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Agilent Technologies Magnis Dx NGS Prep System, User Manual

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Agilent Technologies Magnis Dx NGS Prep System User Manual Download Page 67

Magnis and Magnis Dx NGS Prep System User Guide

67

Protocol Update screen

Purpose: To upload new protocol files into the software from a connected USB disk drive or from 
the Agilent website. See instructions in 

“Install protocol updates” 

on page 45.

To open: From the Home screen, press 

Settings

. On the Settings screen press 

Protocol 

Update

.Then, press 

Update Protocol

.

Figure 43

Protocol Update screen – USB Disk selected

Figure 44

Protocol Update screen – Online Download selected

USB Disk / Online Download

Select the USB Disk option to import a protocol file from a connected USB disk. When the USB 
Disk option is selected, the screen displays a browser of the folders and files on the connected 
USB disk. Select the protocol files you want to install on your system.

Select the Online Download option to download a protocol file directly from Agilent using the 
system’s internet connection. When the Online Download option is selected, the screen displays 
the list of available new protocols. Mark the check boxes next to the protocols you want to install 
on your system.

Summary of Contents for Magnis Dx NGS Prep System

Page 1: ...Dx NGS Prep System User Guide Magnis Dx NGS Prep System P N K1007AA For In Vitro Diagnostic Use Magnis NGS Prep System P N G9710AA For Research Use Only Not for use in diagnostic procedures Revision...

Page 2: ...ce denotes a hazard It calls attention to an operating procedure practice or the like that if not correctly performed or adhered to could result in personal injury or death Do not proceed beyond a WAR...

Page 3: ...ts 18 3 Getting Started 19 Starting Up the Magnis Magnis Dx NGS Prep System 20 Turn on the instrument 20 Log in to the system 20 Managing User Accounts 22 About user access levels 22 Add new user acco...

Page 4: ...and Teach Point Verification 43 Run auto teaching 43 Include teach point verification in the IHC 44 Installing Updates 45 Install protocol updates 45 Install firmware updates 47 5 Performing Maintena...

Page 5: ...r Settings screen 76 Instrument Diagnostic screens 78 Diagnostic Test screen 78 Diagnostic Test Report screen 79 Diagnostic Report Explorer screen 80 Decontamination screen 81 Run Data Explorer screen...

Page 6: ...Magnis and Magnis Dx NGS Prep System User Guide 6 Magnis system issues 94 Library sequencing issues 95...

Page 7: ...ep Procedure 8 Limitations of Use 8 Instrument Specifications 9 Materials Provided 10 Optional Accessories 10 Optional Cleaning Supplies 10 Product Inspection 11 Safety Precautions 11 Environmental Re...

Page 8: ...t to finish automation of library preparation and target enrichment protocols for next generation sequencing NGS The starting material is fragmented genomic DNA gDNA purified from a cell or tissue sam...

Page 9: ...9 C Heater Shaker Magnet module Heater Temperature maximum 75 C Shaker Maximum speed rpm 1800 rpm 5 Chiller module Temperature range 4 12 C Power inlet AC voltage 100 240 VAC AC frequency 50 60 Hz Max...

Page 10: ...Power cord Functional test certificate USB disk with PDFs of the User Guide and Quick Reference Guide Table 3 Optional accessories for use with the system Description Purpose Mouse with USB connector...

Page 11: ...ndard electrical safety precautions should be applied including the following Per North American and IEC requirements install the instrument in a location where branch circuit protection is available...

Page 12: ...autions are still needed During decontamination of the instrument deck with UV light do not look directly or indirectly at the UV light source Always perform decontamination with the instrument door c...

Page 13: ...e Maintain the following minimum distances for cleared space around the instrument Instrument sides 10 cm 4 inches on each side to allow for proper ventilation from the side vents Back of the instrume...

Page 14: ...GS Prep System User Guide 14 2 Hardware Overview Instrument Components 15 Instrument Status Indicator Lights 18 This chapter provides product information on the hardware elements of the Magnis Magnis...

Page 15: ...components Front and sides of instrument Figure 1 Instrument door Waste bin drawer containing disposable tip waste bin LCD touchscreen for display of the firmware software Power button USB ports 2 Si...

Page 16: ...t HSM module for various processing steps Chiller module for reagent storage Tube holders for liquid reagents 6 total Platforms to hold tip boxes 4 Platform to hold Beads Buffers Plate Opening to tip...

Page 17: ...gure 4 Instrument deck Micropipettor Barcode scanner UV tube Instrument deck LED indicator light LED indicator light Gantry Tip box platforms 3 loaded 1 empty Chiller loaded Beads Buffer Plate platfor...

Page 18: ...auto teaching or teach point verification and when a user is setting up a protocol run Blue Ready The lights are illuminated blue anytime the system is idle and the door is closed including at comple...

Page 19: ...hiller temperature 27 Set the time and date 27 Assign an instrument name 28 View the instrument serial number and software version 29 Set up the instrument IP address 29 Set the instrument health chec...

Page 20: ...se the user name and password provided by the Agilent engineer or service provider who installed your system 1 Access the Login screen of the software The Login screen opens automatically after turnin...

Page 21: ...ithin specifications Teach point verification Auto teaching is a process in which the system locates and records the positions of markers called teach points that are printed on the instrument deck Au...

Page 22: ...User Management screen opens listing the available user names and corresponding access levels and statuses Table 7 Actions permitted for Standard and Advanced user account Action Permitted by Standard...

Page 23: ...Next to Access Level select the access level Standard or Advanced for the new user The default selection is Standard See Table 7 on page 22 for a summary of the differences between the two access leve...

Page 24: ...een closes and you are returned to the User Management screen The new user name appears in the list on the User Management screen Edit user accounts Only users with Advanced access are permitted to ed...

Page 25: ...complete to send an email to the user when a protocol run initiated by the user completes Mark Email alert on error occurs to send an email to the user when the instrument encounters an error during a...

Page 26: ...account that you want to disable and press Disable A message box opens asking you to confirm that you want to disable the account 4 Press Yes in the message box to continue All user permissions for t...

Page 27: ...permitted to set the chiller temperature 1 From the Home screen press Settings The Settings screen opens 2 Press System Settings The System Settings screen opens 3 Press Chiller Setting The Chiller S...

Page 28: ...he screen Press the and buttons to adjust the values or type the desired values into the fields Press the AM or PM button to toggle between AM and PM settings To set the time zone expand the drop down...

Page 29: ...ome screen press Settings The Settings screen opens 2 Press System Settings The System Settings screen opens 3 Press Instrument Settings The Instrument Settings screen opens displaying the serial numb...

Page 30: ...e information 5 Press OK to save your changes Set the instrument health check settings Based on this setting the system can include or exclude verification of the teach points as part of the first ins...

Page 31: ...forms after being powered on Or clear the check box to exclude teach point verification from the instrument health checks When the check box is marked each time the instrument is powered on the first...

Page 32: ...tings for the email server Enter the requested information into the fields shown on the screen Figure 16 Mail Server Info expanded Outgoing Mail Server SMTP Enter the host name of the SMTP Simple Mail...

Page 33: ...en Agilent releases a new or updated Magnis protocol 1 From the Home screen press Settings The Settings screen opens 2 Press Connectivity Settings The Connectivity Settings screen opens 3 Press Protoc...

Page 34: ...le 42 Running Auto Teaching and Teach Point Verification 43 Run auto teaching 43 Include teach point verification in the IHC 44 Installing Updates 45 Install protocol updates 45 Install firmware updat...

Page 35: ...nal Perform the 30 minute UV decontamination quick cycle to decontaminate the surfaces of the instrument deck See Decontaminating with UV Light on page 41 You can begin Prepare the reagents and plasti...

Page 36: ...with the cursor Because the steps vary depending on the type or target enrichment you are running you will need to refer to the instructions and screen images provided in the user manual for your Magn...

Page 37: ...ss fully open the instrument door and collect the final library samples i e the green library strip tube from the chiller module 3 Re seal the wells of the strip tube using a fresh foil seal strip the...

Page 38: ...n press Settings The Settings screen opens 3 Press Self Diagnostic The Instrument Diagnostic screen opens 4 Press Run Diagnostic Test The Diagnostic Test screen opens listing all of the available diag...

Page 39: ...irectly on the icon to view more information about the failed test items 8 When finished press Close to close the report View reports for diagnostic tests and instrument health checks Each time the sy...

Page 40: ...lays the report in the Diagnostic Test Report screen The top of the report contains summary information including the date and time of the tests The table lists the tests that were performed organized...

Page 41: ...l labware then make sure that the instrument door is closed 2 From the Home screen press Decontamination The Decontamination screen opens Figure 24 Decontamination screen with Quick cycle selected 3 A...

Page 42: ...protect the deck surfaces from excessive exposure to UV light 1 Verify that the instrument deck is cleared of all labware then make sure that the instrument door is closed 2 From the Home screen press...

Page 43: ...screen press Settings The Settings screen opens 3 On the Settings screen press Auto Teaching The Auto Teach screen opens Figure 26 Auto Teach screen 4 Press Start A message box opens asking you to con...

Page 44: ...ng process continues until completion Include teach point verification in the IHC The system can include teach point verification as part of the initial instrument health check IHC that is performed a...

Page 45: ...ment 3 From the Home screen press Settings The Settings screen opens 4 Press Protocol Update The Protocols screen opens 5 Press Update Protocol The Protocol Update screen opens 6 At the top of the scr...

Page 46: ...tocol s that you want to download and install Figure 29 Protocol Update screen with protocol file selected online 6 Press Download A message box opens notifying you that the protocol was downloaded 7...

Page 47: ...e system s touchscreen users with an Advanced user account can install the new firmware through a USB disk or through an online connection Upload firmware from a USB disk 1 Save the zip folder contain...

Page 48: ...screen press Settings The Settings screen opens 2 Press System Settings The System Settings screen opens 3 Press Firmware Update The Firmware Update screen opens 4 Select Online Update The screen disp...

Page 49: ...o take when cleaning the system components 51 Clean the deck surfaces and instrument exterior 51 Clean the barcode scanner 52 Replacing the UV Tube and Viewing UV Tube Usage 53 Request a UV tube repla...

Page 50: ...es not require calibration however it does require preventive maintenance annually Preventative maintenance is performed by an Agilent service engineer or Agilent authorized service provider This serv...

Page 51: ...erge the barcode scanner or any other instrument component in water Clean the deck surfaces and instrument exterior If needed you can clean the deck surfaces and instrument exterior Cleaning the deck...

Page 52: ...the power supply 2 Use a soft cloth or wipe moistened with water or a mild detergent water solution to clean the window of the barcode scanner If you use a detergent water solution follow with cleanin...

Page 53: ...Agilent Worldwide Technical Support to schedule a UV tube replacement View usage hours for the UV tube After replacing the UV tube the Agilent engineer or Agilent authorized service provider will res...

Page 54: ...arts If at any time the Magnis Magnis Dx NGS Prep System or any of its parts are no longer of use you can return the unneeded items to Agilent as part of the Agilent Product Take Back program See www...

Page 55: ...System Settings screens 72 Instrument Settings screen 72 Date Time Settings screen 73 Chiller Setting screen 74 Connection Settings screen 75 Firmware Update screen 74 Other Settings screen 76 Instrum...

Page 56: ...that protocol updates are available for download When this bell shaped icon is red you can press directly on the icon to open the Protocol Update screen and download the new protocol s The presence of...

Page 57: ...urrence of a system error or failed diagnostic test Press to view information on the error s Time and date Displays the time and date according to the system settings Press to open the Date Time Setti...

Page 58: ...ogged in user at the bottom of the screen then press Log Out The Login screen is also the first screen that opens when the instrument is powered on Figure 34 Login screen Username Type the user name f...

Page 59: ...er manual for your specific Magnis Target Enrichment Kit for details on the screens for the protocol wizard Decontamination Press this button to open the Decontamination screen used for performing UV...

Page 60: ...Settings Opens the System Settings screen for accessing tools to configure system wide settings Export Opens the Export Files screen for exporting post run data files and log files Protocol Update Ope...

Page 61: ...lists the user name access level standard or advanced and status active or disabled of each user account If the table extends to multiple pages use the Page field or arrowheads below the table to navi...

Page 62: ...w account Email address es In this field type the email address of the new user If entering multiple email addresses separate them with a space Email alert on run complete Mark this check box to have...

Page 63: ...cannot edit the user name for existing accounts Access Level Select the access level for the account standard or advanced Password Confirm Password To reset the password for the account type a new pa...

Page 64: ...ystem Settings screen Purpose To access tools for configuring settings that are applicable to the entire system To open From the Home screen press Settings Then press System Settings Figure 40 System...

Page 65: ...em will export all post run data files in that folder System Log folder Contains log files of system level actions such as powering on of the instrument and diagnostic tests Error Log folder Contains...

Page 66: ...new and updated protocols To open From the Home screen press Settings On the Settings screen press Protocol Update Figure 42 Protocols screen Protocols table This table lists the name Protocol column...

Page 67: ...col Update screen Online Download selected USB Disk Online Download Select the USB Disk option to import a protocol file from a connected USB disk When the USB Disk option is selected the screen displ...

Page 68: ...outgoing mail account for email alerts and enabling alerts when a new protocol is available To open From the Home screen press Settings On the Settings screen press Connectivity Settings Figure 45 Co...

Page 69: ...eaching process Close This button returns you to the Settings screen Hardware Usage Tracking screen Purpose To track the usage of the system s UV tube For Agilent engineers and Agilent authorized serv...

Page 70: ...t engineer or Agilent authorized service provider following replacement of the UV tube Close This button returns you to the Settings screen Instrument Diagnostic screen Purpose To run diagnostic tests...

Page 71: ...gnostic Test Opens the Diagnostic Test screen which allows you to select from a list of diagnostic tests Browse Report Opens the Diagnostic Report Explorer screen which contains a list of completed di...

Page 72: ...em Settings Then press Instrument Settings Figure 49 Instrument Settings screen Instrument name This field displays the name of the instrument If desired edit the text in the field to rename the instr...

Page 73: ...the left of the screen are for setting the date In the Day Month and Year fields type the correct values or press the buttons to adjust the values Time settings The settings on the right of the scree...

Page 74: ...Temperature Type the desired temperature for the chiller in C into the field Note that this field is only editable for Advanced users Temperatures from 4 C to 12 C are permitted Firmware Update scree...

Page 75: ...ing the system s internet connection When the Online Update option is selected the screen displays the new the firmware version Update This button opens the license agreement for the new firmware Acce...

Page 76: ...connection settings are set to Obtain IP Address Automatically this button renews the IP address assigned to the system Either the previous IP address is re assigned to the system if it is available o...

Page 77: ...time the system is powered on the first IHC that it performs includes verification of the teach point positions If the system identifies a mis alignment with the teach points it displays an error mes...

Page 78: ...n From the Home screen press Settings On the Settings screen press Self Diagnostic Then press Run Diagnostic Test Figure 56 Diagnostic Test screen Prior to starting diagnostic test Figure 57 Diagnosti...

Page 79: ...ess Self Diagnostic then press Browse Report to open the Diagnostic Report Explorer screen Then select a report and press View Note that this screen opens automatically after completion of diagnostic...

Page 80: ...om the Home screen press Settings On the Settings screen press Self Diagnostic Then press Browse Report Figure 59 Diagnostic Report Explorer screen Diagnostic Report folder This folder contains report...

Page 81: ...to complete Agilent recommends running the extended cycle in the event of a spill or leak that resulted in potential contamination of the instrument deck At the end of the extended cycle the instrumen...

Page 82: ...for each user account The subfolders in the right panel are organized by year then numerically by month The subfolder for the month contains the XML files for all of the protocol runs performed by the...

Page 83: ...screen press Post Run Data On the Run Data Explorer screen use the browser to locate and select the XML file for the protocol run of interest then press Open Press the individual tabs on the Post Run...

Page 84: ...the selected protocol run and the system on which the run was performed Labware Info tab Figure 65 Post Run Data Labware Info tab The Labware Info tab lists the serial number and where available the...

Page 85: ...Data Audit Trails tab The Audit Trails tab provides a list of user actions that occurred during the setup and execution of the protocol run For each action the tab shows the date and time of the acti...

Page 86: ...by step instructions on how to set up and start the run Press the forward arrow button to advance to the next screen If necessary press the back arrow button to return to the previous screen The steps...

Page 87: ...creen press Connectivity Settings Then press Email Alert Settings Figure 67 Email Alert Settings screen Mail Server Info Press this heading to view the settings for the outgoing mail server Figure 68...

Page 88: ...n of new protocols on page 33 To open From the Home screen press Settings On the Settings screen press Connectivity Settings Then press Protocol Alert Settings Figure 70 Protocol Alert Settings screen...

Page 89: ...remaining hh mm ss until completion of the protocol Protocol steps List of protocol steps Current step is highlighted Stop Press the red square next to Stop to abort the run A warning message opens a...

Page 90: ...is the total time hh mm ss that has elapsed since the protocol run started OK This button initiates library sample collection During sample collection the system transfers prepared library solutions...

Page 91: ...are ready Chiller notification The instrument door is now unlocked allowing you to remove from the chiller the green library strip tube containing the libraries Until you fully open the instrument do...

Page 92: ...is Dx NGS Prep System User Guide 92 Figure 75 Run screen when libraries are ready To close the Run screen press the X on the tab NOTE Closing the screen may take several seconds Do not repeatedly pres...

Page 93: ...ooting Troubleshooting Suggestions 94 Magnis system issues 94 Library sequencing issues 95 This chapter contains troubleshooting suggestions to help you solve potential problems and errors encountered...

Page 94: ...52 for instructions Once cleaning is complete repeat the Verify Labware step If only one or a few labware components failed verification then press the error icon at the bottom of the screen and expa...

Page 95: ...power cord inlet and that the other end of the power cord is connected to a wall output that provides 100 240 VAC 1000 W If the problem persists contact Agilent Worldwide Technical Support The touchs...

Page 96: ...7 9770 option 3 4 4 Or send an email to techservices agilent com For Europe Middle East Africa and India Call 00800 345 600 toll free or 49 69 8679 7730 Or send an email to genomics_tech_europe agilen...

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