Highlights of LabKey Server v14.2

• Organize and share files using a new drag-and-drop file uploader (docs)
• Analyze high-volume results using Rserve to execute scripts remotely (docs)
• Integrate specimen information with automated FreezerPro® import (docs)

Resources

• Download LabKey Server 14.2
• Release Notes 14.2

Highlights of LabKey Server v13.3

• Gain insight across data sources by bringing data together using ETL tools (video | docs)
• Optimize specimen management with finer-grained control of allocation, export and editing (video | docs)
• Make the right reports, views and thumbnails visible to the right people (docs | docs | docs)

Resources

• Download LabKey Server 13.3
• Read the full list of 13.3 features
• Watch "sprint" videos

For recent versions of LabKey Server, see:
https://www.labkey.org/wiki/home/Documentation/page.view?name=prevReleases

For older versions of LabKey Server, see:
https://www.labkey.org/project/home/Documentation/Archive/begin.view?

The LabKey team is pleased to announce the release of LabKey Server v2.3. This release represents another important step towards our vision of providing facilities like yours with a centralized scientific data management system (SDMS) for all your experimental and observational study information.

LabKey v2.3 enhancements include:
- A new MS1 module for importing and viewing MS1 features from files generated by the open-source msInspect tool.
- Improvements to peptide-based MS2 run comparisons, including the ability to compare runs from different search engines and view XPRESS quantitation data.
- New facilities for integrating data from participant-completed forms with assay results derived from each participant's biological specimens.
- Better support for viewing dataset "snapshots" and direct, read-only database access to the underlying study tables for users of SQL-based query and reporting tools.
- TZM-bl neutralization assay (NAB) enhancements, including better data upload options, customization of assay parameters and new support for four- and five- parameter curve-fitting graphs.

For more details on features and fixes, please see What's New in 2.3: https://www.labkey.org/wiki/home/Documentation/Archive/2.3/page.view?name=whatsNew
 
To get the new release , please go to the Download Center: https://www.labkey.org/Project/home/Download/begin.view

(Note: The official 2.3 release is build 7806. If you happened to download an earlier build of 2.3, please upgrade to 7806.)

On the download page, you will find the Windows setup program and the built binaries for manual install on other operating systems. Both the setup program and the manual installation support automatic upgrade of prior versions of LabKey Server. We recommend that all existing LabKey users upgrade to version 2.3 (after backing up their databases). Report any problems you may encounter via the support boards on https://www.labkey.org.

Thank you for your continued support,

The LabKey Team

The LabKey Software development team is pleased to announce the immediate availability of LabKey Server Version 2.2. The new version includes improvements in all areas of the product, including:

- LabKey/CPAS for proteomics is now certified as Silver-level compliant with the National Cancer Institute's caBIG(TM) standard. Sample sets and MS2 results stored in LabKey Server are now accessible via caBIG(TM) with the click of a button.

- The Study module includes the new Assay service for managing simple experiments. The Assay designer is a tool for describing the data that will be uploaded or entered by a lab researcher. Once an Assay is described, the pages for capturing information about a run are generated automatically, with defaults and drop-down lists to make data entry fast and easy.

- LabKey Server now integrates with the R scripting language, allowing users to send the data displayed on a grid into an R script. The R script can generate graphs and reports which can then be incorporated into a message board or wiki page.

For more details on features and fixes, please see what's new in 2.2:
https://www.labkey.org/Wiki/home/Documentation/Archive/2.2/page.view?name=whatsNew
 
To get the new release , please go to the Download Center:
https://www.labkey.org/Project/home/Download/begin.view

(Note: The official 2.2 release is build 7153. If you happened to download an earlier build of 2.2, please upgrade to 7153.)

On the download page, you will find the Windows setup program and the built binaries for manual install on other operating systems. Both the setup program and the manual installation support automatic upgrade of prior versions of LabKey Server. We recommend that all existing LabKey users upgrade to version 2.2 (after backing up their database). Report any problems you may encounter via the support boards on https://www.labkey.org


Thank you for your continued support,

The LabKey Team

The LabKey / CPAS development team is pleased to announce the immediate availability of LabKey Server Version 2.1. Version 2.1 includes many new features and performance and usability improvements. As with all versions of LabKey / CPAS since 1.3, it can be safely installed over earlier versions and will automatically upgrade. We recommend that all existing LabKey / CPAS users upgrade to version 2.1.

What's New in LabKey 2.1:
https://www.labkey.org/Wiki/home/Documentation/page.view?name=whatsNew

Download Center:
https://www.labkey.org/Project/home/Download/begin.view

Enjoy!

It was great to meet and talk with so many of you at ASMS 2007. Thanks to everyone who dropped by the booth, came to our lunch sessions, or visited our hospitality suite for a bit of Nintendo Wii action.

I've attached the two presentations I gave during the lunch sessions. The first is an introduction to CPAS; the second covers more advanced topics, in particular, technical details about the pipeline and setting up a production installation.

Adam

(Seattle, WA – May 22, 2007) – The Canary Foundation and the LabKey Software Foundation announced today the fifteen grant recipients of their Bioinformatics Platform Dissemination Award. A total of $225,000 in grants is being awarded to key labs around the world. The Canary Foundation and this award advocate the continued development of common software platforms for research on early cancer detection. See the attached press release for details.

The attached document describes a funding opportunity from the Canary Foundation for the installation and use of the Computational Proteomics Analysis System (CPAS). A total of $225,000.00 is available to fund as many as 15 research groups to use or extend CPAS.

Please note the fast approaching application deadline, May 7, 2007, when a maximum three-page application is due. Only applications received by this date will be assured consideration for funding. Funding decisions will be made by May 15, 2007.

The LabKey / CPAS development team is pleased to announce the immediate availability of LabKey / CPAS Version 2.0. Major new features include Sequest support, a C++ implementation of ProteinProphet yielding dramatic performance improvements, advanced protein search capabilities, and the first released version of the LabKey Flow Cytometry module. For more details see What's New in LabKey / CPAS 2.0.

Many thanks to the Canary Foundation for supporting CPAS distribution.

Enjoy!

The LabKey / CPAS Development Team

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).

We just learned that our CPAS paper is listed as a 2006 Most-Cited Article based on citation data obtained from Thomson ISI. Of course, we are very excited. This is a good time to thank our users who have made the effort to learn this product, and the developers who have contributed to it. It is gratifying to see how many people find this work worthwhile.

http://pubs.acs.org/journals/jprobs/promo/most/most_cited/2006.html

We're happy to announce the release of CPAS 1.7. It is available now via the download page. There are a wide variety of new features, including support for controlling a Mascot pipline in the MS2 module.

For more information:

• What's New in CPAS 1.7
• Download and Installation Instructions

We just released an update to CPAS, version 1.6-5018, available immediately via the download page. This release fixes two issues:

• Extremely slow FASTA loads on SQL Server (Issue #2143)
• "Invalid Email Exception" when attempting new user verification (Issue #2135)

If you've upgraded to CPAS 1.6 and are not experiencing either of these problems then there's no need to upgrade your installation.

The CPAS development team is pleased to announce the release of CPAS release 1.6, available now via the download page. This release improves reliability and adds several key new features.

For more information:

• What's New in CPAS 1.6
• Download and Installation Instructions

Enjoy!

The CPAS development team is pleased to announce the release of CPAS 1.5, available now via the download page. This release improves reliability and adds several key new features.

For more information:

• What's New in CPAS 1.5
• Download and Installation Instructions

Enjoy!

If you haven't seen it yet, check out the "Get Started" documentation here. This tutorial walks you through the process of running X! Tandem searches and importing sample LC/MS-MS ("MS2") data into your local CPAS installation.

We just released an update to CPAS, version 1.4-4355, available immediately via the download page. This release includes a few improvements from the version we distributed for ASMS via CD and our download site. Changes include:

• Fix Mascot2XML pepXML converter on Windows (Issue #1440)
• Allow sorting and filtering on protein annotation columns in protein views (Issue #1439)
• Allow exporting ProteinProphet information to Excel (Issue #1435)
• Improve PeptideProphet discriminant function for native X! Tandem scoring.

If you're running CPAS 1.3 or earlier, now is a great time to upgrade to CPAS 1.4. For a list of new features in 1.4, see What's New in CPAS 1.4.

If you already installed CPAS 1.4 via a CD you received at ASMS or from a download prior to 7/8/06 you should upgrade if you are encourtering any of the above issues or want the latest version of X! Tandem PeptideProphet support.

The Windows installer is the easiest way to install or upgrade an existing CPAS installation. It will upgrade any existing CPAS 1.3 or 1.4 system that was originally installed using the Windows installer.

Attached are presentations from our Monday and Tuesday lunch presentations in the Genologics hospitality suite at the ASMS conference. Special thanks to Genologics for providing the venue, lunches, and logistics that made these presentations possible!

Adam

The CPAS development team is pleased to announce the immediately availability of CPAS version 1.4. New features in this release include:

• Graphical Windows installer now upgrades existing CPAS 1.3 installations.
• Windows setup installs a full proteomics pipeline, now adding PeptideProphet, ProteinProphet, XPRESS quantitation, and various pepXML converters, all developed at the Institute for Systems Biology (ISB) and optimized for Windows by Insilicos.
• CPAS pipeline supports launching and monitoring X! Tandem searches that use the ISB components.
• Preliminary support for PeptideProphet validation using X! Tandem scoring.
• Improvements in Mascot support, user interface, export capabilities, performance, and reliability.

For more information:

• What's New in CPAS 1.4
• Download and Installation Instructions

Enjoy!

-CPAS Development Team

Some of the designers and developers of CPAS from both FHCRC and Labkey will be available at the American Society for Mass Spectrometry conference in the Washington State Convention Center in Seattle, May 29th through June 1.

Even if you are not attending the conference, you are invited to the CPAS information sessions being held in Genologics' Hospitality Suite, room #205:

• CPAS for Proteomics Researchers Monday May 29, 12:15pm to 1:30pm
• CPAS Technical Overview Tuesday May 30, 12:15pm to 1:30pm

The first session is primarily for current and prospective users of CPAS, and will overview installation and use of CPAS. The second session is primarily for supporting prospective CPAS developers. Please let us know if you can attend one or both sessions by signing up at

http://cpas.dataweb.com/ASMS/signup.view

Lunch will be provided for pre-registered attendees. Many thanks to Genologics for their generous sponsorship of these sessions.

You can talk to the labkey development members at the LabKey Software table in the corporate poster area of the Exhibit Hall.

The CPAS development team is proud to announce the immediate availability of CPAS version 1.3. New features include:

• Integration of protein scoring results from ProteinProphet and XPRESS, two algorithms developed by the Institute for Systems Biology
• Tight integration of protein annotations
• Ability to initiate, monitor, and control database searching using an external, cluster-based, analysis pipeline
• Java source code available via both zip download or direct Subversion source control access

For more information:

• What's New in CPAS 1.3
• Download and Installation Instructions
• Media Backgrounder (.doc)

Enjoy!

-CPAS Development Team

The Fred Hutchinson Computational Proteomics Laboratory and LabKey Software are pleased to announce the immediate availability of CPAS, the Computational Portal and Analysis System, version 1.1, with source code. The source availability coincides with the publication of the CPAS Paper in the Journal of Proteome Research.

Learn More:

• About CPAS
• Media Backgrounder (.doc)

Register and Download Software and Source Code:

• New User Registration
• CPAS Download Page

The CPAS development team is proud to announce the immediate availability of CPAS version 1.1.

New features include:

• Improved user interface with simplified web navigation
• Improved pipeline support for submitting and managing MS2 runs with integrated X!Tandem peptide scoring
• Improved experiment annotation support
• Custom site branding
• Simplified upgrade

Download here

Enjoy!

-CPAS Development Team