[PPT Overview from 10.3 Release Webinar]

Scalable Performance and Reliability

  • Improved performance for large datasets.
  • Support for high-thoughput NAb assays. Added support for 384-well plate assay runs, multiple plate upload and processing (up to 8 plates at a time), and cross-plate analysis.
  • Read-only pipeline directories. The pipeline now supports a read-only file system and writing analysis results to a parallel writable file system.
  • Reagent database enhancements. The reagent database can now be customized, including bulk editing. (Available as an add-on module)

Data Management and Integration

  • Conditional formatting. Data formatting can now be changed depending on the value of the data.
  • Customize view enhancements. Custom views are easier to design and create with a new user interface.
  • Improved SQL/XML editor. A more sophisticated SQL and XML editor now supports syntax highlighting, line numbers, and search.
  • Support for MySQL External Data Sources. Access any data you have stored in MySQL databases and use it with all the standard LabKey analysis, query, and visualization tools.
  • Multivalued columns. Single columns can now display multiple values. (Availability is currently limited to the genotyping and reagent modules.)

Next Generation Sequencing and Genotyping

  • Roche 454 GS FLX and Junior instruments. LabKey Server now supports Roche 454 GS FLX and Junior long-read sequencing instruments.
  • Data management. Data management for dictionaries of reference sequences, sample information, metrics, and metadata about each run.
  • Data analysis. Sequences, quality scores, and multiplex identifiers can be analyzed directly or exported to FASTQ files for use in other tools.
  • Galaxy genotyping workflows. LabKey sends reads, sample information, and reference sequences of interest to Galaxy. After the Galaxy workflow runs, LabKey automatically imports the resulting matches and makes them available for single- and multi-run analysis.
  • Metadata management for Illumina sequencing assays. LabKey introduces initial support for the Solexa/Illumina platform.
  • Genotyping and Illumina features are available as add-on modules.

Visualization

  • New visualization tools. LabKey has begun a new effort to expand our visualization tools. The expanded tool set allows for intuitive creation of visualizations, offering users a wide pallet of visualization options. The beta version is available as an add-on module.

Other Enhancements

  • New CSS theme. Provides improved look and feel.
  • Permission settings for custom buttons. Permissions sensitive rendering of custom buttons.
  • User-defined fields in issue tracker. The issue tracker now supports user defined fields and editable email templates.
  • Search. Indexing for custom file properties/metadata; indexing for metadata of MAGE-ML, mzXML, mzML files.
  • Recalculable SILAC ratios. Users can now exclude individual peptide-level quantitation results and recalculate the protein ratio results for runs analyzed with XPRESS or Q3.
  • Enhanced MS2 views and UI. Improved grid views and run comparisons.
  • mspicture support. For MS2 runs, related mspicture files are automatically linked to the run.
  • File based metadata (NAb). Sample metadata can now be uploaded as files, instead of entered manually.
  • New details URL on study.StudyData table.
  • PostgreSQL 9.0. LabKey server now supports PostgreSQL 9.0.
  • New wiki {div} macro allows for the injection of inline CSS styles or CSS classes.

Extensibility and New APIs

Powerpoint summary of 10.3 API and XML Schema Changes.

Perl APIs

  • New Perl API allows you to query, insert and update data.
JavaScript APIs
  • JavaScript APIs now use Ext 3.2.2
  • New container management APIs: LABKEY.Security.createContainer(), LABKEY.Security.deleteContainer(), and LABKEY.Security.getFolderTypes(). Manage projects, folders and workbooks.
  • New LABKEY.Utils.textLink. Returns a string containing a well-formed html anchor that will apply theme specific styling.
  • New LABKEY.Query.saveQueryViews(). Creates or updates a custom view for a given query.
  • Modified LABKEY.QueryWebPart(). 'config.buttonBar' now includes 'permission', 'permissionClass', and 'requiresSelection' to control the visibility of custom buttons.
  • Modified LABKEY.Query.selectRows(). 'showRows' and 'selectionKey' configuration options have been added.
  • Standardized naming convention for AJAX functions. 'success' and 'failure' properties on the 'config' object replace, but are backwards compatible with, the old names: 'successCallback', 'errorCallback', and 'failureCallback'.
XML Schemas
  • tableInfo.xsd
    • New elements <fkMultiValued> and <fkJunctionLookup> to support multivalued columns.
    • New <dimension> and <measure> elements on <ColumnType> to provide metadata for visualizations.
    • New attributes on <ButtonBarItem>:
      • insertPosition, insertBefore, insertAfter to control the placement of buttons added to the button bar.
      • permission and permissionClass to control button visibility.
    • Support for conditional formats with <ConditionalFormatsType>.
    • New <onRender> element on <ButtonBarOptions> to invoke a JavaScript function when the grid is rendered.
LabKey SQL
  • New 'GROUP_CONCAT' aggregate function.
  • New support for 'SELECT *'. It is not longer necessary to use 'SELECT Table.*'.
  • No longer necessary to prefix unambiguous columns with table names or table aliases.
Dataset Persistence
  • Before 10.3, three forms of persistence were used:
    • Metadata was stored in OntologyManager.
    • Data was stored in OntologyManager.
    • Data was also stored in materialized "hard" temp tables.
  • In 10.3, two forms of persistence are used:
    • Metadata is stored in OntologyManager.
    • Data is stored only in OntologyManager maintained "hard" database tables.

Bug Fixes

New Documentation

  • Quick Tutorial series for new users:
    • Data Analysis Tutorial
    • File Management Tutorial
    • Security Tutorial
    • Collaboration Tutorial
  • Manage Views

Upgrade Tips

  • New look and feel. A new CSS theme is available with version 10.3.
    • To upgrade the entire site to the new theme, navigate to Admin -> Manage Site -> Admin Console -> Look and Feel Settings. In the drop down "Web Themes", select 10.3.
    • To upgrade an individual project to the new theme, navigate to Admin -> Manage Project -> Project Settings. In the drop down "Web Themes", select 10.3.
  • Database backup. When upgrading to 10.3, we highly recommend that you perform a database backup.
  • PostgreSQL customers should run a "vacuum" and an "analyze" after the upgrade is complete.

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