What's New in LabKey / CPAS 2.0

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What's New in LabKey / CPAS 2.0 georgesn  2007-04-16 17:54
Status: Closed
 
LabKey Release 2.0 includes many new features and performance improvements, some of which are listed below. For a detailed list of changes since 1.7 browse the issues list.

CPAS

Sequest Support

CPAS can now control a Sequest pipeline.

Performance Improvements

  • ProteinProphet runs up to 100x faster
  • FASTA loading is approximately 10x on SQLServer, 2-3x faster on Postgres
  • MS2 runs load 2-3x faster, or 8x faster if you elect to not load spectra data
  • ProteinProphet data loads approximately 25x faster
  • Browsing the file system through the pipeline is 20x faster on a network drive
  • Many, many improvements to UI responsiveness
Protein Search

You can now search for a protein by name (or gene name, if protein annotations have been loaded) in all the MS2 runs in the current folder and subfolders. See MS2 Dashboard for more information.

Improved Experimental Annotation Support

Moving MS2 runs to other contains now correctly moves experimental annotations. Several key bug fixes for viewing sample properties. Bug fixes for exporting MS2 runs to XAR and importing into another server.

Protein Group Details Page

Clicking on a protein group number now takes you to an improved details page, showing the full sequences for the proteins in the group with peptide coverage.

Error Rate for PeptideProphet and ProteinProphet Probabilities

For newly loaded runs, CPAS now loads both the probability and its associated error rate. The error rates are available as new columns in the grids.

New parameters to control loading into CPAS

You can add new parameters to your search configuration to prevent CPAS from loading some or all of your search results.

  • <note type="input" label="pipeline, load">no</note> will prevent CPAS from loading the results.
  • <note type="input" label="pipeline, load spectra">no</note> will prevent CPAS from loading the MS2 spectra into the database. This can significantly improve MS2 run load time.
MS2 Pipeline Improvements

LabKey will now load data directly into the folder you want instead of forcing you to load it into a top level folder and then moving it later. Just go to the target folder and use the pipeline to Process and Upload. The system will now remember the last location you uploaded data from. You can browse to any directory under the pipeline root. Additionally, all folders now inherit their pipeline setup from their parent folder or project, so you only need to set up the pipeline for the parent folder.

Flow Cytometry

LabKey now analyzes Flow Cytometry Data. This feature is most useful when instrument settings are standardized and identical gates can be applied to each run. Gates can either be defined by uploading a FlowJo workspace, or by using the online gate editor.

LabKey Flow can be set up to automatically calculate the compensation matrix if there are a consistent set of keywords that identify the compensation controls.

LabKey Flow will apply gates, calculate statistics, and generate graphs. All of these analysis results are stored in the database and can be selected, sorted, and filtered.

Advanced users can write their own queries using a SQL-like language to perform quality control and identify outliers.

LabKey Observational Study

The study module registration tool enables researchers to define a vaccine study in terms of the vaccine, the cohorts, a vaccination plan and an assay plan. Created for CAVD.

Shared Core Services

External Modules Support

LabKey Server supports a new directory, externalModules, for third-party modules that are upgraded independently of the core distribution

Visual HTML Editor

The Wiki now offers a WSYWIG HTML editor.

Discuss This

You can now attach discussions to several different types of pages, including wiki pages like this one (see the "Discuss This" link at the bottom of the page).