MassARRAY Typer v

Transcription

1 MassARRAY Typer v MassARRAY Typer v is a maintenance update to Agena Bioscience s MassARRAY Typer v or higher application software. This version provides improved reporting capabilities for Agena Bioscience s pharmacogenetics reports with expanded CNV analysis, updated viewing options of multiple spectra in Typer Analyzer, and iplex Pro Sample ID report bug fixes VERSION NOTES MassARRAY Typer v contains all functionality of previous versions of MassARRAY Typer, including reporting capability for chromosomal breakpoints and translocations using the LungFUSION Panel v1.0 and other reporting improvements. These Release Notes contain instructions for installing Typer v , as well as a description of the software improvements. Installation Instructions... 2 Pre-Installation Requirements... 2 R Package Requirement... 2 Oracle Client Requirement... 2 ODBC requirement (for iplex Pro Sample ID Panel)... 2 Software Installation from AgenaCx.com Download... 2 Preserving Custom Columns in Plate Data View... 3 Preserving Existing Custom Reports... 3 Uninstalling Prior Versions... 4 Installing MassARRAY Typer v Setting the License in Windows Setting the License in Windows XP... 6 Running in Windows Software Improvements... 6 Pharmacogenetic Reports... 6 MassARRAY Typer Improvements... 6 Sample ID Report Bug Fix... 8 Appendix A: Installing R Appendix B: Installing Oracle 11g... 11

2 Installation Instructions Pre-Installation Requirements R Package Requirement MassARRAY Typer v requires R v and various R packages (RODBC, doby, gap, and RSQLite) to be installed. If R is not already installed, please follow the R installation instructions in Appendix A. Oracle Client Requirement To check the ODBC configuration: 1) Go to Start Menu > All Programs > Oracle... > Configuration and Migration Tools > Microsoft ODBC Administrator. 2) Select the System DSN tab and name of your database. Examples: agenadb, sequenomdb 3) Ensure the Data Source Name and TNS Service Name are the same. A: Illustration, Newer Database MassARRAY Typer v requires Oracle client 11g or higher. If you have Oracle 10g client or lower, you will need to update your Oracle client. The Oracle client install instructions are available in Appendix B. To check the Oracle client version on your system, please go to Start Menu > All Programs > Oracle. You will see the Oracle version number in the Menu. ODBC requirement (for iplex Pro Sample ID Panel) B: Illustration, Older Database If you use the iplex Pro Sample ID Panel, please note that in order for the Sample ID software to function properly, the Data Source Name for your database must match the TNS Service Name in the ODBC Data Source Administrator. If they are different, you must update the Data Source Name before running a Sample ID report. You do not need to alter the configuration if you will not be using the iplex Pro Sample ID Panel or if this has already been done when installing a previous version of MassARRAY Typer Software Installation from AgenaCx.com Download Because of path name changes in the installation location of MassARRAY Typer v , this update is a full installation intended to replace most previous 2

3 versions. It is highly recommended to uninstall all previous versions before installing MassARRAY Typer v If you are replacing MassARRAY Typer v , there is no need to uninstall. All other installed previous versions that have not been removed will no longer function after installation of v Preserving Custom Columns in Plate Data View Note: This procedure is only necessary for users upgrading from MassARRAY Typer v who have defined custom columns in the Plate Data View in Typer Analyzer. You will need to save a copy of the file that specifies the column information before installation, and then restore it after the installation. 1) Open Windows Explorer and go to the location where Typer is installed (typically Typer 4.0/bin). 2) Make a backup copy of the ColumnInfo.xml file. 3) After installation is complete, copy your backup ColumnInfo.xml file into the new Typer 4.0/bin folder, overwriting the new one that is there. Preserving Existing Custom Reports new installed files, following the instructions below for General Reports or OncoReports. General Reports 1) In the backup copy you made of ReportInfo.xml, locate the section(s) with your custom report(s). For example, for a report titled MyCustomReport: <report id="12"> <display-name>mycustomreport</display-name> <command-line-params> CMD BATCH --vanilla slave args [params] Reports\MyCustomReport\MyCustomeReport.r </commandline-params> <valid-expt-types>kg</valid-expt-types> </report> 2) Copy the section and paste it into the new ReportInfo.xml after the last report entry. 3) Change the <report id= 12 > to be one higher than the previous entry (e.g., if the previous report was UltraSEEK and was <report id= 13 > change your new entry to <report id= 14 >. Note: This procedure is not necessary for users upgrading from Typer v , as the installer will not overwrite these files when upgrading from v If you have custom OncoReports or custom general reports (e.g., user-created reports, MelaCarta, or reports from Assays by Agena), you will need to save copies before installation, and then restore them after the installation. 1) Open Windows Explorer and go to the location where Typer is installed (typically Typer 4.0/bin). 2) Make backup copies of the ReportInfo.xml, OncoPanel.xml, and ColumnInfo.xml files. 3) After installation is complete: a) Copy your backup ColumnInfo.xml file into the new Typer 4.0/bin folder, overwriting the new one that is there. b) Add the custom reports from the backup copies of the ReportInfo.xml and OncoPanel.xml files to the 3

4 4) At the bottom of the file is a section; <level name="chip"> </level> <reportid id="0"/> <reportid id="1"/> <reportid id="2"/> <reportid id="3"/> <reportid id="4"/> <reportid id="5"/> <reportid id="6"/> <reportid id="7"/> <reportid id="8"/> <reportid id="9"/> <reportid id="10"/> <reportid id="11"/> <reportid id="12"/> <reportid id="13"/> Add your entry(s) with its id (e.g. <reportid id="14"/>) to the bottom of the list before the </level> line. OncoReports 1) In the backup copy you made of OncoPanel.xml, locate the section(s) of the file containing the subproduct entry for your custom report(s). For example, the entry for OncoFOCUS starts like this: <sub_product name="oncofocus Report"> <category expand="false" name="calls"> Many lines of <property> follow and it ends with: </sub_product> 2) Copy the whole sub-product entry for each custom report and paste into the new OncoPanel.xml after the last </sub_product> line in the file (before </product>). For further information or assistance, please contact your local Agena Bioscience Customer Support office. Uninstalling Prior Versions 1) Open Control Panel and select Programs and Features. 2) From the list of programs select MassARRAY Typer and click Uninstall. Note: If you get a window that asks if MathLab should be uninstalled, select No. Installing MassARRAY Typer v ) Log onto the computer under an account that has administrator privileges. 2) Go to AgenaCx.com and navigate to Product Support > Application Updates > TYPER > Typer v ) Click on the Typer v Software Update link and save the file to the desktop. 4) Double-click the file that was saved to the desktop. 4

5 5) Click Next to start the installation of the software. The default DataSource =AGENADB (newer systems) or =SEQUENOMDB (existing systems), default username =system, and default password=manager. Click on Next to proceed. 6) The following dialog allows you to change the location of your install directory and run database scripts. You will need to run the database scripts if you plan to run Sample ID reports or create 24-well plates. Select Yes to run the database scripts if this is the first computer at your site to be updated to MassARRAY Typer v or later. Choose No if your site has already installed MassARRAY Typer v or later on another computer and updated the database. Click on Next to proceed. 8) Click Install to install the software. 9) Software installation will take several minutes. Click Finish to complete the installation. 7) If you chose Yes to run the database scripts you will be asked to enter the database information. 5

6 Setting the License in Windows 7 1) Right-click on the License Manager from the Start Menu for Sequenom. 2) Select Run as Administrator. 3) Select the Typer-4 Product and enter the information for the license obtained from Customer Support 4) Click Done. Setting the License in Windows XP plots are provided that provide the CNV calls for each sample and gene. See the iplex ADME PGx Pro Panel v1.0 User Guide for more detailed information. Note: Users who previously had ADME Reports installed will see the previous report (ADME Report) as well as the new PGx Report v2.0 in the Reports menu, and both reports will be functional. However, only the PGx Report v2.0 contains the enhanced reporting described above. MassARRAY Typer Improvements Font Sizes on Spectrum View The fonts of the various parts of the view can now be independently varied. 1) Left-click on the License Manager from the Start Menu for Sequenom. 2) Select the Typer-4 Product and enter the information for the license obtained from Customer Support. 3) Click Done. Running in Windows 7 The first time MassARRAY Typer is run in Windows 7, it should be started with Run as Administrator. To do this, right click on the Typer entry in the Start Menu and select Run as Administrator. Subsequently, MassARRAY Typer can be started normally. Software Improvements Pharmacogenetic Reports MassARRAY Typer v incorporates a new PGx Report v2.0 into the application package. The new PGx Report v2.0 simplifies and improves the reports for pharmacogenetics testing. All diplotype and CNV calls are provided in a single combined report, and 6

7 Coloring of overlayed spectra remains constant throughout the session Instead of highlighting the selected spectrum in black, the view now indicates selection by bolding the line. Black is always used for a spectrum that has not been added to the overlay list. This means the colors of the overlayed spectra will now remain constant for the duration of a user session. Highlighting of the current selection can be toggled off/on from the context menu or the options dialog. This is useful for printing without showing the selection. This feature allows the user to exclude the UEP peak when zooming into an assay result. It can be done by context menu, options dialog, or toolbar button. Spectrum View Legend Spectrum view now has a legend when spectra are overlayed. The legend can be hidden by using the context menu or the options dialog. Autozoom to analytes only 7

8 Export all cluster plots Instead of having to go through each assay and individually save the cluster plot as an image file, a new feature allows for the generation of an image file of the cluster plot for each assay in the Assay View. From the context menu on the cluster plot view, click Save Assays As, then select the image type (bitmap, PNG, JPEG) from the menu. A folder dialog is displayed to select the desired folder to save into. MassARRAY Typer then generates a file name based on the image and the alleles used for the image. This allows for generation of cluster plots when there are more than two alleles in the assay. The type of cluster plot (height, yield, etc.) generated is controlled by the current type selected in the cluster plot view. Sample ID Report Bug Fix 5) Click Next to start the installation. 6) Click Next to accept the license. MassARRAY Typer v corrects an issue with the software being unable to find data for Sample ID reports where a plate name began with 0. Appendix A: Installing R ) Use the following link to obtain the R environment: 2) Click on Download R for Windows, and save the file to your computer. 3) Open the downloaded.exe file and click Run. 4) Select your language and click OK. 7) Click Next to accept the default installation location. 8

9 8) In the Select Components window, de-select the x64 Files option. 11) Click Next to confirm additional tasks. 9) Click Next to accept default startup options. 12) Installation will start. When it is complete, click Finish. 10) Click Next to confirm start menu folder. 13) After installation is complete, four packages must be installed. Open the RGui window by double-clicking on the R icon on the desktop. 9

10 14) Under the Packages menu, select Install package(s) 17) Under the Packages menu, choose Install packages again, choose gap, and click OK. 15) Choose your location; for example, USA (CA1) and click OK. 18) Under the Packages menu, choose Install packages again, choose RODBC, and click OK. 16) Choose doby and click OK. 10

11 19) Under the Packages menu, choose Install packages again, choose RSQLite, and click OK. 3) Navigate to the client folder and double-click on the setup application file. 4) Click Run. 20) Under the File menu, choose Exit. Click on No in the window that appears. Appendix B: Installing Oracle 11g Note: In order to install Oracle 11g, the user must have administrative privileges on their computer. 1) Download Oracle Client Win32 Software from AgenaCx.com > Product Support > Application Updates > MassARRAY > Oracle. Updates_MassARRAY.aspx?path=oracle 2) Unzip/extract the downloaded file. 11

12 5) Select Administrator and then click Next. 7) Change Oracle Base from C:\app\admin to C:\oracle, then click Next. 6) Select your language and click Next. 8) Click Finish. 12

13 9) If prompted, select Domain Networks and/or Private Networks and Allow Access. 12) Under Local, select Service Naming and then click on the + in the tool bar on the left. 10) Click Close when installation is finished. 13) Enter Net Service Name. Newer databases will be agenadb, older ones will be sequenomdb. Click Next. 11) You now must configure Oracle for access to the database server. Go to Start > All Programs > Oracle-OraClient11g_home1 > Configuration and Migration Tools > Net Manager. 13

14 14) Select TCP/IP and click Next. 17) Click on Finish. 15) Enter the Host Name and Port Number (1521). The Host Name should be the same as the Net Service Name entered in step 13 (i.e., agenadb or sequenomdb). Click on Next. 18) Under the File menu, select Save Network Configuration. Then go to the File menu again and select Exit. 16) Enter the Service Name (BMS) and click Next. 19) You now must create an ODBC entry. The ODBC is the gateway for all third party applications, e.g., MassARRAY Typer, to access the database. For Windows 32 bit systems, navigate to Start > Control Panel > Administrative Tools and doubleclick on Data Sources (ODBC). For Windows 64 bit systems, navigate to C:\Windows\SysWOW64\ODBCAD32 and doubleclick on ODBCAD32.exe. 14

15 20) Go to the System DSN tab and click on Add. 22) Select the TNS Service Name from the drop-down menu. This will be the name you entered earlier, either AGENADB or SEQUENOMDB. If there is a space at the end of the name, delete it. 21) Select Oracle in OraClient11g_home1 and click on Finish. 23) Enter the Data Source Name (either AGENADB or SEQUENOMDB) and the User ID (charles) and click on Test Connection. 15

16 24) Enter the Password (darwin) and click on OK. 27) Click on OK to close the window. 25) Click on OK in the Testing Connection window. Patents and Trademarks MassARRAY, iplex, and SpectroCHIP are registered trademarks of Agena Bioscience, Inc. Agena Bioscience is a trademark of Agena Bioscience, Inc. All other trademarks or service marks set forth herein are the property of their respective owners. 26) Click on OK to close the window. Agena Bioscience s patented nucleic acid analysis by mass spectrometry methods and products are protected under United States patent rights including but not limited to 5,869,242; 6,024,925; 6,440,705; 6,558,623; 6,569,385; 6,730,517; 6,979,425; 6,994,969; 7,019,288; 7,025,933; 7,232,688; 7,285,422; 7,332,275; 7,390,672; 7,501,251; 7,888,127; 7,917,301; 8,003,317; 8,315,805; and 8,349,566 and patents pending including but not limited to US and US , and foreign counterparts including but not limited to, EP B1, EP B1, EP B1, EP B1, EP B1, EP B1, EP B1, and EP B1. [0515] The MassARRAY System, iplex Pro Sample ID Panel, Typer software, and iplex ADME PGx Pro Panel are For Research Use Only. Not for use in diagnostic procedures. RLN-CUS-023 Rev03 4/6/16 16