Applied Biosystems
SDS version 1.3.1 Patch 1
Release Notes
Software Release notes for:
· Applied Biosystems 7300 Real-Time PCR System Sequence Detection Software v1.3.1 Patch 1 (P/N 43508094370897);
· Applied Biosystems 7300 Real-Time PCR System Sequence Detection Software Relative Quantification Study v1.3.1 (P/N 4350814);
· Applied Biosystems 7500 Real-Time PCR System Sequence Detection Software v1.3.1 (P/N 4350819);
· Applied Biosystems 7500 Fast Real-Time PCR System Sequence Detection Software v1.3.1 (P/N 4363619).
These release notes contain the most current information about the Applied Biosystems SDS Software v1.3.1 patch 1. and Relative Quantification (RQ) Study Software v1.3.1 for the Applied Biosystems 7300 Real-Time PCR System, the Applied Biosystems 7500 Real-Time PCR System, and the Applied Biosystems 7500 Fast Real-Time PCR SystemThis software will only upgrade SDS v1.3.1 to SDS v1.3.1 patch 1. . This patch is applicable only for installations that license the Relative Quantitation applications. Please review these notes prior to installing the application patch.
Upgrading from an earlier version of SDS software:
· If you are installing this software on a machine with an existing installation of an earlier version of SDS, DO NOT uninstall the existing software. Uninstalling the previous version and installing this version will result in the inability to operate the connected instrument.
· The upgrade process for SDS Software v1.3.1 may require up to an hour, including loading new firmware to the instrument.
· Upgrades are supported only for a common instrument type or from the 7500 instrument to the 7500 Fast instrument. For example, 7300 SDS v1.3.1 will upgrade only from a previous version of 7300 SDS and 7500 SDS v1.3.1 will upgrade only from a previous version of 7500 SDS, but 7500 Fast SDS v1.3.1 will upgrade from a previous version of 7500 SDSThis software only upgrades SDS v1.3.1 to SDS v1.3.1 patch 1. It will not upgrade any previous versions of SDS software for the 7000, 7300, 7500 or Fast 7500 instruments.
· Place the new version disk in the CD drive and allow the System Setup Wizard to launch automatically. If the System Setup Wizard does not launch automatically, double click the SystemSetupWizard.exe file on the CD to start the installationDownload the installer package onto your desktop. The compressed installer is in WinZip format and can be opened with any software that supports that format. .
· When the instrument is first connected, the software may detect that the instrument firmware is not the latest version. If the instrument firmware is not the most recent, the software will recommend that the most recent version be loaded to the instrument. The new firmware version should be loaded to the instrument for correct performance. The firmware loading requires approximately 40 minutes.
· Please refer to the 7300/7500/7500 Fast Installation and Maintenance guide (p/n 4347828) or the 7300/7500 System Setup and Maintenance video CD (p/n 4352001) for detailed instructionsDouble click on the uncompressed installer and follow the instructions contained in the installer..
Checking Installation Status
· To check the version of an installation, do the following:
1. launch SDS;
2. select from the menu Help>About SDS;
3. from the About SDS dialog box, select the Plug-Ins… button;
4. from the Version Information for Plug-Ins dialog box, find the Application area;
5. identify the Version associated with the Relative Quantification Study application.
· An installation of the released SDS v1.3.1 that can be fixed by this patch will display version “1.3.1.20”.
· An installation that has already been patched will display version “1.3.1.21”.
New FeaturesIssue Addressed
After repeatedly analyzing expression within an RQS assay, the application either stops responding or it executes an invalid operation. If the application stops responding, it must be terminated; it may be terminated by using the operating system Task Manager or by restarting the machine. If the application executes an invalid operation, the operating system will terminate the application and inform the user of the failure. If the user has made any changes to the study without saving prior to the failure, those changes will not be saved to the file.
· This defect does not corrupt the collected data in the RQ Study nor does it produce invalid results.
System Setup Wizard
· The System Setup Wizard guides a user through performing all steps of:
○ an initial instrument installation;
○ a software upgrade or installation; or
○ an instrument recalibration.
· You must complete all steps of the “Unpack and Set Up a New Instrument” procedure from the System Setup Wizard at least once before you may perform the “Calibrate the Instrument” procedure, even if you are running the System Setup Wizard on a machine with an existing SDS installation.
“User Expert” Mode (7500 Fast Only)
· It is now possible to perform an Assay Run in less than 30 minutes when using AB Fast Chemistry and a 7500 Fast instrument by selecting the “User Expert” mode when setting up the run using Fast 7500 thermal cycling mode. When the User Expert mode is engaged, the user selects the instrument filters for which data will be collected, which can reduce the period required for data collection, resulting in a reduced total run time.
Use this feature with discretion: if data is collected that does not cover the dyes used in the plate setup, the system will not generate results.
Firmware Version G2.09
· This version of the SDS software includes version G2.09 of the instrument firmware. After installing this firmware, attempting to revert to a previous version of the firmware will result in a loss of all firmware calibration data.
Usage Notes
Installation
· If you are installing this software on a machine with an existing installation of an earlier version of SDS, please DO NOT uninstall the existing software. Instead, upgrade the software by following the instructions in the Upgrading from an earlier version of SDS software section above. Uninstalling the previous version and installing this version will result in the inability to operate the connected instrument.
Display Settings
· The display graphics require a video controller and system settings exercising at least the High (16 bit) color palette. Using color palette settings with fewer colors will result in the incorrect display of some detectors.
7500 Instrument
· A maximum of five (5) dyes can be processed in each well on the 7500 system. A maximum of four (4) detectors can be applied per well in any one of the following combinations:
· 4 reporters, 1 quencher, 0 passive references
· 4 reporters, 0 quenchers, 1 passive reference
· 3 reporters, 1 quencher, 1 passive reference
· 2 reporters, 2 quenchers, 1 passive reference
· 3 reporters, 2 quenchers, 0 passive reference
It is recommended to include a passive reference in all reactions.
Allelic Discrimination
· Modifying the “Use Pre-Read Data in Analysis” selection causes results to be recalculated and causes allele calls to be re-evaluated. However, if that selection is modified and the “Keep Manual Calls” option is enabled, results will not be recalculated for wells that have manually assigned allele calls. It is recommended that the “Keep Manual Calls” option be disabled before the “Use Pre-Read Data in Analysis” selection is modified unless you want to keep the manual calls you have already made.
RQ Study
· When performing an RQ study, all included RQ assays should have been run on the same instrument. Including RQ assays run on various instruments may produce unexpected results. The software will not allow you to include documents in an RQ study unless they share consistent plate type, instrument type, run mode, and thermal profile information; however, the software does not enforce that all included assays have been run on a single instrument.
· After omitting selected wells in an RQ Study and then resorting the grid, the displayed row positions that were selected remain selected, even if the row content has moved to a different display position due to the grid resorting. It is suggested that you always check the selected rows in the Well information grid after omitting wells and resorting the grid.
· A statistical “p-value” calculation is not supported in this version of the SDS application.
Known Issues
System Setup Wizard
· When performing the “Optical Calibration”, the “Preparing the Plate” page contains a picture in which the plate is labeled “Background plate”. It should be labeled “ROI plate”.
· If the software has already been installed and the System Setup Wizard is launched and the user selects either the “Unpack and Set Up a New Instrument” option or the “Install the SDS Software” option, as part of the wizard series, the “Software Installation” page will be displayed and the “Next >” button will be disabled. You must select “Install / Upgrade SDS Software” in order to continue, although canceling the installer without performing any installation operations will still enable the “Next >” button if the current version of the software is already installed.
Assay Setup
· If a thermal profile is set up using the auto-increment feature, the software typically rejects auto-increment parameter combinations that cannot be executed by the instrument (e.g. starting at 80° C and incrementing 2° C for each of 40 cycles would result in a temperature of 158° C). However, it is possible to enter some parameter combinations for which a run cannot be completed (e.g. by entering negative values or modifying values in an unusual order). If you set up such a thermal profile, the system will allow you to save the document and start the run, but the run will not be completed or may be completed improperly.
· If a document is created in which the plate setup contains any custom dye(s) and the instrument setup uses “User Expert” mode (7500 Fast only), the system will not warn you if the selected filters do not cover the custom dye(s), but it will not analyze the collected data unless the selected filters do cover the custom dye(s).
Instrument Runs
· If an instrument run is stopped while the instrument is waiting for the cover to heat, the software will indicate that the run is terminated and no further data will be collected; however, the instrument will continue to thermally cycle.
· If the instrument front door is open when a run is requested to start, the block will be raised, but a door open error will be displayed and the run will not be performed. Pushing the “Ok” button on the dialog box should lower the block, allowing the plate to be ejected; however, if the “Ok” button on the dialog box is pushed while the instrument’s filter wheel is turning, the block will not be lowered. To avoid that condition, if you are faced with the door open error situation, please wait until the filter wheel stops turning before pushing the “Ok” button on the dialog box.
· If the instrument lamp is not performing properly (defined as not drawing the correct current), the first attempt to perform a run after instrument power up will result in a “Lamp Failure” error. Any further attempts to perform runs on the instrument with the low lamp current condition (without first turning the instrument off and on again) will result in “Instrument Communication Failure” errors. For an instrument with the low lamp current condition, turning the instrument off and then on will reproduce the initial “Lamp Failure” error.
· While an instrument run is in progress, the SDS software requires significant processor utilization to perform data collection activities. In order to allow the workstation the greatest processor usage, it is recommended to avoid the following activities during an instrument run:
§ rapidly changing the well selection for any Results chart;
§ surfing the Internet;
§ writing to a CD or DVD;
§ scanning a disk for viruses;
§ defragmenting a disk; or
§ any other activity that extensively uses the workstation’s processor.
Performing such an activity during an instrument run may result in data loss or run termination.
Instrument Runs (7500 Fast Only)
· If an instrument run is started for which the duration of the data collection step is too short to collect the necessary data, an error will be displayed indicating the minimum duration required. If you experience that error, it is recommended that before attempting to start the run again, you should:
1. increase the data collection step duration to at least the suggested minimum,
2. close the SDS application on the PC,
3. cycle the power on the instrument,
4. re-launch the SDS application, and
5. re-open the document for connection.
· If an instrument run is stopped while it is in progress, it is recommended that before attempting to start another run, you should:
1. close the SDS application on the PC,
2. cycle the power on the instrument, and
3. re-launch the SDS application.
Auto-baselining and Auto CT
· Amplification plots in which the baselines are very steep may not be baselined correctly in Auto Baseline mode. Plots with very steep baselines may appear to have an earlier than expected baseline end cycle. It is suggested that you manually set the start and end cycles on such plots.
· When Auto CT is enabled, amplification plots crossing the threshold in the baseline region will be assigned an ‘undetermined’ CT.
Results Report
· When handling AQ Run results, some wells may be filtered due to noisy Baselines. While these filtered wells do not appear in the analyzed data, they are not reported as “Filtered” in views, exports, and reports.
· For any well that is assigned more than one detector, there is a remote possibility that the second detector assigned to well will be reported as undetected (undet.) even if the signal shown for that detector on the Amplification Plot chart crosses the threshold. That may occur if:
§ The combination of detectors is not assigned to any other well on the plate.
§ The second detector is not assigned as the first detector to any other well on the plate.
§ For each well on the plate to which the second detector is assigned, the first detector assigned to the well is not assigned to any well “before” that well, where the ordering of the wells is:
A1, ... A12, B1, ... H12