Bio-Rad CFX Automation System II User Manual

CFX Automation System II

Instruction Manual

Catalog #184-5075

Bio-Rad Technical Support

For help and technical advice, please contact the Bio-Rad Technical Support department. In the United
States, the Technical Support department is open Monday–Friday, 5:00 AM–5:00 PM, Pacific time.

http://www.bio-rad.com

Bio-Rad Laboratories
Life Science Research
2000 Alfred Nobel Drive
Hercules, CA 94547

Telephone: [phone]
Tele x: 335-358

Toll Fre e: 1-800-4-BIORAD (1-800-424-6723)
Fax: [phone]
Free Fax: [phone]

Online technical support and worldwide contact information are available at www.consult.bio-rad.com.

Legal Notices

Windows and Microsoft Office are trademarks of Microsoft Corporation.

Bio-Rad real-time systems are covered by one or more of the following U.S. patents, their foreign
counterparts, or their foreign patents pending, owned by Eppendorf AG: US Patent Nos. 6,767,512
and 7,074,367.

Bio-Rad’s Hard-Shell PCR plates are covered by one or more of the following U.S. patents, patents pending,
or their foreign counterparts, owned by Eppendorf AG: US Patent Nos. 7,347,977, 6,340,589, 6,528,302.

No part of this publication may be reproduced or transmitted in any form or by any means, electronic
or mechanical, including photocopy, recording, or any information storage or retrieval system, without
permission in writing from Bio-Rad Laboratories.

Bio-Rad reserves the right to modify its products and services at any time. This instruction manual is subject
to change without notice.

Although prepared to ensure accuracy, Bio-Rad assumes no liability for errors, or for any damages resulting
from the application or use of this information.

Copyright © 2014 by Bio-Rad Laboratories, Inc. All rights reserved.

CFX Automation System II | i

Bio-Rad Laboratories Resources

Bio-Rad provides many resources for scientists, including rich technical resources on a wide variety of methods and applications
related to PCR, real-time PCR, and gene expression. Table 1 lists available resources and how to locate what you need.

Table 1. Bio-Rad resources.

Resource How to Contact

Local Bio-Rad Laboratories Find local information and contacts on the Bio-Rad website (www.bio-rad.com) by selecting
representatives your country on the home page, and find the nearest contacts on the Contact Us page. Find the

nearest international office listed on the back of this manual

Technical support scientists Bio-Rad’s technical support scientists provide our customer with practical and expert solutions.

To find local technical support on the phone, contact your nearest Bio-Rad office. For technical
support in the United States and Canada, call 1-800-424-6723 (toll-free), and select the technical
support option

Service support engineers Maintenance and repairs should be carried out only by authorized service support engineers

For service support in the United States and Canada, call 1-800-424-6723 (toll-free), and select

the technical support option to request service support

Technical notes and literature Go to the Bio-Rad website (www.bio-rad.com). Type a term in the Search box and select

Documents tab to find links to technical notes, manuals, and other literature

Writing Conventions Used in This Manual

This manual uses the writing conventions listed in Table 2.

Table 2. Conventions used in this manual.

Convention Meaning

Tip: Provides helpful information and instructions, including information explained in further detail elsewhere in this manual

Note: Provides important information, including information explained in further detail elsewhere in this manual

WARNING! Explains very important information about something that might injure the researcher, damage the instrument, or

cause data loss

X > Y Select X and then select Y from a toolbar, menu, or sof tware window

Safety and Regulatory Compliance

For safe operation of the CFX Automation System II, we strongly recommend that you follow the safety specifications listed in this
section and throughout the manual.

Safety Warning Labels

Warning labels posted on the instrument and in this manual warn you about sources of injury or harm. Refer to Table 3 to review the
meaning of each safety warning label.

Table 3. Meaning of safety warning labels.

CAUTION: Risk of danger! This symbol identifies components that pose a risk of personal injury or damage to

the instrument if improperly handled. Wherever this symbol appears, consult the manual for further information
before proceeding

CFX Automation System IIii |ii |

Instrument Safety Warnings

The warning labels shown in Table 4 are displayed on the instrument and refer directly to the safe use of the CFX Automation System II.

Table 4. Instrument safety warning labels.

Warning about risk of harm to body or equipment.

Risk of puncture injury. Keep clear of plate handler when in operation.

Operating the CFX Automation System II before reading this manual can constitute a personal injury hazard.

For safe use, do not operate this instrument in any manner unspecified in this manual. Only qualified laboratory
personnel trained in the safe use of electrical equipment should operate this instrument. Always handle all
components of the system with care, and with clean, dry hands

Safe Use Specifications and Compliance

Electrical Safety Information and Classification

Table 5 lists the safe use specifications for the CFX Automation System II. Shielded cables (supplied) must be used with this unit to
ensure compliance with the Class A FCC limits.

Table 5. Safe use specifications.

Safe Use Requirements Specifications

Temperature Ambient temperatures of 4–30°C. Relative humidity maximum of 85% noncondensing

WARNING! To reduce the risk of electric shock, do not remove the cover. No user serviceable parts are inside the CFX Automation
System II. Refer to qualified service personnel if help is required.

WARNING! Use this product only in the manner described in this manual. If the equipment is used in a manner not specified by the
manufacturer, the protection provided by the equipment may be impaired.

FCC Warnings and Notes

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Warning. Changes or modifications to this unit not expressly approved by Bio-Rad Laboratories could void the user’s authority to

operate the equipment

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Note. 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. This equipment generates, uses, and can radiate radio frequency energy and, if not
installed and used in accordance 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 case the user will be required to correct the
interference, at his own expense

n

Note regarding FCC compliance. Although this instrument has been tested and found to comply with Part 15, Subpar t B of the FCC

Rules for a Class A digital device, please note that this compliance 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

n

Note regarding Canadian EMC compliance: Le present appereil numerique n’emet pas de buits radioelectrique depassant les

limites applicables aux appareils numeriques de class A prescrites dans le regulement sur le brouillage radioelectrique edicte par le
Ministere des Communications du Canada

Regulatory Compliance

This instrument has been tested, and found to be in compliance with all applicable requirements of the following safety and
electromagnetic standards:

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IEC 61010-1:2010 (3rd Ed.), EN61010-1:2010 (3rd Ed). Electrical Equipment for Measurement, Control, and Laboratory Use - Part 1:

General requirements

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IEC 61010-2-081:2001+A1, EN61010-2-081:2002+A1. Safety Requirements for Electrical Equipment for Measurement, Control and

Laboratory Use. Part 2-081: Par ticular requirements for automatic and semi-automatic laboratory equipment for analysis and other
purposes (includes Amendment 1)

n

CAN/CSA-C22.2 NO. 60101-1:2012 Safety Requirements for Electrical Equipment for Measurement, Control, and Laboratory Use,

Part 1: General Requirements

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CAN/CSA-C22.2 NO. 60101-2-081:2004 Safety Requirements for Electrical Equipment for Measurement, Control, and Laboratory

Use, Part 2-081: Particular Requirements for automatic and semi-automatic laboratory equipment for analysis and other purposes

| iiiCFX Automation System II | iii

n

EN 61326-1:2006 (Class A) Electrical Equipment for Measurement, Control and Laboratory Use. EMC requirements,

Part 1: General requirements

n

UL 61010-1:2012 Safety Requirements for Electrical Equipment for Measurement, Control, and Laboratory Use, Part 1:

General requirements

This equipment generates, uses, and can radiate radio frequency energy and, if not installed and used in accordance 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 case the user will be required to correct the interference at his own expense.

Warranty

The CFX Automation System II and associated accessories are covered by a standard Bio-Rad warranty. Contact your local Bio-Rad
Laboratories office for details of the warranty.

CFX Automation System IIiv |iv |

Table of Contents

Chapter 1. CFX Automation System II Installation ...................... 1

CFX Automation System II Parts ............................................. 1

CFX Automation System II Compatibility....................................... 2

CFX Automation System II Hardware Installation ................................ 3

Software Installation ......................................................10

Enable Computer to Continuously Communicate with Barcode Scanner .............11

Turn Off Windows Automatic Update Feature...................................12

CFX Automation System II Configuration and Calibration ..........................12

Chapter 2. Using the CFX Automation System II ...................... 21

Introduction.............................................................21

Starting an Automation Run ............................................... 22

Adding Plates after Starting an Automation Run.................................24

Canceling an Automation Run ..............................................25

Pausing or Canceling a Single Plate Run in a CFX System.........................25

Emptying the Waste Rack..................................................25

LIMS Information.........................................................25

PrimePCR Information.................................................... 26

Create the Plate List: Additional Features ..................................... 26

Barcode Controls: Advanced Features ........................................27

Modify Settings ......................................................... 29

Statu s Tab ..............................................................31

History Tab ............................................................ 32

Chapter 3. Resources............................................ 33

Maintenance ........................................................... 33

Power Outage.......................................................... 34

Troubleshooting the CFX Automation System II ................................ 34

Frequently Asked Questions ............................................... 36

Ordering Information ............................................ 37

| vCFX Automation System II | v

CFX Automation System IIvi |

1

CFX Automation System II Installation

Read this chapter for information about installing the CFX Automation System II.

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CFX Automation System II Parts

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CFX Automation System II Compatibility

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CFX Automation System II Hardware Installation

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Software Installation

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CFX Automation System II Configuration and Calibration

CFX Automation System II Parts

Arm

Wrist

Tow er

Rear CF X System

Front CFX System

Mounting plate

Fig. 1. CFX Automation System II par ts.

Gripper assembly

Rack 1

Rack 2

Rack 3

Barcode scanner

Base

Foot assembly

Rotary axis Power LED

CFX Automation System II | 1

Chapter 1: CFX Automation System II Installation

Table 6. CFX Automation System II part details.

Part Function

Arm Reach axis. Moves horizontally 11.25 in (28.5 cm) to 19.75 in (50.1 cm) from tower

Wrist Rotates plate to appropriate position (270° rotation)

Gripper assembly Gripper fingers open and close to grasp and release the plate

Tower Vertical axis. Moves the arm up and down

Rotary axis Rotates the arm 340° around the base of the CFX Automation System II

Barcode scanner Scans plates prior to placing them into the CFX System

Rack Holds source and waste plates. Each rack holds a maximum of 32 sealed

96-well plates or 48 sealed 384-well plates

CFX Automation System II Compatibility

Compatible CFX Systems

The CFX Automation System II is compatible with the following CFX Systems:

CFX9 6 Touc h

CFX384 Touch

CFX Connect

CFX96 Touch Deep Well

CFX96

CFX384

™

Real-Time PCR Detection System

™

Real-Time PCR Detection System

™

Real-Time PCR Detection System

™

Real-Time PCR Detection System

™

Real-Time PCR Detection System

™

Real-Time PCR Detection System

Plastics Compatibility

The CFX Automation System II is compatible with Hard-Shell® Low-Profile 96-Well Skirted PCR
Plates and Hard-Shell 384-Well Skirted PCR Plates. Table 7 lists the Bio-Rad catalog numbers
for compatible plates. The same gripper fingers are compatible with both 96- and 384-well
plates. PCR plates not listed in Table 7 may not be compatible with the gripper fingers, plate
handler, or CFX Systems.

For more information, visit www.bio-rad.com/pcrplastics.

Table 7. PCR plate compatibility with CFX Automation System II.

PCR Plate Barcode Well Color Catalog Number

Hard-Shell 384-Well Barcoded White HSP-3905
Skirted Nonbarcoded White HSP-3805

Barcoded White HSP-9955
Hard-Shell Low Clear HSP-9901
Profile 96-Well Skirted Nonbarcoded White HSP-9655
Clear HSP-9601

Seal Compatibility

Bio-Rad Hard-Shell Plates can be sealed with Microseal® 'B' Optically Clear Adhesive Seals
(catalog #MSB-1001). After the plate is sealed, remove the end tabs before loading the plates
into the racks.

Plates may also be heat sealed using Bio-Rad’s PX1
and Optically Clear Heat Seals (catalog #181-4030). This semi-automated heat sealer ensures a
reproducible seal every time, helping minimize sample evaporation during thermal cycling. For
more information, go to www.bio-rad.com/pcrplatesealer.

™

PCR Plate Sealer (catalog #181-4000)

2 | CFX Automation System II2 |

Minimum Computer Requirements

A computer with either Windows 7 or Windows 8 operating system is required to run CFX
Automation Control Software version 2.0 or higher. The software package must be installed on
the computer by a user with administrative privileges.

™

Note: CFX Manager
CFX Automation Control Software.

Table 8 lists the computer system requirements for CFX Manager Software and CFX
Automation Control Software.

Table 8. Computer requirements.

System Minimum Recommended

Operating system Windows 7 or Windows 8 Windows 7 or Windows 8
Drive CD-ROM drive CD-RW drive
Hard drive 10 GB 20 GB
Processor speed 2.0 GHz 2.0 GHz
RAM 1 GB RAM 2 GB RAM
Screen resolution 1,024 x 768 with true-color mode 1,280 x 1,024 with true-color mode
USB USB 2.0 Hi-Speed port USB 2.0 Hi-Speed port
Software Microsoft Office Suite

Software version 3.1.1620 or higher must be installed before installing

Chapter 1: CFX Automation System II Installation

CFX Automation System II Hardware Installation

Getting Started

Determine where the automation system will be installed. Remove any objects from the bench
that will interfere with installation. Unplug and remove the CFX System(s) and computer from the
laboratory bench before installing the plate handler (note the location of any cables connected
to the instruments).

Determine the placement of the CFX System(s), plate handler, and computer on the lab bench.
If a single CFX System will be integrated, the CFX System front panel must face forward and be
located to the right of the plate handler (Figure 2A). If two CFX Systems will be integrated, the CFX
Systems must be installed with their front panels oriented toward the plate handler (Figure 2B).

A B

Fig. 2. Single and dual CFX Automation System II configurations.

| 3CFX Automation System II | 3

Chapter 1: CFX Automation System II Installation

Space Requirements

The CFX Automation System II must be assembled on a sturdy, level lab bench. The benchtop
must be sturdy enough to support the weight of the computer, the plate handler, and the CFX
System(s) without sagging. An uneven surface will result in misalignment of the automation
system. Ensure there are sufficient electrical outlets available for the plate handler, CFX System(s)
and the computer. Table 9 illustrates the space requirements needed for the system.

Table 9. CFX Automation System II dimensions.

Operational Space
Footprint Requirements*

Single CFX Dual CFX Single CFX Dual CFX
Plate Handler System System System System
Dimensions Alone Configuration Configuration Configuration Configuration

Height, cm (in) 97 (38) 97 (38) 97 (38) 97 (38) 97 (38)

Width, cm (in) 53 (21) 91 (36) 99 (39) 91 (36) 114 (45)

Depth, cm (in) 77 (30) 77 (30) 77 (30) 86 (34) 86 (34)

* Operational space includes space for the plate handler arm travel and CFX System lid to open.

Tools required to assemble and install the CFX Automation System II include:

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Adjustable wrench

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Bubble level (provided with the system)

Unpacking the CFX Automation System II

WARNING! Use two people to lift the CFX Automation System II. The plate handler weighs
approximately 110 lb (50 kg). Lift the plate handler with care. Do not lift the plate handler by the
arm. Lift only by the base. Take precautions to avoid injury.

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Examine the carton for damage

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Remove the outer carton

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Remove the startup kit packaging on top of the plate handler. Make sure the startup kit is not
stuck in the top of the outer carton

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Retain the box and packing materials. If the unit needs to be returned for any reason, you
must use the original packing materials and box for shipping. If there has been damage to the
instrument in transit, it is particularly important to retain the packaging for inspection

Parts List

The shipping cartons should include the following items:

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Plate handler with attached barcode scanner

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Three removable racks

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Declaration of Conformity

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Startup kit containing:

- Power cord

- Communications cable [6 ft (1.8 m),
USB-B to USB-A]

- Calibration block

- Mounting plate

- Bubble level

- Eight extra gripper pads

- Two plate lifters for use with CFX384 Systems

- CFX Automation System II instruction manual

- CFX Automation Control Software
installation CD

- Ex tra fus es

- Warranty card

- Software registration card

4 | CFX Automation System II4 |

Position the Mounting Plate and Plate Handler

Position the mounting plate on the bench such that the two holes for the plate handler feet are
on the right and the beveled edge faces up (Figure 3).

Lift the plate handler and place the two left feet inside the designated holes on the mounting
plate. The barcode scanner should be located in the front left.

WARNING! The plate handler weighs 110 lb (50 kg). Do not lift the plate handler by the arm.
Lift only by the base. Take precautions to avoid injury.

Beveled edge faces up

Back lef t foot of the plate handler will be
placed in this hole

Single CFX System configuration. Right feet of
the CFX System will be placed in these holes

Chapter 1: CFX Automation System II Installation

Dual CFX System configuration. Front feet of
the CFX Systems will be placed in these holes

Front left foot of the plate handler will be
placed in this hole

Fig. 3. Mounting plate.

Carefully cut the tie-wrap with the red sticker from the counterbalance rail and remove the
tiewrap and the black split tubing (Figure 4).

Fig. 4. Remove tie-wrap and black split tubing.

| 5CFX Automation System II | 5

Chapter 1: CFX Automation System II Installation

Install the CFX System(s)

1. Install the CFX System(s) in the desired positions.

■n

Single CFX System. Align the right side feet of the CFX System in the mounting plate
such that the CFX System front panel is facing forward (Figure 2)

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Dual CFX Systems. Align the front feet of the CFX Systems in the mounting plate such
that the CFX Systems’ front panels are facing the plate handler (Figure 2)

2. Connect CFX System(s) power cord(s) and communication cable(s). For detailed
instructions on installing the CFX Systems, refer to the CFX Systems instruction manual
(bulletin #10021337).

3. Install the plate lifter (Figure 5) in all 384-well CFX Systems configured with the plate handler.
The plate lifter aids in the removal of 384-well plates by gently lifting the plate slightly out of
the reaction block when the heated lid is opened.

Note: The plate lifter is not required for 96-well CFX Systems. Save unused plate lifters for
potential future use with 384-well CFX Systems.

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Place the plate lifter around the outside of the 384-well block, with the lifters facing up
(Figure 5)

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Gently press down on the long edges of the plate lifter until the four notches on the short
side of the plate lifter push against the 384-well block

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Examine the plate lifter to ensure that it is properly installed

Fig. 5. Plate lifter for 384-well CFX Systems.

Level the Plate Handler

WARNING! This step requires two people. The plate handler weighs 110 lb (55 kg). When
lifting, grasp only the bottom of the plate handler. Do not lift the system by the arm.

Note: The bench top must be able to support the weight of the computer, the plate handler
and the CFX System(s) without sagging. An uneven surface will result in the misalignment of the
plate handler.

Lifters face upward

Press down here

Notches push into block

6 | CFX Automation System II6 |

Chapter 1: CFX Automation System II Installation

Fig. 6. Bubble level in CFX System block.

1. Place bubble level in the center of the CFX System(s) block (Figure 6). Note where the
bubble is within the level.

2. Lift the plate handler arm up high enough to access the tower opening. Place the level
inside the center of the plate handler tower (Figure 7). Compare the position of the
bubble to its position when placed on the CFX System block. Because the CFX Systems
do not have leveling feet, the most important thing is to level the plate handler relative
to the CFX System(s).

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If the bubble position differs significantly in the plate handler tower and CFX System(s),
proceed to step 3

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If the bubble position does not differ significantly when placed in the plate handler tower
and CFX System(s), proceed to step 6

Fig. 7. Bubble level in tower.

| 7CFX Automation System II | 7