CFX Opus 96 Dx, CFX Opus 384 Dx,
and CFX Opus Deepwell Dx
Real-Time PCR Systems
Operation Manual
12014330
12014334
12014335
12014348
12014349
12016659
12016687
Manual revision: October 2022
Software revision: 2.3

CFX Opus 96 Dx, CFX Opus 384 Dx,
and CFX Opus Deepwell Dx Systems
Operation ManualBio-Rad Technical Support
The Bio-Rad Technical Support department in the U.S. is open Monday through Friday, 5:00 AM to 5:00 PM,
Pacific Time.
Phone: 1-800-424-6723, option 2
Email: Support@bio-rad.com (U.S./Canada Only)
For technical assistance outside the U.S. and Canada, contact your local technical support office or click theContact us link at www.bio-rad.com.

NoticeNo part of this publication may be reproduced or transmitted in any form or by any means, electronic ormechanical, including photocopy, recording, or any information storage or retrieval system, without permission
in writing from Bio-Rad.
Bio-Rad reserves the right to modify its products and services at any time. This guide is subject to change
without notice. Although prepared to ensure accuracy, Bio-Rad assumes no liability for errors or omissions, orfor any damage resulting from the application or use of this information.
BIO-RAD, HARD-SHELL, and MICROSEAL are trademarks of Bio-Rad Laboratories, Inc. in certain
jurisdictions.
SYBR is a trademark of Thermo Fisher Scientific Inc. Bio-Rad Laboratories, Inc. is licensed to sell reagents
containing SYBR Green I for use in real-time PCR, for research purposes only.
EvaGreen is a trademark of Biotium, Inc. Bio-Rad Laboratories, Inc. is licensed by Biotium, Inc. to sell
reagents containing EvaGreen dye for use in real-time PCR, for research purposes only.
All trademarks used herein are the property of their respective owner.
Copyright © 2022 by Bio-Rad Laboratories, Inc. All rights reserved.

Revision History

Revision History
Document
CFX Opus Dx Real-Time PCR

Date

Description of Change

January 2021

Ver A, Initial Release

System Operation Manual(Doc ID #10000135538)
CFX Opus Dx Real-Time PCR

May 2021

System Operation Manualn Update to environment
requirements
n Update to descriptions of(Doc ID #10000135538)

LEDs on the LED signal statusbar
CFX Opus Dx Real-Time PCR

May 2022

System Instrument Guiden Updated to support CFX Opus
Deepwell Dx
n Updated Symbols Lexicon(Doc ID #10000135538)

Table
CFX Opus Dx Real-Time PCR
System Operation Manual(Doc ID #10000135538)

October 2022

n Correction to CFX Opus 384
Dx Ramp Raten Correction to Instruments,
Parts, and Accessories
n Add cybersecurity note to
Introduction and Maintenanceand Troubleshooting

Operation Manual | iii

Intended Use
The CFX Opus Dx Real-Time PCR System™ with CFX Maestro Dx SE Software™ is intended to perform
fluorescence-based PCR to detect and quantitative nucleic acid sequences. The system and software areintended for in vitro diagnostic use by trained laboratory technicians. The systems are intended to be usedwith third-party diagnostic nucleic acid tests, which have been manufactured and labeled for diagnostic
purposes.

Symbols Lexicon

Manufacturer

Lot number

Use byFor In Vitro Diagnostic Use

Temperature limit

Catalog number

Consult instructions for use

Number of tests

For use with

Serial number

Prescription use only

Contains latexiv | CFX Opus 96 Dx, CFX Opus 384 Dx, and CFX Opus Deepwell Dx Real-Time PCR Systems

Translations

CE Marking - Regulation(EU) 2017/746 IVDR

Translations
Product documents may be provided in additional languages on electronic media.

Operation Manual | v

vi | CFX Opus 96 Dx, CFX Opus 384 Dx, and CFX Opus Deepwell Dx Real-Time PCR Systems

Table of Contents
Revision Historyiii

Intended Use

iv

Symbols Lexicon

iv

Translationsv

Safety and Regulatory Compliance13

Safety Warning Labels

13

Safety and Regulatory Compliance

15

Safety Compliance

15

Electromagnetic Compatibility (EMC)16

EMC Warnings and Notes

16

Environment Requirements

18

Hazards

19

Biohazards

19

Chemical Hazards

20

Explosive or Flammability Hazards

20

Electrical Hazards

20

Transport

21

Battery21

Disposal

21

Chapter 1 Introduction

23

Main Features

23

Performance Specifications

24

Sample Block Performance Specifications

24

Optical Detection Performance Specifications

25

Finding Out More

Chapter 2 Setting Up the CFX Opus Dx Real-Time PCR System
Site Requirements
Bench Space Requirements

25

27
27
27

Operation Manual | vii

Table of Contents

Environment Requirements

28Power Requirements

28

Network Requirements

29

System Overview

30

Front View

30

Back View

33

Unpacking the System

34

Packaged Instrument Specifications

34

Unpacking the System

36

Connecting the Power and Communication Cables

40

Removing the Shipping Screw

41

Logging In to the CFX Opus Dx Real-Time PCR System

44

Starting the CFX Opus Dx Real-Time PCR System

45

Creating CFX Opus Dx Real-Time PCR System User Accounts

46

Logging In to the CFX Opus Dx Real-Time PCR System

47

Loading the Sample Block49

Shutting Down the CFX Opus Dx Real-Time PCR System

51

Chapter 3 Configuring the CFX Opus Dx Real-Time PCR System

53

Touch Screen Overview

54

Software Files

56

Tools Screen

57

User Tools Screen Options

57

Admin Tools Screen Options

59

Renaming the CFX Opus Dx Real-Time PCR System

61

Setting the Time Zone on the CFX Opus Dx Real-Time PCR System

62

Setting Up a Network Connection on the CFX Opus Dx Real-Time PCR System

63

Setting Up Email Service

68

Changing Email Servers

69

Connecting to a Computer Running CFX Maestro Dx SE Software

69

Calibrating New Dyes

71

Managing Personal User Accounts

72

Setting User Passwords

72

Setting Up Your Email Address

74

Setting Up a Connection to a Shared Network Drive

75

viii | CFX Opus 96 Dx, CFX Opus 384 Dx, and CFX Opus Deepwell Dx Real-Time PCR Systems

Table of Contents

Managing User Accounts

77

Setting the Admin Password

77

Resetting User Passwords

78

Deleting User Accounts

80

Chapter 4 Creating Protocols

81

Parameters and Ranges for Protocol Steps

82

Creating a Protocol

84

Modifying the Settings in a Protocol Step

89

Changing Target Temperature and Hold Time89

Adding or Removing a Temperature Gradient91

Adding or Removing the Ramp Rate

92

Adding or Removing a Temperature Increment

93

Adding or Removing an Extend Time Option

95

Adding or Removing a Beep Alert

95

Changing Parameters in a GOTO Step

96

Setting Sample Volume and Lid Temperature

98

Sample Volume and Temperature Control Modes

98

Lid Temperature

99

Editing a Protocol

100

Editing a Protocol

101

Adding a Protocol Step

104

Deleting a Protocol Step

105

Renaming a Protocol

105

Saving an Edited Protocol

105

Chapter 5 Running Protocols

107

Running a Protocol

108

Running a Saved Protocol

108

Running a Completed CFX Opus Dx Real-Time PCR System Run

112

Monitoring a Run

114

Pausing a Run

115

Skipping Steps in a Protocol

116

Stopping a Run

116

Extracting and Editing a Protocol from a Run

116

Operation Manual | ix

Table of Contents

Chapter 6 Managing Files and Folders

119

The File Browser Screen

120Managing Files and Folders

122

Managing Files on the CFX Opus Dx Real-Time PCR System

123

Managing Folders on the CFX Opus Dx Real-Time PCR System

125

Backing Up and Restoring Files and Folders
File Storage

Appendix A Bio-Rad’s Real-Time PCR Detection Systems and CFX Maestro Dx SE
Software Catalog Numbers
Warranty

127
128

129
129

Appendix B Recommended Plastic Consumables

131

Plastic Consumables for CFX Opus 384 Dx Systems

131

Plastic Consumables for CFX Opus 96 Dx and CFX Deepwell Dx Systems

131

Plastic Consumables for CFX Opus 96 Dx Systems

131

Plastic Consumables for CFX Opus Deepwell Dx Systems

132

Plate Seals and Plate Sealer

132

Appendix C Maintenance and Troubleshooting

133

Cleaning and Maintaining the CFX Opus Dx Real-Time PCR System

133

Maintaining Sufficient Air Flow138

Testing for Sufficient Air Flow138

Fixing Insufficient Air Flow138

Replacing Fuses

139

Upgrading Software and Firmware on CFX Opus Dx Real-Time PCR Systems

143

Shutting Down the CFX Opus Dx Real-Time PCR System

145

Returning the CFX Opus Dx Real-Time PCR System to Bio-Rad

146

Installing the Shipping Plate and Screw
Troubleshooting CFX Opus Dx Real-Time PCR Systems

146
149

Recovering Files

149

Viewing and Exporting Log Files149

Troubleshooting Issues

151

Appendix D Bio-Rad Free and Open-Source Notices for PCR Products
Software Notices
M2Mqtt (paho.mqtt.m2mqtt)

x | CFX Opus 96 Dx, CFX Opus 384 Dx, and CFX Opus Deepwell Dx Real-Time PCR Systems

153
154
154

Table of Contents

Standard Open License Text
EPL 1.0

Appendix E References

158
158

165

Operation Manual | xi

Table of Contentsxii | CFX Opus 96 Dx, CFX Opus 384 Dx, and CFX Opus Deepwell Dx Real-Time PCR Systems

Safety Warning Labels

Safety and Regulatory Compliance
Bio-Rad’s CFX Opus Dx Real-Time PCR Systems (known in this guide as the CFX system) heat and coolvery quickly during operation. Bio-Rad strongly recommends that you follow the safety specifications listed inthis chapter and throughout this guide.
Note: Use only Bio-Rad–supplied USB cables (catalog #12012942) when using the CFX Opus Dx
system.

Safety Warning Labels
Warning labels posted on the CFX Opus Dx system and in this manual warn you about sources of injury or
harm. Table 1 defines each safety warning label.
Table 1. General safety warnings

Icon

Meaning
Operating the CFX Opus Dx system before reading this manual can constitute a
personal injury hazard. The use of this instrument in a manner not specified in thismanual or by Bio-Rad may result in the protection features of the instrument
becoming impaired or disabled.
There are no biohazards or radioactive hazards associated with the CFX Opus Dx
system itself. These hazards only become a concern when they are introduced into
the system via the samples being tested. When handling biohazardous orradioactive samples, adhere to the recommended precaution s and guidelines
specific to your laboratory and location. These guidelines should include cleaning,monitoring, and disposal methods for the hazardous materials you are using.
In addition, as identified above, there is a small risk of explosion, or of expulsion ofliquids or vapors from the sample containers. When working with hazardous
materials the risk of injury from expelled material is compounded with the risk thatthe hazardous material themselves could be dispersed in and around the
instrument. Users should take appropriate precautions for such a situation.

Operation Manual | 13

Safety and Regulatory Compliance

Table 1. General safety warnings, continued

Icon

Meaning
The CFX Opus Dx system operates at temperatures high enough to cause serious
burns. Always allow the sample block to return to room temperature before opening
the lid and removing samples. Even after the sample block has cooled, thesurrounding areas as well as the heater plate can remain hot for quite some time. In
situations where there is not sufficient time to allow the instrument to cool, the useof protective equipment such as thermal gloves or “oven mitts” is recommended.
The safety and performance of any system incorporating a CFX Opus Dx system issolely the responsibility of the assembler of the system.

The CFX Opus Dx system can become hot enough during the course of normal
operation to cause liquids in the samples to boil or vaporize, pressurizing thesample containers. There is the possibility that the sample containers could fail,leading to leaks, fluid spray, or explosive rupture and expelling vapors or liquids inand around the instrument.
Users should always operate the instrument with the lid closed or wear safety
goggles, thermal gloves, and other personal protection equipment during operation
to avoid injury. Opening the instrument while samples are still hot, such as after
aborting a run, can allow pressurized containers to leak, spray, or spurt liquid.
Always allow the samples to cool before opening the lid.
Users should never run a reaction with a lid or seal that is open, loose, punctured,or otherwise damaged because it will increase the likelihood of a dangerous
rupture or explosion.
Users should never run a reaction with volatile reagents that could increase thelikelihood of a dangerous rupture or explosion.

14 | CFX Opus 96 Dx, CFX Opus 384 Dx, and CFX Opus Deepwell Dx Real-Time PCR Systems

Safety and Regulatory Compliance

Safety and Regulatory Compliance
Safety Compliancen

IEC 61010-1:2010 Safety requirements for electrical equipment for measurement, control, andlaboratory use, Part 1: General requirementsn

IEC 61010-2-010:2019 Safety requirements for electrical equipment for measurement, control andlaboratory use — Part 2-010: Particular requirements for laboratory equipment for the heating ofmaterialsn

IEC 61010-2-081:2019 Safety requirements for electrical equipment for measurement, control andlaboratory use — Part 2-081: Particular requirements for automatic and semi-automatic laboratory
equipment for analysis and other purposesn

IEC 61010-2-101:2018 Safety requirements for electrical equipment for measurement, control andlaboratory use — Part 2-101: Particular requirements for in vitro diagnostic (IVD) medical equipmentn

CAN/CSA-C22.2 NO. 61010-1-12:2018 Safety requirements for electrical equipment formeasurement, control, and laboratory use, Part 1: General Requirementsn

CAN/CSA-C22.2 NO. 61010-2-010:19 Safety requirements for electrical equipment formeasurement, control, and laboratory use, Part 2-010: Particular requirements for laboratory
equipment for the heating of materialsn

CAN/CSA-C22.2 NO. 61010-2-081:19 Safety requirements for electrical equipment formeasurement, control, and laboratory use, Part 2-081: Particular requirements for automatic andsemi-automatic laboratory equipment for analysis and other purposesn

CSA-C22.2 NO. 61010-2-101:19 Safety requirements for electrical equipment for measurement,
control and laboratory use — Part 2-101: Particular requirements for in vitro diagnostic (IVD) medical
equipmentn

EN 61010-1:2010 Safety requirements for electrical equipment for measurement, control, andlaboratory use, Part 1: General requirementsn

EN 61010-2-010:2014 Safety requirements for electrical equipment for measurement, control andlaboratory use — Part 2-010: Particular requirements for laboratory equipment for the heating ofmaterials

Operation Manual | 15

Safety and Regulatory Compliancen

EN 61010-2-081:2015 Safety requirements for electrical equipment for measurement, control andlaboratory use — Part 2-081: Particular requirements for automatic and semi-automatic laboratory
equipment for analysis and other purposesn

EN 61010-2-101:2017 Safety requirements for electrical equipment for measurement, control andlaboratory use — Part 2-101: Particular requirements for in vitro diagnostic (IVD) medical equipmentn

UL 61010-1:2012 Safety requirements for electrical equipment for measurement, control andlaboratory use — Part 1: General Requirementsn

UL 61010-2-010:2019 Safety requirements for electrical equipment for measurement, control andlaboratory use — Part 2-010: Particular requirements for laboratory equipment for the heating ofmaterialsn

UL 61010-2-081:2019 Safety requirements for electrical equipment for measurement, control andlaboratory use — Part 2-081: Particular requirements for automatic and semi-automatic laboratory
equipment for analysis and other purposesn

UL 61010-2-101:19 Safety requirements for electrical equipment for measurement, control andlaboratory use — Part 2-101: Particular requirements for in vitro diagnostic (IVD) medical equipment

Electromagnetic Compatibility (EMC)n

IEC 61326-1:2020 Electrical equipment for measurement, control and laboratory use — EMC
requirements — Part 1: General requirements. Tested as a Class A devicen

IEC 61326-2-6:2012 Electrical equipment for measurement, control and laboratory use — EMC
requirements — Part 2–6: Particular requirements – In vitro diagnostic (IVD) medical equipmentn

EN 61326-1:2013 Electrical equipment for measurement, control and laboratory use — EMC
requirements — Part 1: General requirements. Tested as a Class A devicen

EN 61326-2:-6:2013 Electrical equipment for measurement, control and laboratory use — EMC
requirements — Part 2–6: Particular requirements – In vitro diagnostic (IVD) medical equipmentn

FCC Part 15, Subpart B, Sections 15.107 and 15.109. Tested as a Class A digital devicen

CAN ICES-003v6:2019 Interference-causing equipment standard, information technology equipment(including digital apparatus) — Limits and methods of measurement. Tested to Class A limits

EMC Warnings and NotesnWarning: Changes or modifications to this unit, not expressly approved by Bio-Rad, could void theuser’s authority to operate the equipment.

16 | CFX Opus 96 Dx, CFX Opus 384 Dx, and CFX Opus Deepwell Dx Real-Time PCR Systems

Safety and Regulatory CompliancenNote: This equipment has been tested and found to comply with the limits for a Class A digital device,pursuant to part 15 of the FCC Rules. These limits are designed to provide reasonable protection
against harmful interference when the equipment is operated in a commercial environment. Thisequipment generates, uses, and can radiate radio frequency energy and, if not installed and used inaccordance with the instruction manual, may cause harmful interference to radio communications.
Operation of this equipment in a residential area is likely to cause harmful interference, in which casethe user will be required to correct the interference at their own expense.

nNote regarding FCC compliance: Although this instrument has been tested and found to comply
with Part 15, Subpart B of the FCC Rules for a Class A digital device, please note that thiscompliance is voluntary, for the instrument qualifies as an “exempted device” under 47 CFR 15.103(c), in regard to the cited FCC regulations in effect at the time of manufacture.

nNote regarding cables: This instrument was tested for EMC compliance using specially designed
USB cables, which are supplied with the instrument. These cables, or Bio-Rad authorized
replacements, must be used with this instrument to ensure continued compliance with the EMC
emissions limits.

Operation Manual | 17

Safety and Regulatory Compliance

Environment Requirements
The CFX Opus Dx system has been designed to be safely operated under the environmental conditions
listed in the following table.
Table 2. CFX Opus Dx Real-Time PCR System environment requirements

Parameter

Specification

Environment

Indoor use only

Operating altitude

Up to 2,000 meters above sea level

Ambient room temperature

15–31°C*
59–88°F

Transport and storage temperature–20° to 60°C**–4 to 140°F

Relative humidity

20% to 80% (noncondensing)***Operating power

100 to 240 VAC, 50/60 Hz, 850 W Max

Mains supply voltage fluctuation±10%

Maximum power usage<850 watts

Fuses

10 A, 250 V, 5 x 20 mm, fast blow (qty. 2)

Overvoltage category

II

Pollution degree2* Operating the instrument outside of this temperature range may not meet performance specifications.
A room temperature between 5–40°C (41–104°F) is considered safe.
** Store and transport the instrument in its shipping container to meet these temperature conditions.
*** Operating the instrument at 4⁰C should be limited to 18 hours at these conditions. Holds at 4⁰C canbe performed for up to 72 hours if humidity is 20% to 60% (noncondensing).

18 | CFX Opus 96 Dx, CFX Opus 384 Dx, and CFX Opus Deepwell Dx Real-Time PCR Systems

Hazards

Hazards
The CFX Opus Dx system is designed to operate safely when used in the manner prescribed by the
manufacturer. If thesystem or any of its associated components is used in a manner not specified by the
manufacturer, the inherent protection provided by the instrument may be impaired. Bio-Rad is not liable
for any injury or damage caused by the use of this equipment in any unspecified manner, or bymodifications to the instrument not performed by Bio-Rad or an authorized agent. Service of the CFX
Opus Dx system should be performed only by trained Bio-Rad personnel.

Biohazards
The CFX Opus Dx system is a laboratory product. However, if biohazardous samples are present, adhere
to the following guidelines and comply with any local guidelines specific to your laboratory and location.
Note: No biohazardous substances are exhausted during normal operations of this instrument.

General Precautionsn

Always wear a laboratory coat, laboratory gloves, and safety glasses with side shields or goggles.

n

Keep your hands away from your mouth, nose, and eyes.

nCompletely protect any cut or abrasion before working with potentially infectious materials.

nWash your hands thoroughly with soap and water after working with any potentially infectious
material before leaving the laboratory.

n

Remove wristwatches and jewelry before working at the bench.

nStore all infectious or potentially infectious material in unbreakable leak-proof containers.

nBefore leaving the laboratory, remove protective clothing.

n

Do not use a gloved hand to write, answer the telephone, turn on a light switch, or touch anything that
other people may touch without gloves.

n

Change gloves frequently. Remove gloves immediately when they are visibly contaminated.

n

Do not expose materials that cannot be properly decontaminated to potentially infectious material.

nUpon completion of an operation involving biohazardous material, decontaminate the work area with
an appropriate disinfectant (for example, a 1:10 dilution of household bleach).

Operation Manual | 19

Safety and Regulatory Compliance

Surface Decontamination
WARNING! To prevent electrical shock, always turn off and unplug the instrument prior
to performing decontamination procedures.

The following areas can be cleaned with any hospital-grade bactericide, virucide, or fungicide disinfectant:nOuter lid and chassisn

Inner sample block surface and sample block wellsnControl panel and display

To prepare and apply the disinfectant, refer to the instructions provided by the product manufacturer.
Always rinse the sample block and sample block wells several times with water after applying adisinfectant. Thoroughly dry the sample block and sample block wells after rinsing with water.
Important: Do not use abrasive or corrosive detergents or strong alkaline solutions. These agentscan scratch surfaces and damage the sample block, resulting in loss of precise thermal control.

Disposal of Biohazardous Material
Dispose of the following potentially contaminated materials in accordance with laboratory local, regional,
and national regulations:nClinical samples

nReagents

n

Used reaction vessels or other consumables that may be contaminatedChemical Hazards
The CFX Opus Dx system contains no potentially hazardous chemical materials.

Explosive or Flammability Hazards
The CFX Opus Dx system poses no uncommon hazard related to flammability or explosion when used ina proper manner as specified by Bio-Rad Laboratories.

Electrical Hazards
The CFX Opus Dx system poses no uncommon electrical hazard to operators if installed and operated
properly without physical modification and connected to a power source of proper specification.

20 | CFX Opus 96 Dx, CFX Opus 384 Dx, and CFX Opus Deepwell Dx Real-Time PCR Systems

Transport

Transport
Before moving or shipping the CFX Opus Dx system, decontamination procedures must be performed.
Always move or ship the system in a separate container in the Bio-Rad-supplied packaging material,
which protects the system from damage.
For information about transporting the system and to request the appropriate packaging material, contact
your local Bio-Rad office.

Battery
The CFX Opus Dx system uses one 3 V lithium-metal coin cell battery to maintain time settings in theevent of AC power loss. If the time does not remain set after the unit is turned off, it may be an indicationthat the batteries are getting weak.
WARNING! Do not attempt to change the batteries. They are not user serviceable.
Instead, contact Bio-Rad Technical Support for assistance.

For the State of California, USA onlynPerchlorate material — Lithium batteries contain perchlorate material; special handling may apply.
See www.dtsc.ca.gov/hazardouswaste/perchlorate.

Disposal
The CFX Opus Dx systems contain electrical materials; they should not be disposed of as unsorted waste
and must be collected separately, according to European Union Directive 2012/19/EU on waste electricaland electronic equipment — WEEE Directive. Before disposal, contact your local Bio-Rad representative
for country-specific instructions.

Operation Manual | 21

Safety and Regulatory Compliance

22 | CFX Opus 96 Dx, CFX Opus 384 Dx, and CFX Opus Deepwell Dx Real-Time PCR Systems

Main Features

Chapter 1 Introduction
The CFX Opus Dx Real-Time PCR Systems (known in this guide as the CFX Opus Dx system) are
real-time PCR systems with an integrated 96-well or 96-well large volume sample block, depending on thesystem.
Thermal cyclers are essential laboratory equipment for laboratories that run polymerase chain reaction(PCR) for sequencing, cloning, gene expression studies, mutagenesis, and many other applications.
Bio-Rad’s CFX Opus Dx Real-Time PCR Systems are real-time PCR detection systems provide excellent
thermal performance for two-target multiplex PCR and routine detection of single fluorophore
experiments. The fully adjustable heated lid supports a wide range of vessels and sealers, including lowprofile and standard-height PCR plates.
This guide explains how to set up and use the CFX Opus Dx system to perform sensitive quantitative PCR
experiments, manage users, and connect to external data storage on the network and to Bio’s BR.io
application.
Important: Cybersecurity is the protection of assets in cyberspace from cyberattacks. Cybersecurity
is Bio-Rad’s ability to secure its people, information, systems, and reputation in cyberspace.
Cyberspace is the always-on, technologically interconnected world; it consists of people,
organizations, information, and technology.
Fast reaction is important with cybersecurity issues! If you suspect that there may be a cybersecurity
issue concerning your instrument or that cybersecurity has been breached at your site, contact your
Bio-Rad representative for technical support immediately.

Main Features
The main features of the CFX system include:n

WLAN Ethernet network compatibility enables connectivity to your internal network for unlimited data
access and storage on shared network drivesn

USB drive compatibility provides an optional medium for protocol transfer and data storagen

USB ports enable direct connectivity to a computer running CFX Maestro Dx SE SoftwarenProgrammable temperature gradient to quickly and easily identify optimal annealing temperatures

Operation Manual | 23

Chapter 1 Introduction

Performance Specifications
CFX Opus Dx system components provide sensitive detection for precise quantification and target
discrimination. The tables in this section list the sample block and optical detection performance
specifications for the CFX Opus 96 Dx, CFX Opus 384 Dx , and CFX Opus Deepwell Dx systems.

Sample Block Performance Specifications
Table 3. CFX Opus Dx Real-Time PCR System sample block specifications
Item

VolumeSpecification
CFX Opus 96 Dx
Systems

CFX Opus 384 Dx
Systems

CFX Opus
Deepwell Dx
Systems

1–50 µl1–30 µl1–125 µl(10–50 µl(5–30 µl(10–125 µl

Recommended)

Recommended)

Recommended)

Maximum ramp rate

5°C/sec

2.5°C/sec

2.5°C/sec

Average ramp rate

3.3°C/sec

2.0°C/sec

2.0°C/sec

The following specifications apply to all three instruments
Lid temperature

30–110°C

Heating and coolingmethodPeltierTemperature range

4–100°C

Increment-10°C to 10°C/cycle

Gradient
Operational range

30–100°C

Programmable span

1–24°C

Temperature accuracy±0.2°C of programmed target at 90°C

Temperature uniformity±0.3°C well-to-well within 10 sec of arrival at 90°C

24 | CFX Opus 96 Dx, CFX Opus 384 Dx, and CFX Opus Deepwell Dx Real-Time PCR Systems

Finding Out More

Optical Detection Performance Specifications
Table 4. CFX Opus Dx Real-Time PCR System optical detection specifications
Item

Specification
CFX Opus 96 Dx and
CFX Opus Deepwell Dx
Systems

CFX Opus 384 Dx Systems

Excitation

6 filtered LEDs

5 filtered LEDs

Detection

6 filtered photodiodes

5 filtered photodiodes

450-730 nm

450-690 nm

5 targets per well

4 targets per well

12 sec<20 sec

3 sec

8 sec

Yes

Yes

Range of excitation/emission
wavelengths
Multiplex analysis
Scan time

All channels
Single-channel fast scan
FRET
Sensitivity
Dynamic range

Detects 1 copy of target sequence in human genomic DNA
10 orders of magnitude

Finding Out More
The CFX Opus Dx Real-Time PCR System web site (bio-rad.com/CFXOpus) provides access to technicalnotes, manuals, product information, and technical support. This site also provides many technicalresources on a wide variety of methods and applications related to real-time PCR.

Operation Manual | 25

Chapter 1 Introduction

26 | CFX Opus 96 Dx, CFX Opus 384 Dx, and CFX Opus Deepwell Dx Real-Time PCR Systems

Chapter 2 Setting Up the CFX Opus Dx Real-Time
PCR System
This chapter explains how to set up the CFX Opus Dx system at your site.
Tip: Before setting up the CFX Opus Dx system, familiarize yourself with the system and its sample
block, ports, and accessories.

Site Requirements
The tables in this section list the bench space and power requirements necessary to successfully installand use the CFX Opus Dx system. For weight and dimensions of the packaged instrument, see Packaged
Instrument Specifications on page 34.
Note: Install your CFX Opus Dx system on a flat, dry surface with sufficient cool airflow for it to run
properly.

Bench Space Requirements
Caution: The CFX Opus Dx system requires at least 10 cm behind and at
least 5 cm along one side or the top to allow exhaust air to flow properly.

Additionally, ensure you provide sufficient space around the system to disconnect the power cord or toaccess the power switch in case of an emergency.
The lab bench on which you plan to install the CFX Opus Dx system must support its width, depth, height,
and weight. Table 5 lists the specifications of the CFX Opus Dx system to ensure proper installation.
Note: If you plan to connect the CFX Opus Dx system to the computer running CFX Maestro Dx SE
Software, ensure during setup that you have sufficient space near the system for the computer.

Operation Manual | 27

Chapter 2 Setting Up the CFX Opus Dx Real-Time PCR System

Table 5. CFX Opus Dx Real-Time PCR System dimensions and weight

Item

Specification

Dimensions

W: 13 in; 33 cm
D: 22 in; 56 cm
H: 14 in; 36 cm

Weight48 lb; 22 kg

Environment Requirements
For information about environment requirements See Environment Requirements.

Power Requirements
Power to the CFX Opus Dx system must be stable and within specifications to ensure proper operation.
The power cord connected to the power inlet port must be rated for 10 amps or more.
Table 6. CFX Opus Dx Real-Time PCR System power requirements

Item

Specification

Number of power sockets

n One socket for the CFX Opus Dx systemn (Optional) One socket for the computerrunning CFX Maestro Dx SE Software

28 | CFX Opus 96 Dx, CFX Opus 384 Dx, and CFX Opus Deepwell Dx Real-Time PCR Systems

Site Requirements

Network Requirements
The CFX Opus Dx system supports connectivity through USB.
Table 7. CFX Opus Dx Real-Time PCR System networking requirements

Item

Specification

Ethernet port

10/100 BASE-T (RJ45)*

USB ports

USB 2.0 type A (two on rear panel, one on front panel)USB 2.0 type B (one on rear panel)

Operation Manual | 29

Chapter 2 Setting Up the CFX Opus Dx Real-Time PCR System

System Overview
The illustrations in this section display the main components of the CFX Opus Dx system.

Front View

LEGEND
1. Touch screen display

2. Sample block

3. Retractable lid (partially retracted)

4. LED system status bar

5. Air intake vents

6. USB A port

Detailsn

Touch screen display — provides access to all functions necessary to create and run protocols.

n

Sample block — holds the 96-well, 384-well, or Deepwell plate, depending on the instrument.

nRetractable lid — provides access to the sample block.
Note: The CFX Opus Dx system does not have a manual open/close button on the lid. To open
or close the lid, use the button on the Home screen, Run Setup screen, or Run Status screen, or
use the lid control in CFX Maestro Dx SE Software.

30 | CFX Opus 96 Dx, CFX Opus 384 Dx, and CFX Opus Deepwell Dx Real-Time PCR Systems

System Overviewnn

LED system status bar — indicates system status:oGreen (constant) — run is in progress.

oGreen (flashing) — run is paused.

oBlue (flashing) — run has completed (flashes until lid is opened).

o

Red (flashing) — system error.

oOFF — system is idle (not executing a run, lid not moving) or system is shut down.

Air intake vents — allow the system to heat and cool quickly.
Important: Keep all air vents clean and clear of obstruction. Do notinsert any object in the air vents at any time. Fans or other internalmoving parts may collide with the object and cause personal injury
or damage the system. Conductive objects could contact internal
circuitry and cause damage to the system.

n

USB A port — connects the CFX Opus Dx system to a USB drive, mouse, keyboard, or barcode
scanner.

Special Considerations Regarding the CFX Opus Dx Real-Time PCR System Touch
ScreenThe following are special considerations regarding the CFX Opus Dx system’s touch screen. If you haveany questions regarding the touch screen, contact Bio-Rad Technical Support.
WARNING! If any liquid leaks out of a damaged glass cell and comes in contact with yourskin, wash thoroughly with soap and water.

Notes:n

A strong incident light shining on the touch screen for extended periods of time may degrade thequality and performance of the display.

n

Do not expose the touch screen to strong ultraviolet rays or direct sunlight for long periods of
time.

n

Do not touch or scratch the surface of the touch screen with any hard object.

Operation Manual | 31

Chapter 2 Setting Up the CFX Opus Dx Real-Time PCR Systemn

The touch screen self-calibrates the first few seconds after turning on the instrument. During thisprocess, do notoTouch the surface of the touch screenoPlace your hands near the surface of the touch screen

If it cannot successfully calibrate during system initialization, the touch screen might not work
properly for some time. If the problem persists, turn the system off and on or contact Bio-Rad
Technical Support for assistance.

32 | CFX Opus 96 Dx, CFX Opus 384 Dx, and CFX Opus Deepwell Dx Real-Time PCR Systems

System Overview

Back View

LEGEND
1. Power input

2. Power switch

3. Fuses

4. Cooling vents

5. USB Type A ports

6. USB Type B port

7. Ethernet port

Detailsn

Power input — connects to AC power.

nPower switch — turns on or off power to the CFX Opus Dx system.

nFuses — provides access to the fuses.

n

Cooling vents — cools the CFX Opus Dx system.
Important: Do not block the cooling vents. For optimal operation, ensure that air can circulate
behind the CFX Opus Dx system.

n

USB type A ports — transfer data to and from a USB flash drive or connect a USB mouse,keyboard, CFX Opus Dx system WiFi adaptor, or barcode scanner.

n

USB type B port — connects the CFX Opus Dx system to a computer running CFX Maestro Dx SE
Software.

n

Ethernet port — connects the CFX Opus Dx system to your network.

Operation Manual | 33

Chapter 2 Setting Up the CFX Opus Dx Real-Time PCR System

Unpacking the System
This section explains how to properly unpack the CFX Opus Dx system. Read this section before you
begin.
Caution: The packaged CFX Opus Dx system weighs approximately 57 lb (26 kg). Bio-Rad strongly
recommends that you use a pallet jack to move the instrument from the shipping dock to thelaboratory.
Important: Use proper lifting techniques when moving and lifting the
instrument to prevent damage to the instrument and personal injury.
Bio-Radrecommends that two or more people lift the instrument.

Packaged Instrument Specifications
Table 8 lists the specifications of the packaged CFX Opus Dx system. For information about bench space
specifications, see Site Requirements on page 27.
Table 8. Specifications for the packaged CFX Opus Dx Real-Time PCR System

Parameter

Specification

Weight57 lb; 26 kg

Dimensions

Depth: 28 in; 71 cm
Width: 19 in; 48 cm
Height: 19 in; 48 cm

34 | CFX Opus 96 Dx, CFX Opus 384 Dx, and CFX Opus Deepwell Dx Real-Time PCR Systems

Unpacking the System

The image below depicts the CFX Opus Dx system instrument inside its packaging.

Operation Manual | 35

Chapter 2 Setting Up the CFX Opus Dx Real-Time PCR System

Unpacking the System
Install the CFX Opus Dx system on a flat, dry surface with sufficient cool airflow to run properly. The
AC power cord is approximately 5’ in length. Ensure you have sufficient access to the power outlet before
you begin.
Note: Ensure that there is enough clear space on the lab bench for your instrument plus additional
space to maneuver it while installing cables and accessories. If you plan to operate the system via
CFX Maestro Dx SE software, ensure you have space on the lab bench for the computer running thesoftware.
Caution: When handling the instrument, do not grip the LCD screen or retractable lid. To lift the
instrument, position your hands underneath the right and left sides of the instrument.

To unpack the system
1.

Ensure that the path from the shipping dock to the laboratory is clear of obstacles and canaccommodate the packaged CFX Opus Dx system and a pallet jack.

2.

Using a pallet jack, move the instrument container from the shipping dock to the laboratory.
Important: Bio-Rad strongly recommends that you do NOT use a hand truck to move thepackaged instrument.

3.

Release the instrument container next to the lab bench.

4.

Using two people, lift and place container onto the lab bench.

5.

With scissors or a box cutter, cut and remove the exterior straps that secure the container top to thebase.
Tip: The exterior straps are very tight. Hold the straps securely while cutting to prevent injury.

36 | CFX Opus 96 Dx, CFX Opus 384 Dx, and CFX Opus Deepwell Dx Real-Time PCR Systems

Unpacking the System

6.

Remove the plastic clips on the bottom corners by firmly pinching the tabs together and pulling theclips straight out.

7.

Lift the large container top up and out of the base and place it to the side.

You see the CFX Opus Dx system wrapped in plastic sheeting and inserted into the foam packing
structure.

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Chapter 2 Setting Up the CFX Opus Dx Real-Time PCR System

8.

Remove the top foam insert and place it to the side.

9.

Standing in front of the instrument, fold down the front of the cardboard base.

38 | CFX Opus 96 Dx, CFX Opus 384 Dx, and CFX Opus Deepwell Dx Real-Time PCR Systems

Unpacking the System

10. While another person holds the base, grasp the cardboard tray and slide the instrument completely
out of the base.

11. Using the lift points first on one side of the instrument and then the other, gently lift the instrument,
remove the foam inserts, and place them to the side.
12. Using two people, carefully lift the instrument and remove the cardboard tray.
13. Slide the plastic cover toward the back of the instrument to remove.
14. Inspect the instrument for any damage.
Important: If you observe any damage to the system, do not continue.
Instead, contact Bio-Rad Customer Support.

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Chapter 2 Setting Up the CFX Opus Dx Real-Time PCR System

Connecting the Power and Communication Cables
After you unpack the CFX Opus Dx system and install it on the lab bench, you will need to connect thepower cord and (optionally) the communication cables. This section explains how to connect the cord andcables.
Tip: Before connecting the cables, familiarize yourself with the CFX Opus Dx system, its accessory
kit, and power switches.
Important: Ensure you have enough room on the lab bench to reach the power switch on the back of
the system after connecting the power cord and USB Type B and Ethernet cables. Use only the
Bio-Rad-supplied power cord and USB Type B and Ethernet cables.

To connect the CFX Opus Dx system power and communication cables
1.

Locate the accessory kit that shipped with the CFX Opus Dx system.

2.

Remove the AC power cord and USB Type B and Ethernet cables from the accessory kit.
Tip: Store the packing material for future use. If any item is missing or damaged, contact yourlocal Bio-Rad office.

3.

Insert one end of the AC power cord into the power inlet port on back of the system.

4.

Insert the other end of the AC power cord into an available grounded, surge-protected AC outlet.

5.

(Optional) If you plan to connect the CFX Opus Dx system to a computer running CFX Maestro Dx
SE, insert the male end of the supplied USB Type B cable into the USB Type B port on the back of thesystem.

6.

(Optional) If you plan to connect the CFX Opus Dx system to your internal network, insert the
Ethernet cable into the Ethernet port on the back of the system.

40 | CFX Opus 96 Dx, CFX Opus 384 Dx, and CFX Opus Deepwell Dx Real-Time PCR Systems

Removing the Shipping Screw

Removing the Shipping Screw
Important: The CFX Opus Dx system ships with a red shipping screw inserted in the side of the lid tostabilize it during transport. You must remove the shipping screw before you can operate the system.

To remove the shipping screw
1.

Locate the shipping screw plug that ships with the CFX Opus Dx system.
Tip: This might be located in a plastic sheath taped to the front or side of the instrument.

2.

Ensure the power cord is properly inserted into the power input on the back of the instrument.

3.

If you have not yet done so, insert the other end of the power cord into an available grounded, surgeprotected AC outlet.

4.

Press the power switch on the back of the instrument to start the CFX Opus Dx system.

5.

The system recognizes that the shipping screw is inserted and displays a message on the touch
screen instructing you to remove the screw. Tap OK.
The Remove Shipping Screw instructions appear.

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Chapter 2 Setting Up the CFX Opus Dx Real-Time PCR System

6.

To remove the shipping screw, turn it counter-clockwise and then pull it straight out of the accesshole. Set the screw in a safe place.
Caution: Do not insert the shipping screw or any other object in the
shipping screw hole while instrument is operating. Internal moving
parts might collide with the object, which can cause personal injury
or damage the system.

7.

Insert the shipping screw plug into the hole for the shipping screw.
Tip: The plug helps to prevent contamination of internal components.

8.

On the Shipping Screw screen, tap Screw Removed to confirm the screw is removed.

9.

Tap Open Lid to open the lid.

10. Remove the shipping plate from the sample block and set it in a safe place.
Note: Save the screw and plate in a safe and accessible place. You must reinsert the shipping
screw and shipping plate should you need to return the system for any reason.

42 | CFX Opus 96 Dx, CFX Opus 384 Dx, and CFX Opus Deepwell Dx Real-Time PCR Systems

Removing the Shipping Screw

11. On the Shipping Screw screen, tap Close Lid to close the lid.
The CFX Opus Dx system is ready to use and displays the Login screen.

Operation Manual | 43

Chapter 2 Setting Up the CFX Opus Dx Real-Time PCR System

Logging In to the CFX Opus Dx Real-Time PCR System
CFX Opus Dx systems ship with three default users: Admin, Service, and Guest. Users also have theoption to create their own account when first logging in to the system.
Tip: Creating user accounts on the CFX Opus Dx system is optional.
Any user can log in as Guest and access all protocols and runs in the Public folder including the qPCR
files within the default Bio-Rad qPCR folder.
Any user, including the Guest account, can create folders and protocols, edit protocol templates, and run
protocols. When logged in as Guest, users can create subfolders in the Public folder and save their
protocols and run files into the selected folder.
Tip: All folders and files saved into the Public folder are available to all users of the CFX Opus Dx
system.
The CFX Opus Dx system automatically creates a personal folder for each user who creates their own
user account. When logged in, users can create subfolders within their personal folder and save their
protocols and run files into the selected folder.
Note: For the Admin or Service user, all such files are saved into the respective folders. Thesefolders are not accessible to any other user.

44 | CFX Opus 96 Dx, CFX Opus 384 Dx, and CFX Opus Deepwell Dx Real-Time PCR Systems

Logging In to the CFX Opus Dx Real-Time PCR System

Starting the CFX Opus Dx Real-Time PCR System
To start the CFX Opus Dx Real-Time PCR Systemu

If you have not already done so, press the power switch on the back of the instrument to start the CFX
Opus Dx system.
You see the CFX Opus Dx Real-Time PCR System startup screen.

The system performs a series of initialization tests and then displays the Login screen.

Operation Manual | 45

Chapter 2 Setting Up the CFX Opus Dx Real-Time PCR System

Creating CFX Opus Dx Real-Time PCR System User Accounts
Tip: Creating user accounts on the CFX Opus Dx system is optional but highly recommended.
When logged in to the CFX Opus Dx system, you cannCreate and manage a folder structure within a browser environment.

nCreate and edit protocols and then save them to your personal folders.

n

Run a protocol and save the run file to your personal folders.

nDelete protocols and runsin your personal folders.

n

Copy a protocol or run file to a public folder or USB drive.

nConnect to a shared folder on the network to store or access protocol and run files.

nCreate and change your password.

This section explains how to create user accounts on the CFX Opus Dx system.

To create a new user
1.

Do one of the following:nTurn on the CFX Opus Dx system.

n

On the Home screen, tap Logout to log out a currently logged-in user.

The Login list appears.

46 | CFX Opus 96 Dx, CFX Opus 384 Dx, and CFX Opus Deepwell Dx Real-Time PCR Systems

Logging In to the CFX Opus Dx Real-Time PCR System

2.

Tap the Create User icon (3.

Using the alphanumeric keypad that appears, type a user name and then tap OK.

).

The Password dialog appears.
4.

Do one of the following:nEnter and confirm a password using the alphanumeric keypad that appears, and then tap Save
Password.
CFX Opus Dx system passwords can be any combination of alphanumeric characters.
Passwords must be between 4–50 characters.
Tip: Passwords are case-sensitive.

n

Tap Skip Password.

Tip: You can create a password some other time by accessing Tools > User Profile. See Setting
User Passwords on page 72 for more information.
The Home screen appears and displays your user name next to the Logout button.

Logging In to the CFX Opus Dx Real-Time PCR System
When the CFX Opus Dx system starts, the Login list appears and displays the existing users with the mostrecent user at the top.
Important: By default, the Admin account does not have a password. When accessed for the firsttime, Bio-Rad strongly recommends that you create a password for the Admin account and record

Operation Manual | 47

Chapter 2 Setting Up the CFX Opus Dx Real-Time PCR System

the password in a password safe. Resetting a forgotten Admin password requires a phone call to
Bio-Rad Technical Support. See Setting User Passwords on page 72 for more information.

To log in to the Admin account when the CFX Opus Dx system starts
1.

In the Login list, locate and tap Admin.

2.

When prompted, enter the Admin password using the alphanumeric keypad that appears and thentap OK.

To log in to a User account when the CFX Opus Dx system starts
1.

In the Login list, locate and tap your user name.

2.

If prompted, enter your password using the alphanumeric keypad that appears and then tap OK.
Tip: After you create your user account, the keypad does not appear if you did not create apassword.

To log in to the Guest account when the CFX Opus Dx system startsu

In the Login list, locate and tap Guest.
Tip: The keypad does not appear because the Guest account does not have a password.

To change users
1.

On the Home screen, tap Logout to log out the currently logged in user.
The Login list appears.

2.

In the Login list, tap your user name.

3.

If prompted, enter your password using the alphanumeric keypad that appears and then tap OK.
Tip: The keypad does not appear if the user account does not have a password.

To log outu

On the Home screen, tap Logout.

48 | CFX Opus 96 Dx, CFX Opus 384 Dx, and CFX Opus Deepwell Dx Real-Time PCR Systems

Loading the Sample Block

Loading the Sample Block
Bio-Rad strongly recommends that you use only low-profile plates and flat-cap tubes with the CFX Opus
Dx system. Using high-profile plates can crush tubes. Using domed-cap tubes can negatively affect platereads.
For a list of plates and tubes compatible with the CFX Opus Dx system, visit us at or contact your local
Bio-Rad Sales representative.
To ensure uniform heating and cooling of samples, reaction vessels must be in complete contact with thesample block. To ensure adequate contact, do the following:nConfirm that the sample block is clean before loading samples.

nFirmly press the individual tubes, tube strips, or microplates into the block wells.

nWhen using one or a few tubes, use the tube frame or load at least one empty tube in each corner ofthe block to ensure the lid exerts even pressure on individual tubes.

Loading Plates, Tubes and Tube Strips into the Sample Block
Caution: Never run a sample with a lid or seal that is open, loose, punctured, orotherwise damaged. Doing so will increase the likelihood of a rupture, which could cause
injury or contaminate the system.
Important: When running the CFX Opus Dx system, always balance the tube strips or add capped
tubes to the corner wells to ensure the heated lid applies even pressure across the block.

To load plates into the sample block
1.

2.

To open the motorized lid, do one of the following:n

On the Home screen, tap Open Lid.

n

On the Run Setup screen, tap Open Lid.

n

In the Detected Instruments pane of the CFX Maestro Dx SE Software, click Open Lid.

n

In the Detected Instruments pane of the CFX Maestro Dx SE, right click the instrument and click
Open Lid.

n

On the Start Run tab of the Run Setup pane of the CFX Maestro Dx SE, click Open Lid.

Place the microplate, individual tubes, or tube strips with sealed lids in the block.
Important: Ensure that the tubes are completely sealed to prevent leakage.
Tip: For optimal results, load sample volumes of 10–50 µl for the CFX Opus 96 Dx system,
10–125 µl for the CFX Opus Deepwell Dx system, and 5–30 µl for the CFX Opus 384 Dx system.

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Chapter 2 Setting Up the CFX Opus Dx Real-Time PCR System

3.

For accurate data analysis, verify that the orientation of samples in the block is exactly the same as
the orientation of the well contents in CFX Maestro Dx SE.

4.

To close the motorized lid, do one of the following:n

On the Home screen, tap Close Lid.

n

On the Run Setup screen, tap Close Lid.

n

In the Detected Instruments pane in CFX Maestro Dx SE software, click Close Lid.

n

On the Start Run tab of the Run Setup pane of the CFX Maestro Dx SE, click Close Lid.

n

In the Detected Instruments pane of the CFX Maestro Dx SE, right click the instrument and click
Close Lid.

n

In the Run Details pane of the CFX Maestro Dx SE (when right-clicking on the instrument of the
Detected Instruments pane and selecting Run Details), click Close Lid.

Important: Ensure that nothing obstructs the lid when it closes. Although there is a safetymechanism to prevent the lid from closing if it senses an obstruction, do not place anything in theway of the lid before closing.

50 | CFX Opus 96 Dx, CFX Opus 384 Dx, and CFX Opus Deepwell Dx Real-Time PCR Systems

Shutting Down the CFX Opus Dx Real-Time PCR System

Shutting Down the CFX Opus Dx Real-Time PCR System
Important: Follow these instructions to safely and completely shut down the CFX Opus Dx system.

To shut down the CFX Opus Dx system
1.

Ensure that no protocol is running and the system is no longer in use.

2.

If you have not already done so, remove the samples from the block:a.

On the Home screen, tap Open Lid to access the samples.

b.

Remove the samples from the block and then close the lid.

3.

On the Home screen, tap Logout to log out of the system.

4.

On the Login screen, tap Shut Down (5.

When the CFX Opus Dx system has completed the soft shutdown process, press the power switch
on the back of the instrument to power off the system.

) to perform a soft shutdown of the system.

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Chapter 2 Setting Up the CFX Opus Dx Real-Time PCR System

52 | CFX Opus 96 Dx, CFX Opus 384 Dx, and CFX Opus Deepwell Dx Real-Time PCR Systems

Chapter 3 Configuring the CFX Opus Dx RealTime PCR System
After successfully installing the CFX Opus Dx system, you can configure the system according to therequirements at your site. Using the system’s touch screen, the Admin user can perform the following
tasks.
n

Set the CFX Opus Dx system’s time zone and local timenEnable or disable the system’s screen savernRename the systemn

Set up network communicationn

Set up the email servicenConnect the system to a computer running CFX Maestro Dx SE Software

As a CFX Opus Dx system user, you cannCreate your own CFX Opus Dx system log-in accountn

Set or change your passwordn

Set or change your email addressn

Set or change connection to a shared network folder

As a CFX Opus Dx system Guest user, you cann

Set or change your email accountThis chapter explains how to configure the CFX Opus Dx system.

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Chapter 3 Configuring the CFX Opus Dx Real-Time PCR System

Touch Screen Overview
This section provides an overview of the CFX Opus Dx system touch screen features.

LEGEND
1. Connectivity and software version

2. Primary activity menu

3. Instrument details

4. Current logged in user

5. Open/close lid

DetailsnConnectivity and software version — displays the current software version and the type ofoperational connection:oNetwork connection — indicates operational connection to an Ethernet network:– Ethernet network connectiononSoftware version — displays the touch screen software version. To manually install updates,
see Upgrading Software and Firmware on CFX Opus Dx Real-Time PCR Systems on page 143.

Primary activity menu — provides quick access to the primary activities required to create and run
protocols and manage the operation of the CFX Opus Dx system.
o

New Protocol — opens the New Protocol screen in which you can create a new protocol. For
details, see Creating Protocols on page 81.

54 | CFX Opus 96 Dx, CFX Opus 384 Dx, and CFX Opus Deepwell Dx Real-Time PCR Systems

Touch Screen OverviewoFiles — opens the File Browser, where you can manage your files and execute runs. For details
on managing files, see Managing Files and Folders on page 119.

oTools — accesses menus from which users and administrators can perform systemmanagement operations.

o

Run Status — opens the Run Status screen to view the status of the current run.

nInstrument status — identifies the system, its serial number, and current status.

n

Logout action/status — identifies the currently logged in user and enables the user to log out of thesystemoLogout — tap this button to log out of the system. The system then displays the Login list.
Tip: To create a new user account, see Creating CFX Opus Dx Real-Time PCR System
User Accounts on page 46.

onLogged in user — identifies the user currently logged in to the system.

Open/Close Lid — opens or closes the instrument lid.
If the lid is closed, the label is Open Lid. If the lid is open, the label is Close Lid. For details on loadingplates, see Loading the Sample Block on page 49.

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Chapter 3 Configuring the CFX Opus Dx Real-Time PCR System

Software Files
Table 9 lists the CFX Opus Dx system file types.
Table 9. CFX Opus Dx system file types

File Type

Icon

Details

ProtocolContains protocol setup details to perform a PCR run.

Data

Contains the results of an experiment run and PCR analysis.

JSON

A read-only file generated only by CFX Opus Dx systems, thisfile contains the run file data that appear in the details pane in
the File Browser when a run file is selected. This file isgenerated after a run completes. It is exported with the .zpcr
file and saved with the data files when the Save Location iseither a USB drive or a shared network folder.

56 | CFX Opus 96 Dx, CFX Opus 384 Dx, and CFX Opus Deepwell Dx Real-Time PCR Systems

Tools Screen

Tools Screen
From the Tools screen, users and administrators can access a variety of options. These options control
the system. All options available to users are also available to administrators. Only those who log in withan administrator account have access to the Admin options.

User Tools Screen Options
Tip: You do not need to log in with a user account to access the User options. The Guest account canalso access options on the Tools screen.

To access the User Tools screen
1.

On the Home screen, tap Logout, and then log in with your user credentials.

2.

On the Home screen, tap Tools.
The User Tools screen appears.

n

About — view the current software version, serial number, disk space capacity and availability,
as well as total number of run hours and cycles the system has accumulated since the last log
on.

nUser Profile — view user profile options for password, email address, and shared network
account information.
Note: The Guest user can set only their email address.

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Chapter 3 Configuring the CFX Opus Dx Real-Time PCR Systemn

Run Reports — view the run report for each protocol run on the system. Users can export a
specific run report or all run reports to an attached USB drive.
Tip: In addition to exporting run reports, Admin users can trim the list of run reports toremove older or invalid reports as well as recover the .zpcr file of selected runs.

nSystem Logs — view two types of logs:oMessages Log — messages that occur during each run.

oUsage Log — all events that occur during each run.

Note: From this screen, logged-in users can export all message and usage logs to an
attached USB drive. Admin users can export all logs as well as clear all logs from thesystem.
n

Real-Time PCR Demo — view a demonstration of a real-time 96-well, 384-well, or Deepwell
SYBR® or multiplex PCR run on the touch screen.

nShipping Screw — view instructions for removing or installing the shipping screw.

58 | CFX Opus 96 Dx, CFX Opus 384 Dx, and CFX Opus Deepwell Dx Real-Time PCR Systems

Tools Screen

Admin Tools Screen Options
All options available to users are also available to administrators. Only those who log in as Admin haveaccess to the Admin options.

To access the Admin Tools screen
1.

Log in an Admin user.

2.

On the Home screen, tap Tools on the Home screen.
The Tools screen appears and displays the Admin options.
Tip: To view the standard User options, tap User on the bottom of the screen.

Operation Manual | 59

Chapter 3 Configuring the CFX Opus Dx Real-Time PCR SystemnSystem Settings — from this screen, Admin users cano

Set the time zone, date, and time on the systemoEnable or disable password requirement

Note: If a user creates a local user account without a password before you enable thisrequirement, that user will be prompted to create a password at the next log-in attempt.
oEnable or disable the screen saver and set its idle time

Note: The screen saver appears after the system has been idle for a specified amount oftime. The screen saver does not appear while a run is in progress.
oRename the systemn

Network Settings — view details about the current network connection; use this screen toconnect the system to the internal network via Ethernet connection.

nUser Management — reset a user’s password and remove users.

n

System Update — update the system software and firmware from an attached USB drive.
Note: The CFX Opus Dx system installer can include both software and firmware updates.
CFX Opus Dx system firmware updates are not distributed in a separate package.

nDiagnostic Test — perform a series of diagnostic self tests on the system (for use whenservicing the system).

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Tools Screen

Renaming the CFX Opus Dx Real-Time PCR System
Initially, the name of each CFX Opus Dx system is its serial number. You can rename the system for easy
identification.

To rename a CFX Opus Dx system
1.

Log in as an Admin user.

2.

On the Home screen, tap Tools to open the Tools menu.

3.

On the Admin tools screen, tap System Settings to open the System Settings screen.

4.

Tap the Instrument name field and type a new name using the alphanumeric keypad that appears.

5.

Tap Apply to confirm the change in settings.

6.

Tap Back to return to the Tools menu.

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Setting the Time Zone on the CFX Opus Dx Real-Time PCR System
The date and time on the CFX Opus Dx system is synchronized to the time zone configured in yourinstrument’s operating system. If your instrument is connected to the Internet, you can set the time zone
according to your lab’s best practices. You can then set the actual time on the system according to thetime zone in which the system resides.
In this manner, actual local time might differ from the detected time zone. However, run reports generated
from protocols retrieved from computers running CFX Maestro Dx SE that are not in the same time zone
as the CFX Opus Dx system will display the correct time.
The time zone changes are applied immediately to the System Settings Date and Time fields and saved
when you tap Apply. Any changes you made to the date and time prior to setting the time zone are lost.
Changes to Date and Time made after the time zone change are saved and applied in addition to the timezone change when you tap Apply.
Run reports will display local time (that is, the time zone in which the instrument on which experiment is
run is located).
Important: Even if you set the time zone, you must set the correct time. The system does not
automatically detect the local time.
Tip: Time changes due to switching between daylight saving and standard time are performed
automatically when you set the Time zone.

To set the time zone on the CFX Opus Dx system
1.

Log in as the Admin user.

2.

On the Home screen, tap Tools to open the Tools menu.

3.

In the Admin tools screen, tap System Settings to open the System Settings screen.

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Tools Screen

4.

Tap the Time zone field and select the target time zone from the dropdown list that appears.

5.

Tap the Date field and set the date using the calendar that appears.

6.

Tap the Time fields and set the hour, minute, and second fields using the keypads that appear.
Note: The Hour field is a 24-hour field.

7.

Tap Apply to confirm the change in settings.

8.

Tap Back to return to the Tools menu.

Setting Up a Network Connection on the CFX Opus Dx Real-Time
PCR System
When establishing a connection between the CFX Opus Dx system and your internal network, a DHCP
server is required so that the system receives an IP address. The DHCP server should be configured toalways assign the same IP address to the system. See your network administrator for more information.
By default, the CFX Opus Dx system’s IP address is dynamic. That is, the IP address can change eachtime the system restarts. In these cases, the system must reestablish a connection to your internal
network each time it starts. A static IP address never changes; thus the system always reconnects to the
network each time it restarts.
The CFX Opus Dx system connects to your internal network using the DHCP server. This section explains
how to view the dynamic IP or static IP network settings for your CFX Opus Dx system.

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Viewing the Dynamic IP Network Settings
Note: Before starting this procedure, ensure your CFX Opus Dx system is turned off.

To view the dynamic IP network settings
1.

If you have not already done so, insert one end of the provided Ethernet cable into the Ethernet porton the back of the CFX Opus Dx system.

2.

Insert the loose end of the Ethernet cable into the network connection router or hub.

3.

Turn on the system.
The CFX Opus Dx system automatically detects an available IP address and connects to yournetwork. The system displays the Ethernet icon in the lower left corner of the Home screen to indicate
successful Ethernet network communication.

4.

To test the dynamic IP configuration, log into the CFX Opus Dx system as Admin and tap Tools on
the Home screen.

5.

In the Admin Tools list, tap Network Settings.

6.

On the Network Settings screen, tap IP Config.
The IP Config dialog box appears and displays the current dynamic configuration details, forexample:7.

Tap Test to test the connection.

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Tools Screen

A message appears indicating an Internet connection has been found.
8.

Tap OK to close the message and then tap Cancel to close the IP Config dialog box and return to the
Network Settings screen.

9.

On the Network Settings screen, tap Back to return to the Tools screen.

10. If necessary, implement network security measures per your organization’s security and privacy
policies.

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Chapter 3 Configuring the CFX Opus Dx Real-Time PCR System

Setting Up a Static IP Network Connection
Note: Before starting this procedure, ensure your CFX Opus Dx system is turned off.
When setting up a static IP network connection, you must provide the IPv4 address, subnet mask, default
gateway, and primary and alternate DNS server details for your system. See your system administrator
for the appropriate settings.
Note: CFX Opus Dx systems support only IPv4 connectivity. Ensure the settings are appropriate foryour site.

To set up a static IP network connection
1.

If you have not already done so, insert the provided Ethernet cable into the Ethernet port on the backof the CFX Opus Dx system.

2.

Insert the loose end of the Ethernet cable into the network connection router or hub.

3.

Turn on the system.
The CFX Opus Dx system automatically detects an available IP address and connects to yournetwork.

4.

To set up a static IP configuration, log into the CFX Opus Dx system as Admin and tap Tools on the
Home screen.

5.

In the Admin Tools list, tap Network Settings.

6.

On the Network Settings screen, tap IP Config.
The IP Config dialog box appears.

7.

Tap Static IP and provide the IP address, subnet mask, default gateway, and primary and alternate
DNS server details for your site.
n

IP address — the specific numeric address for the CFX Opus Dx systemn

IP subnet mask — the numeric filter used to define the subnet to which the IP address belongsn

IP default gateway — (optional, required if you plan to access the CFX Opus Dx system from
CFX Maestro Dx SE software computers that are on another subnet) the IP address of the nodethat allows communication between subnetsnPrimary and alternate DNS servers — the IP address of the nodes that translate a server nameto its IP address

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Tools Screen

8.

Tap Test to test the connection.
A message appears indicating that an Internet connection has been found.

9.

Tap OK to close the message and then tap Cancel to close the IP Config dialog box and return to the
Network Settings screen.

10. On the Network Settings screen, tap Back to return to the Tools screen.
11. The system displays the Ethernet icon in the lower left corner of the Home screen to indicate
successful Ethernet network communication.

12. If necessary, implement network security measures per your organization’s security and privacy
policies.

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Chapter 3 Configuring the CFX Opus Dx Real-Time PCR System

Setting Up Email Service
You can connect the CFX Opus Dx system to your outgoing email server and have run notifications andreports emailed directly to a specified user account. The CFX Opus Dx system saves the email serverconnection parameters until you change them.
By default, the system ships with Gmail server settings saved. You can create a Gmail account and have
email sent to that account, or you can program the system to send email to a specific account on yoursite’s email server.
This section explains how to connect the system to a custom email server.
Note: Before connecting the system to a custom email server, consult your system administrator forsite-specific email server requirements.

To connect the CFX Opus Dx system to a custom email server1.

On the Home screen, tap Logout and then log in as Admin.

2.

On the Home screen, tap Tools to open the Tools screen.

3.

In the Admin Tools screen, tap Email Settings to open the Email Setup dialog box.
The Email Setup dialog box displays the default Gmail server settings.

4.

Provide the information for your company:nAuthentication — by default Authentication is selected (required for Gmail email servers) andthe Authenticated Account and Account Password fields are active. If your site does not require
account authentication, clear this checkbox.

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Tools Screen

Tip: See your system administrator for the name of the authenticated account and its
password.
oAuthenticated Account — the name of the authenticated account.

oAccount Password — the password for the authenticated account.

5.

Tap Save to save the changes.

6.

(Optional) To verify that the SMTP server settings are correct:a.

Tap Test Email to open the Email Server dialog box.

b.

Provide a valid email address and enter a sample attachment size.
The size limit for attachments is determined by your company’s server. Bio-Rad recommends
testing an attachment size between 0.5 and 5 MB.
Tip: Enter 0 to send a test email with no attachment.

c.

Tap Send Email.
The system sends a test email to the email account.

d.
7.

Tap Cancel to return to the Email Setup dialog box.

Tap Back to return to the Tools screen.

Changing Email Servers
The CFX Opus Dx system saves the connection parameters for one email server at a time. It retains themost recent server connection until you change it.

To change to another email server1.

In the Email Setup dialog box, make the appropriate changes.

2.

Tap Save and then tap Yes to save the changes.

3.

Tap Back to return to the Tools screen.

Connecting to a Computer Running CFX Maestro Dx SE Software
During installation, the CFX Maestro Dx SE software installer automatically installs the instrument drivers
onto the computer. When you start the software, CFX Maestro Dx SE detects the connected instruments.
Important: You must disconnect the CFX Opus Dx system from the CFX Maestro Dx SE computer
before you install the software. You do not need to turn off the system during the software installation.

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Chapter 3 Configuring the CFX Opus Dx Real-Time PCR System

To detect connected instruments
1.

If you have not yet done so, insert the square (male) end of the supplied USB Type B cable into the
USB Type B port located on the back of the CFX Opus Dx system.

2.

Insert the other (port) end into a USB port on the CFX Maestro Dx SE computer.

3.

If the system is not already running, press the power switch on the back of the instrument to turn it on.

4.

Start CFX Maestro Dx SE software.

The software automatically detects the connected instrument and displays its name in the Detected
Instruments pane in the Home window.

Note: If the instrument does not appear in the Detected Instruments pane, verify that the USB cableis properly installed. To reinstall drivers, select Tools > Reinstall Instrument Drivers in the
CFX Maestro Dx SE software Home window.

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Calibrating New Dyes

Calibrating New Dyes
The CFX Opus 96 Dx and CFX Opus 96 Deepwell Dx systems are factory calibrated for commonly usedfluorophores in white-well and clear-well plates. The CFX Opus 384 Dx system is factory calibrated forcommonly used fluorophores in white-well plates only.
For a list of factory calibrated flourophores, channels and instruments, and for instructions on how tocalibrate new dyes, refer to the CFX Maestro Dx SE Software user guide.

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Chapter 3 Configuring the CFX Opus Dx Real-Time PCR System

Managing Personal User Accounts
As a logged in CFX Opus Dx system user, you cann

Set or change your passwordn

Set or change your email addressn

Set or change your shared network driveThis section explains how to manage your personal account.
Important: Guest users can only set or change their email account.

Setting User Passwords
Bio-Rad recommends that you create a password at the time you create your user profile. You canchange your password at any time. The section explains how to set a password if you did not create one
at the time you created your user profile.
Note: If you plan to connect to a shared network drive you must have a password.
Tip: CFX Opus Dx system passwords can be any combination of alphanumeric characters.
Passwords must be between 4–50 characters and are case-sensitive.

To create a user password
1.

From the Home screen, tap Tools.

2.

On The Tools screen, tap User Profile.
The User Profile screen appears.

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Managing Personal User Accounts

3.

In the CFX Opus Dx system Password section, tap

to expand the dialog box and then tap Change

Password.
The Change Password dialog box appears.

4.

Type and confirm your password using the alphanumeric keyboard and then tap Save Password.

5.

Tap Back to return to the Tools screen, and then tap Home to return to the Home screen.

To change your password
1.

On the User Profile screen, expand the Password section and then tap Change Password.

2.

Type your current password using the alphanumeric keyboard that appears, and then tap OK.
The Change Password dialog box appears.

3.

In the Change Password dialog box, type and confirm your password using the alphanumerickeyboard that appears and then tap Save Password.

4.

Tap Back to return to the Tools screen, and then tap Home to return to the Home screen.

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Chapter 3 Configuring the CFX Opus Dx Real-Time PCR System

Setting Up Your Email Address
Adding an email address to your CFX Opus Dx system user account allows you to be notified by email
after a run is completed. This is an option in the Run Setup screen for executing runs. For details, see
Running Protocols on page 107.
Note: Guest users can choose which email account receives notifications after a run completes.
However, the system will continue to send notifications to that email unless the Guest email accountis changed. Bio-Rad recommends that all Guest user accounts use one generic email address sothat Guest users won’t miss notifications.
Note: To receive email notifications from the CFX Opus Dx system, your site administrator must
configure the email service. For details, see Setting Up Email Service on page 68.

To add an email address to your user account1.

From the Home screen, tap Tools, then in the User screen tap User Profile.
The User Profile screen appears.

2.

In the Email Notification section, tap

to expand the dialog box.

3.

Tap the Email Address field and type your email address using the alphanumeric keypad thatappears, and then tap OK.

4.

Tap Back to return to the Tools screen, and then tap Home to return to the Home screen.
Note: You might be able to configure the system to send an email notification to your cell phonedepending on your service provider. Contact your cell phone service provider for specificinformation regarding the email address for your cell phone. Enter your phone's email address(for example, 5552221234@your_service_provider_EmailDomain.net) in the Email Notificationtext box of the User Preferences screen.

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Managing Personal User Accounts

Note: The system might be able to send email notifications to your cell phone if that service issupported by your cell phone provider. Contact your cell phone service provider to obtain specificemail domain information. Enter your phone's email address (for example, 5552221234@your_service_provider_EmailDomain.net) in the Email Notification text box of the User Preferences
screen.

Setting Up a Connection to a Shared Network Drive
Note: You must have a password on the CFX Opus Dx system to connect to a shared network drive.
See Setting User Passwords on page 72 for more information.
You can connect your CFX Opus Dx system user account to a shared drive on your internal network.
When connected, you can create protocols on your CFX Opus Dx system and save protocols and run files
to your network drive. You can also copy protocol files from your network drive to a folder on the CFX
Opus Dx system.

To connect to a shared network drive1.

On the Tools screen, tap User Profile.
The User Profile screen appears.

2.

In the Network Folder section, tap

to expand the dialog box.

3.

In the Folder Path section, type the path to the shared network folder using the following format:\\server_name\folder_name\...\target_folder
Note: You must type the two backslashes (\\) at the beginning of the path, and separate eachfolder with a single backslash.

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Chapter 3 Configuring the CFX Opus Dx Real-Time PCR System

4.

In the Connection section, type the global domain name and user name you use to connect to thatserver in this format:
global_domain_name\user_name
You must include the backslash in the path, for example:
Global\Carln
Tip: This user name might be different than your CFX Opus Dx system user name.

5.

(Optional) Tap Save User Password to save your network password on the CFX Opus Dx system.
You will not be prompted for a password the next time you log in to your CFX Opus Dx system
account.

6.

Tap Connect.

7.

Type the password you use to connect to that server using the alphanumeric keyboard that appears
and then tap OK.
When the connection is successful, the Network Folder status changes to Connected to network
folder:8.

Tap Back to return to the Tools screen, and then tap Home to return to the Home screen.
Tip: The system informs you when the folder to which you are connected is read-only.

To disconnect the CFX Opus Dx system from your network drive
1.

From the Home screen, tap Tools, then in the User screen tap User Profile.
The User Profile screen appears.

2.

In the Network Folder section, tap theicon to expand the dialog box.

3.

Tap Disconnect.

4.

Tap Back to return to the Tools screen, and then tap Home to return to the Home screen.

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Managing User Accounts

Managing User Accounts
The CFX Opus Dx system Admin user can perform limited user management tasks. From the User Profile
screen, the Admin user can create his own password. From the User Management screen, the Admin
user cannReset a user’s passwordnDelete a user accountThis section explains how to set the Admin password and manage user accounts.

Setting the Admin Password
Important: The default Admin user does not have a password. Bio-Rad strongly recommends thatthe user who assumes the Admin role immediately set a password and store that password in a
password safe. Resetting the Admin password requires a call to Bio-Rad Technical Support.
CFX Opus Dx system passwords can be any combination of alphanumeric characters. Passwords must
be between 4–50 characters and are case-sensitive.

To add the Admin password
1.

Log in as an Admin user.

2.

On the Home screen, tap Tools to open the Admin Tools screen.

3.

Tap the User icon on the bottom of the screen to display the User Tools screen then tap User Profile.
The User Profile screen appears.
icon and then tap Change Password.

4.

In the CFX Opus Dx system Password section, tap the

5.

In the Change Password dialog box, type and confirm your password using the alphanumerickeyboard that appears, tap Save Password, and then tap OK.

6.

Tap Back to return to the Tools screen, and then tap Home to return to the Home screen.

To change the Admin password
1.

In the CFX Opus Dx system Password section on the User Profile screen, tap Change Password.

2.

Type your current password using the alphanumeric keyboard that appears, and then tap OK.
The Change Password dialog box appears.

3.

Type and confirm your new password, tap Save Password, and then tap OK.

4.

Tap Back to return to the Tools screen, and then tap Home to return to the Home screen.

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Chapter 3 Configuring the CFX Opus Dx Real-Time PCR System

Resetting User Passwords
In the event that a user forgets his password, the Admin user can create a temporary password. When theuser next logs in, the software prompts the user to reset their password. Users can change their password
at any time and as often as they choose.

To change or add a password for another user
1.

Log in an Admin user.

2.

On the Home screen, tap Tools then in the Admin Tools screen tap User Management.
The User Management screen appears.

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Managing User Accounts

3.

Tap the targeted user name on the Users list.

4.

Tap Reset Password on the bottom toolbar.
The Reset Password dialog box appears.

5.

Type and confirm the temporary password using the alphanumeric keyboard that appears, and thentap Save Password.

6.

Tap Back to return to the Tools screen, and then tap Home to return to the Home screen.

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Chapter 3 Configuring the CFX Opus Dx Real-Time PCR System

Deleting User Accounts
WARNING! Deleting users accounts from the CFX Opus Dx system also permanently
deletes their protocols, run files, and user data. Take care when deleting users from thesystem.
Note: You cannot delete the Admin, Guest, or Service user accounts.

To delete a user account1.

Log in as an Admin user.

2.

On the Home screen, tap Tools then in the Admin Tools screen tap User Management.
The User Management screen appears.

3.

Tap the targeted user name on the Users list.

4.

Tap Remove User on the bottom toolbar.
A warning appears informing you that removing a user permanently deletes their user data.

5.

Tap Cancel to cancel the screen or tap Remove to remove the user account and permanently delete
their data.

6.

Tap Back to return to the Tools screen and then tap Home to return to the Home screen.

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Chapter 4 Creating Protocols
Using the touch screen on the CFX system, you can create and edit protocols, change step parameters,
and set the sample volume and lid temperature.
For each protocol, you can add, edit, or remove any of the following parameters:nPlate “read”

nTemperature gradientsnTemperature incrementsnRamp ratenExtend timen

Alert beepsn

GOTO steps

A protocol can contain the following types of steps:nTemperature — ramps to a target temperature at specified ramp rate and holds that temperature; caninclude a plate read at end of the step.

n

Gradient — applies a temperature differential across the rows of the block; can include a plate read at
end of the step.

n

GOTO — creates a cycle of a specific number of repetitions between certain steps in the protocol.

nMelt Curve — collects fluorescence data at specified temperature intervals between a starting
temperature and an ending temperature; used to perform melt curve analysis. Includes a plate read
after each interval.

The section Parameters and Ranges for Protocol Steps on page 82 lists the options and ranges for
protocol steps. Review the information in this section before creating your protocol.

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Chapter 4 Creating Protocols

Parameters and Ranges for Protocol StepsUse the information in Table 10 to modify the default settings for the steps in your protocol.

Temperature Steps
The target temperature is a value between 4.0 and 100.0°C, set in tenths of a degree. The system ramps
to this temperature and holds that value for a specified amount of time (the hold time).

Gradient Steps
The gradient range is the difference between the lower and upper temperatures in a gradient step. The
maximum allowed range is 24°C. The lower temperature is a value between 30.0 and 99.0°C, set intenths of a degree. The upper temperature range can be set from 31.0 to 100.0°C. The system ramps tothe target temperature gradient across the block and holds that temperature for a specified hold time.
Important: The instrument calculates the gradient value. When you enter a value in the gradientcalculator’s top and bottom fields, the software automatically calculates and assigns thetemperatures for the remaining fields. When you enter a temperature in any field between the top andbottom field, the instrument automatically calculates the remaining fields. You cannot manually entera temperature value in every field.
Table 10. Parameters and ranges for protocol steps

Parameter

Range

Description

Ramp raten For CFX Opus 96 Dx systems:

Instructs the thermal cycler to ramp to

0.1–5°C per sec
n For CFX Opus Deepwell Dx systems:
0.1–2.5° per sec

the target temperature at the specified
rate in that step.
Available only to temperature steps.

n For CFX Opus 384 Dx systems:
0.1–2.5°C per sec
Increment

A number from –10.0 to 10.0°C per cycle inInstructs the thermal cycler to changetenths of a degree

the target temperature of a step witheach cycle, where a positive number
increases the temperature and anegative number decreases thetemperature.
Available only to temperature steps ina GOTO cycle.

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Parameters and Ranges for Protocol Steps

Table 10. Parameters and ranges for protocol steps, continued

Parameter

Range

Description

ExtendA time from –60 to 60 sec per cycle

Instructs the thermal cycler to extend
the hold time with each cycle. A
positive number increases the holdtime and a negative number
decreases the hold time.
Available to both temperature andgradient steps.

Beep(No parameters)

Instructs the thermal cycler to beep tosignal that the thermal cycler has
reached the target temperature forthat step.
Available to both temperature andgradient steps.

Plate read(No parameters)

Instructs the thermal cycler to add aplate read to the selected step.
Available to both temperature andgradient steps.

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Chapter 4 Creating Protocols

Creating a Protocol
Important: While creating your protocol, take care when setting the sample volume and lid
temperature. If the lid temperature is too high, the sample temperature might rise above the target
temperature. For more information about these settings, see Setting Sample Volume and Lid
Temperature on page 98.

To create a protocol
1.

On the Home screen, tap New Protocol to open the New Protocol screen.

2.

To set or change any of the following, tap its respective button or field and enter a value using thealphanumeric keypad that appears:nName — the name of the protocol. The name can consist of up to 32 alphanumeric characters.
Tip: Spaces are considered as a character.

nVolume — the sample/reaction volume in μl.
Note: The volume setting affects the control mode used to determine when the sample
reaches the target temperature. For details, see Sample Volume and Temperature Control
Modes on page 98.

n

Lid temp — the temperature of the lid in °C.

nTemperature — the target temperature of the step. For example:(target temperature set to 95°C)

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Creating a ProtocolnTime — the hold time of the step (between 1 sec and 17:59:59) in the format of HH:MM:SS. For
example:(hold time set to 10 sec)

Tip: To set an infinite hold on a step, tap then

key.

GOTO step number — (for GOTO steps only) the step number to which the GOTO cycle
returns. For example:(GOTO cycle returns to step 2 and repeats the succeeding steps.)n

GOTO cycles — (for GOTO steps only) the number of times to repeat the cycle. The default is
39 times. For example:(repeat the cycle 39 times)

3.

(Optional) If your protocol requires a new temperature, gradient, melt curve, plate read, or GOTO
step:
a.

Select the step in the protocol that will precede the new step and tap Insert at the bottom of thescreen.
The Insert Step dialog appears.

b.

Tap the type of step to insert.
The new step appears in the protocol, highlighted and to right of the selected step. The default
temperature of the new step is 50°C and the default time is 30 sec (0:30). Tap time ortemperature to edit the parameters in the new step.

4.

(Optional) To delete a step, select the step and tap Remove at the bottom of the screen.

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Chapter 4 Creating Protocols

5.

Tap Save to save the protocol.
The Save As dialog box appears:

If you have a local user account, the default save location is your personal folder, which appears as
My Files in the Save As dialog box. Protocols that are saved in that folder or any folder within the My
Files folder structure are visible only to you. Files within your My Files structure are not available to or
shareable with other users.
Alternatively, you can choose to save protocols to a shared network folder if you have enabled thissetting. You can also choose to save to an attached USB drive.
Finally, you can save protocols to a location in the Public folder. Files that are saved in that folder or
any folder within the Public folder structure are visible to and shareable with every CFX Opus Dx
system user in your organization.
Important: Files saved to an alternate location are not concurrently saved on the CFX Opus Dx
system. Consider this before selecting the location.
For Guest users, the default save location is the Public folder. Guest users can save protocols only in
the Public folder structure or to an attached USB drive.

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Creating a Protocol

Tip: For more information about managing files and folders, see Chapter 6, Managing Files andFolders.
6.

In the Save As dialog box:a.

If you have not yet named the protocol, tap the Protocol Name field and type a name for the
protocol in the alphanumeric keyboard that appears.

b.

Do one of the following to determine the file destination:n

Accept the default folder location.

n

Tap the Folder Location link to open the Select Location dialog box and select the newlocation. If necessary, tap Create Folder () to create a new folder in the currently-

selected location. When you are finished, tap Select.
c.
7.

Tap Save to save the protocol or Cancel to return to the New Protocol screen.

In the New Protocol screen, tap Next to open the Run Setup dialog box.

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Chapter 4 Creating Protocols

8.

Adjust the run settings as needed for your protocol:nSample volumen

Lid temperaturen

Scan moden(Optional) Plate IDn

Run file nameTip: This is the name for the run file, separate from the protocol name.

nSave location
Tip: The default location is the user’s personal folder (My Files), you can change this tosave into the same folder as the folder containing the saved protocol, to a shared network
drive, or to a USB drive.

n

Notifications after the run is completed
You can have the system beep and/or send email to a specified email account when the runcompletes.

9.

On the Run Setup screen, tap Run to start the run.

For more information, see Chapter 5, Running Protocols.

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Creating a Protocol

Modifying the Settings in a Protocol Step
While you create your protocol, you can modify the default settings for each step. You can add or remove
any of the following:nTarget temperaturen

Hold timenTemperature gradientsnTemperature incrementsnRamp ratenExtend timen

Alert beeps

You can also modify the default settings of a GOTO step. These tasks are explained in the sections that
follow.

Changing Target Temperature and Hold TimeTo change the target temperature and hold time1.

Select the target step and then tap Options on the bottom toolbar to open the Step Options dialog
box:

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Chapter 4 Creating Protocols

2.

Tap the appropriate option and enter a new value in the keypad that appears.

3.

Tap OK to confirm and close the keypad.

4.

Tap OK to close the Step Options dialog box.

5.

Tap Save to save the changes.

Tip: Alternatively, tap the appropriate field in the target step and enter a new value in the keypad thatappears. Tap OK to close the keypad and return to the protocol.

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Creating a Protocol

Adding or Removing a Temperature GradientTo add a temperature gradient1.

On the protocol, select the target step and tap Options.
The Step Options dialog box appears.

2.

In the Step Options dialog box, tap the Gradient checkbox. The gradient range appears to the right in
the Step Options dialog box.

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Chapter 4 Creating Protocols

3.

To change the gradient range tap either the higher or lower value and enter a new value in the
keypad that appears.
Important: The upper value of the gradient range must be within 24°C of the lower value.

4.

Tap OK to confirm and close the keypad.

5.

Tap OK to close the Step Options dialog box.

6.

Tap Save to save the changes.

To remove the temperature gradient1.

On the protocol, select the gradient step and then tap Options.
The Step Options dialog box appears.

2.

Clear the Gradient checkbox.

3.

Tap OK to confirm and close the keypad.

4.

Tap OK to close the Step Options dialog box.

5.

Tap Save to save the changes.

Adding or Removing the Ramp Rate
The ramp rate option instructs the thermal cycler to ramp to the target temperature at a specified rate inthat step.
To emulate a thermal cycler that runs at a slower ramp rate than the CFX Opus Dx system, change theramp rate of the appropriate protocol step.

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Creating a Protocol

To add a ramp rate
1.

On the protocol, select the target step and tap Options.
The Step Options dialog box appears.

2.

Tap Ramp Rate and enter a value using the keypad that appears.

3.

Tap OK to confirm and close the keypad.

4.

Tap OK to close the Step Options dialog box.

5.

Tap Save to save the changes.

To remove a ramp rate
1.

On the protocol, select the ramp rate step and tap Options.

2.

In the Step Options dialog box, tap Ramp Rate and then tap Off to clear the entry.

3.

Tap OK to confirm and close the keypad.

4.

Tap OK to close the Step Options dialog box.

5.

Tap Save to save the changes.

Adding or Removing a Temperature Increment
A temperature increment raises or lowers the target temperature of a step within each cycle.

To add a temperature increment
1.

On the protocol, select the target step and tap Options.
The Step Options dialog box appears.

2.

Tap Increment.

3.

Enter an increment value using the keypad that appears.
Tip: A positive number increases the temperature, a negative number decreases thetemperature.

4.

Tap OK to confirm and close the keypad.

5.

Tap OK to close the Step Options dialog box.

6.

Tap Save to save the changes.

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Chapter 4 Creating Protocols

To remove a temperature increment
1.

On the protocol, select the temperature increment step and tap Options.

2.

Tap OK to confirm and close the keypad.

3.

Tap OK to close the Step Options dialog box.

4.

Tap Save to save the changes.

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Creating a Protocol

Adding or Removing an Extend Time Option
The Extend option instructs the thermal cycler to extend the hold time with each cycle.

To add or modify an Extend option
1.

On the protocol, select the target step and tap Options.
The Step Options dialog box appears.

2.

Tap Extend and type a value using the keypad that appears.

3.

Tap OK to confirm and close the keypad.

4.

Tap OK to close the Step Options dialog box.

5.

Tap Save to save the changes.

To remove an Extend option
1.

On the protocol, select the extend step and tap Options.

2.

In the Step Options dialog box, tap Extend and then tap 0 (zero) to clear the entry.

3.

Tap OK to confirm and close the keypad.

4.

Tap OK to close the Step Options dialog box.

5.

Tap Save to save the changes.

Adding or Removing a Beep Alert
The CFX Opus Dx system can emit a beep sound when it reaches the target temperature of a protocol
step.

To add a beep alert
1.

On the protocol, select the target step and tap Options.
The Step Options dialog box appears.

2.

Tap the Beep checkbox to select it.

3.

Tap OK to confirm and close the keypad.

4.

Tap OK to close the Step Options dialog box.

5.

Tap Save to save the changes.

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Chapter 4 Creating Protocols

To remove a beep alert
1.

On the protocol, select the beep step and tap Options.

2.

In the Step Options dialog box, tap Beep to clear the checkbox.

3.

Tap OK to confirm and close the keypad.

4.

Tap OK to close the Step Options dialog box.

5.

Tap Save to save the changes.

Changing Parameters in a GOTO Step
The GOTO step instructs the thermal cycler to return to a specific step in the protocol and repeat theseries of steps a specified number of times. This creates a cycle in the PCR experiment. The GOTO stepin Step 4 in the following image instructs the thermal cycler to return to Step 2 and perform 34 additional
repeats, for a total of 35 cycles.

To change parameters in a GOTO step1.

To change the return-to step, tap Step in the GOTO step and type the new step number using the
keypad that appears.

2.

Tap OK to confirm and close the keypad.

3.

To change the number of repeats, tap the repeat X on the GOTO step and type a new value using the
keypad that appears.

4.

Tap OK to confirm and close the keypad.

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Creating a Protocol

5.

Tap OK to close the Step Options dialog box.

6.

Tap Save to save the changes.

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Chapter 4 Creating Protocols

Setting Sample Volume and Lid Temperature
Important: If the lid temperature is too high, the sample temperature might rise above the target
temperature.

Sample Volume and Temperature Control Modes
The CFX Opus Dx system uses one of two control modes to determine when the sample reaches thetarget temperature:n

Calculated mode — when a sample volume setting is greater than zero, the CFX Opus Dx system
calculates the sample temperature based on the sample volume. Bio-Rad recommends using the
calculated mode because it most accurately represents the actual sample temperature.

n

Block mode — when a sample volume setting is zero (0) µl, the CFX Opus Dx system assumes thatthe sample temperature is the same as the measured block temperature.

To change the sample volume
1.

On the New Protocol or Edit Protocol screen, tap Volume at the top of the screen and type a newvalue using keypad that appears.

2.

Tap OK to confirm and close the keypad.

To view the control mode setting for a saved protocol or run file1.

From the Home screen, tap Files to open the File Browser screen.

2.

Tap the location and folder in which the protocol or run file resides, and then tap the file’s name toview its details.

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Setting Sample Volume and Lid Temperature

For example, the image that follows shows that the PCR2 protocol uses the CALC (calculated)
control mode:

Lid Temperature
Note: For the CFX Opus 96 and the CFX Opus Deepwell Dx systems, Bio-Rad recommends a lid
temperature of 105°C. For the CFX Opus 384 Dx system, Bio-Rad recommends a lid temperature of
95°C.
The CFX Opus Dx system’s adjustable heated lid allows you to control the lid temperature. Heating the lid
prevents condensation from forming inside the sample wells. When the CFX Opus Dx system is running,
the heated lid maintains the temperature specified for the protocol being run. Without a heated lid, waterfrom the reagents can be lost to condensation, concentrating the reactants in the tube or plate.
The default lid temperature is 105°C for CFX Opus 96 Dx and CFX Opus Deepwell Dx sample blocks, and95°C for CFX Opus 384 Dx .
Note: When the block is running an infinite hold at a temperature below 30.0°C for the last step in the
protocol, the lid heater maintains 31.0°C.

To change the lid temperature
1.

On the New Protocol or Edit Protocol screen, tap Lid temp at the top of the screen and type a newvalue using keypad that appears.

2.

Tap OK to confirm and close the keypad.

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Chapter 4 Creating Protocols

Editing a Protocol
You can edit any parameter within an existing protocol. You can then save it with the same name into thesame or a different folder, or you can rename the protocol and save it into any folder. A renamed protocol
does not overwrite the original protocol.
Tip: You can also open a completed run file, edit the original protocol parameters, and save theprotocol to another folder or with another name. For details, see Extracting and Editing a Protocol
from a Run on page 116.
Caution: Saving a protocol with the same name in the same folder overwrites the original protocol.
You can have multiple protocols with the same name as long as they are saved in different folders.
The CFX Opus Dx system provides two options with which to edit a protocol:nnDirect interaction with buttons that appear on the protocol:oOn melt curve, temperature, and gradient steps, tap the temperature and step time buttons to set
these parameters. More options are available in the Options dialog.

o

On Goto steps, tap the step number button to change the step at which the Goto cycle begins.
Tap the cycles button to change the number of cycles to repeat.

Tap Options on the bottom toolbar to open the Step Options dialog box, which provides access to all
options available for the selected step.

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Editing a Protocol

Editing a Protocol
To edit a protocol
1.

On the Home screen, tap Files to open the File Browser screen.

2.

Tap the location and folder in which the protocol file resides, and then tap the file’s name to select it.

3.

Tap Edit to open the Edit Protocol screen. The protocol appears in a graphical format.

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Chapter 4 Creating Protocols

4.

To set or change any of the following, tap its respective button or field and enter a value using thealphanumeric keypad that appears:
n

Name

n

VolumeNote: The volume setting affects the control mode used to determine when the sample
reaches the target temperature. For details, see Sample Volume and Temperature Control
Modes on page 98.

5.

n

Lid tempnTemperaturen

Step timen

GOTO step destination (start of cycle)n

GOTO number of cycles(Optional) To add a new step, select a step in the protocol and tap Insert on the bottom toolbar.

In the Insert Step dialog box, tap the type of step to insert. The new step appears to the right of theselected step. See Creating a Protocol on page 84 for more information.
6.

Tap Next to open the Run Setup dialog box and then tap Run to run the protocol.

7.

Tap Save to enter a new file name, folder, and location in which to save the protocol.

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Editing a Protocol

Editing a qPCR Protocol
The CFX Opus Dx system ships with a set of preconfigured sample qPCR read-only protocols. You cancopy the sample qPCR protocols to any folder on the system.
Note: You cannot edit or delete these read-only protocols, even if you make a copy and save them toanother folder.
The sample qPCR files are located in the Public > Bio-Rad qPCR folder, which is also read-only. You
cannot save files to or delete files from this folder.
However, any user, including the Guest user, can rename and save a qPCR protocol to another location
before running it. Renamed protocols are open protocols and can be edited, copied, and deleted.
Note: You must save the renamed qPCR protocol to a location other than the Bio-Rad qPCR folder.
This section explains how to edit a sample qPCR protocol.

To edit a qPCR protocol
1.

On the File Browser screen, tap Public in the left navigation pane and then tap the Bio-Rad qPCR
folder to display the sample qPCR protocols.

2.

Select the target protocol and then tap Edit.
The Edit Protocol screen appears.

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Chapter 4 Creating Protocols

3.

In Name field, type a new name for the protocol.
Tip: You must rename the protocol. Unless you rename it, the system will not save edits to aqPCR protocol regardless of the folder into which you choose to save it.

4.

(Optional) In the Edit Protocol screen, make any necessary changes to the protocol and then tap
Save.

5.

In the Save As dialog box, tap the Folder Location link and select a location in which to save theprotocol.

6.

Verify that you changed the name of the file and then tap Save to save the renamed sample qPCR
file.

7.

On the Edit Protocol screen, do one of the following:n

Tap Next to open the Run Setup to set up and run the protocol.

n

Tap Back to return to the File Browser screen.

Adding a Protocol Step
To add a protocol step1.

Tap the step in the protocol that will precede the new step and tap Insert on the bottom toolbar.
The Insert Step dialog box appears.

2.

Tap the type of step to insert:nTemperaturen

GradientnMelt curve

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Editing a ProtocolnPlate read
Note: The Plate Read option does not insert a step. Instead, it adds a plate read action to theselected step. If a step contains a plate read, it displays the following icon:

n

Goto

The new step appears to the right of the selected step.
Tip: The default target temperature of a new step is 50°C and its default time is 30 sec (0:30).
Tap the step’s time or temperature or tap Options to edit the parameters in the new step.

Deleting a Protocol Step
To delete a protocol stepu

On the protocol, select the target step and tap Remove on the bottom toolbar.

Renaming a Protocol
To rename a protocol
1.

On the protocol, tap Name on the top of the screen.

2.

Type a new name for the protocol using the alphanumeric keyboard that appears.

3.

Tap OK to accept the name and close the keyboard.

Saving an Edited Protocol
To save an edited protocol
1.

On the protocol, tap Save to open the Save As dialog box.

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Chapter 4 Creating Protocols

Important: Saving the protocol with the same name in the same location overwrites the original
protocol. Saving the protocol with a new name or in another location creates a new protocol. The
original file remains unchanged.
2.

Tap the Protocol Name field and type a name for the protocol.

3.

Do one of the following to determine the file destination:n

Accept the existing folder location.

n

Tap the Folder Location link to open the Select Location dialog box and select the new location.
If necessary, tap Create Folder () to create a new folder in the selected location. When you

are finished, tap Select.
Folder Location path displays the path to the selected destination:

4.

Click Save to save the protocol or Cancel to return to the Edit Protocol screen.

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Chapter 5 Running Protocols
From the CFX system you cann

Run a new protocoln

Run a saved protocolnEdit a protocol from a completed run, and then run the edited protocoln

Repeat a completed runnView the status of a runnPause and resume a runnSkip steps in a runnStop a run

This chapter explains how to perform these tasks using the CFX Opus Dx system’s touch screen.

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Chapter 5 Running Protocols

Running a Protocol
CFX Opus Dx system offers several options for running a protocol:n

Run a new protocol.

n

Run a saved protocol.

n

Run a completed run again.

n

Edit a protocol from a completed run, and then run the edited protocol.

This section explains these options in detail.

Running a Saved Protocol
Using the CFX Opus Dx system’s File Browser feature, logged-in users can select and run protocols thatare saved locally in their My Files folderstructure, an attached USB drive, or a shared network folder.
Guest users can run protocols saved in the Public folder structure or an attached USB drive.
Admin users can run saved protocols from any local folder, an attached USB drive, or a shared network
folder.

To run a saved protocol
1.

On the Home screen, tap Files to open the File Browser screen.

2.

Tap the location and folder in which the protocol is saved and then tap the file’s name to select it.

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Running a Saved Protocol

Tip: Protocol files are identified by a protocol icon (icon (
3.

) while run files are identified by a run).

Tap Next.
The Run Setup dialog box appears.

4.

Adjust the run settings as needed for your experiment:

Operation Manual | 109

Chapter 5 Running ProtocolsnSample volumen

Lid temperaturen

Scan moden(Optional) Plate IDo

Tap the Plate ID field and manually enter the plate ID in the alphanumeric keyboard thatappears and then tap OK to accept the plate ID and close the keyboard.

o

Use a USB barcode scanner to scan the plate’s barcode into this field:a.

Connect a barcode scanner to one of the system’s USB ports.
Note: The CFX Opus Dx system only supports barcode scanners that arecompatible with Windows 10 and are ready to use when connected.

nb.

Tap the Plate ID field to view the Plate ID alphanumeric keyboard.

c.

Tap the text field in the keyboard and then scan the barcode to insert the barcode into
the text field.

d.

Tap OK to accept the barcode and close the keyboard.

Run file name — the default file name format is <ProtocolName>_<Date>_<Time>_<SerialNumber>_<UserName>. You can change it to a name of your choice.
Note: The run file name is limited to 64 characters.

nSave Location — the location in which to save the run file. The default location is the folder inwhich the saved protocol is located.
To save the run file in a different location, tap the location link to access the Select Location
dialog and select the new location. If necessary, tap Create Folder () to create a new folder at

the currently-selected location. When you are finished, tap Select.

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Running a Saved ProtocolnNotifications after the run is complete:
o

Beep

= off
= on
o

Email

= off
= on

= disabled because email is not configured.
Your email address appears next to the email icon.
For information about setting up email, see Setting Up Your Email Address on page 74.
5.

As needed, tap Open Lid (and Close Lid) to insert the plate in the sample block.

6.

Tap Run to start the run.

7.

When the run completes, the Status screen displays Protocol Complete. The system saves the run
file into the location with the name indicated in Step 4, for example:

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Chapter 5 Running Protocols

Running a Completed CFX Opus Dx Real-Time PCR System
Run
To run a completed run
1.

On the Home screen, tap Files to open the File Browser screen.

2.

Tap the location and folder in which the completed run file is located, and then tap the file’s name toselect it.

3.

Tap Next.
The Run Setup dialog box appears.

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Running a Completed CFX Opus Dx Real-Time PCR System Run

4.

Adjust the run settings as needed for your experiment.
See Running a Saved Protocol on page 108 for more information.

5.

When the run completes, the system saves the run file into the location with the name indicated in
Step 4.
Tip: To differentiate the second run file from the original if you did not change the name, view thetime stamp on the run file name, for example:

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Chapter 5 Running Protocols

Monitoring a Run
During a run, you can use the status buttons on the Home screen to monitor the run.

To monitor a running protocol
1.

To see the detailed status of a run in progress, tap Run Status on the Home screen.
The Run In-Progress screen appears.

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Pausing a Run

2.

To view the remaining time for the run, tap Time Remaining.

3.

To return to the Run In-Progress screen, tap View Status.

Pausing a Run
From its status screen, you can temporarily pause a run in progress. While the run is paused, the CFX
Opus Dx system continues to heat or cool to the target temperature if it has not been reached, and also
maintains the lid temperature.
Tip: After a power failure, the CFX Opus Dx system displays a warning message. When the power
resumes, the system automatically resumes the run from the point in the protocol that was inprogress at the time of the power failure.
Important: Pausing a step can adversely change the outcome of the PCR reaction. If the protocol ispaused during a temperature step, the PCR reaction stays at the target temperature for a longer holdtime than the protocol step requires.

To pause or resume a running protocol
1.

On the Home screen, tap Run Status.

2.

On the Run In-Progress screen, do one of the following:n

Tap Pause to pause the running protocol.

n

Tap Resume to resume the protocol.

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Chapter 5 Running Protocols

Skipping Steps in a Protocol
From the status screen, you can skip steps in a protocol while it is running if it is necessary to shorten the
protocol.
Notes:n

If the CFX Opus Dx system is currently in an infinite hold, tap Skip Step to exit the hold.

n

If you tap Skip Step while in a GOTO step, the software skips to the next cycle in the GOTO loop. If
the GOTO step is in the last cycle when you tap Skip Step, the CFX Opus Dx system exits the GOTO
loop and continues to the next step in the protocol.

n

By repeatedly skipping steps, it is possible to bypass several cycles of a GOTO loop and shorten the
protocol.

To skip a step in a running protocol
1.

If necessary, on the Home screen, tap Run Status to display the Run In-Progress screen.

2.

Tap Skip Step to skip to the next step or, if in a GOTO cycle, to the next step in the cycle.
Tip: To skip more than one step, tap Skip Step multiple times.

Stopping a Run
You can stop a protocol while it is running. When the protocol is stopped, the block immediately stops
changing temperature.
WARNING! Do not open the lid immediately after stopping a run. Opening the lid
while samples are still hot can allow pressurized containers to leak, spray, or
spurt liquid. Always allow the samples to cool before opening the lid.

To stop a run in progress
1.

Tap Run Status on the Home screen.
The Run In-Progress screen appears.

2.

Tap Stop Run.

Extracting and Editing a Protocol from a Run
You can extract a protocol from a run, edit the protocol, and save it. This is helpful if, for example, you do
not have access to the original protocol file.

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Extracting and Editing a Protocol from a Run

This process creates a copy of the protocol file contained in the run file and does not impact the run file or
the original protocol file. If you want to edit an existing protocol file on the CFX Opus Dx system, see
Editing a Protocol on page 100.
Important: If you save the edited protocol with the same name and into the same location as theoriginal file, the system prompts you whether you want to overwrite the original file. You cannot
recover the original file if it is overwritten. Bio-Rad recommends that you save the file with anothername or in a different location to avoid any loss of data.

To extract and edit a protocol from a run
1.

On the Home screen, tap Files to open the File Browser screen.

2.

Tap the location and folder in which the run file resides, and then tap the file’s name to select it.

3.

Tap Edit to open the Edit Protocol screen. The protocol appears in a graphical format.

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Chapter 5 Running Protocols

4.

To set or change any of the parameters, tap its respective button or field and enter a value using thealphanumeric keypad that appears.
For detailed information about the protocol parameters, see Parameters and Ranges for Protocol
Steps on page 82.
For detailed information about the settings in a protocol, see Creating a Protocol on page 84.

5.

(Optional) To delete a step, select the step and tap Remove at the bottom of the screen.

6.

Tap Save to open the Save As dialog box.

7.

Type a new name for the protocol and (optionally) select a new location in which to save the protocol.

8.

Tap Save to save the protocol or Cancel to return to the Edit Protocol screen.

9.

(Optional) Tap Run Setup to set the run parameters and then run the protocol.

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Chapter 6 Managing Files and Folders
Using the CFX Opus Dx system’s file browser feature, you cannCreate a sophisticated folder structure in which to manage your stored data filesnSave data files directly on the CFX Opus Dx system or to a connected USB drive or shared network
drive

n

Copy files and folders from a shared network driven

Copy files and folders to and from a connected USB drivenRename files and folders on the systemnDelete unnecessary files and folders from the system

This chapter explains how to manage files and folders on the CFX Opus Dx system.

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Chapter 6 Managing Files and Folders

The File Browser Screen
On the CFX Opus Dx system, you manage folders and files using the File Browser screen.
To view the File Browser, tap Files on the Home screen.

The Legend table on page 120 describes the File Browser screen in detail.
LEGEND1

Directories — Potential directories:n My Files — file storage available only to the person logged in to the CFX Opus Dx system.
Tip: This option is not available to users who do not have a local account (that is, users
logged in as Guest).
n Public — file storage available to all users. Use this directory to share files across users.
Tip: This option is available to users who do not have a local account (that is, users
logged in as Guest).
n USB — file storage on a portable USB storage device connected to the CFX Opus Dx system.
n Network — file storage on a network drive connected to the CFX Opus Dx system via
Ethernet or wireless communication (for details, see Setting Up a Connection to a Shared
Network Drive on page 75).

2Sub-directory location — identifies your current location within the selected directory.

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The File Browser Screen

34Create Folder — enables you to create a folder within the current location.
File management options — after selecting a file, the file details pane appears. Management
options include:n Copy — copies the existing file to a specified locationn Delete — deletes the file from its current locationn Rename — renames the file at its current location

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Chapter 6 Managing Files and Folders

Managing Files and Folders
To manage files and folders, tap Files on the Home screen to open the File Browser screen. Table 11 lists
all the folder and file management functions available on the File Browser screen.
Note: Folder and file names have a 32-character limit on the CFX Opus Dx system.
Table 11. List of file and folder functions in the File Browser screen

Options

Function

File options(all file actions occur locally on the instrument)

Copy

Copies the selected file to a specified location on the system or to an attached
USB drive.

DeleteDeletes the file from its current location.

RenameRenames the file at its current location.

Folder options
New Folder

Creates a new folder in the current location.

Copy

Copies the existing folder to a specified location on the system, attached USB
drive, or a connected shared network drive.

DeleteDeletes the folder and all of its contents.

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Managing Files and Folders

Managing Files on the CFX Opus Dx Real-Time PCR System
Using the CFX Opus Dx system’s File Browser, you can copy, rename, and delete protocol and run files
locatednLocally on the systemn

On an attached USBn

On a connected shared network driveThis section explains how to manage files on the CFX Opus Dx system.

Copying Files1.

On the CFX Opus Dx system’s Home screen, tap Files to view the File Browser screen.

2.

On the File Browser screen, navigate to the file you want to copy, then tap the file to view the filedetails pane.

3.

In the file details pane, tap Options and then tap Copy.

The Select Location dialog box appears.
4.

In the Select Location dialog box, do one of the following:nNavigate to an existing folder.

Operation Manual | 123

Chapter 6 Managing Files and FoldersnNavigate to the location to create a folder in which to save the file, then tap Create Folder(

5.

) to create a new folder in that location.

Tap Select to copy the file to the selected location or Cancel to return to the File Browser screen.
Note: If a file with the same name exists at the selected location, a message box appears. Tap
Yes to overwrite the existing file or No to return to the File Browser screen.
The CFX Opus Dx system displays a confirmation message when the file is successfully copied.

Deleting a FileTo delete a file1.

On the Home screen, tap Files to view the File Browser screen.

2.

On the File Browser screen, navigate to the file you want to delete, then tap the file to view the filedetails pane.

3.

In the file details pane, tap Options and then tap Delete.
The Delete confirmation message appears.

4.

Tap Delete to confirm or Cancel to return to the File Browser screen.

The CFX Opus Dx system displays a confirmation message when the file is successfully deleted.

Renaming a File
Notes:n

You can rename only protocol files. Run files cannot be renamed.

n

The protocol files located in the Bio-Rad qPCR folder are read-only and cannot be renamed.
However, you can copy a protocol file to another location, open the file and edit the parameters. You
can then save the edited protocol with a new name.

To rename a file1.

On the Home screen, tap Files to view the File Browser screen.

2.

On the File Browser screen, navigate to the file you want to rename, then tap the file to view the filedetails pane.

3.

In the file details pane, tap Options, then tap Rename and type a new name for the file using the
keypad that appears.

4.

Tap OK to confirm.

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Managing Files and Folders

Managing Folders on the CFX Opus Dx Real-Time PCR System
Using the CFX Opus Dx system’s File Browser, you can copy, rename, and delete protocol and run
folders locatednLocally on the systemn

On an attached USBn

On a connected shared network driveThis section explains how to manage folders on the CFX Opus Dx system.

Creating a New Folder
To create a new folder
1.

On the Home screen, tap Files to view the File Browser screen.

2.

On the File Browser screen, navigate to location in which you want to create the new folder.

3.

Tap Create Folder () and type a name using the alphanumeric keypad that appears and then tap

OK to confirm.
The new folder appears in the File Browser.

Copying a Folder
You can copy a folder in one location on the system and save it and its contents into another location. For
example, you can copy the folder to an attached USB drive, your shared network drive, or to the Publicfolder.
You can also copy a folder and save it into the same location. In this case, you must rename the copied
folder. You cannot have more than one folder with the same name in the same location.

To copy a folder
1.

On the Home screen, tap Files to view the File Browser screen.

2.

On the File Browser screen, navigate to the folder you want to copy and then tap the ellipses for thatfolder to view the Options pane.

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Chapter 6 Managing Files and Folders

3.

In the Options pane, tap Copy.
The Select Location dialog box appears.

4.

In the Select Location dialog box, navigate to the target location.

5.

Tap Select to copy the folder and its contents to the selected location or Cancel to return to the FileBrowser screen.
Note: If a folder with the same name exists at the selected location, a dialog appears. Tap OK toclose the dialog and select another location.

The CFX Opus Dx system displays a confirmation message when the folder and its contents are
successfully copied.

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Backing Up and Restoring Files and Folders

Deleting a Folder
Important: When you delete a folder, its contents are also deleted. Take care when deleting folders
from the CFX Opus Dx system.

To delete a folder
1.

On the Home screen, tap Files to view the File Browser screen.

2.

On the File Browser screen, navigate to the folder you want to delete and tap its ellipses to view the
Options pane.

3.

In the Options pane, tap Delete. The Delete confirmation message appears.

4.

Tap Delete to confirm or Cancel to return to the File Browser screen.

The CFX Opus Dx system displays a confirmation message when the folder and its contents are
successfully deleted.

Backing Up and Restoring Files and Folders
Using the CFX Opus Dx system’s file browser you can quickly back up and restore your protocol and run
files to an attached USB drive or to a shared network folder.
Tip: Bio-Rad recommends that you back up your data files often, and to a location other than the
CFX Opus Dx system. Follow the recommended SOPs in place at your site.
To restore files that are lost during a power failure or system disconnection, see File Storage on page 128.
Notes: You can back up and restore only one file or folder at a time.

To back up or restore files
1.

With the target file open in the File Browser screen, tap Options > Copy.

2.

In the Select Location dialog box, tap the target destination and then tap Select.

To back up or restore folders
1.

In the File Browser screen, tap the ellipses for the target folder and then tap Copy.

2.

In the Select Location dialog box, tap the target destination and then tap Select.

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Chapter 6 Managing Files and Folders

File Storage
The CFX Opus Dx system stores a number of files depending on the system. These files are saved locallyin the selected folder in the File Browser menu, and in the Run Reports menu.
The CFX Opus Dx system stores up to 100 of the most recent run reports in case an interruption to thesystem connection occurs when a run is in progress. For more information on how to recover files from theRun Reports menu, see Recovering Files on page 149.
The CFX Opus Dx system can store the following number of real-time PCR files:n

CFX Opus 96 Dx: Approximately 1000 files (100 are stored in the Run Reports menu; the remainder
are stored in the My Files folder)n

CFX Opus Deepwell Dx: Approximately 1000 files (100 are stored in Run Reports menu; theremainder are stored in the My Files folder)n

CFX Opus 384 Dx: Approximately 500 files (100 are stored in Run Reports menu; the remainder are
stored in the My Files folder)

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Warranty

Appendix A Bio-Rad’s Real-Time PCR Detection
Systems and CFX Maestro Dx SE Software
Catalog Numbers
This appendix lists the catalog numbers for Bio-Rad’s real-time PCR detection systems, software
services, CFX Maestro Dx SE Software, and accessories.
Table 12. Catalog numbers for Bio-Rad’s CFX Opus Dx Real-Time PCR System, accessories, and
CFX Maestro Dx SE Software

Catalog Number

Description

Instruments
12014330

CFX Opus 96 Dx Real-Time PCR System

12014334

CFX Opus 96 Dx Real-Time PCR System, China

12014335

CFX Opus 384 Dx Real-Time PCR System

12014348

CFX Opus 384 Dx Real-Time PCR System, China

12016687

CFX Opus Deepwell Dx Real-Time PCR System

12016659

CFX Opus Deepwell Dx Real-Time PCR System, China

CFX Maestro Dx SE Software and accessories
12014349

CFX Maestro Dx SE Software

12012942

USB cable* (For use with CFX Opus instruments only)

12013205

Ethernet cable * (For use with CFX Opus instruments only)* For continued compliance with EMC standards only use Bio-Rad-approved USB and Ethernet cables withthis instrument.

Warranty
The CFX Opus Dx system and its associated accessories are covered by a standard Bio-Rad warranty.
Contact your local Bio-Rad office for the details of the warranty.

Operation Manual | 129

Appendix A Bio-Rad’s Real-Time PCR Detection Systems and CFX Maestro Dx SE Software Catalog Numbers

130 | CFX Opus 96 Dx, CFX Opus 384 Dx, and CFX Opus Deepwell Dx Real-Time PCR Systems

Appendix B Recommended Plastic Consumables
Plastic Consumables for CFX Opus 384 Dx Systems
For optimal results, Bio-Rad recommends the following consumables for CFX Opus 384 Dx systems:n

HSP3805 — Hard-Shell low-profile 384-well plates with clear shell and white wellsnHSP3865 — Hard-Shell low-profile 384-well plates with black shell and white wells

Plastic Consumables for CFX Opus 96 Dx and CFX Deepwell
Dx Systems
The CFX Opus 96 Dx and CFX Deepwell Dx systems accept low-profile 0.2 ml plates and tubes. Bio-Rad
recommends thethe HSP9655 — Hard-Shell low-profile 96-well skirted PCR plates with white shell andwhite wells for optimal results. These additional plastic consumables will fit the system but may need to bevalidated and optimized for specific workflows:
The CFX Opus 96 Dx and CFX Opus Deepwell Dx systems accept low-profile 0.2 ml plates and tubes.
Bio-Rad recommends the following consumables for optimal results:n

HSP9601 — Hard-Shell low-profile 96-well skirted PCR plates with white shell and clear wellsn

TLS0801 — Low-profile 0.2 ml 8-tube PCR strips without caps, clearn

TLS0851 — Low-profile 0.2 ml 8-tube PCR strips without caps, whiten

TCS0803 — Optical flat 8-cap strip, for 0.2 ml PCR tubes and plates

Plastic Consumables for CFX Opus 96 Dx Systems
These consumables are compatible with CFX Opus 96 systems. However, Bio-Rad recommends theconsumables listed in Plastic Consumables for CFX Opus 96 Dx and CFX Deepwell Dx Systems for
optimal results.
n

MLL9601 — Multiplate low-profile 96-well unskirted PCR plates with clear wellsn

MLL9651 — Multiplate low-profile 96-well unskirted PCR plates with white wells

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Appendix B Recommended Plastic Consumables

Plastic Consumables for CFX Opus Deepwell Dx Systems
These consumables are compatible with CFX Opus Deepwell Dx systems. However, Bio-Rad
recommends the consumables listed in Plastic Consumables for CFX Opus 96 Dx and CFX Deepwell Dx
Systems for optimal results.
n

HSS9665 — high profile, semi skirted PCR plate, black shell, white welln

HSS9601— high profile, semi skirted PCR plate, white shell, clear well

Plate Seals and Plate Sealer
For optimal results, Bio-Rad recommends the following plate seals:n

MSB1001 — Microseal 'B' adhesive seals, optically clear (strong adhesive-based)n

MSC1001 — Microseal 'C' optical seals, optically clear (pressure-activated, adhesive-based)n

1814030 — Optically clear heat seal plate sealer

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Appendix C Maintenance and TroubleshootingThis appendix explains how to clean and maintain the CFX Opus Dx Real-Time PCR System and how totroubleshoot problems that you might have. If you need to return the system to Bio-Rad, see Returning the
CFX Opus Dx Real-Time PCR System to Bio-Rad.
Important: Cybersecurity is the protection of assets in cyberspace from cyberattacks. Cybersecurity
is Bio-Rad’s ability to secure its people, information, systems, and reputation in cyberspace.
Cyberspace is the always-on, technologically interconnected world; it consists of people,
organizations, information, and technology.
Fast reaction is important with cybersecurity issues! If you suspect that there may be a cybersecurity
issue concerning your instrument or that cybersecurity has been breached at your site, contact your
Bio-Rad representative for technical support immediately.

Cleaning and Maintaining the CFX Opus Dx Real-Time PCR
SystemThe CFX Opus Dx system requires little maintenance for proper operation and precise thermal control.
However, with long and constant use, the system will require some cleaning and other maintenance.
The CFX Opus Dx system includes a sensitive optical shuttle system that moves quickly during datacollection and a sample block that must heat and cool quickly. Contamination of these components caninterfere with thermal cycling and data collection.
Avoid contaminating your CFX Opus Dx system by following these guidelines:n

Always clean the outside of any containers before placing them in the block.

n

Never run a reaction with a seal that is open, loose, punctured, or otherwise damaged.

nClean the sample block and inner lid periodically to prevent the buildup of dirt, biohazardous material,or fluorescent solutions (see Table 14 on page 136).

Operation Manual | 133

Appendix C Maintenance and TroubleshootingnClean the outer surface of the CFX Opus Dx system on a regular schedule to remove any debris ordirt that might interfere with proper function (see Table 14). Clean the system to prevent damage tothe air intake or sample bay.

Important: For instructions on handling and cleaning radioactive or biohazardous materials, consult
the guidelines for radiation safety and biosafety provided by your institution. These guidelines also
include hazardous materials disposal methods.

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Cleaning and Maintaining the CFX Opus Dx Real-Time PCR System

CFX Opus Dx Real-Time PCR System Cleaning and Maintenance Safety Warnings
When cleaning and maintaining the CFX Opus Dx system, always consider and follow the warnings listed
in Table 13 that follows.
Table 13. Cleaning and maintenance safety warnings

Warning
To prevent electrical shock, always turn off and unplug the instrument from the electricaloutlet before cleaning it.

A thermal cycler operates at temperatures high enough to cause serious burns. Always
allow the entire instrument to return to room temperature before cleaning.

When handling biohazardous or radioactive samples, adhere to the recommended
precautions and guidelines specific to your laboratory and location. These guidelines
should include cleaning, monitoring, and disposal methods for the hazardous material(s) you are using.
In addition, as identified above, there is a small risk of explosion, or of expulsion ofliquids or vapors from the sample container(s). When working with hazardous materials
the risk of injury from expelled material is compounded with the risk that the hazardous
material themselves could be dispersed in and around the instrument. Users shouldtake appropriate precautions for such a situation.

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Appendix C Maintenance and Troubleshooting

CFX Opus Dx Real-Time PCR System Maintenance
Table 14 lists the components of the CFX Opus Dx system that require maintenance.
Table 14. CFX Opus Dx system maintenance

Component

ActionAir vents

Use a soft brush, damp cloth, or vacuum cleaner to remove light dust
from the air vents. Remove any heavy dust that is deep in the vents witha vacuum cleaner.
Tip: Cleaning the vents allows sufficient airflow for precise thermal
control during a run.

Touch screen

Use any commercially available touch screen cleaning agent and a soft
cloth to clean the touch screen.
Note: Do not spray or pour cleaning agent directly onto the touch
screen.
Note: Do not use abrasive detergents or rough material because
they can scratch the touch screen.

Outside case of the system

Use a damp cloth or tissue to clean spills off the outside case. If
needed, use a mild soap solution and remove the residue completely.
Tip: Cleaning the outside case prevents corrosion.

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Cleaning and Maintaining the CFX Opus Dx Real-Time PCR System

Table 14. CFX Opus Dx system maintenance, continued

Component

ActionSample block

Important: Clean spills immediately to prevent them from drying
inside wells.
Use disposable plastic pipettes with water (recommended), 95%
ethanol, or a 1:100 dilution of bleach in water. Always rinse the wellswith water several times to remove all traces of ethanol, bleach, orsoap.
Note: Consider the following when cleaning the sample block:n If left in the block wells, bleach, ethanol, or soap could corrode theblock and/or destroy tubes and microplates during a run. Always
rinse the block thoroughly after cleaning it with any solution otherthan water.
n Never clean the sample block with strong alkaline solutions (strong
soap, ammonia, or highly concentrated bleach). Never use corrosiveor abrasive cleaning solutions. These cleaning agents can damage
the block, preventing precise thermal control.
n Never heat the block with cleaning solution on or in it. Heating theblock with cleaning solution damages the block and lid, and cancontaminate the optics.
If oil is used, the wells must be cleaned thoroughly and often. Use of oilin the wells is not recommended. Use a solution of 95% ethanol toclean oil on the sample block. Do not allow oil to build up in the block.

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Appendix C Maintenance and Troubleshooting

Maintaining Sufficient Air Flow
The CFX Opus Dx system requires sufficient air flow to heat and cool precisely to the correct target
temperature. If the flow of air is blocked, the thermal cycler cannot ramp to the correct temperature in thespecified time. This section explains how to test the air flow and how to fix low or warm air flow.

Testing for Sufficient Air Flow
The air flow is sufficient when the system heats and cools to the correct target temperatures promptly.
Bio-Rad suggests that you test the air flow when you set up the CFX Opus Dx system in a new location.
You can also measure the air temperature at any time to ensure sufficient air flow.

To determine the presence of sufficient air flow
1.

Set up and start the system.

2.

Adjust the local environment for typical conditions:

3.

nTurn on any nearby equipment, such as fans or other systems.

nOpen any window blinds to reproduce typical conditions during a run.

Run a typical PCR protocol for 30 min.
If more than one system is in the area, run a protocol on all at the same time.
Note: Samples are not required for the test runs. However, you must include an empty
microplate or capped strip tubes. The lid does not heat correctly if it touches the sample block.

4.

Measure the air temperature at the air intake vents.
If the air intake temperature increases above 31°C, see the following section Fixing Insufficient Air
Flow.

Fixing Insufficient Air Flow
If the air temperature near the system is above 31°C, make one or more of the following changes toincrease the flow of cooler air:nAdjust air conditioning to lower the ambient air temperature.

nMove the system to another location.

nProvide more space around the system and between adjacent systems. Arrange the systems so thatthe warm exhaust air from one does not enter the air intake vents of another.

nShield the system from heat sources such as radiators, heat-producing instruments, and brightsunlight.

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Replacing Fuses

Replacing Fuses
Fuses on the CFX Opus Dx system are designed to blow in case of severe power surges or other causesof electrical short. This protects both the user and the system from excessive, potentially damaging
electric currents. Fuses on the CFX Opus Dx system rarely need to be replaced. However, someinstitutions prefer to replace fuses on a regular basis to maintain uninterrupted operation.
If the system does not power up, first verify that the power cord is plugged in to a functioning powersource. Also, verify that the power cord and power source are within the specifications for this system.
Important: Do not attempt to replace the power cord on the CFX Opus Dx system. Instead, contact
Bio-Rad Technical Support.
Finally, verify that the fuses are intact. If the fuses are broken or burned, replace the fuses. This section
explains how to view and replace fuses on the CFX Opus Dx system.
Tip: The system utilizes two 10 A, 250 V, 5 x 20 mm, fast blow fuses.
WARNING! To prevent electrical shock, always turn off and unplug the system from theelectrical outlet before checking the fuses.

To view and replace the fuses
1.

Verify that you have powered off the instrument and unplugged the power cord from the back of the
instrument.
Important: You must unplug the power cord from the instrument to open the fuse door. Trying toopen the fuse door while the cord is plugged in could damage the door.

2.

Using your finger tip, gently pull the black fuse door on the back of the system out toward you.

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Appendix C Maintenance and Troubleshooting

3.

Using a small flathead screw driver, gently pry out the red fuse holder until you can grasp it with yourfingers.

4.

When you can firmly grasp the fuse holder, pull it straight out of the instrument.

5.

Using a finger tip, gently pry the fuse out of the fuse holder.

6.

The fuse holder contains two fuses, one on each side. You must inspect both fuses.

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Replacing Fuses

A bad fuse displays a break or burned spot in the internal metal filament, or measures open with an
Ohm meter. A good fuse has an internal metal filament or measures short (< 1 Ohm). If a fuse is bador damaged, replace it with a new fuse of the same type and rating.
Note: Some fuses used in the CFX Opus Dx system are made from ceramic and cannot be
visually inspected. In this case, you must use an Ohm meter to determine whether the fuse isgood. Alternatively, you can replace the fuse with a known good one without checking.

7.

Assuming the prongs indicate the front of the fuse holder, insert the back end of a 10 A, 250 V, 5 x 20mm, fast blow fuse into the middle bracket. Ensure the front end of the fuse faces the prongs. For
example:8.

With the flat red square on the fuse holder facing upward, insert the fuse holder into the instrument
and firmly press it into position.

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Appendix C Maintenance and Troubleshooting

9.

Close the fuse door, insert the power cord, and turn on the instrument.
Caution: If the CFX Opus Dx system repeatedly blows one or more fuses, there could be
an internal problem with the instrument. Contact Bio-Rad Technical Support forassistance in determining whether it is safe to replace the fuses again or if the instrument
should be repaired.

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Upgrading Software and Firmware on CFX Opus Dx Real-Time PCR Systems

Upgrading Software and Firmware on CFX Opus Dx Real-Time
PCR Systems
Important: Only the Admin user can upgrade software and firmware on CFX Opus Dx systems.
Before upgrading, Bio-Rad recommends that you verify the current version installed on the CFX Opus Dx
system. This section explains how to verify the installed version and how to upgrade the system.
Note: Depending on the type of upgrade, this process can take several minutes to complete.

Verifying the Currently Installed Version
To verify the current version of the CFX Opus Dx system software1.

On Home screen, tap Tools to view the Tools screen.
Tip: If you are logged in as Admin, tap the User icon at the bottom of the screen to view the tools
available to all users.

2.

Tap About and locateOpus Version on the About screen.

3.

Note the currently installed version.
Ensure the version you are upgrading to is newer than the version currently installed.

4.

Tap Back and then tap Home to return to the Home screen.

Upgrading the CFX Opus Dx Real-Time PCR System Software and Firmware
Note: Depending on the type of upgrade, this process can take several minutes to complete.
Important: While the upgrade is in progress, do not shut down the system and do not remove theUSB drive.

To upgrade the software and firmware
1.

From the CFX Maestro Dx SE computer, log into bio-rad.com and go to the Firmware and Software
Updates page to download the installer onto an attached USB drive.

2.

Insert the USB drive into a USB port on the CFX Opus Dx system.

3.

Log in as an Admin user.

4.

On the Home screen, tap Tools to open the Admin tools screen.

5.

In the Admin tools screen, tap System Update.
The Software and Instrument Updates screen appears.

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Appendix C Maintenance and Troubleshooting

6.

(Optional) To get details about the update, tap Details.

7.

Do one of the following:n

To cancel the update, tap Cancel.

n

To proceed, tap Update and follow the prompts.
Note: When the update completes, the system automatically restarts.

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Shutting Down the CFX Opus Dx Real-Time PCR System

Shutting Down the CFX Opus Dx Real-Time PCR System
Important: Follow these instructions to safely and completely shut down the CFX Opus Dx system.

To shut down the CFX Opus Dx system
1.

Ensure that no protocol is running and the system is no longer in use.

2.

If you have not already done so, remove the samples from the block:a.

On the Home screen, tap Open Lid to access the samples.

b.

Remove the samples from the block and then close the lid.

3.

On the Home screen, tap Logout to log out of the system.

4.

On the Login screen, tap Shut Down (5.

When the CFX Opus Dx system has completed the soft shutdown process, press the power switch
on the back of the instrument to power off the system.

) to perform a soft shutdown of the system.

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Appendix C Maintenance and Troubleshooting

Returning the CFX Opus Dx Real-Time PCR System to
Bio-RadImportant: Should you need to return your CFX Opus Dx system instrument to Bio-Rad, your
Bio-Rad Technical Support specialist will provide instructions for decontaminating, packaging, andshipping the instrument. Before you return the instrument, you must install the shipping plate andshipping screw. This section explains these tasks.
Note: Locate the shipping screw and shipping plate that you saved when you installed the system.
You will need these items to properly package the system. Bio-Rad will send you the packaging
material required to safely return the system.
Important: Before you begin, ensure that you have completely backed up all data files to a shared
network drive or a USB drive.

Installing the Shipping Plate and Screw
Tip: This information is also available on the CFX Opus Dx system’s touch screen to ensure you
accurately install the screw.

To install the shipping plate and screw
1.

If necessary, start the CFX Opus Dx system and log in.

2.

Copy all user data to a network drive or an attached USB drive.

3.

On the Home screen, tap Tools to view the User Tools screen.
Note: The Shipping Screw button appears on the User > Tools screen. If you logged in as the
Admin user, tap User at the bottom of the screen.

4.

On the User Tools screen, tap Shipping Screw.
The Shipping Screw screen appears with instructions for installing the shipping screw.

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Returning the CFX Opus Dx Real-Time PCR System to Bio-Rad

5.

Follow the instructions to install the shipping screw.
a.

Tap Open Lid on the bottom button bar.

b.

Place the shipping plate on the sample block.

c.

On the Install Shipping Screw screen, tap Close Lid to close the lid.

d.

Tap Lock Instrument to position the shuttle and lock the lid in place.
The system displays a message confirming that you have installed the shipping plate.

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Appendix C Maintenance and Troubleshootingn

If the shipping plate is installed, tap Yes. The system locks the instrument for shipping.
When lock-down is complete, tap OK and continue with Step e that follows.

n

If the shipping plate is not installed, tap No. The system stops the lock-down process andreturns to the Install Shipping Screw screen.
Repeat the steps in this procedure and ensure to install the shipping plate.

e.

Remove the plug (store it in a safe place) and then install the shipping screw, turning it clockwise
until it is securely in place.

f.

On the Shipping Screw screen, tap Screw Installed to confirm the shipping screw is installed.

6.

Tap Back to return to the Home screen.

7.

Log out of the system and then shut down the CFX Opus Dx system.

8.

Package and ship the system to Bio-Rad according to the instructions provided by Bio-Rad.

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Troubleshooting CFX Opus Dx Real-Time PCR Systems

Troubleshooting CFX Opus Dx Real-Time PCR Systems
This section provides information about exporting system log information that can be used fortroubleshooting purposes. It also lists potential problems and suggested solutions for the CFX Opus Dx
system.

Recovering Files
The CFX Opus Dx system allows for an Admin user to recover up to 100 of the most recent .zpcr files andexport them to a USB drive in case an interruption to the system connection occurs or the system
unexpectedly shuts down while a run is in progress. These files are retrieved from the Run Reports menu.
Note: Only an Admin user can recover files from the Run Reports menu.

To recover files from the Run Reports menu:
1.

Insert a USB drive into a USB port of the CFX Opus system.

2.

Tap Admin to log in as an Admin user.

3.

On the Home screen, tap Tools to open the Tools screen.

4.

Tap User.

5.

Tap Run Reports to access the Run Reports screen.

6.

In the Run Reports screen, select the desired Run Report.

7.

Tap the Recover Data button. The .zpcr file is saved to the attached USB drive.

Notes: You can only recover one .zpcr file at a time.
Once you recover the file, you can drag and drop the .zpcr file into Maestro and view the PCR run in the
Data Analysis window.

Viewing and Exporting Log Files
CFX Opus Dx system message and usage log files contain information that is helpful in troubleshooting
problems with the system. Bio-Rad Technical Support might ask you to provide these files so that they
can better assist you in resolving problems. You can export the log files to an attached USB drive.
The CFX Opus Dx system retains all message and usage log data until it is cleared. Only an Admin user
can clear the log file.

To view and export log files
1.

If you have not yet done so, insert a USB drive into a USB port on the instrument.

2.

On the Home screen, tap Tools and open the User Tools screen.

Operation Manual | 149

Appendix C Maintenance and Troubleshooting

3.

On the User Tools screen, tap System Logs.
The System Logs screen appears, displaying the message logs by default.

4.

5.

Tap Export Logs to export the system logs. The CFX Opus Dx system creates a folder labeled
Exports on the attached USB drive and exports the following files as .txt files:nSystemMessageLognSystemUsageLognDebugLog

n

OSLog

n

FirmwareUpdateLogn

GUILogn

WCFLogClick Back twice to return to the Home screen.

To view the log information, remove the USB drive from the CFX Opus Dx system, insert it into a USB port
on an available computer, and open the log files in a text editing or word processing program.

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Troubleshooting CFX Opus Dx Real-Time PCR Systems

Troubleshooting Issues
Error

Possible causes

Troubleshooting steps

Unable to use USB

Power loss

Turn the CFX Opus Dx system off and thendriveson.

Operation Manual | 151

Appendix C Maintenance and Troubleshooting

152 | CFX Opus 96 Dx, CFX Opus 384 Dx, and CFX Opus Deepwell Dx Real-Time PCR Systems

Appendix D Bio-Rad Free and Open-Source
Notices for PCR ProductsThis document includes licensing information relating to free, open-source, and public-source softwareand data (together, the “MATERIALS”) included with or used to develop Bio-Rad products and services.
The terms of the applicable free, open-source, and public-source licenses (each an “OPEN LICENSE”)
govern Bio-Rad’s distribution and your use of the MATERIALS. Bio-Rad and the third-party authors,licensors, and distributors of the MATERIALS disclaim all warranties and liability arising from all use anddistribution of the MATERIALS. To the extent the OSS is provided under an agreement with Bio-Rad thatdiffers from the applicable OSS LICENSE, those terms are offered by Bio-Rad alone.
Bio-Rad has reproduced below copyright and other licensing notices appearing within the MATERIALS.
While Bio- Rad seeks to provide complete and accurate copyright and licensing information for all
MATERIALS, Bio-Rad does not represent or warrant that the following information is complete, correct, or
error-free. MATERIALS recipients are encouraged to (a) investigate the identified MATERIALS to confirm
the accuracy of the licensing information provided and (b) notify Bio-Rad of any inaccuracies or errors
found in this document so that Bio-Rad may update this document accordingly.
Certain OPEN LICENSES (such as the Affero General Public Licenses, Common Development andDistribution Licenses, Common Public License, Creative Commons Share-Alike License, Eclipse Public
License, Mozilla Public Licenses, GNU General Public Licenses, GNU Library/Lesser General Public
Licenses, and Open Data Commons Open Database License) require that the source materials be madeavailable to recipients or other requestors under the terms of the same OPEN LICENSE.
The corresponding open source software is available for download from the links in the section that
follows.

Operation Manual | 153

Appendix D Bio-Rad Free and Open-Source Notices for PCR Products

Software Notices
M2Mqtt (paho.mqtt.m2mqtt)
Project homepage/download sites:
https://m2mqtt.wordpress.com/
https://www.nuget.org/packages/M2Mqtt/
Bio-Rad source code site:
https://github.com/bio-rad-lsg-open-source/Mqtt-4.3.0.0
External source code site:
https://github.com/eclipse/paho.mqtt.m2mqtt
Project licensing notices:

Eclipse Foundation Software User Agreement
February 1, 2011
Usage Of Content
THE ECLIPSE FOUNDATION MAKES AVAILABLE SOFTWARE, DOCUMENTATION,
INFORMATION AND/OR OTHER MATERIALS FOR OPEN SOURCE PROJECTS(COLLECTIVELY "CONTENT"). USE OF THE CONTENT IS GOVERNED BY THE TERMS
AND CONDITIONS OF THIS AGREEMENT AND/OR THE TERMS AND CONDITIONS OF
LICENSE AGREEMENTS OR NOTICES INDICATED OR REFERENCED BELOW. BY USINGTHE CONTENT, YOU AGREE THAT YOUR USE OF THE CONTENT IS GOVERNED BY
THIS AGREEMENT AND/OR THE TERMS AND CONDITIONS OF ANY APPLICABLE
LICENSE AGREEMENTS OR NOTICES INDICATED OR REFERENCED BELOW. IF YOU
DO NOT AGREE TO THE TERMS AND CONDITIONS OF THIS AGREEMENT AND THE
TERMS AND CONDITIONS OF ANY APPLICABLE LICENSE AGREEMENTS OR NOTICESINDICATED OR REFERENCED BELOW, THEN YOU MAY NOT USE THE CONTENT.
Applicable Licenses
Unless otherwise indicated, all Content made available by the Eclipse
Foundation is provided to you under the terms and conditions of the
Eclipse Public License Version 1.0 ("EPL"). A copy of the EPL isprovided with this Content and is also available at
http://www.eclipse.org/legal/epl-v10.html. For purposes of the EPL,
"Program" will mean the Content.

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Software Notices

Content includes, but is not limited to, source code, object code,
documentation and other files maintained in the Eclipse Foundation
source code repository ("Repository") in software modules ("Modules")and made available as downloadable archives ("Downloads").
l

l

l

l

Content may be structured and packaged into modules tofacilitate delivering, extending, and upgrading the Content.
Typical modules may include plug-ins ("Plug-ins"), plug-in
fragments ("Fragments"), and features ("Features").
Each Plug-in or Fragment may be packaged as a sub-directory or
JAR (Java™ ARchive) in a directory named "plugins".
A Feature is a bundle of one or more Plug-ins and/or Fragments
and associated material. Each Feature may be packaged as a subdirectory in a directory named "features". Within a Feature,
files named "feature.xml" may contain a list of the names andversion numbers of the Plug-ins and/or Fragments associated withthat Feature.
Features may also include other Features ("Included Features").
Within a Feature, files named "feature.xml" may contain a listof the names and version numbers of Included Features.

The terms and conditions governing Plug-ins and Fragments should becontained in files named "about.html" ("Abouts"). The terms andconditions governing Features and Included Features should becontained in files named "license.html" ("Feature Licenses"). Abouts
and Feature Licenses may be located in any directory of a Download or
Module including, but not limited to the following locations:
l
l
l
l
l

The top-level (root) directoryPlug-in and Fragment directories
Inside Plug-ins and Fragments packaged as JARs
Sub-directories of the directory named "src" of certain Plug-ins
Feature directories

Note: if a Feature made available by the Eclipse Foundation is
installed using the Provisioning Technology (as defined below), youmust agree to a license ("Feature Update License") during the
installation process. If the Feature contains Included Features, theFeature Update License should either provide you with the terms andconditions governing the Included Features or inform you where you
can locate them. Feature Update Licenses may be found in the"license" property of files named "feature.properties" found within a
Feature. Such Abouts, Feature Licenses, and Feature Update Licenses
contain the terms and conditions (or references to such terms andOperation Manual | 155

Appendix D Bio-Rad Free and Open-Source Notices for PCR Productsconditions) that govern your use of the associated Content in that
directory.
THE ABOUTS, FEATURE LICENSES, AND FEATURE UPDATE LICENSES MAY REFER
TO THE EPL OR OTHER LICENSE AGREEMENTS, NOTICES OR TERMS AND
CONDITIONS. SOME OF THESE OTHER LICENSE AGREEMENTS MAY INCLUDE (BUT
ARE NOT LIMITED TO):
l

l

l

l

l

l

Eclipse Distribution License Version 1.0 (available at
http://www.eclipse.org/licenses/edl-v1.0.html)
Common Public License Version 1.0 (available at
http://www.eclipse.org/legal/cpl-v10.html)
Apache Software License 1.1 (available at
http://www.apache.org/licenses/LICENSE)
Apache Software License 2.0 (available at
http://www.apache.org/licenses/LICENSE-2.0)
Metro Link Public License 1.00 (available at
http://www.opengroup.org/openmotif/supporters/metrolink/license.html)
Mozilla Public License Version 1.1 (available at
http://www.mozilla.org/MPL/MPL-1.1.html)

IT IS YOUR OBLIGATION TO READ AND ACCEPT ALL SUCH TERMS AND
CONDITIONS PRIOR TO USE OF THE CONTENT. If no About, Feature License,or Feature Update License is provided, please contact the Eclipse
Foundation to determine what terms and conditions govern thatparticular Content.

Use of Provisioning Technology
The Eclipse Foundation makes available provisioning software,examples of which include, but are not limited to, p2 and the Eclipse
Update Manager ("Provisioning Technology") for the purpose ofallowing users to install software, documentation, information and/or
other materials (collectively "Installable Software"). This
capability is provided with the intent of allowing such users to
install, extend and update Eclipse-based products. Information about
packaging Installable Software is available at
http://eclipse.org/equinox/p2/repository_packaging.html("Specification").
You may use Provisioning Technology to allow other parties to install
Installable Software. You shall be responsible for enabling theapplicable license agreements relating to the Installable Software to
be presented to, and accepted by, the users of the Provisioning

156 | CFX Opus 96 Dx, CFX Opus 384 Dx, and CFX Opus Deepwell Dx Real-Time PCR Systems

Software Notices

Technology in accordance with the Specification. By using
Provisioning Technology in such a manner and making it available inaccordance with the Specification, you further acknowledge youragreement to, and the acquisition of all necessary rights to permit
the following:
1. A series of actions may occur ("Provisioning Process") in which auser may execute the Provisioning Technology on a machine ("Target
Machine") with the intent of installing, extending or updating thefunctionality of an Eclipse-based product.
2. During the Provisioning Process, the Provisioning Technology may
cause third party Installable Software or a portion thereof to beaccessed and copied to the Target Machine.
3. Pursuant to the Specification, you will provide to the user theterms and conditions that govern the use of the Installable Software("Installable Software Agreement") and such Installable Software
Agreement shall be accessed from the Target Machine in accordancewith the Specification. Such Installable Software Agreement must
inform the user of the terms and conditions that govern the
Installable Software and must solicit acceptance by the end user inthe manner prescribed in such Installable Software Agreement. Uponsuch indication of agreement by the user, the provisioning Technology
will complete installation of the Installable Software.

Cryptography
Content may contain encryption software. The country in which you are
currently may have restrictions on the import, possession, and use,
and/or re-export to another country, of encryption software. BEFORE
using any encryption software, please check the country's laws,
regulations and policies concerning the import, possession, or use,
and re-export of encryption software, to see if this is permitted.
Java and all Java-based trademarks are trademarks of Oracle
Corporation in the United States, other countries, or both.
/LICENSE:
See EPL-1.0 in the Standard OSS License Text appendix to this document.

Operation Manual | 157

Appendix D Bio-Rad Free and Open-Source Notices for PCR ProductsStandard Open License Text
EPL 1.0
Eclipse Public License - v 1.0
THE ACCOMPANYING PROGRAM IS PROVIDED UNDER THE TERMS OF THIS ECLIPSE
PUBLIC LICENSE ("AGREEMENT"). ANY USE, REPRODUCTION OR DISTRIBUTION
OF THE PROGRAM CONSTITUTES RECIPIENT'S ACCEPTANCE OF THIS AGREEMENT.
1. DEFINITIONS"Contribution" means:a) in the case of the initial Contributor, the initial code anddocumentation distributed under this Agreement, andb) in the case of each subsequent Contributor:i) changes to the Program, andii) additions to the Program;where such changes and/or additions to the Program originate from andare distributed by that particular Contributor. A Contribution'originates' from a Contributor if it was added to the Program bysuch Contributor itself or anyone acting on such Contributor'sbehalf. Contributions do not include additions to the Program which:(i) are separate modules of software distributed in conjunction with
the Program under their own license agreement, and (ii) are notderivative works of the Program.
"Contributor"
Program.

means

any

personorentitythat

distributes

the"Licensed Patents" mean patent claims licensable by a Contributor
which are necessarily infringed by the use or sale of its
Contribution alone or when combined with the Program.
"Program" means the Contributions distributed in accordance with thisAgreement.
"Recipient" means anyone who receives
Agreement, including all Contributors.

theProgram

158 | CFX Opus 96 Dx, CFX Opus 384 Dx, and CFX Opus Deepwell Dx Real-Time PCR Systems

under

this

Standard Open License Text

2. GRANT OF RIGHTSa) Subject to the terms of this Agreement, each Contributor hereby
grants Recipient a non-exclusive, worldwide, royalty-free copyrightlicense to reproduce, prepare derivative works of, publicly display,
publicly perform, distribute and sublicense the Contribution of such
Contributor, if any, and such derivative works, in source code andobject code form.
b) Subject to the terms of this Agreement, each Contributor hereby
grants Recipient a non- exclusive, worldwide, royalty- free patent
license under Licensed Patents to make, use, sell, offer to sell,
import and otherwise transfer the Contribution of such Contributor,
if any, in source code and object code form. This patent license
shall apply to the combination of the Contribution and the Program
if, at the time the Contribution is added by the Contributor, such
addition of the Contribution causes such combination to be covered by
the Licensed Patents. The patent license shall not apply to any othercombinations which include the Contribution. No hardware per se islicensed hereunder.
c) Recipient understands that although each Contributor grants thelicenses to its Contributions set forth herein, no assurances areprovided by any Contributor that the Program does not infringe thepatent or other intellectual property rights of any other entity.
Each Contributor disclaims any liability to Recipient for claims
brought by any other entity based on infringement of intellectual
property rights or otherwise. As a condition to exercising the rights
and licenses granted hereunder, each Recipient hereby assumes sole
responsibility to secure any other intellectual property rights
needed, if any. For example, if a third party patent license isrequired to allow Recipient to distribute the Program, it isRecipient's
responsibility
toacquirethat
licensebeforedistributing the Program.
d) Each Contributor represents that to its knowledge it has
sufficient copyright rights in its Contribution, if any, to grant the
copyright license set forth in this Agreement.
3. REQUIREMENTS
A Contributor may choose to distribute the Program in object code
form under its own license agreement, provided that:a) it complies with the terms and conditions of this Agreement; andOperation Manual | 159

Appendix D Bio-Rad Free and Open-Source Notices for PCR Productsb) its license agreement:i) effectively disclaims on behalf of all Contributors all warranties
and conditions, express and implied, including warranties orconditions of title and non-infringement, and implied warranties orconditions of merchantability and fitness for a particular purpose;ii) effectively excludes on behalf of all Contributors all liability
for damages, including direct, indirect, special, incidental andconsequential damages, such as lost profits;iii) states that any provisions which differ from this Agreement are
offered by that Contributor alone and not by any other party; andiv) states that source code for the Program is available from such
Contributor, and informs licensees how to obtain it in a reasonable
manner on or through a medium customarily used for software exchange.
When the Program is made available in source code form:a) it must be made available under this Agreement; andb) a copy of this Agreement must be included with each copy of theProgram.
Contributors may not remove or alter any copyright notices contained
within the Program.
Each Contributor must identify itself as the originator of its
Contribution, if any, in a manner that reasonably allows subsequent
Recipients to identify the originator of the Contribution.
4. COMMERCIAL DISTRIBUTION
Commercial
distributorsofsoftwaremay
acceptcertain
responsibilities with respect to end users, business partners and thelike. While this license is intended to facilitate the commercial useof the Program, the Contributor who includes the Program in acommercial product offering should do so in a manner which does notcreate potential liability for other Contributors. Therefore, if aContributor includes the Program in a commercial product offering,such Contributor ("Commercial Contributor") hereby agrees to defend
and indemnify every other Contributor ("Indemnified Contributor")
against any losses, damages and costs (collectively "Losses") arisingfrom claims, lawsuits and other legal actions brought by a third
party against the Indemnified Contributor to the extent caused by theacts or omissions of such Commercial Contributor in connection with160 | CFX Opus 96 Dx, CFX Opus 384 Dx, and CFX Opus Deepwell Dx Real-Time PCR Systems

Standard Open License Text

its distribution of the Program in a commercial product offering. The
obligations in this section do not apply to any claims or Losses
relating to any actual or alleged intellectual property infringement.
In order to qualify, an Indemnified Contributor must: a) promptly
notify the Commercial Contributor in writing of such claim, and b)
allow the Commercial Contributor to control, and cooperate with theCommercial Contributor in, the defense and any related settlement
negotiations. The Indemnified Contributor may participate in any suchclaim at its own expense.
For example, a Contributor might include the Program in a commercial
product offering, Product X. That Contributor is then a Commercial
Contributor. If that Commercial Contributor then makes performance
claims, or offers warranties related to Product X, those performance
claimsandwarranties
aresuchCommercial
Contributor's
responsibility alone. Under this section, the Commercial Contributor
would have to defend claims against the other Contributors related tothose performance claims and warranties, and if a court requires anyother Contributor to pay any damages as a result, the Commercial
Contributor must pay those damages.
5. NO WARRANTY
EXCEPT AS EXPRESSLY SET FORTH IN THIS AGREEMENT, THE PROGRAM ISPROVIDED ON AN "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
KIND, EITHER EXPRESS OR IMPLIED INCLUDING, WITHOUT LIMITATION, ANY
WARRANTIES OR CONDITIONS OF TITLE, NON-INFRINGEMENT, MERCHANTABILITY
OR FITNESS FOR A PARTICULAR PURPOSE. Each Recipient is solely
responsible for determining the appropriateness of using anddistributing the Program and assumes all risks associated with its
exercise of rights under this Agreement, including but not limited to
the risks and costs of program errors, compliance with applicablelaws, damage to or loss of data, programs or equipment, andunavailability or interruption of operations.
6. DISCLAIMER OF LIABILITY
EXCEPT AS EXPRESSLY SET FORTH IN THIS AGREEMENT, NEITHER RECIPIENTNOR ANY CONTRIBUTORS SHALL HAVE ANY LIABILITY FOR ANY DIRECT,INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES(INCLUDING WITHOUT LIMITATION LOST PROFITS), HOWEVER CAUSED AND ON
ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR
TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF
THE USE OR DISTRIBUTION OF THE PROGRAM OR THE EXERCISE OF ANY RIGHTS

Operation Manual | 161

Appendix D Bio-Rad Free and Open-Source Notices for PCR Products

GRANTED HEREUNDER,DAMAGES.

EVENIF

ADVISED

OF

THE

POSSIBILITY

OF

SUCH

7. GENERAL
If any provision of this Agreement is invalid or unenforceable underapplicable law, it shall not affect the validity or enforceability of
the remainder of the terms of this Agreement, and without further
action by the parties hereto, such provision shall be reformed to theminimum
extentnecessarytomakesuch provision
valid
and
enforceable.
If Recipient institutes patent litigation against any entity(including a cross-claim or counterclaim in a lawsuit) alleging that
the Program itself (excluding combinations of the Program with othersoftware or hardware) infringes such Recipient's patent(s), then such
Recipient's rights granted under Section 2(b) shall terminate as ofthe date such litigation is filed.
All Recipient's rights under this Agreement shall terminate if it
fails to comply with any of the material terms or conditions of thisAgreement and does not cure such failure in a reasonable period oftime after becoming aware of such noncompliance. If all Recipient's
rights under this Agreement terminate, Recipient agrees to cease use
and distribution of the Program as soon as reasonably practicable.
However, Recipient's obligations under this Agreement and any
licenses granted by Recipient relating to the Program shall continue
and survive.
Everyone is permitted to copy and distribute copies of thisAgreement, but in order to avoid inconsistency the Agreement is
copyrighted and may only be modified in the following manner. The
Agreement Steward reserves the right to publish new versions(including revisions) of this Agreement from time to time. No one
other than the Agreement Steward has the right to modify thisAgreement. The Eclipse Foundation is the initial Agreement Steward.
The Eclipse Foundation may assign the responsibility to serve as theAgreement Steward to a suitable separate entity. Each new version of
the Agreement will be given a distinguishing version number. The
Program (including Contributions) may always be distributed subject
to the version of the Agreement under which it was received. In
addition, after a new version of the Agreement is published,
Contributor may elect to distribute the Program (including its
Contributions) under the new version. Except as expressly stated in
Sections 2 (a) and 2 (b) above, Recipient receives no rights or

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Standard Open License Text

licenses to the intellectual property of any Contributor under thisAgreement, whether expressly, by implication, estoppel or otherwise.
All rights in the Program not expressly granted under this Agreement
are reserved.
This Agreement is governed by the laws of the State of New York andthe intellectual property laws of the United States of America. No
party to this Agreement will bring a legal action under thisAgreement more than one year after the cause of action arose. Eachparty waives its rights to a jury trial in any resulting litigation.

Operation Manual | 163

Appendix D Bio-Rad Free and Open-Source Notices for PCR Products

164 | CFX Opus 96 Dx, CFX Opus 384 Dx, and CFX Opus Deepwell Dx Real-Time PCR Systems

Appendix E References1.

Breslauer KJ et al. (1986). Predicting DNA duplex stability from the base sequence. Proc Natl Acad
Sci USA 83, 3,746–3,750.

2.

Sugimoto N et al. (1996). Improved thermodynamic parameters and helix initiation factor to predictstability of DNA duplexes. Nucleic Acids Res 24, 4,501–4,505.

Operation Manual | 165

Appendix E References

166 | CFX Opus 96 Dx, CFX Opus 384 Dx, and CFX Opus Deepwell Dx Real-Time PCR Systems

10000135538 Ver G US/EG

Sig 0122