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labarchive-integration

Electronic lab notebook API integration. Access notebooks, manage entries/attachments, backup notebooks, integrate with Protocols.io/Jupyter/REDCap, for programmatic ELN workflows.

Author

@K-Dense-AI

Category

Development Tools

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LabArchives Integration

Capabilities Overview


Automate management of LabArchives electronic lab notebooks via the REST API to enable notebook backups, entry management, attachment uploads, and third-party tool integration.

Applicable Scenarios

  • Automated lab data backups: Regularly back up entire electronic lab notebooks, including all entries and attachments, to ensure research data security. Supports export in JSON or 7z formats, with optional inclusion or exclusion of attachment files—suitable for research institutions that need to retain data for compliance.

  • Research workflow automation and integration: Connect LabArchives with research tools like Jupyter Notebook, Protocols.io, REDCap, etc., to automate the full pipeline from data collection to record keeping. For example, Jupyter analysis results can be pushed directly to the notebook, and experimental protocols can be synchronized from Protocols.io.

  • Bulk experiment record management: Programmatically create and modify experiment entries, bulk upload data files (PDFs, images, data files, scientific-format files), and add unified metadata and annotations across multiple project notebooks to improve lab data management efficiency.

    • Core Features

  • Notebook operations and management

    • - List all notebooks a user has access to
    - Full notebook backups (attachments optional)
    - Retrieve notebook member lists and permission settings
    - Retrieve notebook IDs for integration with project management systems

  • Entries and attachments management

    • - Create new experiment record entries
    - Add annotations and comments to entries
    - Upload various file attachments (documents, images, data files, scientific-format files)
    - Support bulk upload operations

  • Third-party platform integration

    • - Jupyter Notebook embedding/export
    - Protocols.io protocol synchronization
    - REDCap clinical data capture integration
    - Integration with research software such as GraphPad Prism, SnapGene, Geneious

    Frequently Asked Questions

    How do I obtain an access key for the LabArchives API?


    You need an enterprise LabArchives license with API access enabled. Contact your LabArchives administrator to obtain an Access Key ID and Access Password. User authentication requires an email and an external app password (not the regular login password). When configuring, choose the correct regional endpoint: US/International, Australia, or UK.

    How can I automatically back up a LabArchives notebook using Python?


    Use the provided notebook_operations.py script or the labarchives-py Python package. Basic flow: first obtain the UID via user authentication, then call the notebook_backup API method. Example command: python3 scripts/notebook_operations.py backup --uid USER_ID --nbid NOTEBOOK_ID. Backups can be in JSON format (without attachments) or as a 7z archive (including attachments).

    Which third-party tools does LabArchives support integrating with?


    Official integrations include Protocols.io (protocols), GraphPad Prism (data analysis), SnapGene (molecular biology), Geneious (bioinformatics), Jupyter Notebook, REDCap (clinical data), Qeios (research publishing), and SciSpace (literature management). New integrations use OAuth authentication; older integrations may use API key authentication.