Welcome to the second edition of the LabKey eNewsletter, your #1 source for the most current information on LabKey's systems and activities in the life science community. In reading the newsletter you’ll see we’ve added a Tips and Tricks section, designed specifically to help LabKey users become even more productive in their use of the system. Let us know what you think, and definitely feel free to forward your own ideas and suggestions.

What's coming in version 8.1

LabKey's 8.1 release is on track for general distribution in early April, thanks in great part to our clients who are providing excellent feedback on LabKey Server’s new capabilities and to LabKey's blue-chip development team for responding so quickly to their input. Key items to look for in this release 8.1 include;

Support for both ELISpot and Microarray assays: LabKey’s fully customizable assay designer helps you sidestep data management bottlenecks by expanding the number of data types you can bring into the system.

• ELISpot: You can customize run metadata and plate templates, upload raw data files from CTL and AID instruments and store the data in standard LabKey data tables with sortable/filterable data grids.
• Microarray: You can leverage the pipeline to process TIFF files and upload MageML files into the LabKey Server database.

New framework of API’s for reports and view: A new, flexible framework of APIs for reports and views lets you quickly develop and deploy grids and charts without help from LabKey’s core development team. These new features include:

• Charting APIs, which include image map support.
• Server-side API, which provide basic query functionality.

Browser-based FTP uploads: simplify your workflow with LabKey’s new drag and drop capability for moving data files in the LabKey system.

• The Beta File Repository provides reliable, checksummed delivery of flow data to the server via drag and drop directly onto a web browser.

UI improvements: designed by working hand in hand with clients with the goal of speeding your data processing and discovery efforts.

• Datagrid paging: LabKey now keeps track of selections on multiple pages of large datasets, so you can work with large amounts of data more efficiently.
• R script sharing: Source scripts for R views can be made available to non-admins, allowing easier sharing.

Stay tuned to this newsletter and LabKey’s web site at www.labkey.com for details on version 8.1’s availability and where to download the bits.

LabKey systems are helping flow cytometry core labs AND its customers become more productive

Flow cytometry core facilities typically provide a breadth of instrumentation and expertise to university researchers, their collaborators and a small number of outside commercial organizations. Today, the majority of cytometry core labs aggregate the data they collect for their customers onto centrally managed FTP servers through a series of time-intensive manual steps. Investigators then retrieve data from the server, provided they are authenticated users. Data backup is usually provided via the exchange of physical media, a process that can lead to errors in copying or transfer.

LabKey Flow enables cytometry core labs to implement a new standard operating procedure that makes managing and distributing data to their customers easier, more secure and more reliable for both investigators and core lab staff. Operators save newly generated data from their cytometers into LabKey Flow’s relational database. Data goes into a “release queue” so that the core lab can rapidly assess the quality of the data prior to distributing it to investigators. This simple but important quality control step helps each lab build and maintain its reputations for quality, an essential attribute for any service-focused core lab.

LabKey Flow does not just help core labs distribute flow cytometer data to their customers. It also provides investigators with a central repository for management of all flow projects, including both raw experimental data and analyzed results. By establishing a secure, shared repository for all their data, investigators eliminate the pain of searching for data hidden away on student desktop systems or, even worse, having to re-run experiments because of data lost during student departures. Investigators can even use LabKey’s web-based interface to share their projects with remotely located collaborators, or to provide full access to the system conveniently from home offices.

The ability to save analytical results from applications like FlowJo back into LabKey Flow provides tremendous additional benefits in efficiency and reliability. With LabKey Flow, you simply log into your project file and all the raw experimental data and analyzed results are available for your review – raw data, graphics, tables and charts are all at your fingertips. Investigators can also take advantage of LabKey Flow’s query language, which makes it easy to query across multiple flow data sets or projects. They can even run sophisticated analysis scripts using LabKey’s built-in support for R, import/export data between applications like Microsoft Excel, and interface with their own analytical algorithms. Users of LabKey Flow can make full use of the best tools that are out there today.

For a complete copy of this case study in action, please send email to info@labkey.com.

Tips and Tricks

For observational studies, did you know you can drop charts right into participant views, right alongside participant data? Just follow these five simple steps:

1. Go to a participant view by clicking on a Participant ID in any dataset grid view.
2. Expand one of the datasets listed for the participant by clicking on the dataset’s name.
3. Use the handy “add chart” link to launch the chart-building tool.
4. Use the tool’s simple interface to design and save your chart.
5. Success! This chart is now available in every participant view. From any participant view, just expand the dataset you used to create the chart and see how data from the selected participant graphs up.

You can see a full blown example here in the Demo Study, available on LabKey’s web site. Just expand the “Physical Exam” section to see a weight chart right alongside the full record of data from the participant’s physical exam.