Instrument, Software, and Database Integrations
LabKey software solutions are designed with non-disruptive integration in mind, making it possible to easily extend the highly flexible LabKey Server platform through integration with other systems. LabKey software products have been successfully integrated with the following assay types, instruments, and software systems. These lists are not exhaustive, and new integrations are regularly built to support user needs. If you do not see your particular instrument, file format, or software system below, contact LabKey for help parsing your data and or to discuss options for support.
Assay Instruments and File Types
In addition to the specialized support for following assay instruments and file types, LabKey Server can import any tabular data, such as Excel, CSV, and TSV files, through a general purpose assay design.
| Assay Type | Description | File Types | Support Documentation on LabKey.org |
| ELISA | LabKey Server features graphical plate configuration for your experiments. | Excel | ELISA Assay |
| ELISpot | LabKey Server features graphical plate configuration for your experiments. | Excel, TXT | ELISpot Assay |
| Fluorospot | LabKey Server features graphical plate configuration for your experiments. The current implementation uses the AID MultiSpot reader. | Excel | FluoroSpot Assay |
| Flow Cytometry - FlowJo | Analyze FCS files using a FlowJo workspace. | FCS, JO, WSP | Flow Cytometry |
| Flow Cytometry - FCSExpress | LabKey Server can be used as the data store for an FCS Express installation. | FCS | FCS Express |
| HPLC | View multiple, overlayed curves and calculate the areas under curves. A file listener automatically loads new results directly from the instrument. | TXT, Excel | High-Performance Liquid Chromatography |
| Luminex® | Import multiplexed bead arrays based on xMap technology. | Bio-Plex Excel | Luminex |
| Microarray - Agilent | LabKey Server automates running the Feature Extractor software on the instrument generated TIFF file, and then associates the resulting MAGE-ML data file, along with a PDF QC report, a JPEG thumbnail, and other outputs with sample information and customizable, user-entered run-level metadata. | CSV, JPEG, TIFF, MAGE-ML | Microarray |
| Microarray - Affymetrix | The current implementation has been successfully integrated with GeneTitan. | Excel, CEL | Microarray |
| Mass Spectrometry | Perform searches against FASTA sequence databases using tools such as XTandem, Sequest, Mascot, or Comet. Perform validations with PeptideProphet and ProteinProphet and quantitation scores using XPRESS or Q3. | mzXML | Proteomics |
| NAb | Low- and high-throughput, cross plate, and multi-virus plates are supported | Excel, CSV, TSV | Neutralizing Antibody Assays |
Research and Lab Software
| Software | Description | Support Documentation on LabKey.org |
| Access | Use Microsoft Access tools on data housed in LabKey using an ODBC connection. | External ODBC Connections |
| Excel | Excel 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. | External ODBC Connections |
| FCSExpress | Use LabKey as the data store for FCSExpress. | FCS Express |
| FreezerPro | Synchronize to data in a FreezerPro server. | FreezerPro Integration |
| Galaxy | Use LabKey Server in conjunction with Galaxy to create a sequencing workflow. | |
| Illumina | Build a workflow for managing samples and sequencing results generated from Illumina instruments, such as the MiSeq Benchtop Sequencer. | |
| ImmPort | Automatically synchronize with data in the NIH Immport database. | About ImmuneSpace |
| Libra | Work with iTRAQ quantitation data. | Using Quantitation Tools |
| Mascot | Work with Mascot server data. | Set Up Mascot |
| OpenEMPI | Connect LabKey data to an Enterprise Master Patient Index. | OpenEMPI (Enterprise Master Patient Index) |
| PeptideProphet | View and analyze PeptideProphet results. | View PeptideProphet Results |
| ProteinProphet | View and analyze ProteinProphet results. | Using ProteinProphet |
| Protein Annotation Databases | UniProtKB 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 |
| Q3 | Load and analyze Q3 quantitation results. | Using Quantitation Tools |
| R | LabKey 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 | Use RStudio to design and save reports. | RStudio Integration |
| RStudio Pro | Connect to an RStudio Pro installation | Connect to RStudio Pro |
| REDCap | Synchronize with data in a REDCap server. | REDCap Survey Data Integration |
| Scripting Languages | LabKey Server supports all major scripting languages, including R, JavaScript, PERL, and Python. | Configure Scripting Engines |
| Skyline | Integrate with the Skyline proteomics tool. | Panorama - Targeted Proteomics |
| Spotfire | Use the JDBC driver to access LabKey data from Spotfire | Spotfire |
| Tableau | Visualize LabKey data in Tableau via an ODBC connection. | External ODBC Connections |
| XPRESS | Load and analyze XPRESS quantitation data. | Using Quantitation Tools |
| XTandem | Load and analyze XTandem results. | Set Up for Proteomics Analysis |
Databases
| Database | Description | Support Documentation on LabKey.org |
| PostgreSQL | PostgreSQL can be installed as a primary or external data source. | Install PostgreSQL |
| MS SQL Server | MS SQL Server can be installed as a primary or external data source. | Install Microsoft SQL Server |
| SAS | SAS can be installed as an external data source. | External SAS Data Sources |
| Oracle | Oracle can be installed as an external data source. | External Oracle Data Sources |
| MySQL | MySQL can be installed as an external data source. | External MySQL Data Sources |
| Amazon Redshift | Configure an Amazon Redshift database as an external data source | Redshift Data Sources |
Authentication Software
| Authentication Provider | Description | Support Documentation on LabKey.org |
| CAS | Use CAS single sign on. | CAS Single Sign On (SSO) |
| Duo | Use Duo Two-Factor sign on. | Duo Two-Factor Authentication |
| LDAP | Authenticate with an existing LDAP server. | Configure LDAP |
| SAML | Configure a SAML authentication provider. | Configure SAML Authentication |
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