Monday, November 22, 2010

GeneSifter Lab Edition 3.16

Recently, we released GeneSifter Laboratory Edition (GSLE) 3.16. Over 40 new features were added to improve laboratory workflow support, enhance multiplexing, make orders and their data easier to manage, and extend the system's application programming interfaces (APIs).

Laboratory Workflow Support

Several new features will make working in the lab easier and improve data tracking and how GSLE is used. Workflows now include the ability to validate data using data ranges, and use laboratory defined lists to track the details about how samples are processed.  For Next Gen Sequencing (NGS), sample multiplexing has been extended to make it possible to define multiplexes and associate Barcodes, MIDs, or Indexes (or whatever else you like to call the little adapter tags) at any step of your process. Also, for those who use specific naming conventions to track process steps, sample naming conventions can be defined for process steps.  Finally, to use the above features and view data, the workflow editor has been streamlined to simplify data entry, workflows can be versioned to track your lab's process improvements, and a new report builder makes workflow data easy to access and view.

To better track samples organized in tubes, plates, slides, flowcells, freezers, buildings, and the universe, we have introduce a new tool called containers. Containers can be defined by the laboratory and are used to link samples to specific actions like sample storage or a data collection run. For example, Illumina flowcells can be created and have samples added. The flowcell can be run immediately or stored following cluster generation.  When samples are added to a flowcell, a new visual interface simplifies adding mixtures of multiplexed samples, single samples in individual lanes, or single samples spread over several lanes. Other kinds of containers track sample storage and can be updated with bed scanners to track the arrangement of samples as they move through the lab. And, containers can contain workflows to manage more complex procedures.

Order and Sample Management

Details matter, and GSLE 3.16 improves how you view them. Lab samples (templates) views now show all laboratory data associated with a sample on a single page. These data are organized in sections that can be collapsed so you can see the big picture, or focus on specific details. We also updated views of orders to make it easier to view their progress and made the orders easier to access when viewing data for release.

API Support

Some groups use GSLE as a stand alone system, others use GSLE in conjunction with external systems in commercial and very high-throughput production environments.  To support the later case, GSLE has a set of rich data-driven APIs that enable system to system communication. In 3.16, the APIs have been extended to edit certain kinds of stored data, add large batches of laboratory samples, upload container maps  to track samples, and manipulate charge codes with accounting systems.

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