QuantStudio 3D AnalysisSuite Server System

Transcription

1 QUICK REFERENCE QuantStudio 3D AnalysisSuite Server System Installation, Maintenance, and Administration Catalog Number and Pub. No Rev. C IMPORTANT! This document does not provide adequate detail to integrate the QuantStudio 3D AnalysisSuite Server System into all possible network architectures. Because your laboratory network can contain advanced features (such as firewalls), Thermo Fisher Scientific recommends that you consult a network administrator before connecting your server. Product overview QuantStudio 3D AnalysisSuite Software The QuantStudio 3D AnalysisSuite Software performs statistical analysis of digital PCR experiments and can be used to calculate the absolute or relative number of target nucleic acid sequences in a biological sample. See Perform a software upgrade on page 9 for instructions to upgrade your software. Compatible instruments AnalysisSuite Software can analyze the results of digital PCR experiments run on the QuantStudio 3D Digital PCR Instrument that have been exported as experiment data (.eds) files. Note: Refer to the QuantStudio 3D Digital PCR System User Guide (Pub. no. MAN ) for detailed information on the instrument operational and data workflow. QuantStudio 3D Digital PCR System data flow For each imaged Digital PCR Chip, the QuantStudio 3D Digital PCR Instrument generates and saves a single experiment (.eds) file that contains the processed imaging data and the results from the preliminary analysis on the instrument. Depending on the chosen data destination, the instrument transfers the saved imaging data directly to the AnalysisSuite Server System or Thermo Fisher Cloud data storage service for immediate access by the AnalysisSuite Software, or to a network file server or other external storage device such as a USB drive for later manual import. QuantStudio 3D AnalysisSuite Server System The QuantStudio 3D AnalysisSuite Server System is a Linux -based file server system from Thermo Fisher Scientific that hosts the server-based QuantStudio 3D AnalysisSuite Software using an Internet Protocol (IP) address configured in the system. The AnalysisSuite Server System requires an administrator to manage user accounts and comes pre-configured with the following components and settings. Dell PowerEdge T110 II base unit with a 1.86TB capacity hard drive, 16GB RAM, single quadcore 2.4GHz processor, and RAID1 controller Note: The hard drive can hold up to 180,000.eds files generated by the QuantStudio 3D Digital PCR System. The maximum number of.eds files is an estimate that can vary based on the specific number, size, and type of chip data you import into the system. Red Hat Enterprise Linux operating system Apache Tomcat application server that runs the AnalysisSuite Software PostgreSQL database server that stores the data for the server and software Google Chrome browser Automatic configuration of Internet Protocol (IP), Domain Name Service (DNS), and Windows Name Service (WINS) settings via Dynamic Host Configuration Protocol (DHCP) Note: Refer to the manufacturer's documentation accompanying the server or go to the manufacturer's website for the network requirements, specifications, and product details. For Research Use Only. Not for use in diagnostic procedures.

2 Note: For more information on the server-based AnalysisSuite Software, refer to the QuantStudio 3D AnalysisSuite Software Help. Install the QuantStudio 3D AnalysisSuite Server System Installation Installation of the QuantStudio 3D AnalysisSuite Server System can be completed within one hour. The installation requires participation at all times. Plan to spend most of the installation working with the device. The time required to install the AnalysisSuite Server System can vary depending on the type of networking solution that you choose (automatic DHCP or static IP). This document does not provide procedures to integrate the server into a static IP network architecture. See Before you begin on page 2 for more information and for additional installation requirements. Materials required The following materials are required to install the QuantStudio 3D AnalysisSuite Server System: Item Quantity Part number Dell PowerEdge T110 II Tower Server [1] Dell Flat Panel Monitor, 23 inches (or equivalent) with cable Dell Quiet Key USB Keyboard [2] Dell Laser USB Mouse [2] GB USB drive Power cord [3] RJ45 CAT6 Ethernet cable USB drive [1] Includes an additional USB drive to re-image the Red Hat Enterprise Linux operating system (if needed). [2] Supplied with the server. [3] Supplied with the server and monitor. Supplies 13A/125V depending on the geographic location of the installation. Note: The information in this table is subject to change. For the latest information, go to the Thermo Fisher Scientific website or contact Customer Support. Before you begin Before you install the AnalysisSuite Server System: Unpack and inspect the materials required for installation as listed in Materials required on page 2. If you have not received one or more of the components or if any components are damaged, contact Thermo Fisher Scientific support or your service representative for assistance. Confirm that the installation site meets the environmental and electrical requirements explained in the manufacturer's documentation accompanying the server or on the manufacturer's website. Read Additional protective devices on page 2 and if necessary, obtain the additional components to install. Collect your network policy for obtaining IP addresses (automatic DHCP or static IP) from a network administrator. If your network requires a static IP address assignment, consult a network administrator before connecting the AnalysisSuite Server System to your laboratory network. Additional protective devices We recommend several electrical devices to protect the systems in environments with large voltage and power fluctuations. 2 QuantStudio 3D AnalysisSuite Server System Quick Reference

3 Power line regulator Use a 1.5-kVA power line regulator in areas where the supplied power fluctuates in excess of ± 10% of the normal voltage. Power fluctuations can adversely affect the function of the systems. Note: A power line regulator monitors the input current and adjusts the power supplied to the systems. It does not protect against a power surge or failure. Surge protector Use a 10-kVA surge protector (line conditioner) in areas with frequent electrical storms or near devices that are electrically noisy, such as refrigerators, air conditioners, or centrifuges. Short-duration, high-voltage power fluctuations can abruptly terminate the function of, and thereby damage the components of, the systems. Note: A dedicated line and ground between the systems and the building s main electrical service can also prevent problems caused by power fluctuations. Install the server 1. Connect the system components. a. Connect the keyboard, mouse, and the monitor to the server according to the manufacturer s documentation. Note: Make sure at least one USB port on the front of the server is available to install the software (see Install the QuantStudio 3D AnalysisSuite Software to the server on page 4). Note: If the monitor comes with a white VGA cable already attached, remove the cable. Install the blue DVI cable, USB, and power cable according to the manufacturer s documentation. b. Connect the server to the local network using the Ethernet cable. Do not use a wireless connection. c. Connect the monitor and the server to the power sockets. 2. Press the power button on the front of the server, then wait 1-2 minutes for it to start. IMPORTANT! Do not interrupt the power up sequence until it is finished. If the server does not start, contact Thermo Fisher Scientific support or your service representative for assistance. The server is ready to install the AnalysisSuite Software when the desktop displays the initial SAA Server login screen. Log into the AnalysisSuite Server System as the Administrator After attaching the server to your network and powering up the server: 1. At the initial SAA Server login screen, select the appliance-admin (server Administrator) user. 2. Enter ServerAdmin!! for the server administrator password, then press Enter. You may need to enter the password again. 3. At first login, the server Administrator must change the UNIX password. The password: Must be a minimum of 8 characters long Must consist of alphabetic and numeric characters Can contain hyphens, but not as the first or last characters in the name Cannot include spaces or special characters ( ; : " < > * + = \?, ) Note: Any updates to the Administrator password for the AnalysisSuite Server System do not affect the Administrator password for the AnalysisSuite Software. If you cannot login using the new server Administrator password, an additional server Administrator user account (appliance-admin-rescue) is available using the default password specified above. If your network requires a static IP address assignment, consult a network administrator to reconfigure the server for static IP operation. QuantStudio 3D AnalysisSuite Server System Quick Reference 3

4 Install the QuantStudio 3D AnalysisSuite Software to the server 1. Log in as the server Administrator and wait for the server desktop to appear. 2. Insert the USB drive into a USB port on the front of the server. The following five files display. install.command launches a script to install the software (see below) upgrade.command launches a script to backup data on the desktop and upgrade the software (See Perform a software upgrade on page 9) uninstall.command launches a script to uninstall the software; a shortcut to this script is added to the server desktop (see below) quantstudio3d-<version>s.rpm archive of files and metadata that are packaged for use by the install.command script and are required to install the software to the server, where <version> is the current released version of the software shared i386.rpm archive of shared static files that are packaged for use by the install.command script and are required to install the software to the server 3. Double-click install.command, then click Run In Terminal. 4. At the prompt, enter the server Administrator password you created in Log into the AnalysisSuite Server System as the Administrator on page 3, then press Enter. The installation process starts after you press Enter. Once the installation is complete, six shortcuts should be available on the server desktop: IP Address launches a script to display the IP address of the server (see Obtain the IP address of the server on page 5) Monit launches a tool that monitors the status of software running on the server Note: Use this tool to determine if the services for the software and server are still running and to restart them as needed (see Monitor the services on the server on page 10). Backup QuantStudio 3D AnalysisSuite Data launches a script to back up the server database (see Back up the data on the server on page 12) Restore QuantStudio 3D AnalysisSuite Data launches a script to restore the server database from a backup (see Restore the data on the server on page 13) QuantStudio 3D AnalysisSuite launches the AnalysisSuite Software (see Access the AnalysisSuite Software on the server on page 6) 4 QuantStudio 3D AnalysisSuite Server System Quick Reference

5 Uninstall QuantStudio 3D AnalysisSuite launches a script to remove the AnalysisSuite Software from the server (see Uninstall the software from the server on page 14) 5. Press any key to exit the window. The installation of the AnalysisSuite Server System is complete and the components are ready for use. Obtain the IP address of the server The IP address of the server is required to access the server from a browser on another computer. The server Administrator should provide each user with the current IP address of the server. Note: The IP address of the server may change periodically, depending on your laboratory network policy for obtaining IP addresses (automatic DHCP or static IP). Consult your network administrator for more information. 1. Log into the server as the Administrator (see Log into the AnalysisSuite Server System as the Administrator on page 3). 2. Double-click IP Address on the server desktop. 3. Note the IP address displayed in the window, then press any key to exit. To access the AnalysisSuite Software from a browser on another computer, a user should enter IP address>/quantstudio3d, where <server IP address> is in the example shown above. See Access the software from another computer on page 6 for more information. Provide the IP address of the server to all users who will access the AnalysisSuite Software from a browser on another computer. Up to 35 concurrent users can access the software using the IP address of the server. QuantStudio 3D AnalysisSuite Server System Quick Reference 5

6 Use the server system Manage users in the AnalysisSuite Software Only users with an Administrator account in the AnalysisSuite Software can create and enable new user accounts. For optimal performance, access to the software should be limited to a maximum of 35 concurrent users. Follow the instructions in the QuantStudio 3D AnalysisSuite Software Help to manage users in the software. Access the AnalysisSuite Software on the server System requirements When deployed in server configuration, the QuantStudio 3D AnalysisSuite Software is accessed as a web-based application that can be run using any Internet browser that meets the hardware and operating system requirements in the following table: Browser Hardware Operating system Google Chrome [1] Microsoft Internet Explorer Mozilla Firefox Client computer Microsoft Windows 7 v21 or later v10.0 or later None [2] Server computer (Dell PowerEdge T110 II server) Red Hat Enterprise Linux v21 or later None [3] v or later [1] Recommended browser for all platforms [2] Browser not supported for this platform [3] Browser not available for this platform Access the software from the server desktop 1. Double-click QuantStudio 3D AnalysisSuite on the server desktop. By default, the software opens in the Google Chrome browser. 2. At first login to the software as the administrator, enter Administrator as the username and Password as the password. Note: If you cannot sign in to the software, contact Thermo Fisher Scientific Customer Support or Servicedesk@lifetech.com. Note: Thermo Fisher Scientific recommends that you change the administrator password after initial login to the software. Refer to the QuantStudio 3D AnalysisSuite Software Help for information about managing your profile. Access the software from another computer To access the software from a client account on another computer: 6 QuantStudio 3D AnalysisSuite Server System Quick Reference

7 1. Confirm that your computer has a network connection and that it is connected to the same network as the server. Note: If your computer does not have a network connection, contact a Thermo Fisher Scientific Sales Representative for information on available AnalysisSuite Software deployment options. 2. Open a browser window and go to IP address>/quantstudio3d, using the <server IP address> you received from your server administrator (see Obtain the IP address of the server on page 5). In the example shown below, the <server IP address> is Note: Using your browser settings, confirm that cookies and JavaScript are turned on for the website to function correctly. If you cannot access the website, then contact Thermo Fisher Scientific Customer Support or Servicedesk@lifetech.com. 3. Log into the software as: Administrator enter the user name and password from Access the software from the server desktop on page 6 End-user enter the user name and password you received from your server administrator Note: If you cannot sign in to the software, contact Thermo Fisher Scientific Customer Support or Servicedesk@lifetech.com. Use the AnalysisSuite Software For information on using the server-based AnalysisSuite Software to create and analyze projects from chip data stored on the AnalysisSuite Server System, see the QuantStudio 3D AnalysisSuite Software Help. Transfer data to the server You must transfer the digital PCR experiment data (.eds) files generated by imaging Digital PCR Chips from the QuantStudio 3D Digital PCR Instrument to the shared storage location on the AnalysisSuite Server System before you can access the data on the server (see Access the data on the server on page 8). Based on the data destinations outlined in QuantStudio 3D Digital PCR System data flow on page 1, if you choose to connect the instrument to: The AnalysisSuite Server System Chip data files are automatically uploaded to the shared storage location on the server at the end of each instrument run, for immediate access by the server-based AnalysisSuite Software. An external storage device such as a USB drive Insert the device into the USB port on the front of the server and manually upload the chip data files to the shared storage location on the server. A network file server Navigate to and transfer chip data files from the mapped location on the network file server to the shared storage location on the AnalysisSuite Server System. The Thermo Fisher Scientific cloud data storage service Chip data files are automatically uploaded to a user-specific data destination on the cloud at the end of each instrument run, for immediate access by the cloud-based AnalysisSuite Software. Note: For more information on configuring the transfer of chip data files from the instrument to the server, see the QuantStudio 3D Digital PCR System User Guide. QuantStudio 3D AnalysisSuite Server System Quick Reference 7

8 Access the data on the server To access the data on the server from another computer: 1. Confirm that your computer is connected to the same network as the server. 2. In the address bar of the Windows file explorer window, enter \\<server IP address>\quantstudio3d, where <server IP address> is in the example shown below. Chip data files saved to the shared storage on the server will be listed in the Import Data screen of the AnalysisSuite Software, under Available to import from shared storage. Note: For more information on importing chip data into a project, see the QuantStudio 3D AnalysisSuite Software Help. 8 QuantStudio 3D AnalysisSuite Server System Quick Reference

9 Perform a software upgrade Back up data on the AnalysisSuite Server System before performing an upgrade to the server-based AnalysisSuite Software (see Back up the data on the server on page 12). Use a USB to perform a software upgrade Use the following procedure to perform a software upgrade to the server-based AnalysisSuite Software. 1. Obtain the files required for an upgrade on a USB drive. You will receive a USB drive from Thermo Fisher Scientific containing the files required to upgrade the software on the server. You can download and extract the files onto a USB drive yourself by visiting QuantStudio 3D AnalysisSuite Local Appliance Software and clicking Download. 2. Navigate to and open the USB drive folder. 3. Double-click upgrade.command. A confirmation message opens. Note: If double-clicking upgrade.command does not prompt confirmation request to upgrade, you may need to make the command executable. To do so, right-click upgrade.command, select Properties, then select Allow executing file as program in the Permissions tab. Click Close, and attempt to double click upgrade.command again. 4. Click Run in Terminal. The following window displays. Ignore the Operation not permitted message. It does not affect the upgrade. 5. Press any key to exit. A Terminal prompt opens. 6. Enter the server administrator password created in Log into the AnalysisSuite Server System as the Administrator on page 3, then press Enter. QuantStudio 3D AnalysisSuite Server System Quick Reference 9

10 Maintain the server system Only users with a server Administrator account can perform the following maintenance functions. Note: For additional information, or if you experience issues with server performance, contact Thermo Fisher Scientific Customer Support. Maintain the server Monitor the services on the server Perform the following if you experience a failure in server performance, or as needed to monitor server performance: 1. Double-click the Monit shortcut on the server desktop. 2. Enter the User Name admin and the password monit, then click Log In. The shortcut launches the Monit Service Manager tool that monitors the status of processes and programs running on the server. Use this tool to determine if the following services are still running and to restart them as needed: SAA-Server ssh (service) tomcat 7 (application server) 10 QuantStudio 3D AnalysisSuite Server System Quick Reference

11 postgresql (database server) Note: Use this tool to monitor the space available on the server. If the Space usage for the Filesystem approaches 80-90%, contact Thermo Fisher Scientific Customer Support for information on additional space options. 3. If a service displays the following status: Green (Running) No action required Red (Does not exist) Select the link for the service, then click Restart service Note: If restarting one or more services does not improve the server performance, make sure to back up the data on the server (see Back up the data on the server on page 12), then reboot the server. If you are still experiencing a failure in server performance, contact Thermo Fisher Scientific Customer Support. QuantStudio 3D AnalysisSuite Server System Quick Reference 11

12 Back up the data on the server This procedure requires a different device or destination (external hard drive, network location, etc.) for the data archive. Note: The data destination must contain enough space to store the data archive before the backup process can begin. Users will not be able to access the server-based AnalysisSuite Software during the backup process. Perform the following at least once a week, or according to your laboratory network policies: 1. Double-click the Backup QuantStudio 3D AnalysisSuite Data shortcut on the server desktop. 2. Enter the server Administrator password you created in Log into the AnalysisSuite Server System as the Administrator on page 3, then press Enter. The shortcut launches a script to perform a full backup of the server database, including experiment data (.eds) files and user accounts. 3. At the prompt, enter the path where the data will be archived. Note: The archive path is case sensitive and cannot include spaces. The example path is /media/usb_hardrive, where media is the location of the external device, and usb_hardrive is the label of your device (in the example below, the label is usb). 4. Press Enter. An archive of the database will be copied to the destination folder you entered above. The example destination is /media/usb_hardrive//quantstudio3d_backup_<mm_dd_yyyy>.tar.gz. 5. When the backup process is complete, make a note of the archive path shown in the window, then press any key to exit. Note: If the backup process is incomplete due to insufficient disk space, select a higher capacity device or destination for the data archive and try again. For all other issues, make sure to record the issue then contact Thermo Fisher Scientific Customer Support or Servicedesk@lifetech.com. Note: You will need to enter the archive path in order to restore the data on the server (see Restore the data on the server on page 13). In the example above, the path is /media/usb//quantstudio3d_backup_09_20_2013.tar.gz. You can also find the archive location if you double-click Computer on the server desktop, then navigate to location you entered in step 3 above. 12 QuantStudio 3D AnalysisSuite Server System Quick Reference

13 Restore the data on the server Perform the following after backing up the data on the server: Note: Users will not be able to access the AnalysisSuite Software during the restoration process. 1. Double-click the Restore QuantStudio 3D AnalysisSuite Data shortcut on the server desktop. 2. Enter the server Administrator password you created in Log into the AnalysisSuite Server System as the Administrator on page 3, then press Enter. The shortcut launches a script to perform a full backup of the server database, including experiment data (.eds) files and user accounts. 3. At the prompt, enter the path where the data was archived (see Back up the data on the server on page 12), then press Enter. When the restoration process is complete, all users that were in the server database at the last successful backup should be able access the AnalysisSuite Software, including the projects and settings stored in the database. Note: If the backup process is incomplete, make sure to record the issue then contact Thermo Fisher Scientific Customer Support or Servicedesk@lifetech.com. 4. Press any key to exit the window. QuantStudio 3D AnalysisSuite Server System Quick Reference 13

14 Maintain the AnalysisSuite Software on the server Uninstall the software from the server Back up data on the AnalysisSuite Server System before removing the server-based AnalysisSuite Software (see Back up the data on the server on page 12). 1. Log in as the server Administrator. 2. Double-click Uninstall QuantStudio 3D AnalysisSuite on the server desktop, then click Run In Terminal. Note: If this script was not copied from the USB drive to the server desktop at install, insert the USB drive into a USB port front of the server, then double-click uninstall.command. on the 3. At the prompt, enter the server Administrator password you created in Log into the AnalysisSuite Server System as the Administrator on page 3, then press Enter. Once the uninstallation is complete, the AnalysisSuite Software is removed from the server, the server database is cleared, and the shortcuts are removed from the server desktop. 4. Press any key to exit the window. Customer and technical support Visit thermofisher.com/support for the latest in services and support, including: Worldwide contact telephone numbers Product support, including: Product FAQs Software, patches, and updates Order and web support Product documentation, including: User guides, manuals, and protocols Certificates of Analysis Safety Data Sheets (SDSs; also known as MSDSs) Note: For SDSs for reagents and chemicals from other manufacturers, contact the manufacturer. Limited product warranty Life Technologies Corporation and/or its affiliate(s) warrant their products as set forth in the Life Technologies' General Terms and Conditions of Sale found on Life Technologies' website at If you have any questions, please contact Life Technologies at 14 QuantStudio 3D AnalysisSuite Server System Quick Reference

15 The information in this guide is subject to change without notice. DISCLAIMER TO THE EXTENT ALLOWED BY LAW, LIFE TECHNOLOGIES AND/OR ITS AFFILIATE(S) WILL NOT BE LIABLE FOR SPECIAL, INCIDENTAL, INDIRECT, PUNITIVE, MULTIPLE, OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR ARISING FROM THIS DOCUMENT, INCLUDING YOUR USE OF IT Thermo Fisher Scientific Inc. All rights reserved. All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified. Dell and PowerEdge are trademarks of Dell, Inc. Red Hat is a registered trademark of Red Hat, Inc. Linux is a registered trademark of Linus Torvalds Apache and Tomcat are trademark of the Apache Software Foundation. Google is a registered trademark and Chrome is a trademark of Google, Inc. UNIX is a registered trademark of the Open Group. Microsoft, Windows, and Internet Explorer are registered trademark of Microsoft Corporation. Mozilla and Firefox are registered trademarks of Mozilla Corporation. For support visit thermofisher.com/support or techsupport@lifetech.com thermofisher.com 6 April 2016