Version 8.1 represents a important step forward in the ongoing evolution of LabKey Server and its applications. Enhancements support LabKey's mission of providing the premier scientific data management system (SDMS) for experimental and observational study information.

New capabilities introduced in this release are summarized below. For a full query listing all improvements made in 8.1, see: Items Completed in 8.1.

Refer to errata to work around minor behavior changes associated with upgrading from v2.3 to v8.1.

CPAS

MS2 Enhancements

  • Use spectra counting to compare runs via label-free quantitation.
  • Produce Venn diagrams to visualize overlap between run groups.
  • Gain deeper insights into your data through improved protein annotation.
    • Access more FASTA file formats thanks to improved parsing of FASTA files.
    • Choose from a wider range of display names for proteins.
  • Enjoy better access to R tools from MS2.
  • Compare run groups more easily.
MS1 Enhancements
  • Automate MS1 searches via the pipeline.
  • Compare MS1 runs based on shared peptide identifications.
  • Mine data you have already uploaded and searched:
    • Search for features by peptide sequence
    • Find similar features by mz and retention time

Assays

New Data Types. LabKey Server’s fully customizable assay designer helps you sidestep data management bottlenecks. Version 8.1 expands the number of data types you can bring into the system:

  • ELISpot Assays
    • Customize run metadata and plate templates, upload raw data files from CTL and AID instruments and store data in standard LabKey data tables with sortable/filterable data grids.
  • Microarray Assays
    • Assay types have been expanded to include Microarrays. Leverage Labkey's data pipeline to use Agilent's feature extraction software on TIFF files and upload MageML files into the LabKey Server database.
List Enhancements
  • File columns for Lists. You can now define columns of type 'File' for lists, just like you can for assay run and upload set domains.
  • Multiline text fields in Lists. UI now supports multiline text fields in insert/update/details views. It also allows embedded carriage returns.

Study

New Study Demo & Tutorial. LabKey.org now provides a suite of sample datasets and views to help you get you up and running in using the Study Application.

  • Use these samples to explore the power of Study for organizing and visualizing your datasets.
  • The Study Demo Tutorial guides you through setting up the Study Demo on your own server, including custom datagrid views, charts and R views.
Pre-Prepared Specimen Reports. The Demo Study lets you sample Labkey's new suite of built-in reports. Interactive reports available now include summaries for specimen types by timepoint, participants by timepoint and requested vials by both type and timepoint.

Study cohort support. A participant’s cohort can now be automatically determined based on CRF data. Any dataset or visit can be manually assigned to a specific cohort if desired. The study overview page, participant views, and specimen reports now reflect cohort information.

Flow

Initial Implementation of File Repository. Provides reliable, checksummed delivery of flow data to the server via drag and drop directly onto a web browser.

  • You can now perform FTP uploads from the browser.
  • MD5 checksums to ensure accuracy of the upload
FlowJo Improvements
  • Support for importing FlowJo templates.
  • Support for importing auto-compensation scripts.
Flow Filtering/Scripting Enhancements
  • Run a flow script against a subset of all wells; e.g., filter for all wells that are "8 color".

Developer Tools

New API Framework for Creating Reports and Views. The new set of APIs for reports and views provides a flexible framework for users to quickly develop and deploy grids and charts without help from LabKey’s core development team. The first release of this growing suite of APIs provides:

  • Javascript client-side APIs, which allow you to retrieve and modify data queries, plus design and render live chart and grid views. The chart APIs provide image map support for existing JFreeCharts generated by the reporting system.
  • Server-side APIs, which provide basic query functionality
  • Complete, javadoc-style API Reference documentation

Reports and Views

These enhancements to Labkey's 8.1 core UI and infrastrucure will speed your data processing and discovery efforts.

R View Enhancements

  • Source scripts for R views can be made available to non-admins, allowing easier sharing.
  • All users can now easily flip between an R View, the R script for the View, the source datagrid for the View and the handy page of “Help” text. Each of these items appears on its own tab in the R View Builder.
  • Inherited R views. R views in a parent folder can be made available to data grids in child folders, helping you leverage your efforts.
  • The custom view used to create an R view is now listed inside the view and you can edit the view as well.
  • Saved R Views respect the filters added to the URL for a custom view so that the user can run these saved views on a subset of the full dataset.
  • R views can now be run against grid views different than the original source grid view. This lets you write a script once and run it against different datasets.
Data Grid View Enhancements
  • LabKey now keeps track of selections on multiple pages of large datasets, so you can work with large amounts of data more efficiently. Selections on multiple pages of data are remembered, so you can perform operations on these rows as a group, no matter where the rows appear in your dataset.
  • Choose the number of rows to display in any grid view: 40, 100, 250, 1000, selected rows or all rows
  • Scoping options for queries and custom views. Custom views can be inherited from parent folders.
  • New "Is One Of" Filter. Use the new "Is One of" criterion to filter data while designing custom data grid views.
Improved Chart Designer UI
  • Simple yet flexible, the designer lets you plot multiple y-values simultaneously using one or many y-axes. Produce one or many subplots, covering each or every participant.
Discoverability and Display Improvement
  • Reports and Views appear in the "View" drop down menu above any data grid view.
  • Data visualizations can now be featured more prominently on portal pages via the new "Reports" webpart.

Admin

Seamless Authentication for Single-Sign-On

  • When single sign-on is configured, links from a partner site to LabKey automatically redirect to the single sign-on authority if LabKey considers the browser unauthorized. LabKey uses the referrer to determine whether to redirect unauthorized user to the single-sign-on link. This makes the authentication process seamless.
Recursive Folder Deletion
  • "Manage Folders" now allows you to delete a folder/project even when it has subfolders. Previously it was necessary to delete subfolders individually before deleting a top-level folder.
Support for PostgreSQL 8.3
  • LabKey now supports PostgreSQL 8.3
Browser-based FTP uploads: simplify your workflow with LabKey’s new drag and drop capability for moving data files in the LabKey system.
  • File Repository (Beta): This handy tool provides reliable, checksummed delivery of data to the server via drag and drop directly onto a web browser.
Wiki Link Checker
  • This new tool allows you to verify that all the links in your wiki pages lead to valid pages of content.

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