Submission guide

Overview

Research files must be deposited on Zenodo through the submitter's own Zenodo account.

GitHub issues are used for public submission tracking and curator communication. GitHub is not used to store submitted research files.

Before submitting

Confirm that:

• The output has a substantial connection to automation in biology.
• You are authorised to deposit the files and metadata.
• The authors and contributors are correctly identified.
• An appropriate licence or rights statement has been selected.
• The record does not expose confidential or unlawfully shared personal data.
• The title, description, keywords, and resource type are accurate.

Route A: Submit an unpublished Zenodo draft

Use this route when the record has not yet been published.

1. Sign in to Zenodo.
2. Visit the Automation in Biology community: https://zenodo.org/communities/biologyautomation
3. Start a new upload.
4. Upload the research files.
5. Complete the required metadata.
6. Select an appropriate licence or rights statement.
7. Add relevant keywords.
8. Add related identifiers where applicable.
9. Save and preview the draft.
10. Submit the draft to the Automation in Biology community for review.
11. Open a submission issue in this GitHub repository.
12. Include the Zenodo record or review URL.
13. Address any changes requested by the curators.
14. The curator may accept, request changes, or decline the submission.

Route B: Submit an existing published Zenodo record

Use this route when the record is already published on Zenodo.

1. Open the published Zenodo record.
2. Open the community-submission controls.
3. Search for Automation in Biology.
4. Select the community with identifier biologyautomation.
5. Submit the record for community review.
6. Open a submission issue in this GitHub repository.
7. Include the published Zenodo record URL.
8. Address any questions or metadata-change requests from the curators.

Required metadata

A submission should provide:

• A clear and specific title
• A meaningful description or abstract
• Complete creator information
• ORCID identifiers where available
• An appropriate resource type
• Relevant keywords
• A licence or rights statement
• A version number for versioned outputs
• Links to related outputs where applicable
• Funding information where applicable

Recommended keywords

Use specific keywords that accurately describe the output. Examples include:

• automation in biology
• laboratory automation
• robotic experimentation
• automated sample preparation
• high-throughput experimentation
• autonomous laboratory
• self-driving laboratory
• biofoundry
• automated microscopy
• automated phenotyping
• workflow management
• laboratory information management system
• scientific software
• reproducible protocol
• synthetic biology automation

Do not add unrelated keywords solely to increase visibility.

Software submissions

Software records should preferably include:

• A versioned release
• Installation instructions
• Usage documentation
• Dependency information
• A source-code repository
• A software licence
• Tests or validation information where available
• A CITATION.cff file where appropriate
• Release notes or a changelog

Dataset submissions

Dataset records should preferably include:

• A README
• A data dictionary
• Collection or generation methods
• File-format descriptions
• Reuse conditions
• Related code or workflows
• Quality-control information
• Ethical and privacy information where applicable

Protocol and workflow submissions

Protocol and workflow records should preferably include:

• Required equipment
• Required software
• Required materials or reagents
• Input and output descriptions
• Step-by-step instructions
• Version information
• Expected results
• Known limitations
• Safety considerations where applicable

Papers and book chapters

Paper and chapter submissions should preferably include:

• A complete citation
• Publication or preprint status
• The associated DOI where available
• Links to related software, datasets, or protocols
• A clear explanation of the role of automation in the work

Privacy and sensitive information

Do not place the following in a public GitHub issue:

• Personal data about research participants
• Confidential peer-review material
• API keys or passwords
• Private access tokens
• Restricted datasets
• Unpublished patent-sensitive details
• Private correspondence
• Files that you are not authorised to share

Use an appropriate private communication channel when a submission requires confidential handling.

After submission

The GitHub issue may be labelled:

• submission
• under-review
• changes-requested
• accepted
• declined
• withdrawn

The GitHub issue is a public tracking record. The Zenodo community request is the authoritative submission reviewed by the curators.