Sunday, November 1, 2009

GeneSifter Laboratory Edition Update

GeneSifter Laboratory Edition has been updated to version 3.13. This release has many new features and improvements that further enhance its ability to support all forms of DNA sequencing and microarray sample processing and data collection.

Geospiza Products

Geospiza's two primary products, GeneSifter Laboratory Edition (GSLE) and GeneSifter Analysis Edition (GSAE), form a complete software system that supports many kinds of genomics and genetic analysis applications. GSLE is the LIMS (Laboratory Information Management System) that is used by core labs and service companies worldwide that offer DNA sequencing (Sanger and Next Generation), microarray analysis, fragment analysis and other forms of genotyping. GSAE is the analysis system researchers use to analyze their data and make discoveries. Both products are actively updated to keep current with latest science and technological advances.

The new release of GSLE helps labs share workflows, perform barcode-based searching, view new data reports, simplify invoicing, and automate data entry through a new API (application programming interface).

Sharing Workflows

GSLE laboratory workflows make it possible for labs to define and track their protocols and data that are collected when samples are processed. Each step in a protocol can be configured to collect any kind of data, like OD values, bead counts, gel images and comments, that are used to record sample quality. In earlier versions, protocols could be downloaded as PDF files that list the steps and their data. With 3.13, a complete workflow (steps, rules, custom data) can be downloaded as an XML file that can be uploaded into another GSLE system to recreate the entire protocol with just a few clicks. This feature simplifies protocol sharing and makes it possible for labs to test procedures in one system and add them to another when they are ready for production.

Barcode Searching and Sample Organization

Sometimes a lab needs to organize separate tubes in 96-well racks for sample preparation. Assigning each tube's rack location can be an arduous process. However, if the tubes are labeled with barcode identifiers, a bed scanner can be used to make the assignments. GSLE 3.13 provides an interface to upload bed scanner data and assign tube locations in a single step. Also, new search capabilities have been added to find orders in the system using sample or primer identifiers. For example, orders can be retrieved by scanning a barcode from a tube in the search interface.

Reports and Data

Throughout GSLE, many details about data can be reviewed using predefined reports. In some cases, pages can be quite long, but only a portion of the report is interesting. GSLE now lets you collapse sections of report pages to focus on specific details. New download features have also been added to better support access to those very large NGS data files.

GSLE has always been good at identifying duplicate data in the system, but not always as good at letting you decide how duplicate data are managed. Managing duplicate data is now more flexible to better support situations where data need to be reanalyzed and reloaded.

The GSLE data model makes it possible to query the database using SQL. In 3.13, the view tables interface has been expanded so that the data stored in each table can be reviewed with a single click.


Core lab's that send invoices will benefit from changes that make it possible to download many PDF formatted orders and invoices into a single zipped folder. Configurable automation capabilities have also been added to set invoice due dates and generate multiple invoices from a set of completed orders.

API Tools

As automation and system integration needs increase, external programs are used to enter data from other systems. GSLE 3.13 supports automated data entry through a novel self-documenting API. The API takes advantage of GSLE's built in data validation features that are used by the system's web-based forms. At each site, the API can be turned on and off by on-site administrators and its access can be limited to specific users. This way, all system transactions are easily tracked using existing GLSE logging capabilities. In addition to data validation and access control, the API is self-documenting. Each API containing form has a header that includes key codes, example documentation, and features to view and manually upload formatted data to test automation programs and help system integrators get their work done. GSLE 3.13 further supports enterprise environments with an improved API that is used to query external password authentication servers.

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