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Centralize and align all of your R&D data in one secure system.

The LabKey Server SDMS integrations offer flexible data import designed to capture and harmonize virtually any type of life science research data. Scientific data can be captured and integrated with related demographic, clinical and sample data to form a “single source of truth” for R&D data. Data integrity is maintained via quality control features and automation tools that reduce the need for error-prone manual processes.

SDMS integrations allow you to:

Model and import virtually any type of R&D data, from any source
Harmonize lab data with clinical, demographic and sample related data
Create workflows that shape your data and automate quality control
Secure your data with permission-based access and comply with HIPAA, FISMA and CFR Part 11

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

Assay Data Integration

Capture structured data from lab instruments and harmonize with related R&D data.

Support for mass spectrometry, Luminex, flow cytometry, proteomics and other instrument types
Generate unique assay design to provide structure and context for tabular instrument data
Use scripts to clean, shape or automate calculation of values during import
Automate data capture using APIs, script-based pipelines and file upload triggers

Quality Control

Improve data integrity with quality control tools, workflows and automation.

Use data validators and range checks to verify data integrity and accuracy
Use quality control reports to track key QC metrics
Automate quality control checks and data cleanup measures
Define QC workflows to support your internal processes and standards

Data Transformation & Alignment

Transform data to achieve alignment between disparate data sources.

Use Python, R, or Java scripting to clean, shape or automate the calculation of values
Attach sequential scripts to assay designs to run multiple transformations and reshape data files prior to import
Use ontologies to reconcile data with controlled vocabularies to aligning terms, hierarchies, and the meaning of specific data columns and values

Study Data

Connect longitudinal study data with related assay and sample data.

Integrating clinical and demographic data for participants, cohorts, and groups
Organize and manage longitudinal study data in a central, secure environment for more efficient curation, analysis, and publishing.
Manage access to study data at all phases from operational execution to post-publication.

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LabKey Server SDMS Integrations
Assays
Standard Assays	Import any type of tabular data using custom assay designs.
ELISA	LabKey Server features graphical plate configuration for your experiments.
ELISpot	LabKey Server features graphical plate configuration for your experiments.
Fluorospot The current implementation uses the AID MultiSpot reader.	LabKey Server 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	LabKey Server 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 LabKey Server.
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