusion is decided by the Zenodo community curators.
• Acceptance indicates relevance to the community scope; it is not peer review or scientific endorsement.
• Submitters remain responsible for authorship, licensing, ethics, privacy, copyright, and record accuracy.

R packages and R-universe

Automation in Biology uses a separate R-universe registry for accepted R packages:

• R-universe registry repository: https://github.com/biologyautomation/biologyautomation.r-universe.dev
• Published R-universe: https://biologyautomation.r-universe.dev/

The separation is intentional:

• This repository, biologyautomation/biologyautomation, is the community's submission, curation, governance, documentation, and general accepted-software registry.
• The R-universe registry, biologyautomation/biologyautomation.r-universe.dev, contains packages.json and indexes accepted software that is also a valid R package.
• Non-R software is not added to the R-universe registry.
• R packages remain subject to the same Automation in Biology submission and curation process as other software; R-universe is an additional package-distribution and discovery layer, not a separate acceptance process.

An R package may remain hosted in its original public Git repository. Inclusion in the Automation in Biology R-universe does not require transferring ownership of the package repository to the biologyautomation GitHub organization.

Documentation

• Submission guide
• Curation policy
• Contributing guide
• Code of conduct
• Security policy

Zenodo community

Community identifier: biologyautomation

Community URL: https://zenodo.org/communities/biologyautomation

Repository scope

This repository contains:

• Submission forms
• Documentation
• Validation workflows
• Protected Zenodo acceptance automation
• Public issue-based submission tracking
• General accepted-software registry automation
• Community governance information

The separate Automation in Biology R-universe registry is used specifically to index accepted R packages for publication through biologyautomation.r-universe.dev.

This repository is not an archival repository for submitted research outputs. Zenodo is the authoritative location for deposited records, files, licences, versions, DOIs, and community membership.

Licence

The documentation and templates in this repository are available under the MIT Licence included in the LICENSE file.

Research outputs deposited on Zenodo retain the licences selected by their respective depositors.

Accepted repository registry

Accepted software repositories are recorded in this repository in two formats:

• Accepted repositories
• Machine-readable registry

After the Zenodo acceptance workflow applies the accepted label, a second GitHub Actions workflow independently verifies that the record is publicly present in the biologyautomation community, opens a generated registry pull request, and merges that pull request after safety checks.

Accepted repositories that are valid R packages may additionally be listed in the separate biologyautomation.r-universe.dev registry for building and distribution through R-universe. Other accepted software remains represented by the general registry in this repository.