bioMerieux NucliSENS easyMAG User manual

bioMérieuxS.A. 69280Marcyl'Etoile/France
RCS Lyon 673 620 399
Tel. [phone] - Fax [phone]
http://www.biomerieux.com
4501 - 1991 - B - en - 2009/09 – P/N 4501 - 1991
USER MANUAL
EN

User Manual iii
Warning
The content of this manual is based on the Software release 2.0.
This manual is periodically updated. Theupdates shall be includedin the new
releases of the Software.
Information supplied in this manual may be subject to modifications before
the products described become available.
This manual may contain information or references relating to certain
bioMérieux S.A. products, software or services which are not available in the
country of release; this shall not mean that bioMérieux S.A. intends to market
such products, software or services in such country.
To request copies of publications or for any technical request, contact
bioMérieux S.A. or your local distributor.
Trademarks
bioMérieux, the blue logo, NucliSENS, EasyQ, NASBA, easyMAG,
miniMAG and NucliSENtral are used, pending and/or registered trademarks
belonging to bioMérieux S.A. or one of its subsidiaries.
Windows is a trademark belonging to Microsoft Corporation.
Extran is a trademark belonging to Merck KGaA.
Decon is a trademark belonging to Decon Laboratories.
Java is a trademark belonging to Sun Microsystems, Inc. The jaxb-api.jar,
jaxb impl.jar, jaxb libs.jar, jaxb xjc.jar, jaxp api.jar and jax qname.jar are
redistributed as whole binary jars.
Sun is a trademark belonging to Sun Microsystems, Inc. and are subject to
Sun license terms.
W3C is a trademark belonging to the Massachusetts Institute of Technology.
TouchWare is a trademark belonging to 3M Company.
Pentium is a trademark belonging to Intel Corporation.
CorelDRAW is a trademark belonging to Corel Corporation.
Any other name or trademark is the property of its respective owner.
This product includes software developed by the Apache Software
Foundation (http://www.apache.org/). Apache Xerces and Xalan are part of
the Apache XML project. Commons Command Line Interfaces, Commons IO
and Commons Lang (all Apache libraries). Commons BeanUtils, Commons
Collections, Commons Digester and Commons Logging are part of the
Apache Jakarta Commons project. All aforementioned Apache projects are
trademarks of The Apache Software Foundation.
For further open source licensing issues pertaining to Apache Software
Foundation, visit http://www.apache.org/LICENSE.
IMPORTANT! Use of the instrument and manual implies acceptance of the
clauses below and the clauses set out in the regulatory booklet. Users are
invited to refer to these clauses.

iv User Manual
This product includes software developed by Teodor Danciu (http://
jasperreports.sourceforge.net.) Copyright © 2001-2004 Teodor Danciu
([email protected]ge.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. For further information pertaining to the
Mozilla Public License, visit http://www.mozilla.org.
This product includes 7-zip software developed by Igor Pavlov. The 7za.exe
is redistributed as a whole binary file. The 7-zip source code version is
available under the terms of the GNU LGPL License from the 7-zip web site
at http://www.7-zip.org. For further information pertaining to the GNU LGPL
License, visit http://www.gnu.org/copyleft/lesser.html.
This document includes images from CorelDRAW 10 which are protected by
the copyright laws of the U.S., Canada and elsewhere. Used under license.
© 2007-2009 bioMérieux S.A.
Photos: bioMérieux / Printed in France / bioMérieux S.A. RCS Lyon 673 620 399

User Manual v
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 All
B2009/09 Modification of legal
and regulatory
information
Covers, ii, iii, iv, v, vi,
vii, viii, 1-2, 1-5, 1-7,
1-8, 1-9, 1-10, 1-11,
2-8, 4-16, 6-2, 8-14

vi User Manual

User Manual vii
Due to software evolution slight changes in the dialog boxes displayed in this
document may occur. When a modification is made that may have adverse
effects on operating the system using this document, an update or
amendment will become available.
Every effort has been made to ensure the information contained in this
document is current and accurate as of the date of publication or revision and
that it is consistent with the product it describes. However, no guarantee is
given or implied that the document is error-free or that it is accurate with
regard to any specifications. bioMérieux reserves the right to make changes
to this document without notification.
Intended Use
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.
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.
The user must not connect, install, replace or decommission equipment or
software that is not approved by bioMérieux, or configure equipment or
software in a manner that is not approved by bioMérieux.
If the equipment is operated in a manner not specified by bioMérieux, the
protection offered by the equipment may be impaired.
Installation, commissioning, repairs and decommissioning must only be
carried out by trained qualified service personnel authorized by bioMérieux.
The equipment is heavy and should not be lifted without following correct
procedures. The equipment should not be lifted or re-located without the
assistance of bioMérieux Field Service Support.
Supplementary information to this User Manual is supplied in the Addendum
to the NucliSENS easyMAG User Manual, which accompanies this manual.
Contact your local representative to obtain an additional copy.
Sub-assembly Weight
‘Dry’ Instrument including LCD monitor and keyboard 128 kg
Computer 8 Kg

viii User Manual
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. Customer acknowledges and agrees that use
of the System for testing of sample types or for indications other than those
described in the package inserts is done solely at the Customer's own risk.
The Customer acknowledges and agrees that it is Customer's sole and
exclusive responsibility to validate the System for any such intended use, and
to determine whether the System is suitable for that intended use. The
performance of any validation studies and the subsequent use of the System
based on Customer's validation studies shall be the Customer's sole risk and
responsibility.
Warranty
bioMérieux disclaims all warranties, express or implied, including any implied
warranties of MERCHANTABILITY AND FITNESS FOR A PARTICULAR
USE. bioMérieux shall not be liable for any incidental or consequential
damages. IN NO EVENT SHALL BIOMÉRIEUX'S LIABILITY TO
CUSTOMER UNDER ANY CLAIM EXCEED A REFUND OF THE AMOUNT
PAID TO BIOMÉRIEUX FOR THE PRODUCT OR SERVICE WHICH IS THE
SUBJECT OF THE CLAIM.

Table of Contents
User Manual ix
Warning iii
Trademarks iii
Revisions
1Safety
Safety Information 1-2
Safety Precautions 1-3
Caution Messages 1-8
Abbreviations 1-10
Conventions 1-11
2 Introduction
Functional Overview 2-2
System Capabilities 2-9
About The User Manual 2-11
3 System Basics
Overview 3-2
Using The System 3-4
About NucliSENS easyMAG Reagents 
And Disposables 3-10
Limitations 3-16
Specific Symbols 3-16
4 Hardware Description
Work Area 4-2
Processing Area 4-8
Reagent Area 4-11
Computer And Peripherals 4-13
Back Of The Instrument 4-16
5 Software Description
Software Basics 5-2
Online Manual 5-11
Menu Bar 5-12
Preparing The System For Use 5-17
Creating Assay Protocols 5-26
6 Operating Procedures
Preparing For Operation 6-2
During Operation 6-22
View Extraction Results 6-29
Shutting Down The System 6-35
7 Device Status
Connect / Disconnect Instrument 7-4
Initialize Instrument 7-4
Clear Incidents 7-5
Stop Instrument 7-5
Connect/Disconnect NucliSENtral 7-6
Clear Alarms 7-7
8 Cleaning And Maintenance
Introduction 8-3
Schedule 8-4
Spills 8-4
Routine Maintenance 8-6
Decontamvination Procedures 8-10
Replacing Filters And Fuses 8-15
Data Maintenance 8-20
User Maintenance Check List 8-22
A Instrument Specifications
General A-2
Operating Conditions A-2
Shipping Conditions A-2
System Input Requirements A-2
Processing A-2
Barcode Reader A-2
Equipment Identification A-3
B Barcode Reader Configuration
Factory Supported Barcode Symbologies B-2
Barcode Reader Configuration B-3
C Touch Screen Re-calibration
Re-Calibrating The Touch-Screen C-2
D Software Reference
Daily Use Menu D-2
Instrument Menu D-26
Settings Menu D-31
Maintenance Menu D-39
Help Menu D-45
E Addendum
Generic Extraction, Additional Information E-2
Index

xUser Manual

1Safety
Safety Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1-2
Safety Precautions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1-3
Warning Messages. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1-3
Caution Messages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1-8
Magnetic Devices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1-9
Abbreviations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1-10
Conventions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1-11

1-2 User Manual
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.
A warning triangle means: ‘Attention’. Consult the appropriate documentation
or accompanying text before proceeding. Personal injury or damage to the
system may occur if correct instructions are not followed.
Warnings and cautions appear both on the equipment and in the
documentation, where appropriate.
All users must be familiar with the following symbols and their meanings:
This label warns that there is danger of damage from static
electricity to components in the area of this label. When
working in the area of sensitive components wear a properly
connected grounding strap.
This label warns that there are items in the vicinity that may
be hot enough to cause burns. Before working in an area
where this label is present, switch off the instrument and
allow sufficient time for cooling.
This label warns of the possibility of crushing. Keep
extremities away from this area when parts of the instrument
are moving.
This label warns of the possibility of pinching. Do not allow
fingers or other extremities to intrude into an area containing
this symbol while the instrument is operating.
This label warns that a strong magnetic field exists within the
vicinity of this label.
This label warns that signals emitted by the instrument may
adversely affect the correct operation of pacemakers.
This label warns that a substance is harmful by inhalation,
harmful if swallowed, irritating to eyes and irritating to the
respiratory system.
This label warns that a substance is corrosive and may attack
either metal and / or naked skin.

User Manual 1-3
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.
Warning Messages
Electric Shock Precautions
Bio-hazardous Materials Precautions
Before undertaking electrical safety or other compliance testing on the instru-
ment, contact bioMérieux.
When working around the instrument fans with the power switched on, take
care not to place fingers near the fans.
Electronic equipment can be the source of electrical shocks. 

Installation, service and repair should only be carried out by authorized and
qualified bioMérieux personnel.
Power outlet. Risk of electric shock. 

All power switches should be off when connecting or disconnecting cables to
power outlets.
We recommend connecting this instrument to a main power circuit that is pro-
tected with a ground fault circuit interrupter.
All in vitro diagnostic equipment, patient samples, blood-based internal con-
trols and quality control (QC) products assayed on this system, as well as all
waste in the waste containers, should be treated as potentially bio-hazardous
materials.


Ensure that appropriate decontamination is carried out if hazardous materials
are spilt on or into the equipment or surrounding areas.

1-4 User Manual
Safety
Safety Precautions
Waste Material 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. Wear appropriate laboratory safety clothing,
including protective eye wear and gloves, when working around the aspirate
head.
Treat waste material, including consumable items, and any components com-
ing into contact with waste material as having the potential hazards of the
samples and reagents used in both preparing and processing the samples.


Handle and dispose of waste materials, including consumable items like
Aspirator Disposables and sample strips, according to local, state, and fed-
eral procedures and regulations, and safety procedures at the installation
site.


All users should be familiar with the MSDS for all materials used in the proce-
dures relating to this instrument, and the correct procedures for handling
these materials.


Specifically, treat all waste material from the instrument as being potentially
biohazardous and corrosive, and do not allow to contact acidic materials.
Material in the waste bottle, drip tray, waste bottle connector, drip tray drain
connector, and service pressure gauge connector may be potentially biohaz-
ardous.


Treat this material as having the potential hazards of the samples and
reagents used in both preparing and processing the samples.


Wear appropriate laboratory safety clothing, including protective eye wear
and gloves, when operating with these items.


Handle and dispose of waste materials, according to local, state, and federal
procedures and regulations, and safety procedures at the installation site for
hazardous chemicals and potentially biohazardous material.

User Manual 1-5
Safety
Safety Precautions
Samples
Hazardous Chemicals Precaution
Crystallized Drops
Avoid direct contact with samples as they may be bio-hazardous. Wipe up
spills immediately and decontaminate affected areas using procedures
approved at the installation site. Wear protective gloves, a lab coat, safety
glasses or goggles.
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. The quantities that may be released
depend on the volumes of both the buffer and the acidic material. Refer to the
MSDS for NucliSENS easyMAG Lysis Buffer and NucliSENS easyMAG
Extraction Buffer 1 for further information.


Avoid contact with skin, eyes and clothing. 

If spilt, isolate spill area. Do not allow entering drains or watercourses. Clean
up the spill with absorbent material (for example, tissue) and clean affected
area with copious amounts of water.
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 drops, and dusts may be generated.


Avoid generation of dusts. 
Harmful by inhalation. 
Do not breathe dust. 
Avoid contact with skin, eyes and clothing. 
Wear protective gloves (nitrile rubber), a lab coat, safety glasses or goggles. 

Wipe up GuSCN drops immediately. Remove crystallized drops carefully with
distilled water and clean the area with a fiber free towel containing a 5% Ext-
ran solution. After cleaning with the 5% Extran solution, clean the affected
area with 70% Ethanol. Then wipe the area clean using a fiber-free towel con-
taining a small amount of silicon oil. This to prevent any GuSCN crystals to
re-occur.

1-6 User Manual
Safety
Safety Precautions
Crystallized Spills
Mechanical Safety Precautions
As with any mechanical system, certain precautions must be taken when
operating the instrument. The instrument has a protective cover intended to
prevent the user coming into contact with any moving parts and aerosols.
This cover is equipped with safety sensors that stop instrument operation
when the cover is opened. bioMérieux does not assume any liability for
damage caused as a result of de-activation of the safety sensors
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. 
Harmful by inhalation. 
Do not breathe dust. 
Avoid contact with skin, eyes and clothing. 
Wear protective gloves (nitrile rubber), a lab coat, safety glasses or goggles. 
Respiratory protection required when dusts are generated (Filter FFP2,
according to EN149).


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. Then clean the area with the 5%
Extran solution, and clean the affected area with 70% Ethanol. Finally wipe
the area clean using a fiber-free towel containing a small amount of silicon oil.
This to prevent any GuSCN crystals to re-occur.
DO NOT remove or raise the protective hood when the instrument is in oper-
ation.
The reagent door falling suddenly has the potential to cause injury. 
Take care when working in the reagent bay.
Pinching hazard. 
There are moving mechanisms inside the cover around the area of the aspi-
rate head. Do not put hands or any part of the body in or near the working
area.

User Manual 1-7
Safety
Safety Precautions
Hazardous Magnetic Fields 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.
Burn hazard. 
Hot parts are accessible when the drip tray is removed. Do not insert body
parts into this area while the instrument is operating, or for at least ten min-
utes after power to the instrument is turned off.
This product contains very strong permanent magnet arrays. 

Extreme care should be taken when handling tools and other magnetic mate-
rial in close proximity to the magnet arrays, as sudden high mechanical
forces may be generated.


Magnetically sensitive items such as computer discs and tapes, audio and
video cassettes, and credit cards should be kept well clear of the magnet
arrays, as these items may be damaged by strong magnetic fields.
People wearing a pacemaker should not use this product, as the strong mag-
netic fields associated with this product may adversely affect or damage the
pacemaker.

1-8 User Manual
Safety
Caution Messages
Caution Messages
Samples
Make sure that samples do not contain fibres, dust or other insoluble
contaminants. If insoluble contaminants are contained in a sample, correct
assay results may not be obtained.
Handling Of Cleaning And Disinfecting Solutions
Cleaning and disinfecting solutions have corrosive properties. Always wear
protective (chemical resistant) gloves and safety glasses when handling
cleaning and disinfecting solutions.
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
Buffer 1 Spills
Do not allow the NucliSENS easyMAG Lysis Buffer, NucliSENS easyMAG
Extraction Buffer 1 or waste from the instrument to contact acidic materials.
NucliSENS easyMAG Lysis Buffer can potentially release cyanide gas on
contact with acid. The quantities that may be released depend on the
volumes of both the buffer and the acidic material. Refer to the MSDS for the
lysis buffer for further information.
Damage To Packaging Materials
Inspect all incoming reagent and disposable packaging for damage. Damage
to the packaging does not prevent the contents from being used. However, if
the outer packaging is damaged the user must satisfy himself that the
contents are intact before using them. Materials must not be used if damage
is suspected.
Third Party Software
Only software that has been validated together with the NucliSENS
easyMAG User Software may run on the NucliSENS easyMAG computer
(PC). bioMérieux assumes no liability for adverse reactions to third party
software installed without the written permission of bioMérieux.
Burn hazard. 
Hot parts are accessible when the drip tray is removed. Do not insert body
parts into this area while the instrument is operating, or for at least ten min-
utes after power to the instrument is turned off.

User Manual 1-9
Safety
Caution Messages
Data Manipulation
Any manipulation of measured/calculated data by a user may cause incorrect
results to be reported. The system has been designed to inhibit the
modification of data by a user. However, if this should occur, bioMérieux
assumes no liability for the data in the system, or results reported from such
data.
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. Use an industry standard virus scanner and ensure that it
has been updated for the most recent virus detection files.
Data Protection
To prevent data loss it is advised to make regular backups of the computer
system. See section “Backups” on page 8-20.
Computer Configuration
The computer and its operating system have been carefully configured for
optimal NucliSENS easyMAG performance. Altering the configuration may
severely hamper the usability of the instrument.
Magnetic Devices
Devices that emit strong magnetic fields may affect measurement data, or
cause the instrument to malfunction. Do not operate such devices in the
immediate vicinity of the instrument when it is in use.
The screen saver function of Windows XP is disabled by default. 

Do not enable the screen saver as this may detrimentally affect software per-
formance.
Do not put the computer in stand-by mode. 

When the computer is put in stand-by mode it will disconnect from the instru-
ment.

1-10 User Manual
Safety
Abbreviations
Abbreviations
In this manual the following abbreviations are used:
Abbreviation Definition
CE Conformité Européenne
DNA Deoxyribonucleic Acid
EN European Norm
FCC Federal Communications Commission
GuSCN Guanidinethiocyanate
ISO International Organization for Standardization
IVD In Vitro Diagnostic
LAN Local Area Network
LCD Liquid Crystal Display
LED Light Emitting Diode
LLS Liquid Level Sensor
MAOI Monoamine Oxidase Inhibitors
MSDS Material Safety Data Sheet
NAD Nucleic Acid Diagnostics
QC Quality Control
RNA Ribonucleic Acid
UL Underwriters Laboratories Inc.
US United States