Applied Biosystems RapidFinder Software Version 1.0 and SDS Software Version Beta Release 10/05 Release Notes (PN Rev A)

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1 Applied Biosystems RapidFinder Software Version 1.0 and SDS Software Version Beta Release 10/05 Release Notes (PN Rev A) Software Release notes for: Applied Biosystems RapidFinder Software v1.0 (7300 Real-Time PCR System) (P/N ) RapidFinder Software v1.0 (7300 Real-Time PCR System with RQ Study) (P/N ) Applied Biosystems RapidFinder Software v1.0 (7500 Real-Time PCR System) (P/N ) Installation Refer to the RapidFinder Software Version 1.0 Install User Bulletin for information. Upgrading from an earlier version of SDS software: If you are installing this software on a computer with an earlier version of the SDS software installed, 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 from v to takes approximately 10 minutes. Upgrading from a version earlier than to v may require up to an hour, including loading new firmware to the instrument. Upgrades are supported only for a common instrument type. For example, 7300 SDS v will upgrade only from a previous version of 7300 SDS and 7500 SDS v will upgrade only from a previous version of 7500 SDS. 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 installation. Note: 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. 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 ) for detailed instructions. Part Number Rev. A Page 1 of 8

2 Known Issues with RapidFinder Software v1.0 Beta Release General Issues DO NOT SAVE A RAPIDFINDER PLATE in the SDS Software. RapidFinder plates saved in the SDS software cannot be opened by the RapidFinder software or the SDS software, and RapidFinder results may be invalidated. If you attempt to launch the SDS software version while the RapidFinder software is running, the SDS software does not start. The SDS software cannot run at the same time as the RapidFinder software. Any comments entered in the Comment field (on the Enter Plate Information, Select Plate to Pipette, and Select Plate to Run pages) are not included in printed reports or exported results. Creating a Plate If you click Close when the Enter Sample Names page or the Select Pipetting Option pages are displayed (then click OK in the Save Changes dialog), the settings on these pages are not saved. Settings on previous pages are saved. Pipetting a Plate When pipetting a plate that does not have positive controls specified, the Close Tubes Before Pipetting Positive Controls page is displayed instead of the Close Tubes page. IMPORTANT! After you pipette the plate, make sure reagents are in the bottom of the wells. If available, use a centrifuge with a plate adapter to briefly centrifuge the plate (<1500xg). If an expected plate does not appear in the Select a Plate to Pipette list, make sure you have confirmed the plate configuration (on the Main page, select Open Plate in Progress, then click Next on all pages including the Confirm Plate Configuration page). If the plate still does not appear in the Select a Plate to Pipette list, click Close to return to the Main page, click View Results, click any plate in the list, click Close to return to the Main page, then click Pipette a Plate. The plate list should be reset and correctly list all plates. When pipetting plates, do not select Pipette Another Plate as your next step. Return to the Main page, then select Pipette a Plate to pipette another plate. Running a Plate Before starting a run on the Run page, change the Number of PCR Cycles from 50 to 45. On the Run page, the Cycle Counter (Cycle n of n) and Time Remaining clock do not display the correct number of cycles run or the time remaining in the run. However, the run will complete successfully. Do not enter a Run Operator name on the Select a Plate to Run page. If you do, the plate is not available to run. Viewing Results Part Number Rev. A Page 2 of 8

3 For all "Negative" Sample results, check the By Well results for the sample to ensure that there are no By Well Warnings associated with the sample. If there are, you may want to rerun your samples. If you enter a Run Operator name, then click Next, then click Close, the plate is not available in the Select a Plate to Run list the next time you view the page. To make the plate available, select Create/Edit a Plate from the Main page, select Open Plate in Progress, select the plate in question, then click Next on all pages including the Confirm Plate Configuration page. Creating Templates If you create a template using the name of an existing template, a message box is displayed asking if you want to overwrite the template. The existing template is overwritten, even if you select No in the message box. If you create a template from a plate and use the name of an existing template, the software does not detect whether the template name already exists. The existing template will be overwritten. New Features in the SDS Software v1.3.2 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. 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 SDS Software 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. Part Number Rev. A Page 3 of 8

4 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 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. Part Number Rev. A Page 4 of 8

5 Known Issues SDS Software 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. 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. Part Number Rev. A Page 5 of 8

6 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. Auto-baselining and Auto C T 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 C T is enabled, amplification plots crossing the threshold in the baseline region will be assigned an undetermined C T. 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 Allelic Discrimination When the display of an AD scatter plot is refreshed, inconsistencies might arise between the plot selection and the table selection. Selecting another tab and then returning to the scatter plot can refresh the scatter plot view. One of the Apply, OK, or OK & Reanalyze buttons must be selected to change the Quality Value setting in the Analysis Settings dialog. Pushing the Enter key alone after inserting a new value does not commit the change. Part Number Rev. A Page 6 of 8

7 Preferences When setting preferences for the Image Viewer, user-entered parameters may not be validated. When setting preferences for the Amplification Plot, user-entered parameters may not be validated. Printing The Background Assay Report does not print in landscape mode, only in portrait mode. Instrument Communication In the event that the software loses communication with the instrument during a run (e.g. a cable is disconnected or there is a hardware malfunction), the best method for resetting the system and reconnecting the software is to: 1. quit the software application on the PC (SDS or System Setup Wizard), 2. cycle the power on the instrument, 3. re-launch the software application on the PC, and 4. re-open the document for connection. Part Number Rev. A Page 7 of 8

8 Notice to Purchaser: License Disclaimer Purchase of these software products alone does not imply any license under any process, instrument or other apparatus, system, composition, reagent or kit rights under patent claims owned or otherwise controlled by Applera Corporation, either expressly or by estoppel. Applied Biosystems is a registered trademark and AB (Design) and Applera and RapidFinder are trademarks of Applera Corporation or its subsidiaries in the US and certain other countries. Part Number Rev. A Page 8 of 8