Highlights

Version 2.2 represents a important step forward in the ongoing evolution of LabKey Server and its applications. In this release, LabKey introduces the following new capabilities:

Assays

Assays are experimental data sets that have well-defined structures and sets of associated properties. When a set of experimental runs is ready for upload, LabKey uses assay definitions to automatically generate appropriate data entry pages. These forms use intelligent defaults and pre-defined picklist choices (termed Lists) to reduce the burden of data entry and improve accuracy. Assays are a powerful solution to a common problem faced by lab researchers: ensuring that sufficient information is collected for each run such that variations can be explained by replicating and comparing runs. LabKey Server makes it possible for researchers to define their own criteria for "sufficient" information without requiring software or database expertise to do so.

R Integration

LabKey users can now take advantage of a powerful and widely-used scripting language to analyze and chart Study and Assay data. A single menu command pushes the data into R and executes a script that a user has created himself or run from a library of saved scripts. Script results in the form of reports and charts can be incorporated back into LabKey portal and wiki pages. Module developers can take advantage of R integration to enhance the flexibility of any data view.

caBIG(TM) Support

With version 2.2, the CPAS proteomics application on LabKey Server is now certified as caBIG(TM) Silver-level compliant. Compliance enables researchers to publish MS2 experiment data such that it is accessible to remote application programs written to the standard caBIG(TM) interface, as defined by the US National Cancer Institute. Support for caBIG enables LabKey Server to participate in data search and exchange applications across the cancer research community. With caBIG(TM) support, LabKey Server becomes the fastest and easiest way to achieve caBIG(TM)-compliance for datasets, including samples and MS2 protein identifications.

New Feature Details by Module

Study

Assays
  • Assay results can be entered via forms or uploaded from spreadsheets after an assay schema has been defined.
  • Results can be reviewed for correctness, then "published" into a study, where they can be rolled-up by participant or by visit.
  • LabKey now supports the definition of Luminex assay schemas and the upload and publication of Luminex datasets.
R Integration
  • The R environment can be configured from the site administration page.
  • LabKey provides a built-in editor for authoring R scripts
  • Live R Views can be displayed and managed securely
  • Long-running R scripts can execute as Pipeline jobs.
Customizable Date and Number Display Formats
  • LabKey now supports customization of display formats on both a field-by-field and a study-wide basis.
  • Example: Studies can now display dates as “04MAY07” rather than the internationally ambiguous “04/05/07”. (Note: not all display formats are supported for data input).
  • Customized formats apply to dataset views and specimen views.
Additional Specimen Tracking Fields
  • LabKey has added five additional storage location fields and a flag for determining specimen availability

Flow Cytometry

Upload, Store, and Display FlowJo-Calculated Statistics
  • Users can now upload and display FlowJo-calculated statistics on a LabKey Server, for quality control checks or for shared access.
  • Upload process will optionally read graphs from the FlowJo workspace or generate graphs at the server from the uploaded statistics.
Sample-Specific Gate Editing
  • New gate editor enables users to edit the existing gate template of an analysis script for a given sample using an interactive web page on the LabKey Server.
  • New gate templates must still be uploaded from Flo Jo.

ms2

Enhancements to Protein and Peptide Views
  • GO charts are now available for protein views
  • Proteins can be exported from ProteinProphet views (in addition to peptides)
Pipeline Enhancements.
  • XpressProteinRatioParser and Q3ProteinRatioParser performance have improved.
  • LabKey now supports multi-instrument PeptideProphet.
  • Terminal modifications are now handled correctly.
  • Sequest cluster pipeline performance has improved.

Administration

Enhanced Integration with External Tables

  • Rows can be inserted and edited in external, user-defined tables that are identified by a Query. These can be accessed via a checkbox on the Schema Administration page on the Query tab. A defined Primary Key is required.
  • Formatting or "lookup" relationships in an external schema can be specified via an XML file
Search Improvements.
  • Administrators can determine whether searches include subdirectories
  • Administrators can control the search path order
Use LabKey Server for Remote Authentication
  • Users can access other servers securely based on their LabKey login, via a redirection exchange with the LabKey login page.

Collaboration

File Management Enhancements
  • Uploaded files on message boards and wiki pages can now be saved in accessible directories.
  • The Files web part enables project administrators to configure and manage uploaded files, including:
    • Configure save directories by uploading user, assay, study, or other field value
    • View files for all readers
    • Upload files for all uploaders
    • Shows all files in directory
    • Shows user for files uploaded through UI
  • Site administrators can configure system defaults
  • Improved reliability in tracking files across move and undelete actions and an upload log file
  • Available to developers of other modules asa an attachment service
Embed Live Content into Wiki Pages
  • Data views can be embedded in wiki pages
    • Static and dynamic content can be embedded with complex layout in a single page, without custom modules
  • The content of one wiki page can be embedded in other wiki pages.
    • Duplication of content is no longer necessary.
Issue Tracker Improvement
  • Editing an Issue now adds a user to future notification emails.
Messaging Improvement
  • Users can now access their email preferences from the "Discuss This" section.

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