System Integration: Instruments and Software

The lists in this topic include some of the assay types, instruments, and software systems that have been successfully integrated with LabKey Server. These lists are not exhaustive and not intended to exclude any specific instrument or system. In general, LabKey Server can import any tabular data, such as Excel, CSV, and TSV files.

LabKey Server is designed with non-disruptive system integration in mind: it is highly flexible and can be extended to work with many kinds of software systems. If you do not see your particular instrument, file format, or software system below, contact LabKey for help parsing your data and to discuss options for support.

Assay Instruments and File Types

Assay TypeooooooooDescriptionFile TypesooooDocumentationooooooooooooo
ELISALabKey Server features graphical plate configuration for your experiments.ExcelELISA Assay
ELISpotLabKey Server features graphical plate configuration for your experiments.Excel, TXTELISpot Assay
FluorospotLabKey Server features graphical plate configuration for your experiments. The current implementation uses the AID MultiSpot reader.ExcelFluoroSpot Assay
Flow Cytometry - FlowJoAnalyze FCS files using a FlowJo workspace.FCS, JO, WSPFlow Cytometry
Luminex®Import multiplexed bead arrays based on xMap technology.Bio-Plex ExcelLuminex File Formats
Mass SpectrometrySupport for many aspects of proteomics research, including searches against FASTA sequence databases (X!Tandem, Sequest, Mascot, or Comet).
Perform validations with PeptideProphet and ProteinProphet and quantitation scores using XPRESS or Q3.
mzXMLMass Spectrometry
NAbLow- and high-throughput, cross plate, and multi-virus plates are supportedExcel, CSV, TSVNAb (Neutralizing Antibody) Assays

Research and Lab Software

ExcelExcel spreadsheet data can be loaded into LabKey for integration and analysis. You can also connect any LabKey data back to Microsoft Excel via an ODBC connection.Tutorial: Inferring Datasets from Excel and TSV Files and ODBC: External Tool Connections
GalaxyUse LabKey Server in conjunction with Galaxy to create a sequencing workflow. 
IlluminaBuild a workflow for managing samples and sequencing results generated from Illumina instruments, such as the MiSeq Benchtop Sequencer. 
ImmPortAutomatically synchronize with data in the NIH Immport database.About ImmuneSpace
LibraWork with iTRAQ quantitation data.Using Quantitation Tools
MascotWork with Mascot server data.Set Up Mascot
OpenEMPI(Premium Feature) Connect LabKey data to an Enterprise Master Patient Index.Enterprise Master Patient Index Integration
PeptideProphetView and analyze PeptideProphet results.Step 3: View PeptideProphet Results
ProteinProphetView and analyze ProteinProphet results.Using ProteinProphet
Protein Annotation DatabasesUniProtKB Species Suffix Map, SwissProt, TrEMBL, Gene Ontology Database, FASTA.
Data in these publicly available databases can be synced to LabKey Server and combined with your Mass Spec data.
Loading Public Protein Annotation Files
Q3Load and analyze Q3 quantitation results.Using Quantitation Tools
RLabKey and R have a two-way relationship: you can make LabKey a client of your R installation, or you make R a client of the data in LabKey Server. You can also display the results of an R script inside your LabKey Server applications; the results update as the underlying data changes.R Reports
RStudio(Premium Feature) Use RStudio to design and save reports.Premium RStudio Integration
RStudio Workbench(Premium Feature) Connect to an RStudio Workbench installation.Connect to RStudio Workbench
REDCap(Premium Feature) Synchronize with data in a REDCap server.REDCap Survey Data Integration
Scripting LanguagesLabKey Server supports all major scripting languages, including R, JavaScript, PERL, and Python.Configure Scripting Engines
SkylineIntegrate with the Skyline targeted mass spectrometry tool.Panorama: Targeted Mass Spectrometry
XPRESSLoad and analyze XPRESS quantitation data.Using Quantitation Tools
X!TandemLoad and analyze X!Tandem results.Step 1: Set Up for Proteomics Analysis

ODBC/JDBC Integrations (Premium Features)

AccessUse Microsoft Access tools on data housed in LabKey.ODBC: External Tool Connections
AWS GlueUse the JDBC driver preconfigured within Glue to connect to LabKey data.Integration with AWS Glue
ExcelOpen LabKey schema and tables directly in Excel.ODBC: External Tool Connections
JMPUse JMP to analyze LabKey data.ODBC: External Tool Connections
MATLABUse MATLAB to analyze LabKey data.ODBC: External Tool Connections
SpotfireUse the LabKey JDBC driver to access LabKey data from Spotfire.Integration with Spotfire
SSRSUse SQL Server Reporting Services for creating, publishing, and managing reports.ODBC: External Tool Connections
Tableau DesktopVisualize LabKey data in Tableau via an ODBC connection.Integrate with Tableau


PostgreSQLPostgreSQL can be installed as a primary or external data source.External PostgreSQL Data Sources
MS SQL Server(Premium Feature) MS SQL Server can be installed as a primary or external data source.External Microsoft SQL Server Data Sources
SAS(Premium Feature) SAS can be installed as an external data source.External SAS/SHARE Data Sources
Oracle(Premium Feature) Oracle can be installed as an external data source.External Oracle Data Sources
MySQL(Premium Feature) MySQL can be installed as an external data source.External MySQL Data Sources
Redshift(Premium Feature) Configure an Amazon Redshift database as an external data source.External Redshift Data Sources

Authentication Software

Authentication ProviderDescriptionDocumentation
CAS(Premium Feature) Use CAS single sign on.Configure CAS Authentication
Duo(Premium Feature) Use Duo Two-Factor sign on.Configure Duo Two-Factor Authentication
LDAP(Premium Feature) Authenticate with an existing LDAP server.Configure LDAP Authentication
SAML(Premium Feature) Configure a SAML authentication provider.Configure SAML Authentication

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