Dear Subscriber,

Welcome to the third edition of the LabKey eNewsletter, your #1 source for the most current information on LabKey's open source solutions for accelerating biomedical research and facilitating collaboration. Let us know what you think, and definitely feel free to forward your own ideas and suggestions.

What's coming in version 8.1

The latest version of LabKey Server is now available for download.  Enhancements are too numerous to inventory here, so make sure to read the full list of What’s New in v8.1 on www.labkey.com.  Just a few:

PROTEOMICS ENHANCMENTS:

• Spectra counting for comparing runs via label-free quantitation. Demo available.
  
• Automated MS1 searches via the new MS1 pipeline, including MS1 feature-MS2-peptide matching.
• Single MS1 run views, MS1 comparisons views and MS1/MS2 data integration.
  
• Venn diagrams for visualizing overlap between runs in ProteinProphet-based comparisons.
• Improved protein annotation and access to additional FASTA file formats.

OBSERVATIONAL STUDY ENHANCEMENTS:

• Pre-prepared specimen reports. See examples in the Study Demo.
• Support for segmenting study participants by cohort.
  

ADMINISTATIVE FEATURES:

• Seamless authentication via single-sign-on.
• PostgreSQL 8.3 support.

Meet the Team at ASMS

Do you have a particularly challenging problem in processing, analyzing and managing your proteomics data, be it MS2 data, MS1 data or label-free quantitation based on statistical analysis across many runs? Come share the challenges you face with LabKey developers and program managers in Booth #111 at the upcoming ASMS meeting at the Denver Convention Center. We may have a solution to help. For a full schedule of events, please browse our ASMS event calendar. 

Workshop:  Customizing LabKey Server for Proteomics

Attend our free luncheon workshop at ASMS on Thursday, June 5th from 12:00 to 1:00 in Convention Center Room 402. The workshop will highlight how easy it is to customize the open source LabKey Server to meet your specific proteomics application or workflow.  Topics include;

• Accelerating proteomics research by extending LabKey Server with an adaptable enterprise pipeline, presented by Brendan MacLean, a senior LabKey developer.
• Adding a universal search engine interface to LabKey Server to improve protein identification using X!Tandem™, Mascot™ or SEQUEST™, presented by Bill Nelson from the KBRIN Bioinformatics Core at the University of Kentucky
• Customized data analysis using LabKey Server and R, plus capturing meta data using LabKey Server’s assays feature, presented by Peter Hussey, LabKey Partner.

Multi- and Clustered-Server Solutions

Learn more about LabKey Server’s adaptable enterprise pipeline for processing proteomics data across multiple clustered servers. Come chat with Brendan MacLean, senior LabKey developer, on Wednesday, June 4th at ASMS from 10:30 to 2:30 at Poster #181.

LabKey Launches Updated Website

Thanks in large part to our client’s strong support over the past several years, LabKey is happy to announce the launch of our new website. Visit us at www.labkey.com and let us know what you think.

Tips and Tricks

Our new Study Demo & Study Tutorial provide a suite of sample datasets and views than can help you explore the power of LabKey's observational study platform.  The Study Tutorial guides you through setting up the Study Demo on your own server, including the creation of custom data-grid views, charts and R views.  The demo samples can help you learn how to use LabKey Server to organize, analyze and visualize your observational study data.