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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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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

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LabKey SDMS Integrations
Assays
Standard Assays	Import any type of tabular data using custom assay designs.
ELISA	SDMS features graphical plate configuration for your experiments.
ELISpot	SDMS features graphical plate configuration for your experiments.
Fluorospot The current implementation uses the AID MultiSpot reader.	SDMS features graphical plate configuration for your experiments.
Flow Cytometry - FlowJo	Analyze FCS files using a FlowJo workspace.
Luminex	Import multiplexed bead arrays based on xMap technology.
Mass Spectrometry Perform validations with PeptideProphet and ProteinProphet and quantitation scores using XPRESS or Q3.	Perform searches against FASTA sequence databases using XTandem, Sequest, Mascot, or Comet.
NAb	Low- and high-throughput, cross plate, and multi-virus plates are supported.

Software
Scripting Languages	SDMS supports all major scripting languages, including R, Java, SAS, JavaScript, and Python.
Access	Use Microsoft Access tools on data housed in LabKey using an ODBC connection.
Excel You can also connect any LabKey data back to Microsoft Excel via an ODBC connection.	Excel spreadsheet data can be loaded into LabKey for integration and analysis.
R Display the results of an R script inside your LabKey Server applications with the results updating as the underlying data changes.	Make LabKey a client of your R installation, or make R a client of the data in SDMS.
RStudio	Use RStudio to design and save reports.
RStudio Workbench	Connect to an RStudio Workbench installation.
Rserve	Execute R reports against a remote Rserve instance.
Tableau	Visualize LabKey data in Tableau via an ODBC connection.
Spotfire	Use the JDBC driver to access LabKey data from Spotfire
MATLAB
Plotly Dash	Supported via HTTP proxy.
REDCap	Synchronize with data in a REDCap server.
Informatica EDC	Uses the JDBC driver to access LabKey data
OpenEMPI	Connect LabKey data to an Enterprise Master Patient Index.
Medidata Rave / CDISC ODM	Connect directly with, and import data from Medidata Rave servers.
Skyline	Integrate with the Skyline targeted mass spectrometry tool
Trans Proteomic Pipeline (TPP) Tools include XTandem, Comet, PeptideProphet, ProteinProphet, XPRESS, Q3, and Libra	Analyze mass spectrometry proteomics tools and view their results.
Protein Annotation Databases Databases include UniProtKB Species Suffix Map, SwissProt, TrEMBL, Gene Ontology Database and FASTA.	Data in publicly available databases can be synced and combined with your Mass Spec data.
Jupyter Notebook	Create and share computational documents.
DbVisualize	Uses the JDBC driver to access LabKey data.
Mascot	Work with Mascot server data.

Databases
PostgreSQL	Configure PostgreSQL as a primary or external data source.
Amazon S3	Configure Amazon S3 as a primary or external data source.
SAS	Configure SAS as an external data source.
Oracle	Configure Oracle as an external data source.
MySQL	Configure MySQL as an external data source.
Amazon Redshift	Configure an Amazon Redshift database as an external data source.

Authentication
LDAP	Configure authentication with an existing LDAP server.
CAS	Configure single sign-on using CAS
SAML	Configure authentication against a SAML provider.
Duo	Configure two-factor authentication via the Duo service