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Connect your instruments, tools, and data in one place

LabKey integrations pull your R&D data sources into a single structured system — instrument outputs, assay results, sample records, and clinical data all captured, linked, and audit-ready. Quality control and permissions are built into how data moves, not added after the fact.

LabKey integrations let you:

Import virtually any type of R&D data, from any source
Build workflows that shape and validate data as it enters the system
Control access and meet compliance requirements for HIPAA, FISMA, and CFR Part 11

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Integration	LIMS Enterprise	SDMS	Description
Assays
Standard Assays	✓	✓	Import any type of tabular data using custom assay designs.
Software
Client APIs	✓	✓	Our APIs support all major scripting languages, including R, Java, JavaScript, and Python.
Excel	✓	✓	Microsoft Excel spreadsheet data can be imported to and exported from LabKey for integration and analysis.
Jupyter Notebook	✓	✓	Import Jupyter notebooks as reports and run them against live LabKey data.
MCP (Model Context Protocol)	✓	✓	Connect AI agents directly to your LabKey data using the MCP server. Pull sample records, run searches, and retrieve results using natural language, without leaving your AI tool or exporting data.
Medidata Rave / CDISC ODM		✓	Connect directly with, and import data from Medidata Rave servers.
Plotly Dash	✓	✓	Supported via HTTP proxy.
R	✓	✓	Connect LIMS Enterprise and SDMS to R. Connect SDMS to RStudio to query data, design and save reports, or link an existing RStudio Workbench installation. Display the results of an R script with the results updating as the underlying data changes.
REDCap		✓	Synchronize with data in a REDCap server.
Skyline		✓	Integrate with the Skyline targeted mass spectrometry tool.
Databases
Oracle	✓	✓	Configure Oracle as an external data source.
Microsoft SQL Server	✓	✓	Configure Microsoft SQL Server as an external data source.
MySQL	✓	✓	Configure MySQL as an external data source.
PostgreSQL	✓	✓	Configure PostgreSQL as a primary or external data source.
Authentication
CAS	✓	✓	Configure single sign-on using CAS.
Duo		✓	Configure two-factor authentication via the Duo service.
LDAP	✓	✓	Configure authentication with an existing LDAP server.
SAML	✓	✓	Configure authentication against a SAML provider.
TOTP	✓	✓	Configure two-factor authentication using any TOTP-compatible authenticator app.
ODBC/JDBC Connections Use these standardized interfaces to connect a variety of analysis tools to LabKey data. These are tools we have tested with ODBC and JDBC.
Access	✓	✓	Use Microsoft Access tools on data housed in LabKey using an ODBC connection.
DbVisualizer	✓	✓	Uses the JDBC driver to access LabKey data.
Excel	✓	✓	Uses the ODBC driver to access LabKey data.
Informatica EDC	✓	✓	Uses the JDBC driver to access LabKey data.
MATLAB	✓	✓
Spotfire	✓	✓	Uses the JDBC driver to access LabKey data from Spotfire.
Tableau	✓	✓	Visualize LabKey data in Tableau via an ODBC connection.
Cloud Resources
Amazon Redshift	✓	✓	Configure an Amazon Redshift database as an external data source.
Amazon S3	✓	✓	Configure Amazon S3 as a primary or external data source.
Snowflake	✓	✓	Configure Snowflake as an external data source.

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Import and align virtually any type of data source, from any source.

Assay & Instrument Data

Capture data from lab instruments and connect it directly to the samples it came from. Assay results, run configurations, and instrument outputs land in structured, searchable records.

Connect assay configurations to capture instrument data in structured, analyzable formats
Connect unique assay designs to provide structure and context for tabular instrument data
Link samples to assay results for automatic, in-context analysis
For automated pipelines, LabKey LIMS captures instrument data directly via API, file watchers, and import scripts — no manual intervention required

Quality Control

Data quality is enforced at the point of capture, not cleaned up after the fact. Validation rules and standardized workflows keep records accurate from the start.

Use data validation and usage modes to verify R&D data before it enters your records
Use custom views and exportable reports to track QC metrics across studies and experiments
Guide users through protocol steps to catch deviations before they become audit findings
Automate quality control checks and data clearance through configurable workflow rules

Data Transformation & Alignment

Raw data rarely arrives in the format you need. LabKey reshapes incoming data to match your structure before it hits your records.

Use transformation scripts to assign alignment between disparate data sources
Use field mapping and no-code metadata schemas to standardize inputs across sources
For complex multi-source pipelines, LabKey SDMS and LabKey LIMS support automation at scale
Reconcile source data by aligning names, hierarchies, and the meaning of scientific data columns and values

Study & Longitudinal Data

Connect samples to the full context of the research they belong to — protocols, subjects, study phases, and assay results all linked in one place.

Link every sample to its protocol, subject, and study phase for in-context analysis
Track how samples and data evolve across a study from a single record
Manage access to study-level data at all phases from experimental execution to post-publication
For organizations managing data across multiple studies, LabKey SDMS provides centralized cross-study data access and dataset alignment tools built for longitudinal research