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
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,
| Assay Typeoooooooo | Description | File Typesoooo | Documentationooooooooooooo |
|---|
| 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 |
| Luminex® | Import multiplexed bead arrays based on xMap technology. | Bio-Plex Excel | Luminex File Formats |
| Mass Spectrometry | Support 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. | mzXML | Mass Spectrometry |
| NAb | Low- and high-throughput, cross plate, and multi-virus plates are supported | Excel, CSV, TSV | NAb (Neutralizing Antibody) Assays |
| Software | Description | Documentationooooooooooooooooooo |
|---|
| 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. | Tutorial: Inferring Datasets from Excel and TSV Files and ODBC: External Tool Connections |
| 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 | (Premium Feature) Connect LabKey data to an Enterprise Master Patient Index. | Enterprise Master Patient Index Integration |
| PeptideProphet | View and analyze PeptideProphet results. | Step 3: 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 | (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 Languages | LabKey Server supports all major scripting languages, including R, JavaScript, PERL, and Python. | Configure Scripting Engines |
| Skyline | Integrate with the Skyline targeted mass spectrometry tool. | Panorama: Targeted Mass Spectrometry |
| XPRESS | Load and analyze XPRESS quantitation data. | Using Quantitation Tools |
| X!Tandem | Load and analyze X!Tandem results. | Step 1: Set Up for Proteomics Analysis |
