Attendant PC; an external computer resource included as part of the GS Junior System that manages most of the system’s functions, including controlling sequencing runs, image processing, signal processing, and data analysis.

Configuration; GS Sequencer application tool to manage Operators and Run Groups.

Data Processing Types; the series of digital images captured by the camera during the sequencing Run are processed to generate the sequence data in two steps: image processing and signal processing. Signal processing parameters differ for Amplicon libraries from other library types. The specification of which data processing step or steps to carry out on the GS FLX+ Instrument at the time of the sequencing Run and which type of library is being Run constitute the Data Processing type option. The choices are: None (no processing), Image Processing Only, Full Processing for Shotgun or Paired End, and Full Processing for Amplicon.

Data set; the set of files generated by Sequencing Run and Data Processing jobs. The Sequencing Run data set artifacts are located in the $RIGDATA directory under its R_ directory name. The data processing data set are stored under the D)_directories under their associated Run data set directories.

Data tab; GS Sequencer application tab lists the Run and Data processing data sets currently on the local instrument. There are an additional four actions to manage the data sets: copying (to a DataRig, a CPU for data analysis), removing data sets (that have been backed up), backup (to archive), and browsing sequencing Run data sets (launching the GS Run Browser). A context area to the right of the list displays summary information for the selected items in the data set list.

DataRig; an external (off-instrument) computing resource that is used for data display, processing or analysis. Examples include, but are not restricted to, the cluster or GS FLX+ Computing Station. A DataRig frees a GS FLX+ Instrument or GS Junior Attendant PC to perform a new sequencing Run before a previous Run has been fully processed and analyzed.

GS FLX+ Computing Station; the recommended DataRig for use with a GS FLX+ Instrument.

GS FLX+ Instrument; an instrument to sequence DNA using the 454 Sequencing System. The instrument components include a PTP device for loading a bead-immobilized library of DNA fragments; a fiber optic bundle camera for capturing raw images of the PTP device during the sequencing Run; a fluidics system for delivering sequencing reagents to the wells of the PTP device during the Run; and a computer with software to control the GS FLX+ Instrument, carry out data processing, and store sequencing Run data sets.

GS FLX+ on-instrument applications; systemStart, systemStop, GS Sequencer, GS Run Browser, GS Run Processor Manager (via the GS Run Browser).

GS Run Browser; an application on the GS FLX+ Instrument or DataRig to view sequencing Run data and launch data processing jobs.

GS Run Processor Manager; tool in the GS Run Browser application to launch data processing jobs on the GS FLX+ Instrument or a DataRig.

GS Sequencer; an application used to set up and carry out sequencing Runs and other procedures, manage Operators and sequencing Run data sets, and monitor the instrument health.

Instrument Status Area; in the default application window of the GS Sequencer after login, contains GS FLX+ Instrument component sensor monitors. Components include PTP Device & Loading Area, Camera, Reagent Cassette & Loading Area.

Instrument tab; GS Sequencer application tab, default screen after login, contains procedure summary information and Instrument status.

Operator; a person that uses the GS Sequencer application to configure and set up sequencing Runs, manage sequencing data sets, or browse sequencing Run data on the GS FLX+ Instrument.

Overview tab; GS Run Browser application tab, contains summary data of the sequencing Run, summary data of the processing results, if carried out, and the GS Run Processor Manager used to launch data processing or reprocessing jobs for the currently selected Run data set.

PicoTiterPlate (PTP) device; a device for loading a bead-immobilized library of DNA fragments for a sequencing Run on the GS FLX+ Instrument. Each device has a unique six-digit ID stamped on its edge.

Raw image; the data captured during a sequencing Run from the GS FLX+ Instrument fiber optic bundle camera. Consists of images of the PTP device taken during each nucleotide flow, capturing the light released by the sequencing reaction in each well of the PTP device.

Run Group; Operators (via their Operator ID) can be grouped into logical associations called Run Groups. These groups are not used directly by the 454 Sequencing System software, but are available to LIMS and other data management applications.

Instrument Procedure Wizard; a dialog launched from the GS Sequencer Start button to configure and launch a sequencing Run or other procedures. It consists of a series of questions used to provide the system with information about the Run. When all required Run information has been entered and the PTP device has been correctly loaded into the GS FLX+ Instrument, the sequencing Run can be launched by clicking the ‘Start’ button in the last Instrument Procedure Wizard window. Required information: Procedure to carry out (Pre-wash, sequencing Run, or Service), PTP ID, Run name and Run Group, sequencing kit type (XLR70, XL+), PTP device type (bead loading gasket; 2, 4, 8, or 16 regions), number of cycles to Run (cycles of 4 nucleotide flows; 100, 150, 200, or 400), data processing type (see above), backup option.

Sequencing Run; the process of using a bead-immobilized DNA library loaded onto a PTP device, the 454 Sequencing System method and the GS FLX+ Instrument to produce read data on a DNA sample from raw images of sequencing reactions as they occur on the PTP device.

systemStart; an application, located on the instrument desktop, used to start or reinitiate GS FLX+ Instrument operation background processes.

systemStop; an application, located on the instrument desktop, used to stop GS FLX+ Instrument operation background processes.