Page 1 USER MANUAL bioMérieux S.A. 69280 Marcy l'Etoile / France RCS Lyon 673 620 399 Tel. 33 (0)4 78 87 20 00 - Fax 33 (0)4 78 87 20 90 http://www.biomerieux.com...
Page 3: Trademarks
Warning The content of this manual is based on the Software release 2.0. This manual is periodically updated. The updates shall be included in the new releases of the Software. Information supplied in this manual may be subject to modifications before the products described become available.
Page 4 This product includes software developed by Teodor Danciu (http:// jasperreports.sourceforge.net.) Copyright © 2001-2004 Teodor Danciu (teodord@users.sourceforge.net.) All rights reserved. This product includes iText software developed by Bruno Lowagie. The iText 1.02b.jar is redistributed as a whole binary jar. The iText source code version is available under the terms of the Mozilla Public License from the iText web site at http://www.lowagie.com.
Page 5: Revisions
Revisions The list of revisions below summarizes replacements or additional pages in your User Manual. Version Date of printing Modifications Pages modified A - 2.0 2007/07 Creation Covers, ii, iii, iv, v, vi, Modification of legal vii, viii, 1-2, 1-5, 1-7, 2009/09 and regulatory 1-8, 1-9, 1-10, 1-11,...
Page 6 User Manual...
Page 7 Important Information The NucliSENS easyMAG is an in vitro diagnostic medical device. The components of the NucliSENS easyMAG system are supplied only for the purposes of the intended use specified. The NucliSENS easyMAG has been designed to safeguard the user and specimens, provided it is operated according to the instructions in the accompanying documentation.
Page 8 Technical Assistance For technical assistance, including spare parts and consumables, contact your local bioMérieux representative. Disclaimer bioMérieux specifically disclaims all warranties, express or implied, of the suitability of the instrument and disposables (the ‘System‘) and disclaims all liability, whether direct, indirect or consequential, for any use other than as set, forth in the package insert.
Page 9: Table Of Contents
About The User Manual 2-11 User Maintenance Check List 8-22 3 System Basics A Instrument Specifications Overview General Using The System Operating Conditions About NucliSENS easyMAG Reagents  Shipping Conditions And Disposables 3-10 System Input Requirements Limitations 3-16 Processing Specific Symbols 3-16...
Page 10 User Manual...
Page 11 1 Safety Safety Information ......... . . 1-2 Safety Precautions .
Page 12: Safety
Safety Safety Information Safety Information It is essential that the warnings, cautions and safety requirements contained in this document are read and understood by the user before operating the system. Warning symbols have been placed on the instrument to draw the user’s attention to areas of potential hazards.
Page 13: Safety Precautions
Safety Safety Precautions Safety Precautions Particular attention must be paid to the following safety precautions. If these safety precautions are ignored, the user may suffer injury. Each individual precaution is important. Before undertaking electrical safety or other compliance testing on the instru- ment, contact bioMérieux.
Page 14 Safety Safety Precautions Hazardous chemicals (i.e. guanidine thiocyanate) are used in the reagent bay. Avoid contact with skin, eyes and clothing. Wear appropriate laboratory safety clothing, including protective eye wear and gloves, when working in the reagent bay or handling the reagent bottles. Potentially hazardous chemicals and potentially biohazardous material are present in the aspirate head.
Page 15 Wear protective gloves, a lab coat, safety glasses or goggles. Hazardous Chemicals Precaution Do not allow the NucliSENS easyMAG Lysis Buffer, NucliSENS easyMAG Extraction Buffer 1 or waste from the instrument to come into contact with acidic materials. NucliSENS easyMAG Lysis Buffer can potentially release cyanide gas on contact with acid.
Page 16 Safety Safety Precautions Crystallized Spills The potential for exposure of the respiratory tract may occur in case of clean- ing crystallized lysis buffer; extraction buffer 1; Guanidine thiocyanate  (GuSCN) containing waste spills, and dusts may be generated.   Avoid generation of dusts.
Page 17 Safety Safety Precautions  The heater can be hot enough to cause burns. Do not touch the heater while the instrument is operating, and allow at least ten minutes after turning off power to the instrument before touching the heater. ...
Page 18: Caution Messages
Spillages Any liquid spilt on the NucliSENS easyMAG may result in the malfunctioning of the system. If liquid is spilt on the NucliSENS easyMAG, wipe it up immediately and apply disinfectant. NucliSENS easyMAG Lysis Buffer and NucliSENS easyMAG Extraction...
Page 19: Magnetic Devices
Computer Virus Infection The NucliSENS easyMAG system must be kept free from computer viruses. To this end bioMérieux advises to perform a virus scan on all media, removable and otherwise, prior to transferring data to or from the NucliSENS easyMAG system.
Page 20: Abbreviations
Safety Abbreviations Abbreviations In this manual the following abbreviations are used: Abbreviation Definition Conformité Européenne Deoxyribonucleic Acid European Norm Federal Communications Commission GuSCN Guanidinethiocyanate International Organization for Standardization In Vitro Diagnostic Local Area Network Liquid Crystal Display Light Emitting Diode Liquid Level Sensor MAOI Monoamine Oxidase Inhibitors...
Page 21: Conventions
Safety Conventions Conventions In this manual the following conventions are used: DANGER: for safety reason.  CAUTION: to ensure that the instrument is maintained in good working condition. IMPORTANT: to allow optimum use of the instrument.  Procedures Procedures describe actions to be followed by the user in order to safely accomplish a task.
Page 22 Safety Conventions 1-12 User Manual...
Page 23: Introduction
2 Introduction Functional Overview......... . 2-2 Front View.
Page 24: Functional Overview
Introduction Functional Overview The NucliSENS easyMAG platform is intended for the automated isolation (purification and concentration) of total nucleic acids (RNA/DNA) from biological specimens. For in vitro diagnostic use. Figure 2-1: The NucliSENS easyMAG system Functional Overview This section provides an overview of the NucliSENS easyMAG, briefly describing the major areas and their function.
Page 25 Eluate, Waste Samples Figure 2-2: Major interactions of the NucliSENS easyMAG system The user places sample strips and sample, aspirator, and reagents into the instrument, and identifies the samples and protocol required to the software. The computer controls the instrument by issuing commands that run a protocol.
Page 26: Front View
NucliSENtral feature is configured (activated). Front View Figure 2-3 shows the major areas at the front of the NucliSENS easyMAG.  The sections following describe the function of each of these areas. Figure 2-3: Front view of the NucliSENS easyMAG The following list identifies the items in Figure 2-3, and these items are described in the following sections.
Page 27 Introduction Functional Overview Reagent Module The reagent module contains the reagent platforms and reagent mass sensors. There are four 1 L reagent bottles that are placed on platforms. The platforms are part of a mass sensing system, which detects the amount of reagent in each reagent container.
Page 28 Introduction Functional Overview When a run is started, the sample strip carriage moves into the processing area, which contains the mechanisms the instrument uses to process the samples. These mechanisms, including Aspirator disposables, and the aspiration, dispensing, magnet, and heater mechanisms, are discussed in “Processing Area”...
Page 29: Back View
 In this view the electronics compartment is at the left, and the fluidics compartment is at the right. Figure 2-4: Back view of the NucliSENS easyMAG The items identified in Figure 2-4 are: 1. Main power input and fuses 5.
Page 30 Introduction Functional Overview Serial Number This number is unique to each instrument, and should be quoted when requesting support. Fans There is a fan in each of the back panels (electronics at the left and fluidics at the right). The fans should rotate under normal conditions. Communications Connection This is the cable that connects the computer to the instrument.
Page 31: System Capabilities
Buffer 3 if that was not the last reagent dispensed before the instrument was last shut down. The NucliSENS easyMAG system offers a number of tools and features to help the users. A handheld barcode reader helps with entering sample and reagent ID's, and also to identify a particular location for a reagent or sample strip.
Page 32 Extraction Buffer 3 (elution buffer). b. Removes all unwanted material from the sample strip. c. Dispenses NucliSENS easyMAG Extraction Buffer 3 (elution buffer). d. Heats the fluid in the sample strip. e. While maintaining fluid temperature, flushes the Magnetic Silica by repeatedly...
Page 33: About The User Manual
About The User Manual About The User Manual Scope And Audience This document is intended for users of the NucliSENS easyMAG system. It does not contain technical service procedures, which must be performed by bioMérieux or its representatives. User Qualification...
Page 34 Introduction About The User Manual 2-12 User Manual...
Page 35 Software And Data Management ......3-3 Principle Of The NucliSENS easyMAG Method ....3-3 Using The System .
Page 36: System Basics Overview
For information and advice on prehandling steps for handling specific sample matrices, contact your local bioMérieux representative or Global Customer Service. The NucliSENS easyMAG system is intended to be used as a universal stand-alone tool for nucleic acid extraction. NucliSENS easyMAG uses one single set of reagents, independent of the sample type and the nature of the nucleic acid to be isolated.
Page 37: Protocols
The system supports sample and reagent identification via a barcode reader. Principle Of The NucliSENS easyMAG Method The NucliSENS easyMAG system is based on a generic method for binding nucleic acids from complex biological samples to Magnetic Silica. The system works with a liquid specimen. A specimen is mixed with a lysis buffer containing a chaotropic agent (GuSCN).
Page 38: Using The System
Figure 3-1 on page 3-5. With the second scenario, called the ‘off board’ workflow, the lysis step is performed manually, away from the NucliSENS easyMAG instrument, using a dedicated lysis tube. After sample lysis, the lysates are transferred manually to the sample strips loaded on the instrument.
Page 39 System Basics Using The System start instrument magnetic silica control prepare run sample start a run pre-mix add samples aliquot add lysis buffer incubate sample to 8-well strip add pre-mix homogenize samples 8-tip electronic pipette extraction run on instrument concentrate silica wash elution deliver clear end-product...
Page 40 System Basics Using The System Lysis buffer start instrument sample magnetic silica control prepare run start a run pre-mix mix sample in lysis transfer lysed aliquot incubate (lysis) samples to vessels to 8-well strip add pre-mix homogenize sample 8-tip electronic pipette extraction run on instrument concentrate silica wash...
Page 41: Detailed Description Of The 'On Board' Workflow
System Basics Using The System Detailed Description Of The ‘On Board’ Workflow  On board workflow 1. Start the instrument • Start the instrument and log in to the software. 2. Prepare a run • Introduce the identification code of the samples to be processed into the software.
Page 42 System Basics Using The System • Vortex the prepared mixture. Do not centrifuge the mixture. • Aliquot 125 µl portions into an 8-well strip using, optionally, a programma- ble electronic multichannel pipette. 7. Add pre-mix to lysed sample • Transfer 100 µl pre-mix from 8-well strip to sample strips containing the lysed samples and properly homogenize the mixture, for example using a programmable electronic multichannel pipette.
Page 43: Detailed Description Of The 'Off Board' Workflow
System Basics Using The System Detailed Description Of The ‘Off Board’ Workflow  Off board workflow 1. Start the instrument See step 1 of the ‘on board’ workflow. 2. Prepare a run See step 2 of the ‘on board’ workflow. 3.
Page 44 • NucliSENS easyMAG Magnetic Silica (Z011MS) is used as a solid phase for binding the released nucleic acids to facilitate washing of sam- ple components and guanidine that could interfere with nucleic acid detec- tion.
Page 45: About Nuclisens Easymag Reagents And Disposables
NucliSENS easyMAG Disposables (Z10XXX) have the following functions: • NucliSENS easyMAG Sample Strips provide 8 reaction vessels. They are designed to contain 2 ml of lysis buffer, up to 1ml of sample, Magnetic Silica (Z011MS) and an optional internal control.
Page 46: Storage
• Storage of NucliSENS easyMAG Lysis Buffer at 2 to 8 °C may give rise to the appearance of crystals due to the high salt concentration. These crys- tals have to be dissolved during reagent preparation.
Page 47 All other tubes should be kept closed and physically separated from the one being handled. • NucliSENS easyMAG sample strips and aspirator disposables are for single use only. Re-use of disposables will lead to sample contamination and invalid results. •...
Page 48: Materials And Accessories Needed But Not Provided
System Basics About NucliSENS easyMAG Reagents And Disposables • Crystallized spills: Remove crystallized spills carefully. Spray the area carefully with water and absorb using absorbent material (for example fiber free tissue), clean the affected area with copious amounts of water. Then clean the area with a fiber free towel containing a 5% Extran solution.
Page 49: Reagent Preparation
8 samples. If less than 8 samples are to be pro- cessed, any remaining reagents must be closed, marked with the date of opening, and returned to storage as soon as possible. After opening, the NucliSENS easyMAG Magnetic Silica can be stored for a maximum of 14 days. •...
Page 50: Limitations
The NucliSENS easyMAG system fully supports the use of an internal control. It is recommended to use internal controls for monitoring the per- formance of the extraction process.
Page 51: Hardware Description
4 Hardware Description “Functional Overview” on page 2-2 gives a brief introduction to the main hardware items. This section provides a more detailed description of the hardware components and operations involving those components. Work Area ..........4-2 Sample Loading Area .
Page 52: Work Area
The sample strip carriage moves into the processing area for the samples to be processed. Figure 4-1: The Sample loading area of the NucliSENS easyMAG The items in Figure 4-1 are: 1. Sample strip carriage arms.
Page 53: Sample Strips
Hardware Description Work Area Sample Strips Sample strips are plastic disposables containing a row of eight vessels that can hold sample and all reagents necessary for the extraction process (refer to Figure 4-2). The sample strips can be loaded (clipped) into the sample strip carriage at the front of the processing area when the carriage is in the load / unload position at the front of the work area.
Page 54 Hardware Description Work Area  To load a sample strip Figure 4-3: Loading a sample strip 1. Hold the sample strip by the indent. 2. Slide the edges of the strip into the sample strip carriage arms, beneath the tabs in either arm. 3.
Page 55: Sample Strip Carriers
Hardware Description Work Area Sample Strip Carriers Sample strip carriers can hold three sample strips upright to aid the user with pipetting samples or solutions in and out of the strips when away from the instrument. They are also intended to be used as an aid to transporting the sample strips between instruments and / or rooms.
Page 56: Drip Tray
Figure 4-5: Drip tray partially removed Before operating the NucliSENS easyMAG instrument, make sure that the drip tray is in place. Do not reach into the instrument while the instrument is on, as there are moving and heated parts that could cause injury.
Page 57: Sample Tray
Note that the barcode reader holder may be attached to either side of the sample tray. Figure 4-6: View of the front of the NucliSENS easyMAG showing the sample tray extended from under the instrument...
Page 58: Processing Area
Hardware Description Processing Area Processing Area The processing area contains moving mechanical parts and heaters, and is covered to prevent injury. The process door can be lifted to allow placement of Aspirator Disposables and to load samples, however the process door must be closed for the instrument to run samples.
Page 59 Hardware Description Processing Area  To load an Aspirator Disposable 1. Hold the aspirator disposable by the indent, with the pipette tips facing down and the body of the disposable facing away from the user. 2. Slide the sides of the disposable on an angle down into the aspirate head. Rotating spring-loaded nozzle Retaining leaf-spring engages Leaf-spring pushes...
Page 60: Magnets
Hardware Description Processing Area  To unload an Aspirator Disposable 1. Hold the disposable by the indent, and gently lift until the disposable is released. 2. Slide the disposable up out of the aspirate head. The connection point of the Aspirator Disposables should be inspected for reagent salt buildup and washed weekly.
Page 61: Reagent Area
Hardware Description Reagent Area Reagent Area The reagent area is a module that can swing away from the instrument for access by service personnel. There is space for four reagent bottles on platforms in the reagent area. A cover is provided to protect the reagent area from the surrounding environment.
Page 62: Carbon Filter
Hardware Description Reagent Area Do not replace a bottle while a run is in progress. If a reagent bottle is removed during a run a bubble may be introduced to the reagent tube, lead- ing to a short dispense. A warning alarm (W112) will be issued if a bottle is removed when a run is in progress.
Page 63: Computer And Peripherals
Hardware Description Computer And Peripherals Computer And Peripherals The computer communicates with the NucliSENS easyMAG instrument via a cable connection. The user uses the keyboard and touch-screen that are connected to the computer to control the NucliSENS easyMAG instrument. A barcode reader is also connected to the computer; this reader identifies reagents and samples to the software.
Page 64: Barcode Reader
If this happens, release the trigger and start again. The barcode reader has been pre-configured by bioMérieux with factory settings. However, the NucliSENS easyMAG can be made to work with other barcode families than those included in the factory settings. Please refer to the barcode reader user manual for instructions on how to prepare the reader.
Page 65: Computer Connections
Hardware Description Computer And Peripherals Computer Connections The following table details the required connections between the instrument and computer for the NucliSENS easyMAG system: Connector Function Identification Style Keyboard Color = violet LCD monitor None - unique connector Touch screen Labeled ‘Touch-screen’...
Page 66: Back Of The Instrument
Back Of The Instrument Back Of The Instrument An overview of the features at the back of the NucliSENS easyMAG are given in “Back View” on page 2-7. This section provides more detail on those features that may require user intervention.
Page 67: Waste Connections
Hardware Description Back Of The Instrument Waste Connections The figure illustrates the waste connections from the NucliSENS easyMAG. Figure 4-13: Waste connections from the NucliSENS easyMAG 1 Drip tray overflow 4 Service pressure gauge connector 2 Outlet to waste bottle...
Page 68 Hardware Description Back Of The Instrument  To empty the waste container Use the waste bottle stand to help prevent the bottle tipping over. If the bottle tips over the filter may become wet and blocked and require replacing. Make sure to keep the filter dry when you dispose of the waste.
Page 69: Software Description
5 Software Description Software Basics ..........5-2 Barcode Reader .
Page 70: Software Basics
The application software has an intuitive graphic interface designed to guide the user through tasks. The NucliSENS easyMAG system has a touch-screen monitor allowing the user to interact directly with the graphic interface. This makes the NucliSENS easyMAG system easy to use, and reduces the possibility of user errors.
Page 71: Touch-Screen
Software Description Software Basics Touch-screen The software is typically operated by tapping buttons on the touch-screen. These buttons can also be operated by using the keyboard mouse. The wearing of gloves is recommended when touching the touch-screen. Throughout the rest of this document, instructions to ‘click’ or ‘select’ an element can be considered to be the same as ‘touch’.
Page 72: Logging In / Logging Out
Software Description Software Basics Logging In / Logging Out The Login dialog box allows users to login to the system. The Login dialog box is displayed when the system is started up, and when no user is logged in. When logged in, the current user can logout by clicking the Key button on the status bar.
Page 73: Screen Layout
Menu bar: main menu bar and sub-menu bar • Action bar • Work area • Status bar Figure 5-2: NucliSENS easyMAG graphic interface 1 Main tool bar 5 Action bar 2 Sub-tool bar 6 Status bar 3 Work area title 7 Alarms area...
Page 74 Software Description Software Basics An icon, differing by its color and its shape, represents each state: Figure 5-3: Alarm states Color and shape Meaning Green and square: Orange and triangle: Indicates a warning. Red and circle: An error occurred. (The system can be partially or completely stopped.) Each alarm is an active button, which allows displaying information in a specific working area.
Page 75 Software Description Software Basics Menu Bar The Menu bar consists of navigation items within the software. Each button of the main bar represents a function or a group of functions. If the button represents a group of functions, a sub-navigation bar is accessible to allow the selection of an individual function.
Page 76 Software Description Software Basics Work Area Tabbed Windows In a few work areas the windows are tabbed. Each window tab provides a different view on the task at hand. Within the Execute Run work area for example, there is a tab for monitoring progress of the run that is being executed, and another tab for displaying details about any errors or warnings that may have occurred.
Page 77: Confirmation Dialogs
Software Description Software Basics Confirmation Dialogs Confirmation dialog boxes are displayed for various operations such as when modifying or deleting data. Figure 5-7: Confirmation dialog The software requires confirmation if the user wishes to continue. Click Yes to continue with the action, click No to abort the action. Warning Message Dialogs Warning message dialogs indicate that the chosen action was not performed as expected.
Page 78: Error Message Dialogs
Software Description Software Basics Error Message Dialogs Error message dialogs inform the user that one or more errors have occurred when starting lysis buffer dispensing, starting an extraction run or starting a maintenance protocol. An error can be caused by one or more alarms. The error message dialog shows the error related alarms, which can be selected by the user.
Page 79: Online Manual
Start Add remark Online Manual The NucliSENS easyMAG application software has an online user manual available to help the user find information quickly and conveniently. Clicking the Help button on the main menu bar or the User Manual button on the sub-menu bar will provide the online user manual to the user.
Page 80: Menu Bar
Software Description Menu Bar Menu Bar The main menu bar at the top of the screen provides a main menu with sub- menu items, that give access to the different work areas of the application. The following menu and sub-menu items are accessible from the main menu bar, depending on the access rights of the current user.
Page 81 Software Description Menu Bar Settings Application Settings User Administration Maintenance Maintenance Protocol Inventory Assay Development Help About User Manual User Manual 5-13...
Page 82: Daily Use Menu
Daily Use Menu The Daily Use menu contains menu items which are used on a daily basis when performing extractions on the NucliSENS easyMAG. Define Extraction Requests Use this work area to enter extraction requests into the software, simply by scanning sample tubes.
Page 83: Instrument Menu
Application Settings work area. From within this work area, the workflow preferences, communication settings for the barcode reader, and communication settings for the NucliSENS easyMAG instrument and NucliSENtral can be set. It is also possible to enable or disable the various sounds used within the application software.
Page 84: Maintenance
Routine Maintenance The Routine Maintenance work area provides functions to perform routine maintenance protocols on the NucliSENS easyMAG Instrument. From this work area, the user is able to select and start daily, weekly, and monthly routine maintenance protocols.
Page 85: Preparing The System For Use
Preparing The System For Use User Administration The NucliSENS easyMAG system makes use of user names and access rights to track which user is currently operating the system, and also to restrict access to areas of the system by unauthorized persons. Each user has a unique user name and is assigned to one or more security groups with predefined access rights.
Page 86: Security Groups
Software Description Preparing The System For Use Security Groups The system supports four security groups: • Laboratory Technician • Laboratory Manager • Maintenance Engineer • System Administrator A user must be assigned to at least one of these groups to be able to login. The following table lists the permitted actions for users in each security group.
Page 87 Software Description Preparing The System For Use    Load Run (all views)    Dispense lysis buffer    Start    Delete    Reagents inventory    Abort    Print ...
Page 88 Software Description Preparing The System For Use  Maintenance Start   Reagents inventory Abort    Protocol Inventory   Import   Activate   De-activate   Delete   Enable NucliSENtral   Disable NucliSENtral ...
Page 89 Software Description Preparing The System For Use  To create a new user 1. Select the Create New User action button. The New User dialog box is displayed. Figure 5-11: New User dialog 2. Enter the user name and full name into the designated fields. 3.
Page 90: Protocol Inventory
Please note however that a user cannot delete their own account. Protocol Inventory The NucliSENS easyMAG system uses extraction protocols to instruct the instrument how to perform an extraction run. Some instrument maintenance activities are supported by one or more maintenance protocols that can be executed on the instrument in a manner similar to extraction protocols.
Page 91 Software Description Preparing The System For Use Protocols can be activated or deactivated. Only active assay protocols or generic extraction protocols can be selected when extraction requests are defined. Assay protocols have a status assigned, depending on their state of promotion defined in the Assay Development work area.
Page 92 Software Description Preparing The System For Use  Activating a protocol Above the protocols list a filter button is shown. Clicking this button will change the list contents from ‘All Protocols’ to ‘Active Protocols’ and vice- versa. 1. Set the filter of the protocol list to ‘All protocols’. Select an inactive assay ...
Page 93 Software Description Preparing The System For Use  Deleting a protocol 1. Select a protocol to delete in the Protocol list. 2. Select the Delete action button. A confirmation dialog is displayed. 3. Press either the Yes button on the confirmation dialog to confirm deletion or No to cancel the action.
Page 94: Creating Assay Protocols
Creating Assay Protocols The NucliSENS easyMAG software enables assay protocol creation. Assay development is needed for NucliSENS easyMAG to be able to recognize LIS orders related to a specific sample and assay, and to be able to pass the extraction information to NucliSENS EasyQ including the sample/ assay combination.
Page 95: Create New Assay
Software Description Creating Assay Protocols Create New Assay Follow the procedure below to create a new assay. 1. Open the Assay Development work area in the Maintenance menu. 2. Click the Create new assay action button to open the Create new assay dialog box.
Page 96 Software Description Creating Assay Protocols 3. Enter or select assay information in the corresponding fields: Assay Enter the name of the new assay protocol. Name Version Enter a numeric value in the two corresponding text fields to identify the assay protocol version number. The third digit is automatically added by the system.
Page 97: Edit Assay
Software Description Creating Assay Protocols Edit Assay Follow the procedure below to edit an existing assay. 1. Open the Assay Development work area in the Maintenance menu. 2. Select an assay protocol to be edited in the All unreleased assays list. 3.
Page 98: Promote Assay
Software Description Creating Assay Protocols Promote Assay Follow the procedure below to promote an existing assay. 1. Open the Assay Development work area in the Maintenance menu. 2. Select a ‘Development’ or ‘Trial’ status assay protocol to be promoted in the All assays list.
Page 99: Activate/Deactivate Assay
Software Description Creating Assay Protocols Activate/Deactivate Assay Follow the procedure below to activate/deactivate an existing assay. 1. Open the Assay Development work area in the Maintenance menu. 2. Select an assay protocol to be activated/deactivated in the All assays list. 3.
Page 100: Application Settings
Software Description Creating Assay Protocols Application Settings The NucliSENS easyMAG application environment can be set to support specific needs for a certain lab or customer situation. The following application settings can be changed: • Workflow preferences related to executing a run according to a predefined workflow •...
Page 101 • Default on board lysis addition (On/Off): When lysis addition is to be performed by the NucliSENS easyMAG instrument, click on the On-board Lysis Incubation button. This setting is a default that can be overruled when new runs are defined.
Page 102 • Default on board silica incubation (On/Off): When lysis incubation is to be performed by the NucliSENS easyMAG instrument, click on the On-board Silica Incubation button. This setting is a default that can be overruled when new runs are defined.
Page 103 Check to activate communication via NucliSENtral. • Application ID: Enter a unique identification of NucliSENS easyMAG to be able to participate in NucliSENtral data communication. The Application Id entered here must be the same as entered in the Adminis- trator software of NucliSENtral.
Page 104 Software Description Creating Assay Protocols • Port: Enter the port of the NucliSENtral network. This value needs to be in the range between 1024 and 65535. • Address: Enter the IP address of the NucliSENtral network. The required syntax for this value is xxx.xxx.xxx.xxx, where xxx needs to be in the range 0 –...
Page 105: Maintenance
Software Description Creating Assay Protocols Maintenance The NucliSENS easyMAG system requires regular maintenance. Some maintenance activities must be performed by the instrument. For this purpose ‘maintenance protocols’ are available; refer to “Cleaning And Maintenance” on page 8-1 for further details.
Page 106 Software Description Creating Assay Protocols  To install maintenance reagents 1. Select the required protocol in the protocol list. Detailed information of the protocol is shown in the detail window. When reagents are required for the selected protocol, they will be presented in the required reagents list. 2.
Page 107: Operating Procedures
6 Operating Procedures This chapter directs the user through the procedures that are required to operate the NucliSENS easyMAG system. The main procedure that the user will encounter is known as a Routine Extraction. Preparing For Operation ........6-2 Starting Up The System .
Page 108: Preparing For Operation
It is allowed to run the NucliSENtral administrator application next to the NucliSENS easyMAG software. Starting Up The System To start both the NucliSENS easyMAG instrument and software, proceed as follows: 1. Power up the computer and the touch screen.
Page 109: General Laboratory Procedures
Extraction requests which already have been received through NucliSENtral may disappear from the list due to processing ot this request on another NucliSENS easyMAG. Click Daily Use on the main menu bar to display the sub-menu items. The preparation is divided into three steps: 1.
Page 110: Define Extraction Request
Operating Procedures Preparing For Operation Define Extraction Request Requesting extractions for samples is the first task in the routine extraction workflow. This involves entering sample information into the system and ordering extractions for the samples. The user enters sample information in the Define Extraction Requests work area, either by manual entry (typing or scanning) or by using the Auto-generate new extraction requests function.
Page 111 Operating Procedures Preparing For Operation 2. Modify the default settings for extraction Protocol, sample input Volume, Eluate volume, sample Matrix, Type and Priority as required. When a test request is received from NucliSENtral, some extraction request properties are read-only in order to provide the integrity of information across the NucliSENtral system.
Page 112 Operating Procedures Preparing For Operation The following action buttons are available in this sub-menu. Auto-Generate New Extraction Requests Clicking the Auto-generate new extraction requests button allows the user to generate several new extraction requests at once, based on the settings in the Extraction Request area.
Page 113 Operating Procedures Preparing For Operation Edit Extraction Requests In the Define Extraction Requests work area the user can change extraction request information. Follow the procedure below to edit previously submitted information. 1. Select the desired extraction request to be edited in the Unassigned extraction request list.
Page 114: Organizing Runs
Operating Procedures Preparing For Operation Select The Relevant Protocol For specific sample types, different choices in protocols for the NucliSENS easyMAG are available. Make sure that the correct protocol is selected for the sample type which is in the extraction request. New protocols are available through your local bioMérieux representative.
Page 115 Operating Procedures Preparing For Operation Creating A New Run If no runs are ready to be processed, a new one needs to be created. Follow the procedure below to create a new run. Figure 6-4: The New Run dialog 1. Click the New Run button. The New Run dialog box appears. The run name (prefix) is automatically generated by the system, as defined in Application Settings.
Page 116 Operating Procedures Preparing For Operation Moving Extraction Requests To A Run Follow the procedures below to move extraction requests to a run. 1. To quickly assign extraction requests to a run, click the Auto fill run button. All compatible extraction requests from the list will be moved to the run layout (maximum 24 extraction requests)....
Page 117 Operating Procedures Preparing For Operation  It is possible to move requests to a run by scanning sample's barcode. When unassigned test request list contains one test request regarding scanned sample, this request will be highlighted and automatically moved to ...
Page 118 Operating Procedures Preparing For Operation Editing A Run Run information that can be modified includes the run's name and workflow options. Follow the procedure below to edit a run. 1. From the Run list, select the run to be edited. 2.
Page 119: Load A Run
Operating Procedures Preparing For Operation Load A Run Before executing an extraction run the samples need to be prepared and loaded on the instrument. This task is handled in the Load Run work area. Figure 6-5: Load Run work area The Load Run work area’s main window has four tabs, visible in the upper right-hand side corner.
Page 120 Operating Procedures Preparing For Operation In addition to the buttons on the Action bar, there is a group of five small buttons in the barcode Input window in the lower left part of the Load Run work area. These buttons indicate whether a scanned barcode represents a sample strip, a sample, internal control, silica or diluent.
Page 121 Repeat this for all sample strips. Step 2: Install On Board Reagents Reagents need to be present in the NucliSENS easyMAG system before starting a run. When run(s) have been organized, the system indicates whether the required reagents are present or need to be loaded onto the system.
Page 122 The bar to the left of each bottle indicates the volume of that particular bottle. The NucliSENS easyMAG reagents have an on board stability of 1 month. Do not remove the bottles at the end of a work shift; leave them in place to ensure the liquid system remains 'closed’.
Page 123 Operating Procedures Preparing For Operation Emptying The Waste Container  Waste contains a mixture of biological and chemical components. It is important that the waste container is emptied regularly with the appropri- ate degree of caution (see below). To empty the waste container, always start by selecting the Empty out waste container action button from the Reagent Inventory work area.
Page 124 Operating Procedures Preparing For Operation  Waste Dispose of chemical and biological waste in compliance with corresponding local laws and regulations. We recommend contacting either the authorities in charge, or approved waste disposal companies, who will advise on how to dispose of this type of waste.
Page 125 Operating Procedures Preparing For Operation  To assign kit reagents to extraction requests 1. Select the Assign Kit reagents tab in the Load run work area. In the top columns of the Kit Reagents all reagents that have been introduced to the run are listed.
Page 126 1. Install the lysis buffer according to the procedure “Step 2: Install On Board Reagents” on page 6-15. 2. Close the process door of the NucliSENS easyMAG instrument. 3. Select the Dispense Lysis action button and the addition of the lysis buffer will start for all installed strip positions that contain primary samples.
Page 127 Operating Procedures Preparing For Operation Step 5: Perform Lysis Incubation (when necessary) In the case of lysis buffer addition performed by the instrument, the lysis incubation step starts automatically with the incubation time set by the extraction protocol. Step 6: Add Internal Control ...
Page 128: During Operation
Before the run is being executed the software has already checked that the reagent bottle levels are sufficient to complete the run. Do not open the process door when the NucliSENS easyMAG is in opera- tion. If the process door is raised, processing will pause. If this happens in the first 20 minutes of the run for longer than 20 seconds, the aspirator needles may clog.
Page 129: Execute A Run
Operating Procedures During Operation Execute A Run After the run has been started in the Load Run work area, the system automatically moves on to the Execute Run work area Progress view. The user can monitor run progress here. Figure 6-9: Execute Run Progress work area The Execute Run work area’s main window has three tabs, visible in the upper right-hand side corner.
Page 130: Unloading Samples
Remarks can be added to a selected extraction request or to a run. Unloading Samples When the run has finished, and the NucliSENS easyMAG is idle, the extracted samples should be unloaded within 30 minutes from the NucliSENS easyMAG.
Page 131: Nucleic Acid Extracts Storage
Operating Procedures During Operation Nucleic Acid Extracts Storage The user is responsible for validation of the storage procedures and conditions used in their laboratory. Eluates can typically be stored at room  temperature (± 22 °C) for 2 hours, at 2 to 8 °C for 8 hours and 1 month at ...
Page 132: View Run Layout
Operating Procedures During Operation View Run Layout The run layout can be displayed in the Layout work area. Information is shown about the order of samples on the corresponding strips and carriers and also more sample-related details can be shown by selecting individual samples.
Page 133: View Incidents
Operating Procedures During Operation View Incidents The software issues errors and warnings when, during the extraction, a situation occurs that should be brought to the attention of the user. All such incidents are recorded in the Incidents view of the Execute Run work area, along with any remarks.
Page 134: Run Status
Operating Procedures During Operation The incident can have three severity states: error, warning, information. The severity states are indicated by an icon. Error - Something occurred that led to failure of the extraction process for either a single sample strip position, for a complete sample strip or even for an entire run.
Page 135: View Extraction Results
Operating Procedures View Extraction Results View Extraction Results A run is finished when the extraction was performed successfully, when the run was failed by the system, or when the run was aborted by the user. The results of all finished runs can be inspected in the View Results work area. Run results can be assessed, printed, exported, deleted and transferred to the NucliSENtral network.
Page 136 Operating Procedures View Extraction Results The View Results work area’s main window has five tabs, visible in the upper right-hand side corner. Run view - the user uses this view to determine whether or not the run has completed successfully. This view also displays when the run was performed, by whom and on what instrument.
Page 137: Assessing A Run
Operating Procedures View Extraction Results Assessing A Run Assessing a run is a means of indicating that the run is fully finished and can be ‘archived’. Assessing a run does not delete it from the system but does remove it from the active (‘unassessed’) list. After a run has finished executing, the execution status can be one of the following: •...
Page 138: Printing Run Information
Operating Procedures View Extraction Results Printing Run Information  To print the run related information 1. Select the filter option to view all unassessed runs or all runs. 2. Select a run to be printed. 3. Select the Print action button. Press OK to print the run. When a run is printed the operator is asked to mark the run assessed.
Page 139: Issuing A Repeat Extraction
Operating Procedures View Extraction Results Issuing A Repeat Extraction When a sample needs to be retested a repeat extraction can be initiated. An identical extraction request will be automatically generated and can be assigned to be processed.  To initiate a repeat extraction Only for samples in unassessed runs a repeat extraction can be initiated.
Page 140: Add Remark
Operating Procedures View Extraction Results Add Remark Additional text information can be added to a run.  To add additional information to a run 1. Select the filter option to view all unassessed run or all runs. 2. Select the runs to which the additional information shall be added. 3.
Page 141: Shutting Down The System
Operating Procedures Shutting Down The System Send Run Results Manually Assessed Run results with assay protocols assigned to at least one sample can be resent to the NucliSENtral network.  To resend results 1. Select the filter option to view all runs. 2.
Page 142 Operating Procedures Shutting Down The System 6-36 User Manual...
Page 143: Device Status
7 Device Status Connect / Disconnect Instrument ....... . 7-4 Initialize Instrument .
Page 144 Device Status The Device Status work area presents a graphical overview of the NucliSENS easyMAG system and the status of each of the system modules. By means of the alarm icons, the occurrence of system related incidents will be brought to the attention of the user. There are two ways to navigate to the Device Status work area: via the alarm icons in the event that an incident has occurred or via the sub-menu item Device Status.
Page 145 Device Status The Device Status work area displays details of the following devices, each of which is accessed by its own button: Software Instrument Reagent Bay Aspirator Sample Dispenser Heater Mixer Magnetic Silica Capture For each of the devices, a device button is available on the left side of the work area.
Page 146: Connect / Disconnect Instrument
Device Status Connect / Disconnect Instrument Connect / Disconnect Instrument When the connection to the instrument is not active and the instrument device button is selected, the detail panel for the instrument shall display state ‘Disconnected’. To activate the connection, press the Connect instrument action button. To be able to connect to the instrument, the instrument has to be powered on, the power indicator must be green, a physical connection must be available, and instrument connection settings must be valid.
Page 147: Clear Incidents
Device Status Clear Incidents Clear Incidents When the instrument has observed a warning (alarm control of the device shows an orange triangle), the warning usually can be fixed by the user without having to reinitialize the instrument. Errors can not be cleared with the Clear incidents button. To clear errors, please use the Initialize instrument button To clear the incidents, select a device, then select the clear incident button.
Page 148: Connect/Disconnect Nuclisentral
Device Status Connect/Disconnect NucliSENtral Connect/Disconnect NucliSENtral The NucliSENtral Status work area presents an illustration of a typical NucliSENtral configuration and provides the NucliSENtral connection status as well as an overview of NucliSENtral alarms. By means of the alarm icons, the occurrence of system related incidents will be brought to the attention of the user.
Page 149: Clear Alarms
Device Status Clear Alarms Connect / Disconnect NucliSENtral When the connection to the NucliSENtral is not active and the Connection Alarm button is selected, the detail panel for the NucliSENtral status shall display state ‘Disconnected’. To activate the connection, press the Connect NucliSENtral action button. To be able to connect to the NucliSENtral network, the NucliSENtral network settings have to be entered in the Application Settings work area under NucliSENtral communication.
Page 150 Device Status Clear Alarms User Manual...
Page 151 8 Cleaning And Maintenance Introduction ..........8-3 Schedule .
Page 152: Cleaning And Maintenance
Cleaning And Maintenance Before undertaking electrical safety or other compliance testing on the instru- ment, contact bioMérieux. Treat all equipment, samples, blood-based internal controls and quality con- trol (QC) products assayed on this system, as well as all waste in the waste containers, as potentially biohazardous material.
Page 153: Introduction
Cleaning And Maintenance Introduction Introduction The NucliSENS easyMAG system is designed to limit the required amount of maintenance by the user. Liquid Level Sensing and extraction protocols that include fluidic system rinse procedures, ensure that the system is kept clean automatically.
Page 154: Schedule
Inspect weekly 8-15 Reagent bottle filter Inspect weekly 8-16 Waste bottle filter Inspect weekly 8-16 NucliSENS easyMAG service Every six months Decontamination procedures As required 8-10 The following solutions are used in the maintenance procedures: • Pyrogen-free sterile water •...
Page 155 Cleaning And Maintenance Spills Other Spills Crystallized drops The potential for exposure of the respiratory tract may occur in case of clean- ing crystallized lysis buffer; extraction buffer 1; Guanidine thiocyanate con-  taining waste drops, and dusts may be generated. ...
Page 156: Routine Maintenance
Cleaning And Maintenance Routine Maintenance Routine Maintenance Daily Cleaning The NucliSENS easyMAG should be cleaned and inspected after each day of use as follows: • Empty and dispose the contents of the waste bottle into the chemical waste system according to the local waste procedure, the waste contains guanidine thiocyanate.
Page 157: Inspect Filters
Cleaning And Maintenance Routine Maintenance Inspect Filters • Inspect the reagent cap vent filters, they should be dry and free of crys- tals. Replace the filters as required. An indication for a blocked filter is the fact that the bottle builds up a slight under-pressure. ...
Page 158: Barcode Reader
Cleaning And Maintenance Routine Maintenance Barcode Reader The window of the reader is sensitive. While cleaning the reader observe the following precautions: • Do not allow any abrasive material to touch the window • Do not spray water or other cleaning liquids directly into the window •...
Page 159: Clean Dispense Needle
To clean the tubing execute the ‘Clean Dispense needles’ maintenance protocol that performs a rinse of both the macro and micro dispense circuit using NucliSENS easyMAG extraction buffer 3. To execute the protocol, navigate to the Maintenance work area and select the ‘Clean Dispense needles’...
Page 160: Decontamvination Procedures
NucliSENS easyMAG and its replaceable assemblies and components. Disinfection is done to protect users, field service personnel, factory repair personnel, and any others who may come in contact with the NucliSENS easyMAG or its replaceable assemblies and components. ...
Page 161: Preparing The System For Service
Cleaning And Maintenance Decontamination Procedures Preparing The System For Service Whenever the system needs to be serviced it must be cleaned properly first to protect the service engineer. Cleaning the system for service involves some manual cleaning actions and executing 4 maintenance protocols. These protocols were designed to first remove all traces of the reagents from the system and than clean the system with Cleaning solution and Ethanol followed by a rinse with Water.
Page 162: Preparing The System For Transport
Cleaning And Maintenance Decontamination Procedures  Replace liquid (EtOH) 1. Clean the cover of the dispense needles wash station with cleaning solution. Be careful not to damage the dispense needles. 2. Load 3 empty sample strips and 3 aspiration disposables onto the instrument.
Page 163: Template Decontamination
See “Safety Precautions” on page 1-3.  The NucliSENS easyMAG instrument is a relatively closed system that uses reagents that are replaced regularly and single-use disposables. This should help in keeping the system clean. A suspected template contamination of the reagents can be resolved by following the procedures described below.
Page 164: Decontamination Of The Equipment At The End Of Its Life Cycle
Cleaning And Maintenance Decontamination Procedures 7. Select and run the ‘Replace liquid (OCL)’ protocol from the Maintenance work area to flush with mild sodium hypochlorite. 8. Remove the 4 reagent bottles and empty its content. Rinse the bottles thoroughly with pyrogen-free sterile water. 9.
Page 165: Replacing Filters And Fuses
Cleaning And Maintenance Replacing Filters And Fuses Replacing Filters And Fuses Some filters and fuses might need replacement at some point. Often this will be done as part of the preventive maintenance procedure. The following paragraphs offer some guidance should the user be confronted with the necessity to replace an item.
Page 166: Fuse Replacement
Cleaning And Maintenance Replacing Filters And Fuses Reagent Filter This is the filter that is placed on the end of the reagent bottle straw. Figure 8-3: Picture showing the reagent filter To replace this filter, pull it out of the straw and push in a new filter. Replacement reagent filters must be obtained through bioMérieux.
Page 167 Cleaning And Maintenance Replacing Filters And Fuses Figure 8-4: Fuses Replacement fuses must be obtained through the instrument manufacturer. Do not substitute fuses. User Manual 8-17...
Page 168 Cleaning And Maintenance Replacing Filters And Fuses Figure 8-5: Maintenance and decontamination flow chart 8-18 User Manual...
Page 169 Cleaning And Maintenance Replacing Filters And Fuses Pyrogen-free sterile water Maintenance protocols: ‘Clean Waste (H2O)’, ‘Replace liquid (H2O)’ 70% ethanol, REF: 284048 Maintenance protocol: ‘Replace liquid (ETOH)’ Hypochlorite Maintenance protocol: ‘Replace liquid (OCL)’ Cleaning solution Figure 8-6: Maintenance protocol reagent barcodes User Manual 8-19...
Page 170: Data Maintenance
Preparation The NucliSENS easyMAG computer comes with a CD RW drive and Ahead Nero's InCD pre-installed. Writing a CD is a safe way of preserving a backup should the harddisk of the application PC fail. Please format a rewritable CD for use with InCD (packet writing protocol) before attempting to write backups to the CD RW.
Page 171: Backing Up The Database
OK. The computer shall close the software and display the Windows XP desktop. Open Windows Explorer. Navigate to the drive and folder where the NucliSENS easyMAG user software is installed.Typically, the software is installed in D:\bioMérieux\easyMAG. In the folder, select the folder named ‘Database’ and compress the entire folder using ‘Send To - Compressed (zipped) folder’...
Page 172: User Maintenance Check List
Navigate to the backups folder on the CD-RW. Alternatively, navigate to the backup storage folder on the hard-drive. Select the compressed backup to restore. Expand the backup into the folder where the NucliSENS easyMAG User Software is installed. Make sure the installation folder now contains a folder named Database.
Page 173 Cleaning And Maintenance User Maintenance Check List User Manual 8-23...
Page 174 Cleaning And Maintenance User Maintenance Check List 8-24 User Manual...
Page 175: A Instrument Specifications
A Instrument Specifications General ...........A-2 Operating Conditions .
Page 176: General
Instrument Specifications General General Dimensions 1000 mm wide by 650 mm deep by 530 mm high (excluding computer, LCD monitor & keyboard) Weight 128 kg (dry instrument including LCD monitor & keyboard) 8 kg (computer) Operating Conditions Temperature 15 ºC to 30 ºC Humidity Maximum 80 % RH non-condensing at 30 ºC DB Power Supply...
Page 177: Equipment Identification
Windows XP Professional, parallel port for printing, serial port, 2 x USB 2.0 ports. Only the bioMérieux supplied NucliSENS easyMAG computer is to be used with this instrument. Monitor / Touch-screen Minimal configuration: 15" SVGA LCD Touch screen Monitor, 1024 x 768 pixels, 60 Hz, true colors.
Page 178 Instrument Specifications Equipment Identification User Manual...
Page 179: B Barcode Reader Configuration
Gryphon Defaults .........B-3 BioMérieux NucliSENS easyMAG Defaults.....B-3 Installation Procedure And Configuration Of The Gryphon D130 ...
Page 180: Factory Supported Barcode Symbologies
Barcode Reader Configuration Factory Supported Barcode Symbologies This appendix provides instructions for re-configuring the barcode reader to its bioMérieux factory settings. Before changing the barcode reader configuration please ensure that the reader communication settings in the ‘Application Settings’ work area are correct.
Page 181: Barcode Reader Configuration
Perform the following steps in the given order to re-configure the barcode reader. USB-Com Interface Selection Serial emulation mode is required for the NucliSENS easyMAG system. Scan the barcode below to configure the reader for serial emulation mode: Gryphon Defaults...
Page 182: Installation Procedure And Configuration Of The Gryphon D130 Barcode Reader
Restoring Default Setting The D130 barcode reader is supplied with correct settings to use on NucliSENS easyMAG. This procedure is only required if the settings are changed (as described in section above). However, this procedure can be used to ensure the correct settings are used.
Page 183: Codabar Barcode Decoding
CODABAR encoding is required then the barcodes below can be scanned to enable that mode in the reader. In the NucliSENS easyMAG user manual a section Barcode reader is adapted (Appendix B). In this section it is stated that the barcode reader can be configured by scanning the shown barcodes.
Page 184 Barcode Reader Configuration Barcode Reader Configuration 4. The barcode scanner (Datalogic Serial Emulation) is not usually set to COM4 by default. If the barcode scanner is already set to COM4, proceed to step 7 to complete the installation. Otherwise continue on to step 5 to assign the correct COM port.
Page 185: C Touch Screen Re-Calibration
C Touch Screen Re-calibration Re-Calibrating The Touch-Screen .......C-2...
Page 186: Re-Calibrating The Touch-Screen
Touch Screen Re-calibration Re-Calibrating The Touch-Screen Re-Calibrating The Touch-Screen This appendix provides instructions for re-calibrating the touch screen. This procedure requires that the touch screen be operating at least to some degree. If however the touch screen is not operating sufficiently well to follow this procedure, then it will need to be re-installed, repaired or replaced.
Page 187 Touch Screen Re-calibration Re-Calibrating The Touch-Screen Figure C-1: ELO Touchscreen Properties dialog box 5. The calibration screen will appear. Follow the instructions on screen to perform a three-point calibration. Press each time the calibration point in the allowed timeframe for about one second. This has to be performed for all three points.
Page 188 Touch Screen Re-calibration Re-Calibrating The Touch-Screen 6. Check the calibration and press the green tick if it is OK (otherwise repeat the calibration by selecting the blue repeat arrow) Figure C-2: Calibration confirmation dialog box User Manual...
Page 189  To re-calibrate the touch screen (NEC) 1. Minimize or terminate the NucliSENS easyMAG application software. In the case of termination, do not shut down the operating system. 2. On the desk top, click the TouchWare icon. The TouchWare Properties...
Page 190 Done button. If however, the touch screen needs to be re-calibrated, then click the Calibrate button. 7. When the TouchWare Properties screen is re-displayed, exit the program by clicking the Close button. 8. Maximize or restart the NucliSENS easyMAG application software. User Manual...
Page 191: D Software Reference
D Software Reference This appendix provides a summary of all software screens and their associated controls. Daily Use Menu ..........D-2 Define Extraction Requests Work Area .
Page 192: Daily Use Menu
Software Reference Daily Use Menu Daily Use Menu Define Extraction Requests Work Area The Define Extraction Requests work area is the work area where the user creates extraction requests. The user identifies the primary or lysed sample, and selects the requested extraction type. Figure D-1: Define Extraction Requests work area Unassigned Unassigned...
Page 193 The extraction request has high priority. Application Indicates on which application the extraction request was created. Contains application type and application Id when not created on this NucliSENS easyMAG, otherwise it contains a 'locally created' indication. Timestamp Creation date of the extraction request.
Page 194: Organize Runs Work Area
Software Reference Daily Use Menu Organize Runs Work Area The Organize Runs work area is where the user combines extraction requests that are to be processed together into runs. A run can be created by selecting extraction requests from the Unassigned list and moved into the run, either manually or by means of scanning the sample ID barcodes.
Page 195 Incident description or text of the remark. Application Indicates on which application the incident was created. Contains application type and application Id when not created on this NucliSENS easyMAG, otherwise it contains a 'locally created' indication. Timestamp Creation date of the incident or remark.
Page 196: Load Run Work Area
Software Reference Daily Use Menu Load Run Work Area The Load Run work area is where the user actually loads disposables and samples. The run can be started when all status indicators are ok, indicated with a green square. Please select what kind of information will be scanned or typed in the Barcode Input area.
Page 197 Software Reference Daily Use Menu Info Info This area identifies the run that is being loaded. Unique name of the run, defined when the run was created. Protocol Extraction protocol and version number for this run. Size Number of extraction requests assigned to the selected run.
Page 198 Software Reference Daily Use Menu Load Run Work Area – Assign Kit Reagents View The Assign Kit Reagents view displays the installed kit reagent lots and sample IDs of the extraction request run that is being loaded. If more than one kit reagent should be used in one run they have to be assigned to the extraction requests.
Page 199 Software Reference Daily Use Menu Kit Reagents Kit Reagents This table lists all kit reagent lots available for a run. Silica bioMérieux product ID / lot ID for Silica Internal Control bioMérieux product ID / lot ID for Internal Control Diluent bioMérieux product ID / lot ID for Diluent Assigned Kit Reagents...
Page 200 Software Reference Daily Use Menu Load Run Work Area – Layout View The Layout view displays the sample IDs of the extraction request run that is being loaded. Sample strips and aspirator disposables are displayed solidly when they are actually placed in their holders on the instrument. The sample strip ID is displayed immediately below the sample strip image.
Page 201 Software Reference Daily Use Menu Barcode Input Barcode This area is where the user scans barcodes. Select the Input type first. Type Click this button to scan or type in a sample strip barcode. Click this button to scan or type in a sample barcode.
Page 202 Software Reference Daily Use Menu Load Run Work Area – Incidents View When the user loads a run, several errors and warnings can occur. The Incidents view allows the user to view detail information about such incidents. In addition this view lists user remarks. To view details, select an incident or remark in the upper list.
Page 203 Incident description or text of the remark. Application Indicates on which application the incident was created. Contains application type and application Id when not created on this NucliSENS easyMAG, otherwise it contains a 'locally created' indication. Timestamp Creation date of the incident or remark.
Page 204: Execute Run Work Area
Software Reference Daily Use Menu Execute Run Work Area The Execute Run work area is automatically displayed when the user starts the run from the Load Run work area. Execute Run Work Area – Progress View The Progress view displays the expected amount of time to complete the run. Similar to the Load Run work area the arrow-like images represent the steps that are to be taken: capture, wash, elution and finish.
Page 205 Software Reference Daily Use Menu Execute Run Work Area – Layout View The Layout view displays information about the assignment of vessels on the sample strips. Detailed information about every sample can be displayed. Figure D-8: Execute Run work area - Layout view Layout Column 1 Displays the barcode and vessels of sample strip A with...
Page 206 Application Indicates on which application the extraction request was created. Contains application type and application Id when not created on this NucliSENS easyMAG, otherwise it contains a 'locally created' indication. Created by Identification of the user who originated the extraction request.
Page 207 Incident description or text of the remark. Application Indicates on which application the incident was created. Contains application type and application Id when not created on this NucliSENS easyMAG, otherwise it contains a 'locally created' indication. Timestamp Creation date of the incident or remark.
Page 208: View Results Work Area
Software Reference Daily Use Menu View Results Work Area The user inspects the results of completed runs in the View Results work area. The View Results work area lists both successful runs and runs that have failed due to errors. Four different views allow the user to focus on different aspects of a completed run: General view –...
Page 209 Software Reference Daily Use Menu Run List Unassessed Lists the runs that have not yet been assessed. runs only Click the funnel button to show all runs, assessed and unassessed. Reset the sorting of the runs according to their start date. Column 1 Displays a symbol if errors, warnings and remarks pertain to the run.
Page 210 Software Reference Daily Use Menu View Results Work Area – Results View The Results view shows result data for all samples and related information. Figure D-11: View Results work area - Results view Samples 1...24 Each number represents a single vessel in a sample strip. Vessels where a sample is loaded display the sample ID and the used protocol.
Page 211 Sample type, for example plasma or whole blood. Application Indicates on which application the extraction request was created. Contains application type and application Id when not created on this NucliSENS easyMAG, otherwise it contains a 'locally created' indication. Created by User that created the extraction request Timestamp Creation date of the extraction request.
Page 212 Software Reference Daily Use Menu View Results Work Area – Incidents View The Incidents view shows incidents and remarks assigned to the selected run. Figure D-12: View Results work area - Incidents view D-22 User Manual...
Page 213 Application Indicates on which application the incident was created. Contains application type and application Id when not created on this NucliSENS easyMAG, otherwise it contains a 'locally created' indication. Timestamp Time when the incident occurred or the remark was added.
Page 214 Software Reference Daily Use Menu View Results Work Area – Assigned Kit Reagents View The Assigned Kit Reagents view shows the kit reagents that have been assigned to the samples and were used during the extraction process. Figure D-13: View Results work area - Assigned Kit Reagents view Assigned Kit Reagents 1-24 Sample position.
Page 215 Software Reference Daily Use Menu View Results Work Area – Reagents View The Reagents view shows the product and lot numbers of the reagents that were used during the extraction process. The bottles are displayed on the screen exactly as they are placed on the instrument.
Page 216: Instrument Menu
Software Reference Instrument Menu Instrument Menu Reagent Inventory Work Area The Reagent Inventory work area displays the type and volume of bottled reagent installed on the instrument. This work area supports the user in installing and identifying the right reagents. The Reagent Inventory work area is displayed when the Reagent Inventory sub-menu is chosen from the Instrument menu.
Page 217 Software Reference Instrument Menu Info Info This area identifies the run that is being loaded. Unique name of the run, defined when the run was created. All unassessed runs can be selected from the drop-down box. Protocol Extraction protocol and version number for this run. Size Number of extraction requests assigned to the selected run.
Page 218: Device Status Work Area
Software Reference Instrument Menu Device Status Work Area The Device Status work area shows detailed information about the status of each of the devices that the system is made up of. Figure D-16: Device Status work area D-28 User Manual...
Page 219 Software Reference Instrument Menu Overview Overview Click a button to view detailed status information about an instrument device (sub-system.) View the status of the software. View the status of the instrument. View the status of the reagent bay. View the status of the aspiration device. View the status of the sample device.
Page 220: Nuclisentral Status Work Area
Figure D-17: NucliSENtral Status work area Overview Overview Illustration of a typical NucliSENtral configuration. Details Device Name of the NucliSENtral network. Connection Status of NucliSENS easyMAG connection to State NucliSENtral. Network Status of the NucliSENtral network. State Incidents Lists incidents concerning the data communication through NucliSENtral.
Page 221: Settings Menu
Software Reference Settings Menu Settings Menu The Settings menu contains work areas in which the user or system administrator can configure several aspects of the system. Application Settings Work Area The Application Settings work area contains five categories. Select a category in the left part of the work area in order to view or modify application settings belonging to that category.
Page 222 Software Reference Settings Menu Application Settings Work Area – Workflow In the example below, the workflow is configured for the Generic 1.0.6 protocol using primary samples and on-board lysis buffer dispensing and incubation as well as silica incubation. Sample tracking and reagents tracking are disabled.
Page 223 Software Reference Settings Menu Workflow On-board Enable this option (yellow) to have the Defaults Lysis instrument incubate the samples in lysis Incubation buffer. Disable this option (white) to incubate the samples in lysis buffer off-board, for example in a protective cabinet. On-board Enable this option (yellow) to have the Silica...
Page 224 Software Reference Settings Menu Application Settings Work Area – Barcode Reader The Barcode Reader category is used to view or modify communication settings pertaining to the barcode reader. When the barcode reader is not connected, please connect it first and then re-start the software.
Page 225 Software Reference Settings Menu Application Settings Work Area – Instrument Communication Changing these settings may cause the communication between the instru- ment and the software to be lost Figure D-20: Application Settings work area - Instrument Communication Details Instrument Port number used by the instrument connection. Port IP Address IP address of the instrument.
Page 226 Enable this option to activate NucliSENtral NucliSENtral communication and to enter the NucliSENtral network settings. Application ID Enter a unique identification of NucliSENS easyMAG to be able to participate in NucliSENtral data communication. Port Enter the port of the NucliSENtral network.
Page 227 Software Reference Settings Menu Application Settings Work Area – Sounds In the example below a beep or short tune shall sound when a protocol finishes execution or when a dialog is displayed. The occurrence of an alarm shall also be signalled by a beep. Figure D-22: Application Settings - Sound Details Alarm sound Sound a beep whenever an alarm occurs.
Page 228: User Administration Work Area
Software Reference Settings Menu User Administration Work Area The User Administration work area is for adding or removing user accounts. Users are members of pre-defined security groups. Being a member of one or more security groups determines what functionality a user has access to. Figure D-23: User Administration work area Users Users...
Page 229: Maintenance Menu
Software Reference Maintenance Menu Maintenance Menu Maintenance Work Area The Maintenance work area is where the user performs routine maintenance protocols. Similar to the Load Run work area, the user must make sure that all reagents required for a certain maintenance protocol are installed. Figure D-24: Maintenance work area User Manual D-39...
Page 230 Software Reference Maintenance Menu Protocols Protocols Lists the available maintenance protocols. Select one to view details. Name Name of the maintenance protocol. Version Version of the maintenance protocol. Details Protocol Name of the maintenance protocol. Name Version Version of the maintenance protocol. Release Release date of the maintenance protocol.
Page 231: Protocol Inventory Work Area
Software Reference Maintenance Menu Protocol Inventory Work Area The Protocol Inventory work area is where all protocols are maintained. When a new assay, extraction protocol or maintenance protocol becomes available, it can be imported here. Protocols can be activated and deactivated to govern which protocols can actually be executed.
Page 232 Software Reference Maintenance Menu Details Name Name and version of the protocol. Type Assay The selected protocol is an assay protocol. An assay protocol uses an extraction protocol to perform the actual extraction. Extraction The selected protocol is an extraction protocol Maintenance The selected protocol is a maintenance...
Page 233: Assay Development Work Area
Software Reference Maintenance Menu Assay Development Work Area The Assay Development work displays all customer-created assay protocols with details. New assay protocols can be created or existing assay protocols be edited. Assay protocols can be activated and deactivated to govern which protocols are currently displayed in the list.
Page 234 Software Reference Maintenance Menu Column 3 ‘Released’ assay protocol ‘Trial’ assay protocol ‘Development’ assay protocol. Version Version of the assay protocol. Details Name Name and version number of the selected assay protocol. Status Active The assay protocol can be executed. Inactive The assay protocol cannot be executed.
Page 235: Help Menu
Software Reference Help Menu Help Menu About Work Area The About work area contains three categories. Select a category in the left part of the work area in order to display information belonging to that category. Overview Select one of the categories to display information about the application, system or third-party software.
Page 236 Software Reference Help Menu About Work Area – Application Info Here information about the application software is displayed. Figure D-27: About work area - Application Info D-46 User Manual...
Page 237 Software Reference Help Menu Application Info Product Name of the application software. Company Manufacturer of the application software. Version Version number of the application software. Build Detailed version number of the application software. Version Release Release date of the application software. Date Transla- Installed languages of the application software.
Page 238 Software Reference Help Menu About Work Area – System Info Here information about the system is displayed. Figure D-28: About work area - System Info System Info Memory Information about memory usage of the system. Usage Free Amount of currently free memory (kb). Memory Used Amount of used memory by the system (kb).
Page 239 Software Reference Help Menu About Work Area – Credits Here licensing information about third-party software is displayed. Figure D-29: About work area - Credits Credits Licenses Statement about third-party software used by the application software. User Manual D-49...
Page 240: User Manual Work Area
Software Reference Help Menu User Manual Work Area If the User Manual work area is opened, the user manual file opens and is displayed in a separate window. The user can browse for information in this electronic user manual. Figure D-30: User Manual work area D-50 User Manual...
Page 241: E Addendum
Principle Of The Method ........E-3 NucliSENS easyMAG Platform ......E-3 Warnings And Precautions .
Page 242: Generic Extraction, Additional Information
Addendum Generic Extraction, Additional Information Generic Extraction, Additional Information User Manual...
Page 243: Intended Use
NucliSENS easyMAG platform in conjunction with downstream analysis and detection platforms. Principle Of The Method The NucliSENS easyMAG nucleic acid extraction method is based on Boom chemistry using magnetic silica particles. Briefly, under high salt conditions, nucleic acid will bind to the silica particles.
Page 244: Warnings And Precautions
The NucliSENS easyMAG platform has been validated for plasma, serum, CSF, blood, sputum and stool specimen. Some specimen types (sputum and stool) require preparation steps prior to the use on the NucliSENS easyMAG platform. Consult your local bioMérieux representative for detailed instructions on these procedures.
Page 245: Performance Characteristics
Viral Nucleic Acid Recovery In order to detect and analyze rare nucleic acids from microorganisms, such as viruses, the NucliSENS easyMAG platform has been used to extract viral nucleic acids from different specimen types. Viral recovery of nucleic acid was measured by spiking a fixed amount of intact viral particles to primary specimens.
Page 246 Removal Of Downstream Application Inhibitors Removal of inhibitors was verified by analysis of NucliSENS easyMAG extracts from different specimen types (plasma, serum, blood, CSF, sputum and stool), spiked with fixed amounts of intact viral particles. Diluted and undiluted extracts were assayed in real time PCR to obtain Ct values.
Page 247: Reliability Characteristics
Boom chemistry for total nucleic acid extraction for all specimen types tested. Reagents And Disposables The NucliSENS easyMAG platform uses one set of reagents to perform generic extraction. Using the platform with reagents and disposables not released by bioMérieux for the purpose of processing specimens on the NucliSENS easyMAG instrument may result in damage or harm to the platform, the user or the patient.
Page 248: Troubleshooting
Addendum Generic Extraction, Additional Information Troubleshooting Error Priority Description Error Trigger Condition Solution Code Instrument 2231 FATAL Waste Trap The waste trap sensors are in an Contact your local bioMérieux Error on erroneous combination - the high representative. Initialization sensor is inactive, the full sensor is active.
Page 249 Addendum Generic Extraction, Additional Information Error Priority Description Error Trigger Condition Solution Code Instrument 2244 FATAL Waste trap The waste trap high sensor is Contact your local bioMérieux High after still active after the initialization representative. initialization procedure has attempted to drain the waste trap.
Page 250 Addendum Generic Extraction, Additional Information Error Priority Description Error Trigger Condition Solution Code Instrument 2308 WARNING Fluidics fan The fan in the fluidics area has The system will continue failed been detected as stopped or functioning but your local disconnected. bioMérieux representative should be contacted to solve the problem.
Page 251 (3) Operating temperature (3) Lower the environmental too high resulting in a temperature in which the premature elution during NucliSENS easyMAG platform the last wash step. is operating. (4) High nucleic acid (4) In some cases (e.g. sputum/ background.
Page 252: Symbols
Addendum Generic Extraction, Additional Information Symbols Catalog number Caution, see instructions for use Availability For The NucliSENS easyMAG Platform Article Catalog Sufficient for number NucliSENS Lysis Buffer (2 ml/tube) 200292 48 extractions NucliSENS easyMAG Lysis Buffer 280134 384 extractions ...
Page 253 Index Buttons – common 5-11 About The User Manual 2-11 Activating a protocol 5-24 Adding – calibrator 6-21 Calibrate touch screen (ELO) C-2 – lysis 6-20 Calibrator – magnetic beads 6-21 – adding 6-21 – run remarks 6-34 Carbon filter 4-12 Administration –...
Page 254 Index Dialogs – confirmation 5-9 General laboratory procedure 6-3 – error 5-10 Groups 5-18 – warning 5-9 Gryphon D130 Barcode Reader Dimensions A-2 – Configuration B-4 Disabling a protocol for NucliSENtral 5-25 – Installation B-4 Disconnect NucliSENtral 7-7 – Restoring default setting B-4 Disconnecting the instrument 7-4 Gryphon Defaults B-3 Drip tray 4-6...
Page 255 Moving extraction requests 6-10 6-12 – enabling 5-25 – importing 5-23 – inventory 5-16 5-22 – meaning 5-22 NucliSENS easyMAG reagents 3-10 – types 3-3 NucliSENtral – Connect 7-7 – Connect/disconnect 7-6 – Disconnect 7-7 Reader NucliSENtral Communication Settings 5-35 –...
Page 256 Index Replacing Scenario. See Workflow – carbon filter 8-15 Scope of manual 2-11 – filters 8-15 Security groups 5-18 – fuse 8-16 Select the relevant protocol 6-8 – reagent bottle 4-12 Send run results manually 6-35 Requesting extractions 6-4 Service schedule 8-6 Reseting a password 5-21 Settings 5-32 Restoring the database 8-22...
Page 257 Index Warning – dialogs 5-9 Warnings – reagents 3-11 Waste – connections 4-17 Waste container – emptying 4-18 6-17 Weight A-2 Work area 5-7 Work area tabbed windows 5-8 Work List – printing 6-19 Workflow options. See Workflow scenarios Workflow scenarios 3-4 User Manual...
Page 258 Index User Manual...

bioMerieux NucliSens EasyMag User Manual

Table of Contents

Revisions

1 Safety

2 Introduction

3 System Basics

System Basics

3 System Basics Overview

Principle of the Nuclisens Easymag Method

About Nuclisens Easymag Reagents and Disposables

4 Hardware Description

5 Software Description

6 Operating Procedures

7 Device Status

8 Cleaning and Maintenance

8 Cleaning and Maintenance

A Instrument Specifications

B Barcode Reader Configuration

D Software Reference

E Addendum

Quick Links

Chapters

Need help?

Questions and answers

Related Manuals for bioMerieux NucliSens EasyMag

Summary of Contents for bioMerieux NucliSens EasyMag