The lists below describe 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. Also 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 Typeoooooooo | Description | File Typesooooooooooooooooooo | Documentationooooooooooooo |
|---|
| ELISA | LabKey Server features graphical plate configuration for your experiments. | Excel | ELISA Assay Tutorial |
| 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 | HPLC - High-Performance Liquid Chromatography |
| Luminex® | Import multiplexed bead arrays based on xMap technology. | Bio-Plex Excel | Luminex File Formats |
| 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 | NAb (Neutralizing Antibody) Assays |
Research and Lab Software
| Software | Description | Documentationooooooooooooooooooo |
|---|
| FCSExpress | Use LabKey as the data store for FCSExpress. | FCS Express |
| FreezerPro | Synchronize to data in a FreezerPro server. | Import FreezerPro Data |
| Galaxy | Use LabKey Server in conjunction with Galaxy to create a sequencing workflow. | Example Workflow: LabKey and Galaxy |
| Illumina | Build a workflow for managing samples and sequencing results generated from Illumina instruments, such as the MiSeq Benchtop Sequencer. | Example Workflow: LabKey and Illumina |
| 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 |
| 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 |
| 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 |
| XPRESS | Load and analyze XPRESS quantitation data. | Using Quantitation Tools |
| XTandem | Load and analyze XTandem results. | Step 1: Set Up for Proteomics Analysis |
Databases
Authentication Software
