GeneSifter Lab Edition 3.15

Last week we released GeneSifter Laboratory Edition (GSLE) 3.15.  From NGS quality control data, to improved microarray support, to Sanger sequencing support, to core lab branding, and many others, there are a host of features and improvements for everyone that continue to make GSLE the leading LIMS for genetic analysis.

The three big features include QC Analysis of Next Generation Sequencing (NGS) Data and Microarrays, and core lab branding support.

• To better troubleshoot runs, and view data quality for individual samples in a multiplex, the data within fastq, fasta, or csfasta (and quality) files are used to generate quality report graphics (figure below). These include the overall base (color) composition, average, per base, quality values (QVs), box and whisker plots showing median, lower and upper quartile, and minimum and maximum QVs at each base position, and error analysis indicating the number of QVs below 10, 20 and 30. A link is also provided to conveniently view the sequence data in pages, so that GBs of data do not stream into your browser.
• For microarray labs, quality information from CHP and CEL files and a probe intensity data from CEL files are displayed. Please contact support@geospiza.com to activate of Affymetrix Settings and configure the CDF file path and power tools. 
• For labs that use their own ordering systems, a GSLE data view page has been created that can be embedded in a core lab website. To support end user access, a new user role, Data Viewer, has been created to limit access to only view folders and data within the user's lab group. Please contact support@geospiza.com to activate the feature.  
• The ability to create html tables in the Welcome Message for the Home page has been returned to provide additional message formatting capabilities. 

Laboratory Operations
Several features and improvements introduced in 3.15 help prioritize steps, update items, improve ease of use, and enhance data handling.

Instrument Runs

• A time/date stamp has been added to the Instrument Run Details page to simplify observing when runs were completed. 
• Partial Sanger (CE) runs can be manually completed (like NGS runs) instead of having to have all reactions be complete or fail the remaining. 
• The NGS directory view of result files now provides deletion actions (by privileged users) so labs can more easily manage disk usage. 

Sample Handling

• Barcodes can be recycled or reused for templates that are archived to better support labs using multiple lots of 2D barcode tubes. However, the template barcode field remains unique for active templates. 
• Run Ready Order Forms allow a default tag for the Plate Label to populate the auto-generated Instrument Run Name to make Sanger run set up quicker. 
• The Upload Location Map action has been moved to the side menu bar under Lab Setup to ease navigation. 
• The Template Workflows “Transition to the Next Workflow” action is now in English: “Enter Next Workflow.”
• All Sanger chromatogram download options are easier to see and now include the option to download .phd formatted files. 
• The DNA template location field can be used to search for a reaction in a plate when creating a reaction plate.
• To redo a Sanger reaction with a different chemistry, the chemistry can now be changed when either Requeuing for Reacting is chosen, or Edit Reactions from within a Reaction Set is selected.

Orders and Invoices 
More efficient views and navigation have been implemented for Orders and Invoices.

• When Orders are completed, the total number of samples and the number of results can be compared on the Update Order Status page to help identify repeated reactions. 
• A left-hand navigation link has been added for core lab customers to review both Submitted and Complete Invoices. The link is only active when invoicing is turned on in the settings. 

System Management 
Several new system settings now enable GSLE to be more adaptable at customer sites.

• The top header bar time zone display can be disabled or configured for a unique time zone to support labs with customers in different time zones. 
• The User account profile can be configured to require certain fields. In addition, if Lab Group is not required, then Lab Groups are created automatically. 
• Projects within GSLE can be inactivated by all user roles to hide data not being used. 

Application Programming Interface
Several additions to the self-documenting Application Programming Interface (API) have been made.

• An upload option for Charge Codes within the Invoice feature was added.
• Form API response objects are now more consistent.
• API keys for user accounts can be generated in bulk.
• Primers can be identified by either label or ID.
• Events have been added. Events provide a mechanism to call scripts or send emails (beyond the current defaults) when system objects undergo workflow changes.  

Presently, API's can only be activated on local, on-site, installations.