gh-k-dense-ai-claude-scientific-skills-scientific-skills/skills/labarchive-integration/references/integrations.md

LabArchives Third-Party Integrations

Overview

LabArchives integrates with numerous scientific software platforms to streamline research workflows. This document covers programmatic integration approaches, automation strategies, and best practices for each supported platform.

Integration Categories

1. Protocol Management

Protocols.io Integration

Export protocols directly from Protocols.io to LabArchives notebooks.

Use cases:

• Standardize experimental procedures across lab notebooks
• Maintain version control for protocols
• Link protocols to experimental results

Setup:

1. Enable Protocols.io integration in LabArchives settings
2. Authenticate with Protocols.io account
3. Browse and select protocols to export

Programmatic approach:

# Export Protocols.io protocol as HTML/PDF
# Then upload to LabArchives via API

def import_protocol_to_labarchives(client, uid, nbid, protocol_id):
    """Import Protocols.io protocol to LabArchives entry"""
    # 1. Fetch protocol from Protocols.io API
    protocol_data = fetch_protocol_from_protocolsio(protocol_id)

    # 2. Create new entry in LabArchives
    entry_params = {
        'uid': uid,
        'nbid': nbid,
        'title': f"Protocol: {protocol_data['title']}",
        'content': protocol_data['html_content']
    }
    response = client.make_call('entries', 'create_entry', params=entry_params)

    # 3. Add protocol metadata as comment
    entry_id = extract_entry_id(response)
    comment_params = {
        'uid': uid,
        'nbid': nbid,
        'entry_id': entry_id,
        'comment': f"Protocols.io ID: {protocol_id}<br>Version: {protocol_data['version']}"
    }
    client.make_call('entries', 'create_comment', params=comment_params)

    return entry_id

Updated: September 22, 2025

2. Data Analysis Tools

GraphPad Prism Integration (Version 8+)

Export analyses, graphs, and figures directly from Prism to LabArchives.

Use cases:

• Archive statistical analyses with raw data
• Document figure generation for publications
• Maintain analysis audit trail for compliance

Setup:

1. Install GraphPad Prism 8 or higher
2. Configure LabArchives connection in Prism preferences
3. Use "Export to LabArchives" option from File menu

Programmatic approach:

# Upload Prism files to LabArchives via API

def upload_prism_analysis(client, uid, nbid, entry_id, prism_file_path):
    """Upload GraphPad Prism file to LabArchives entry"""
    import requests

    url = f'{client.api_url}/entries/upload_attachment'
    files = {'file': open(prism_file_path, 'rb')}
    params = {
        'uid': uid,
        'nbid': nbid,
        'entry_id': entry_id,
        'filename': os.path.basename(prism_file_path),
        'access_key_id': client.access_key_id,
        'access_password': client.access_password
    }

    response = requests.post(url, files=files, data=params)
    return response

Supported file types:

• .pzfx (Prism project files)
• .png, .jpg, .pdf (exported graphs)
• .xlsx (exported data tables)

Updated: September 8, 2025

3. Molecular Biology & Bioinformatics

SnapGene Integration

Direct integration for molecular biology workflows, plasmid maps, and sequence analysis.

Use cases:

• Document cloning strategies
• Archive plasmid maps with experimental records
• Link sequences to experimental results

Setup:

1. Install SnapGene software
2. Enable LabArchives export in SnapGene preferences
3. Use "Send to LabArchives" feature

File format support:

• .dna (SnapGene files)
• .gb, .gbk (GenBank format)
• .fasta (sequence files)
• .png, .pdf (plasmid map exports)

Programmatic workflow:

def upload_snapgene_file(client, uid, nbid, entry_id, snapgene_file):
    """Upload SnapGene file with preview image"""
    # Upload main SnapGene file
    upload_attachment(client, uid, nbid, entry_id, snapgene_file)

    # Generate and upload preview image (requires SnapGene CLI)
    preview_png = generate_snapgene_preview(snapgene_file)
    upload_attachment(client, uid, nbid, entry_id, preview_png)

Geneious Integration

Bioinformatics analysis export from Geneious to LabArchives.

Use cases:

• Archive sequence alignments and phylogenetic trees
• Document NGS analysis pipelines
• Link bioinformatics workflows to wet-lab experiments

Supported exports:

• Sequence alignments
• Phylogenetic trees
• Assembly reports
• Variant calling results

File formats:

• .geneious (Geneious documents)
• .fasta, .fastq (sequence data)
• .bam, .sam (alignment files)
• .vcf (variant files)

4. Computational Notebooks

Jupyter Integration

Embed Jupyter notebooks as LabArchives entries for reproducible computational research.

Use cases:

• Document data analysis workflows
• Archive computational experiments
• Link code, results, and narrative

Workflow:

def export_jupyter_to_labarchives(notebook_path, client, uid, nbid):
    """Export Jupyter notebook to LabArchives"""
    import nbformat
    from nbconvert import HTMLExporter

    # Load notebook
    with open(notebook_path, 'r') as f:
        nb = nbformat.read(f, as_version=4)

    # Convert to HTML
    html_exporter = HTMLExporter()
    html_exporter.template_name = 'classic'
    (body, resources) = html_exporter.from_notebook_node(nb)

    # Create entry in LabArchives
    entry_params = {
        'uid': uid,
        'nbid': nbid,
        'title': f"Jupyter Notebook: {os.path.basename(notebook_path)}",
        'content': body
    }
    response = client.make_call('entries', 'create_entry', params=entry_params)

    # Upload original .ipynb file as attachment
    entry_id = extract_entry_id(response)
    upload_attachment(client, uid, nbid, entry_id, notebook_path)

    return entry_id

Best practices:

• Export with outputs included (Run All Cells before export)
• Include environment.yml or requirements.txt as attachment
• Add execution timestamp and system info in comments

5. Clinical Research

REDCap Integration

Clinical data capture integration with LabArchives for research compliance and audit trails.

Use cases:

• Link clinical data collection to research notebooks
• Maintain audit trails for regulatory compliance
• Document clinical trial protocols and amendments

Integration approach:

• REDCap API exports data to LabArchives entries
• Automated data synchronization for longitudinal studies
• HIPAA-compliant data handling

Example workflow:

def sync_redcap_to_labarchives(redcap_api_token, client, uid, nbid):
    """Sync REDCap data to LabArchives"""
    # Fetch REDCap data
    redcap_data = fetch_redcap_data(redcap_api_token)

    # Create LabArchives entry
    entry_params = {
        'uid': uid,
        'nbid': nbid,
        'title': f"REDCap Data Export {datetime.now().strftime('%Y-%m-%d')}",
        'content': format_redcap_data_html(redcap_data)
    }
    response = client.make_call('entries', 'create_entry', params=entry_params)

    return response

Compliance features:

• 21 CFR Part 11 compliance
• Audit trail maintenance
• Data integrity verification

6. Research Publishing

Qeios Integration

Research publishing platform integration for preprints and peer review.

Use cases:

• Export research findings to preprint servers
• Document publication workflows
• Link published articles to lab notebooks

Workflow:

• Export formatted entries from LabArchives
• Submit to Qeios platform
• Maintain bidirectional links between notebook and publication

SciSpace Integration

Literature management and citation integration.

Use cases:

• Link references to experimental procedures
• Maintain literature review in notebooks
• Generate bibliographies for reports

Features:

• Citation import from SciSpace to LabArchives
• PDF annotation synchronization
• Reference management

OAuth Authentication for Integrations

LabArchives now uses OAuth 2.0 for new third-party integrations.

OAuth flow for app developers:

def labarchives_oauth_flow(client_id, client_secret, redirect_uri):
    """Implement OAuth 2.0 flow for LabArchives integration"""
    import requests

    # Step 1: Get authorization code
    auth_url = "https://mynotebook.labarchives.com/oauth/authorize"
    auth_params = {
        'client_id': client_id,
        'redirect_uri': redirect_uri,
        'response_type': 'code',
        'scope': 'read write'
    }
    # User visits auth_url and grants permission

    # Step 2: Exchange code for access token
    token_url = "https://mynotebook.labarchives.com/oauth/token"
    token_params = {
        'client_id': client_id,
        'client_secret': client_secret,
        'redirect_uri': redirect_uri,
        'grant_type': 'authorization_code',
        'code': authorization_code  # From redirect
    }

    response = requests.post(token_url, data=token_params)
    tokens = response.json()

    return tokens['access_token'], tokens['refresh_token']

OAuth advantages:

• More secure than API keys
• Fine-grained permission control
• Token refresh for long-running integrations
• Revocable access

Custom Integration Development

General Workflow

For tools not officially supported, develop custom integrations:

1. Export data from source application (API or file export)
2. Transform format to HTML or supported file type
3. Authenticate with LabArchives API
4. Create entry or upload attachment
5. Add metadata via comments for traceability

Example: Custom Integration Template

class LabArchivesIntegration:
    """Template for custom LabArchives integrations"""

    def __init__(self, config_path):
        self.client = self._init_client(config_path)
        self.uid = self._authenticate()

    def _init_client(self, config_path):
        """Initialize LabArchives client"""
        with open(config_path) as f:
            config = yaml.safe_load(f)
        return Client(config['api_url'],
                     config['access_key_id'],
                     config['access_password'])

    def _authenticate(self):
        """Get user ID"""
        # Implementation from authentication_guide.md
        pass

    def export_data(self, source_data, nbid, title):
        """Export data to LabArchives"""
        # Transform data to HTML
        html_content = self._transform_to_html(source_data)

        # Create entry
        params = {
            'uid': self.uid,
            'nbid': nbid,
            'title': title,
            'content': html_content
        }
        response = self.client.make_call('entries', 'create_entry', params=params)

        return extract_entry_id(response)

    def _transform_to_html(self, data):
        """Transform data to HTML format"""
        # Custom transformation logic
        pass

Integration Best Practices

1. Version control: Track which software version generated the data
2. Metadata preservation: Include timestamps, user info, and processing parameters
3. File format standards: Use open formats when possible (CSV, JSON, HTML)
4. Batch operations: Implement rate limiting for bulk uploads
5. Error handling: Implement retry logic with exponential backoff
6. Audit trails: Log all API operations for compliance
7. Testing: Validate integrations in test notebooks before production use

Troubleshooting Integrations

Common Issues

Integration not appearing in LabArchives:

• Verify integration is enabled by administrator
• Check OAuth permissions if using OAuth
• Ensure compatible software version

File upload failures:

• Verify file size limits (typically 2GB per file)
• Check file format compatibility
• Ensure sufficient storage quota

Authentication errors:

• Verify API credentials are current
• Check if integration-specific tokens have expired
• Confirm user has necessary permissions

Integration Support

For integration-specific issues:

• Check software vendor documentation (e.g., GraphPad, Protocols.io)
• Contact LabArchives support: support@labarchives.com
• Review LabArchives knowledge base: help.labarchives.com

Future Integration Opportunities

Potential integrations for custom development:

• Electronic data capture (EDC) systems
• Laboratory information management systems (LIMS)
• Instrument data systems (chromatography, spectroscopy)
• Cloud storage platforms (Box, Dropbox, Google Drive)
• Project management tools (Asana, Monday.com)
• Grant management systems

For custom integration development, contact LabArchives for API partnership opportunities.