Icycler Thermal Service Manual Rev E-2 PDF

Life Science Group
The iCycler™
Thermal Cycler
Service Manual
Part Number 1001862E

PROPRIETARY NOTICE
Information contained in this manual is copyrighted by Bio-Rad Laboratories, Inc. None of the contents may be
reproduced in full or in part by any person without the prior written approval of Bio-Rad Laboratories, Inc. This
manual is intended to provide information to assist the qualified field or instrument service technician to repair,
maintain, and order replacement parts for the instrument supplied. Every reasonable effort has been made to
keep the information in this manual current and accurate as of the date of publication or revision. However, no
guarantee is given of implied that the manual is error-free or accurate about any specification.
Copyright 2006 by Bio-Rad Laboratories, Incorporated. All rights reserved.

Bio-Rad Laboratories Inc, Life Science Group
2000 Alfred Nobel Drive
Hercules, California 94547
Telephone: 1-800-424-6723
100-1862E 02/06 I
About this manual This document is part of Life Science Group’s commitment to provide you,
the service professional, with adequate information to effectively support
instruments. Additional copies of this service document may be ordered using
part number 100-1862.
We welcome and appreciate any suggestions you may have to improve our
service documentation. Please address your comments or suggestions to:
Technical Editor, Global Service Support Dept.

Bio-Rad Laboratories, Life Science Group
Hercules, CA 94547
FAX Number: 510 741-5885
II 100-1862E 02/06
Revision Control List
Document: iCycler Service Manual

Part Number: 100-1862
Date Issued: February, 2006
Each page of this manual has the catalog number, and revision level and revision date for that page. Subse-
quent revisions to a page will be indicated by changes to the revision level and revision date for that page. A
summary of changes for all revisions is listed in the following table. Pages in this manual are at revision A
unless otherwise noted below.
Page Changed
Revision Description Date
Number By
P Preliminary BG 7-99
A New Release BG 3-2000
B 2-1 Minor correction on Section 2.2.1 SF 5-01
3-3 to 3-9 Added additional tools, new test points, “Note:” on 384
Well.
4-6 Added new sections 4.2.10 thru 4.2.13. Revised section
4.2.9.
5-4 Added new section 5.6.5 of the Instrument Check Diag-
nostic.
6-3 to 6-4 Added new troubleshooting information.
7-2 to 7-3 Added new spare parts
8-1 Added new drawing section
C 3-1 to 3-8 Updated “ About this section”, “Block Heater Cycling SF 9-02
Test”, “Lid Heater Cycling Test” sections
4-1 Updated “Replacement/Adjustment Matrix” section
4-7 to 4-9 Added “Dual 48 Well Lid Assembly”, “Dual 48 Well
Sample Block Assembly”, “Dual 48 Well Lid Heater
Assembly” sections
5-1 Updated “Test Equipment” section
5-3 Updated “Instrument Check Diagnostic” section
5-5 to 5-7 Added “Chassis Calibration for the Dual 48 Well Reac-
tion Module”, “Chassis Calibration Verification”, “Cali-
bration Fixture Verification” sections
6-1 to 6-4 Updated “Troubleshooting Guide” section
7-2 to 7-3 Updated “Recommended Spares List” section
7-3 to 7-4 Added “Tools” section
8-1 Added “Installation” section
9-1 to 9-2 Added “Preventative Maintenance” section
10-1 Updated “Drawings” section
11-1 to 11-6 Added Appendix
section
100-1862E 02/06 III

D 3-1 to 3-25 Revised Section 3 of System Checkout to include use of SF 3-03
Thermal Validation Tool Kit
5-3 to 5-4 Updated Instrument Check Diagnostics section 5.5.4 and
added new flow chart
6-1 to 6-5 Revised Section 6 of Troubleshooting section
7-2 to 7-6 Revised Section 7.5 Spare Parts and added parts photos
8-1 to 8-2 Updated Installation section
11-1 to 11- Updated Appendix section
12
11-11 Added Section 11.4 Save/Restore Procedure
11-12 Added Section 11.5 Power-On Self Test
E 3-1 Added Section 3.2 Customer Catalog Items SF 2-06
3-2 to 3-5 Added Sections 3.4 Visual Check, Sections 3.5 Fuse
Installation, Sections 3.6 Installation Procedure
4-1 to 4-2 Updated Safety section 4.3 and added safety labels.
4-2 Updated Section 4.5 Startup and Preliminary Checks
4-3 Updated Section 4.6 Instrument Check Diagnostic
4-4 to 4-6 Added Section 4.7 Operational Test
4-6 to 4-22 Updated complete Section 4.8 Thermal Validation, Sec-
tion 4.9 Hart Meter to PC Setup/Hyperterminal, Section
4.10 96 Well/60 Well/2 x 48 Well Lid Heater Test, 4.11
384 Well Lid Heater Test
5-1 to 5-2 Updated Section 5.3 Preventative Maintenance and PM
report
6-10 to 6-12 Added Section CPU Board Kit (10005213)
7-1 Updated Section 7.4 Firmware Download to include
v4.006
7-7 to 7-8 Added Section 7.12 Chassis Serial Number Setting
8-1 Revised and reformatted Troubleshooting Guide table
8-6 to 8-7 Added Section 8.3 Chassis Test Points
8-8 to 8-10 Added Section 8.4 Sample Block Test Points
9-2 to 9-10 Revised and reformatted service parts with photos
10-1 Updated Drawing section with revised drawings
11-1 to 11-3 Revised and reformatted Installation Qualification
Report (IQ)
11-4 to 11-6 Revised and reformatted Operational Qualification
Report (OQ)
IV 100-1862E 02/06
Table of Contents
Page
Section 1. Introduction
1.1 General Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-1
1.2 Service Philosophy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-1
1.3 Safety Precautions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-1
1.4 Conventions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-1
Section 2. System Overview

2.1 About this Section . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-1
2.2 Product Description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-1
2.2.1 General Description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-1
2.2.2 Technical Description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-1
2.3 Theory of Operation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-2
2.3.1 Operating Principles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-2
2.3.2 Control Circuits . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-3
Section 3. Installation
3.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-1
3.2 Customer Catalog Items . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-1
3.3 Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-1
3.4 Visual Check . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-2
3.5 Fuse Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-3
3.6 Installation Procedure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-3
3.6.1 Instrument Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-3
3.6.2 System Checkout . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-5
Section 4. System Checkout

4.1 About this Section . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-1
4.2 System Verification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-1
4.3 Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-1
4.4 Tools and Materials . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-2
4.5 Startup and Preliminary Checks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-2
4.6 Instrument Check Diagnostic . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-3
4.7 Operational Test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-4
4.7.1 Run Display Options - Debug Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-4
4.7.2 Setup and Run Protocol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-4
4.8 Thermal Validation - OPTIONAL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-6
1001862E 02/06 V
Table of Contents
Page
4.8.1 Thermal Validation Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-6
4.8.2 General . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-6
4.8.3 Kit Contents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-7
4.8.4 96 Well/2 x 48 Well Probe Setup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-7
4.8.5 60 Well Probe Setup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-9
4.8.6 384 Well Test Setup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-11
4.8.7 Hart Digital Meter Setup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-12
4.9 Hart Meter to PC Setup/Hyperterminal Configuration . . . . . . . . . . . . . . . . . 4-12
4.9.1 Validation Protocol Setup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-14
4.9.2 Running Thermal Validation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-15
4.9.3 Validation Software Calculation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-18
4.10 96 Well/60 Well/2 x 48 Well Lid Heater Test . . . . . . . . . . . . . . . . . . . . . . . 4-20
4.11 384 Well Lid Heater Test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-21
Section 5. Preventative Maintenance

5.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-1
5.2 Tools and Materials . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-1
5.3 Preventative Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-1
5.3.1 Firmware . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-1
5.3.2 Inspection of iCycler Chassis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-1
5.3.3 Inspection of Reaction Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-1
5.3.4 Perform System Checkout . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-1
Section 6. Removal and Replacement

6.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-1
6.2 Replacement/Adjustment Matrix . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-1
6.3 Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-2
6.4 Removal and Replacement Procedures . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-3
6.4.1 Tools Required . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-3
6.4.2 Reaction Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-3
6.4.3 Top Case . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-3
6.4.4 CPU Board . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-5
6.4.5 LCD Backlit Display (9206089) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-5
6.4.6 Main Assembly ( 8008650-01 ) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-6
6.4.7 Fan Bracket Assembly ( 8008127 ) . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-6
6.4.8 Standard Lid Assembly . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-7
6.4.9 Sample Block Assembly ( 96/60/384 Well ) . . . . . . . . . . . . . . . . . . . . . 6-7
6.4.10 2 x 48 Well Lid Assembly (800-5960 per pair) . . . . . . . . . . . . . . . . . . 6-7
6.4.11 2 x 48 Well Sample Block Assembly (100-3561) . . . . . . . . . . . . . . . . 6-8
VI 1001862E 02/06
Table of Contents
Page
6.4.12 2 x 48 Well Lid Heater Assembly ( 800-5963 per pair ) . . . . . . . . . . . 6-9
6.4.13 96/60/384 Well Lid Heater Harness Assembly . . . . . . . . . . . . . . . . . . 6-9
6.4.14 Battery Replacement( 9006020 ) . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-9
6.5 CPU Board Kit (10005213) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-10
Section 7. Adjustment and Calibration

7.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-1
7.2 Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-1
7.3 Test Equipment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-1
7.4 Firmware Download . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-1
7.5 Display Contrast Setting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-1
7.6 Date and Time Setting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-2
7.7 Instrument Check Diagnostics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-2
7.8 Chassis Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-2
7.9 Chassis Calibration Verification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-4
7.10 Calibration Fixture Verification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-5
7.11 Displaying Temperature . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-5
7.12 Chassis Serial Number Setting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-7
Section 8. Troubleshooting
8.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-1
8.2 Troubleshooting the iCycler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-1
8.3 Chassis Test Points . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-6
8.4 Sample Block Test Points . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-8
Section 9. Parts Information

9.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-1
9.2 Parts Orders - US Domestic Operations . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-1
9.3 Parts Orders - International Subsidiaries . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-1
9.4 Returning Defective Parts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-1
9.5 iCycler Thermal Cycler Spare Parts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-2
9.6 Tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-10
Section 10. Drawings

10.1 About this Section . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-1
10.2 Drawings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-1
10.2.1 Instrument Check Flow Chart . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-1
10.2.2 Schematics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-1
1001862E 02/06 VII

Table of Contents
Page
10.2.3 Assembly Drawings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-1
Section 11. Appendix

11.1 Installation Qualification Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11-1
11.2 Operational Qualification Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11-4
11.3 Save/Restore Protocol Procedure. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11-7
VIII 1001862E 02/06

Introduction
Section 1
Introduction
1.1 General Information

This manual is the reference to be used for troubleshooting, repair, and maintenance of the i Cycler Thermal
Cycler. It is intended to be used by trained technicians and engineers familiar with safety precautions relative to
working with hazardous voltages and thermally hot components. The procedures in this manual assume that
the reader is familiar with the operation of the iCycler thermal cycler. Complete operating instructions are con-
tained in the i Cycler instruction manual. Information presented in the instruction manual is not repeated in this
Service Manual unless there is a compelling reason to do so.
1.2 Service Philosophy

This manual is designed to support mail in products. Regional service centers are the first level of service,
where faulty assemblies can be most effectively repaired at a central repair facility. The second level of service
is performed at our factory instrument service facility in Richmond, California, where additional service proce-
dures requiring resources not available at regional service centers are performed.
1.3 Safety Precautions

Hazardous voltages exist in the i Cycler thermal cycler. Besides the regular safety precautions observed while
working with hazardous voltages, the following should be observed when servicing this unit:
• When power is required, the unit should be plugged into an outlet with a properly grounded receptacle. The
use of 2-prong plug adapters is not recommended.
• The use of extension cords may compromise the safety of the operator and is not recommended.
• Ensure that fuses installed in the unit are of the correct rating.
• Ensure that none of the ventilation openings in the unit are blocked. Excessive heat buildup in the unit may
cause failures.
• Under normal operation, various surfaces of this equipment become hot enough to cause burns.
1.4 Conventions
The following conventions are used throughout this manual.:
• Left and right sides of the unit are as viewed from the front, operator’s position, unless otherwise stated.
• Dimensions are in inches, unless otherwise stated.
• Pressure is in pounds per square inch.
Warning: The iCycler is equipped to operate at 120 V or 220 V. It is shipped in its 120 V configuration. To
operate at 220 V, refer to “Voltage Conversion” in the Alignment and Calibration section of this manual.
100-1862A 03/00 1-1

System Overview
Section 2
System Overview
2.1 About this Section

This section of the manual provides an overview of the iCycler thermal cycler including safety information and
theory of operation.
2.2 Product Description
2.2.1 General Description

The iCycler thermal cycler dispenses sample into tubes where they are heated and cooled to amplify target
DNA into multiple samples.
The iCycler is made up of a custom keypad and a quarter-size VGA display. The keypad is used to enter
information. The screen prompts you for information and displays your input and current activity. Displays
are given both graphically and textually. The iCycler allows you to create libraries of protocols for controlling
simulations, as well as defining usernames and user preferences.
When a protocol is running, you may create or modify other protocols, and if you have the dual block, you
can run two independent protocols simultaneously. The graphics are constantly updated as conditions are
programmed or as the instrument progresses through a protocol. At the conclusion of a protocol, the iCycler
will provide a succinct Run Report and offer an optional, more comprehensive Validation Report. The iCycler
stores these reports for 30 days, or they may be backed up to a PC computer connected to the iCycler.
2.2.2 Technical Description

The iCycler consists of a chassis and a reaction module which plugs into the chassis. See Figures 2-1 and
2-2. The reaction modules come in several varieties, including 96 well, 60 well, 384 well, and dual 48 well
units. The iCycler chassis unit have instrument calibration capability for the Dual 48 well Reaction Module
.The same chassis is used for each type of reaction module. Single or dual operation is sensed automati-
cally at startup.
Figure 2-1: iCycler Thermal Cycler
100-1862B 05/01 2-1

System Overview
iCycler Reaction Module
iCycler Chassis
Figure 2-2: iCycler Thermal Cycler
Chassis
The chassis consists of a power supply, keyboard and LCD display, and control components. The power
supply is on the Main PCB, and most of the control is on the CPU PCB. The Main PCB has a line to 48 VDC
converter module which is soldered into the Main PCB.
Temperature sensing
Temperatures are sensed by precision interchangeable thermistors, with an accuracy of ± 0.1 degree from 0
to 70 degrees C, and ± 0.15 degree above 70° C. On a single block system there are 4 thermistors potted
into the block with a special thermally conductive epoxy. The lid sensing thermistors are of the same type,
YSI type H, but the immersion probes have a different value and are YSI type B. Both types have 10K ohm
resistance at 25 degrees C. For more information, see the appendix.
The resistance of the thermistors is read using an op amp circuit, which partially linearizes the output with
temperature, and a 12 bit A/D, so raw readings are between 0 and 4095. A high resistance represents a low
temperature. The scale runs from 0 to 130 ° C for the type H thermistors. If a probe is open it will read 0
degrees, and if shorted, 131 degrees. An abnormally low value could be caused by poor contact on one of
the two connectors where the Reaction Module plugs into the chassis.
2.3 Theory of Operation
2.3.1 Operating Principles

Refer to Figure 2-3, which is an expanded view of the parts near the Peltier thermoelectric (TE) modules.
The peltier modules are bidirectional heat pumps. When current is passed in one direction, they pump heat
up, and in the other direction they pump heat down.
The temperature of the heat sink is kept at approximately 40 degrees Celsius by a control circuit which
adjusts the fan speed. This circuit is not directly controlled by the microprocessor, except that there is a full
high speed override, which can be activated for test purposes.
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System Overview
The Peltier modules must be thermally coupled to the heat sink with minimum thermal resistance to perform
properly. This is done using a thermally conductive, slightly elastic sheet of material between the modules
and the heatsink. Constant pressure must be applied, which is achieved by nine screws. These screws are
special, and have low thermal conductivity, and must be replaced with the same type of screw when ser-
viced. There are two banks of Peltier elements, front and rear. This allows for balancing the temperature in
this direction.
Above the Peltier modules are two sheets of Grafoil™, which is a paper material made of graphite threads.
The Grafoil is both thermally conductive and electrically conductive, so the sheets are used as Joule or
resistance heaters as well as a thermally conductive gasket. The Grafoil is cut in a serpentine pattern to
increase the resistance and to control the heating pattern. At high temperature, there are significant edge
losses which would make the edge of the sample block cooler than the middle. The heaters provide for more
power near the edge to make up the difference. The two Joule heaters also allow for balancing the tempera-
ture left and right by regulating the amount of heat to each.
The Joule heaters only work when the temperature is above 40 ° C and when heating the block. When the
sample block is near the heatsink temperature, there is no need for balancing, as the power requirement is
very low. When cooling down to a low temperature for storage, there is no need for extremely accurate tem-
perature uniformity.
Figure 2-3:
2.3.2 Control Circuits

The outputs to the Peltiers, the Joule heaters and lid heaters are all current controlled. The control is done
using 8 bit DACs for the Peltiers and Joule heaters. However, originally 12 bit DACs were used, so control
valves are shown between 0 and 4095 for these. The Peltier circuits are reversible, with an H bridge. The
current for these goes between minus 8.85 amps and plus 8.85 amps.
The lid heaters use 8 bits, so control values are between 0 and 255. The lid heaters run between 0 and 1.74
amps for single system, under normal conditions, and half of this for the dual system. There is a fast warmup
mode, and in this mode the current available is 4.4 amps for the single system and 2.2 amps for the dual.
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Installation
Section 3
Installation
3.1 Introduction
This section of the manual guides you through the installation and setup of the iCycler Thermal Cycler. A Instal-
lation Qualification Report or IQ should be completed with each installation checkout. The IQ Report shall pro-
vide verification that the instrument has passed the requirements in the Installation section. A report checklist is
provided in the Appendix section. This section represents and meets the Installation Qualification or IQ of the
instrument.
When used with NIST traceable standards as part of an IQ protocol, installation procedures in this section meet
installation validation requirements.
3.2 Customer Catalog Items

Catalog Number Description
170-8720 iCycler Thermal Cycler With 96 x 0.2 ml Reaction Module
170-8722 iCycler Thermal Cycler With 2 x 48 x 0.2 ml Reaction Module
170-8724 iCycler Thermal Cycler With 60 x 0.5 ml Reaction Module
170-8726 iCycler Thermal Cycler With 384-Well Reaction Module
170-8703 96 x 0.2 ml Reaction Module
170-8705 2 x 48 x 0.2 ml Reaction Module
170-8707 60 x 0.5 ml Reaction Module
170-8709 384-Well Reaction Module
3.3 Safety
Electrical
High Voltage Circuits: The MyCycler contains high voltage circuits. Instrument must have power discon-
nected before servicing.
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Installation
Thermal
Thermally Hot Components: The sample block and lid heater of the iCycler can reach temperatures of
100°C during operation of the instrument. The heated lid should remain closed at all times during operation
to prevent accidental skin burns. Always allow the sample block to return to its idle temperature before
opening the lid and removing samples. Take caution to avoid touching the heated lid when lid temperature
control is on. When placing or removing samples, open the heated lid all the way up to allow maximum
clearance and to avoid the heated lid from falling on hands. Make sure that no object obstructs the lid before
opening it. Instrument must be allowed to cool to safe temperature before servicing.
Electro Static Discharge (ESD)

The iCycler contains ESD sensitive parts. Observe ESD precautions when handling these parts. Wear
grounding wristband and store parts in ESD shielded bags.
3.4 Visual Check

1. Check this instrument for any signs of damage which may have occurred during shipping.
2. The following items are included with the iCycler Thermal Cycler and Reaction Module:
• iCycler Thermal Cycler Chassis
• Power Cord
• Instruction Manual
• Fuses (4 each of 4A and 2 each of 8A)
• Warranty Card
• Reaction Module
• Sealing Ring
• Immersion Probe
• Sample Reagent Kit, iTAQ DNA
• Reagent, dNTP Mix
• MTT, 0.2 ml Thin, Natural, 1000 box
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Installation
3.5 Fuse Installation

AC Voltage Fuse Amperage Part Number Fuse Type Size
100 - 120V 8.0A 9008933 Slow Blow T, 250V 5 x 20 mm
220 - 240V 4.0A 9000234 Time Lag T, 250V 5 x 20 mm
3.6 Installation Procedure
3.6.1 Instrument Installation

1. Place the chassis unit on a clean, sturdy table or bench. Allow for 10 cm (4 inches) clearance at the rear of the
instrument to allow for proper ventilation. It is important to keep the instrument in a clean, relatively dust free
environment to ensure optimum performance.
2. Install the Reaction Module in the chassis unit by locking down both green latches.
3. Check that the sliding dust cover is installed and secured. Dust cover must be installed for optimum temperature
uniformity performance. See Figure 3-1.
Dust Cover
Figure 3-1:
4. Check that the voltage selector switch and the fuses in the power entry module are set for proper AC line voltage.
Configure as required. See Figures 3-1 and 3-2.
Caution: iCycler Thermal Cycler Chassis is shipped with the fuse and voltage selector switch configured for
US line voltage or 100/120 VAC. If operating for 220/240 V, configure the voltage setting and replace the fuses
to 4.0A.
1001862E 02/06 3-3

Installation
Figure 3-2: Figure 3-3:

5. Connect the power cord to the connection on the back if the instrument.
6. Turn on the power switch and verify the display fades from dark to normal illumination and the fan sounds from
high to low speed.
7. Verify current firmware version, which is v4.006 or above when the display immediately appears.
8. Check that the display illuminates and unit performs successful initialization during the power-on self test without
fault errors. This typically takes about less than a minute. If successful, the display will appear as shown in Figure
3-4.
Figure 3-4:
9. Press Enter at Registered User, then press Enter again to get to home screen as shown in Figure 3-5. If no regis-
tered user, create a new user name and select a pin option to get to home screen.
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Installation
Figure 3-5:
3.6.2 System Checkout

This section tests system performances and functionality to manufacturer specifications.
1. Perform the complete System Checkout in Section 4 to perform and meet Operational Qualification or OQ require-
ments.
1001862E 02/06 3-5

System Checkout
Section 4
System Checkout

This section describes the procedures for the complete System Checkout of the iCycler Thermal Cycler unit.
All testing is to be performed with the instrument in the fully assembled condition.
Note: This procedure refers to the 96 well, 60 well, 384 well, and Dual 48 Well Block iCycler Reaction
Modules and iCycler Chassis units.
4.2 System Verification

Verification testing is the only method for determining if the iCycler Thermal Cycler is functioning correctly and
if calibration is within published specifications. Perform the tests below to verify system integrity. All testing is to
be performed with the instrument in the fully assembled condition. An Operational Qualification Report should
be completed with each system checkout. This report checklist shall provide verification that the instrument
has passed the tests in the System Checkout section. The OQ Report is provided in the Appendix section. This
section represents and meets the Operational Qualification (OQ) of the instrument.
When used with Bio-Rad Approved NIST traceable equipment as part of an OQ protocol, checkout procedures
in this section meet system validation requirements.
4.3 Safety
Electrical
High Voltage Circuits: The iCycler contains high voltage circuits. Instrument must have power discon-
Thermal
100-1862E 02/06 4-1

System Checkout

4.4 Tools and Materials

• Thermal Validation Kit (100-6494)
• Mineral Oil (163-2129)
• Laboratory Tape
• Needle Nose Plier
4.5 Startup and Preliminary Checks

This section performs initial startup checks of the thermal cycler and Reaction Module.
2. Turn on the power switch and verify the display fades from dark to normal illumination and the fan sounds from
high to low speed.
3. Verify current firmware version, which is v4.006 or above when the display immediately appears.
4. Check that the display illuminates and unit performs successful initialization during the power-on self test without
fault errors. This typically takes about less than a minute. The list below shows what is actually being checked
during the power-on self-test.
Detects presence of block
Checks for stuck keyboard key
Verifies test pattern in display memory
Checks for lid over temperature
Checks code space in ROM
Checks code space in RAM
Checks block sensor uniformity
Checks block sensor for over temperature
Checks lid heating and disable lid heat
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System Checkout
Resumes running any active protocol; if no active protocols then continues tests
Cycles LCD contrast, and the display setting is held if stop key is pressed
Cools block for 4 seconds (or heats if already below 15 degrees C)
Heats block for 4 seconds
Checks that heating and cooling accomplished ramps
5. If the self-test is successful, the display will appear as shown in Figure 4-1.
Figure 4-1:
6. Press Enter at Registered User, then press Enter again to get to home screen as shown in Figure 4-2. If no regis-
tered user, create a new user name and select a pin option to get to home screen.
Figure 4-2:
4.6 Instrument Check Diagnostic

This section performs a 6 minute functional check of the sample block, lid, edge heaters and chassis.
Note: The Instrument Check function in the firmware for the 2 x 48 Well Reaction Module is deactivated and
NOT in use. The 96, 60, and 384 well modules remain functional for Instrument Check.
1. At the home screen, select Utilities (F4).
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System Checkout
2. Select Instrument Check in Utilities to automatically run a 10 stage diagnostic routine. This diagnostic will run a 5
stage block heat/cool tests, lid test, and edge heater test for approximately 6 minutes.
3. At the completion of Instrument Check, threshold data values will be indicated on the screen.
4. Reference to the Instrument Check Flow Chart in Section 10 Drawings for analysis of instrument conditions
5. All indications aof a Normal Block and Continue Instrument Usage in the flow chart represent a functional iCycler
Thermal Cycler instrument. Any failure indications, replace the recommended faulty part.
4.7 Operational Test

This section describes running a Standard-2 protocol to check for proper instrument operation.
4.7.1 Run Display Options - Debug Menu

This section describes setting to debug service mode called Run Display Options.
1. At the home screen, select Utilities (F4).
2. Select Service Options and press Enter.
3. Enter 94547 for PIN number and press Enter.
4. Select Run Display Options and press Enter.
5. Select YES for Debug Mode Run Display? and press Enter. See Figure 4-3.
Figure 4-3:
6. Press Done (F5) twice to return to home screen.
4.7.2 Setup and Run Protocol

1. At the home screen, select Protocol Library (F1).
2. Select BIO-RAD/Two-step Amplification/STANDARD-2 protocol and press Enter.
3. Select Edit Template and press Enter.
4. Edit Cycle 2:(30x) to Cycle 2:(5x) for a final protocol as in Table 4-1 and Figure 4-4.
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System Checkout
Table 4-1 Edit Standard Protocol

Step # Set Point Tempera- Cycle Time Cycles
ture
Step 1 95°C 04:00 (1x)
Step 2 95°C 00:30 (5x)
Step 3 65°C 00:30 (5x)
Step 4 72°C 07:00 (1x)
Step 5 4°C Infinite (1x)
4 Sensor Block Readings
Lid Temperature
Figure 4-4:
5. Press Done (F5).

6. Press Begin Run (F5).
7. When the REM.TIME timer elapses, confirm the actual ALG TEMP (Right Side) is within ± 0.5°C of the set
ALG TEMP (Left Side) as the unit cycles through from 95°C, 65°C, 72°C, and 4°C. See Figure 4-5. The 4 upper
temperature sensor readings should also be within ± 0.5°C of the set temperature. See Figure 4-5. This test takes
about 18 minutes to end at 4°C hold. Setpoint Actual
Figure 4-5:
8. For 4°C, confirm the actual display sensor readings and ALG TEMP (Right Side) read mostly between 3.0°C to
5.0 °C in about 2.0 to 2.5 minutes in regular room temperatures of 21-23°C. Generally, higher room tempera-
tures of 23°C may affect time for instrument to cool to 4°C.
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System Checkout
9. For 105°C lid temperature, confirm the actual display sensor reading is 105°C ±3.0°C as shown in Figure 4-6.
Figure 4-6:
10. Press Pause Run (F4), then End Run (F3) to stop the infinite hold of 4°C run.
11. Press Run Report (F2) to view errors or exceptions of the validation report. See Figure 4-7.
Figure 4-7:
12. Disable the Run Display Options in Service Mode to NO for Debug Mode Run Display?
4.8 Thermal Validation - OPTIONAL

This section describes performing thermal validation of the sample block when attached to chassis unit to oper-
ate. This section is OPTIONAL and generally performed through a Thermal Validation contract or OQ protocol/
field service contract. This procedure is useful for diagnosing and verification of temperature uniformity prob-
lems. Generally, this section is used in-house or for Thermal Validation service contracts.
4.8.1 Thermal Validation Kit

This section provides illustration of the Thermal Validation Kit for test of 96 Well, Dual 48 Well, 60 Well, and
384 Well Reaction Modules.
Caution: Hot surfaces are present in the sample block and lid. Exercise extreme caution when using the
Thermal Validation Kit components.
4.8.2 General
• Verification testing of the iCycler Thermal Cycler is performed using the Thermal Validation Kit.
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System Checkout
• The Thermal Validation software CD requires use of a PC and is compatible with Windows 95, 98, NT, 2000, or XP
operating systems and Microsoft Excel Versions 97/2000.
• The Hart 1521 temperature meter and 5611 thermistor probe in this kit are extremely accurate; the meter is accurate
within +/- 0.025 °C (-200 °C to 100 °C) and the probe accurate within +/- 0.025 °C (0°C to 100 °C) .
• The thermometer and thermoprobe within this kit are calibrated and traceable to the National Institute of Standards
and Technology (NIST). A calibration certificate is provided with the kit. The calibration interval for each of the
thermometer and thermoprobe is one year at the regional offices.
4.8.3 Kit Contents

• Hart Scientific Model 1521-LLK Hand Held Thermometer
• Hart Scientific Model 5611-BR Modified Bio-Rad Thermistor Probe
• Lid Probe Adaptor
• Excel Validation software CD
• 60 well adaptor with removal screw
• Latch rod
• serial cable
• Power supply
• 200 ul and 600 ul vials
• Instructions CD (iCycler and MyCycler Service Manuals)
• NIST Calibration Certification
Figure 4-8: Thermal Validation Kit Figure 4-9: Kit Contents
4.8.4 96 Well/2 x 48 Well Probe Setup

This section provides a procedure for setting up the probe for 96 well or 2 x 48 Well Block sample well mea-
surement.
1. Open sample compartment.
2. For 2 x 48 well block measurement, remove both plastic block shield before proceeding.
3. For 96 well measurement, remove the green sealing ring before proceeding.
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System Checkout
4. Place the 5 each of 200ul vials on wells B2, G2, E7, B11 and G11 to prevent touching of the thermistor probe and
to simulate actual heater position. For Dual Block, insert the tubes in the location equivalent to the 96 well areas.
See Figure 4-10.
B2
B11
E7
G2
G11
Figure 4-10: Designated Wells for 200ul Vials
5. Coat the probe tip in mineral oil by dipping. This will help make the probe seat better. See Figure 4-11.
A1 Well
Figure 4-11:
6. Carefully insert the temperature probe to the first test point A1 well in the sample block. Verify proper seating of
the probe into the well by pressing down the probe into the well without damaging the probe connection. Tape
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System Checkout
down the probe wire to inner light baffle plate to prevent probe disturbance. See Figure 4-12. It is extremely
important to maintain surface contact between the probe tip and the tested well.
Well A1
Probe
Side View Tape wire in inner baffle plate
Figure 4-12: Probe Cable Hold Down Tape

7. Carefully close chamber and latch down sample compartment. Reopen the compartment and reinspect for proper
probe seating in the test well.
4.8.5 60 Well Probe Setup

This section provides a procedure for setting up the probe 60 well sample well measurement.
1. Open sample compartment
2. For 60 well measurement, remove the sealing ring before proceeding.
3. Place three large vials on wells B3, B8, E5 to prevent damage to the thermistor probe. The larger Microtest vol-
ume tubes for the 60 well block are used as spacers.
4. Coat the 60 well adaptor in mineral oil.
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System Checkout
5. Attach the 60 well probe adaptor to the probe tip. See Figure 4-13.
Probe
60 Well Adaptor
Figure 4-13: 60 Well Adaptor and Probe Figure 4-14: 60 Well Measurement
down the probe wire to inner light baffle plate to prevent probe disturbance. It is extremely important to maintain
surface contact between the probe tip and the tested well. See Figure 4-14.
8. To remove the 60 well adapter from the well after test completetion, insert the screw and turn it two to three turns
clockwise and pull to remove by using a nose plier. See Figures 4-15 and 4-16.
Removal Screw
60 Well Adaptor
Figure 4-15: 60 Well Adaptor and Removal Screw Figure 4-16: 60 Well Adaptor Removal
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System Checkout
4.8.6 384 Well Test Setup

This section provides a procedure for setting up the probe for 384 well sample well measurement.
1. Open sample compartment.
2. Coat the probe tip in mineral oil.
down the probe wire to inner light baffle plate to prevent probe disturbance. It is extremely important to maintain
surface contact between the probe tip and the tested well. See Figure 4-17.
Figure 4-17:
5. Install latch rod as shown in Figure 4-18.
Place Here
Place Here
Figure 4-18:
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System Checkout
4.8.7 Hart Digital Meter Setup

This section describes setting up the handheld meter to the PC.
1. Connect the thermoprobe to the handheld thermometer port. See Figure 4-19.
Lid Probe Adaptor
Probe
Hart Temperature Meter
Figure 4-19:
2. Connect the power supply to the jack of the handheld thermometer.

3. Plug the power supply to the AC outlet.
4. Connect the phono plug end of the DB-9 Serial Cable on the port of the thermometer and the 9 pin serial end to
COM1 port of the PC.
5. Press the power switch button on the handheld thermometer to turn on the power. Wait for approximately a minute
for the thermometer to initialize.
4.9 Hart Meter to PC Setup/Hyperterminal Configuration

This section describes the setup of the Hart temperature meter to PC and configuration using Hyperterminal.
HyperTerminal provides real time temperature measurements of the well under test.
1. In Windows, select Start>Programs>Accessories>Communications>HyperTerminal.
2. At the Connection Description pop up window, enter your name and select the icon as indicated in Figure 4-20.
Figure 4-20:
3. Click OK.
4. At the Connect To pop up window, enter Country/Region, Area Code, Phone Number, COM1 or COM2. See
Figure 4-21.
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System Checkout
Figure 4-21:
5. Click OK.
6. At the COM1 Properties pop up window, set Bits per second to 2400, Data bits to 8, Parity to None, Stop bits to
1, and Flow Control to Hardware or None. See Figure 4-22.
Figure 4-22:
7. Click OK and the Hyperterminal screen will appear as shown in Figure 4-23.
Figure 4-23:
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System Checkout
8. At the menu bar, select Transfer>Capture Text. DO NOT PRESS START UNTIL INSTRUCTED LATER IN
THE PROCEDURE.
9. Type in path for a file name (example: 96W Test.TXT) with a .txt extension in preferred directory on the desktop,
C:\96W Validate Test.TXT. For dual 48 well block test, separate .TXT files of same name but with -R.txt or -R.txt
for each left and right blocks are required.
4.9.1 Validation Protocol Setup

This section describes setting up thermal validation protocol for the validation test.
1. Turn on the iCycler Thermal Cycler power and verify the firmware version of the thermal cycler is 4.006 and
above. Allow for successful self-test completion.
2. Press Enter at Registered User, then press Enter again to get to home screen. If no registered user, create a new
user name and select a pin option to get to home screen.
3. At the home screen, select Protocol Library (F1).
4. Select BIO-RAD/Service Validation/SVC STANDARD or SVC Dual (2 x 48 Well) protocol and press Enter.
Figure 4-24:
5. Select Run Template and press Enter.

6. Press Enter and select temperature mode to Block Measurement Mode.
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System Checkout
4.9.2 Running Thermal Validation

This section describes running Hyperterminal and iCycler validation protocol.
1. At the Hyperterminal screen, press Start as shown in Figure 4-25.
Figure 4-25:
2. Press Begin Run (F5) on the thermal cycler as shown in Figure 4-26.
Figure 4-26:
3. The instrument will run the Thermal Validation protocol as shown in Figure 4-27 and protocol tables on next page.
The estimated test time is about 45 minutes.
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System Checkout
Figure 4-27:
9 6 , 6 0 a n d 3 8 4 W e l l T h er m a l Va lid a ti on P r o to c ol
Cycle # Step # Setpoint Temperature Cycle Time

Cycler 1: (1x) Step 1: 40°C 00:10
Cycle 2: (9x) Step 1: 90°C 01:00
Step 2: 55°C 01:00
Step 3: 72°C 01:00
Step 4: 38°C INFINITY
2 x 4 8 We ll T he r m al Val id at io n P r ot o co l
Cycle # Step # Setpoint Temperature Cycle Time

Cycler 1: (1x) Step 1: 40°C 00:10
Cycle 2: (6x) Step 1: 90°C 01:00
Step 2: 55°C 01:00
Step 3: 72°C 01:00
Step 4: 38°C INFINITY
4. At the end of the 72°C run, the unit will PAUSE and HOLD at 38°C until the probe is moved to the next well for
measurement.
5. Lightly coat the probe tip in mineral oil and move it to the next designated test well as described in the proper order
of the test point tables on the next page. When closing sample compartment be extremely careful not to damage the
probe cable.
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System Checkout
96 Well Test Point Table 4-2

The standard sample block has 96 wells, 9 of which are designated test points in the proper order from left to
right when moving the test probe.
A1 A6 A12 D1 D6 D12 H1 H6 H12

The 60 well sample block has 60 wells, 9 of which are designated test points in the proper order from left to
right when moving the test probe.
A1 A5 A10 C1 C5 C10 F1 F5 F10

The 384 well sample block has 384 wells, 9 of which are designated test points in the proper order from left
to right when moving the test probe.
A1 A12 A24 H1 H12 H24 P1 P12 P24
Note: When testing only for the 384 Well Reaction Module, the 384 Well Algorithm Defeat function must be
defeated to allow the unit to run from “Algorithm Measurement Mode” to “Block Measurement Mode” in the
“Run Setup” screen.The 384 Well Algorithm Defeat function can be accessed by selecting “Utilities” >
“Device Configuration” > “Calibration Mode Only” > “Yes” at the “384 Well Algorithm Defeat” pop-up
screen.To prevent any possible application problems by the customer, the 384 Well Algorithm Defeat
function must be used to reset from block mode to the customer’s original algorithm mode after all external
block and lid temperature measurements have been performed.
2 x 49 Well Test Point Table 4-5

The 2 x 48 well sample block has two separate 48 wells, 6 for each side of which are designated test points
in the proper order from left to right when moving the test probe.
A1 B3 A6 H1 G4 H6
L eft S id e 48 Well B lo ck Tes t Po in t
A1 B3 A6 H1 G4 H6
Ri gh t Si d e 4 8 We ll Bl o ck Tes t Po in ts
6. Press the F4 Resume Run key to resume the temperature run.

7. Repeat steps 4 through 6 for the remaining 8 wells.
8. At the end of the complete data collection, press End Run (F3) and Home Screen (F5) to return to home. See
Figure 4-28.
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System Checkout
Figure 4-28:
9. At Hyperterminal menu bar, select Transfer>Capture Text>Stop.

10. Locate the saved .txt validation data file in the C drive directory.
4.9.3 Validation Software Calculation

This section describes performing the temperature accuracy and uniformity calculations from the .TXT data
file collected using the Thermal Validation.xls and Validation Entry Form .xls Excel software.
1. Launch the Validation Entry Form Excel software. See Figure 4-29.
Figure 4-29:
2. Click the 96/60/384 Wells Data (9 points) button, then click OK at the message alert. See Figure 4-30.
Note: Click the Dual Block Left Data button, then Dual Block Right Data buttons if performing calculation
for the 2 x 48 well block.
Figure 4-30:
3. Locate the saved data file in the directory C:\Validation. Click Open.
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System Checkout
4. After data transfer, press the 96/60/384 Wells Result button, then click Enable Macros. The software will begin
the calculations, print to a printer and return to the validation screen. See Figure 4-31.
Note: For 2 x 48 well, analyze the Left Wells Result first, then Right Wells Result last.
Figure 4-31:
5. After calculation, click Type Data for Certificate Cover and the screen in Figure 4-32 will appear.
Figure 4-32:
6. Enter the iCycler serial number, Hart meter serial number and temperature probe serial number. Enter Hart meter
and temperature probe calibration dates and due dates.
7. Click Print iCycler Certificate to print the certificate. The printout will indicate a Pass or Fail for temperature
accuracy and uniformity based on temperature specification for the iCycler.
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System Checkout
Caution: TIf the temperature results fail for accuracy and/or uniformity, clean all test wells with a cotton swab
and alcohol. Clean the thermal probe tip with alcohol. Apply one to two drops of mineral oil in each test well,
then repeat the Validation Test. It is extremely important that the probe tip is seated into the test well and
making surface contact. Proper probe cable hold down with tape and cable dressing are also important to
prevent potential probe to well “pop out”.
8. When exiting the validation software, do not save the Thermal Validation.xls. The Data Entry file can be saved,
but will automatically save this file under the same .TXT name.
Note: Accuracy is determined by recording all of the measured, designated test points for the well block,
then taking the total average and subtracting the total average from the set temperature. Uniformity is deter-
mined by subtracting the single lowest test point measurement from the single highest test point temperature
measurement from all of the designated test points for the well block and subtracting the two measurements.
4.10 96 Well/60 Well/2 x 48 Well Lid Heater Test

This section tests for the temperature of the 96 or 2 x 48 Well lid heater(s) at the default setting of 105°C.
1. Open sample compartment and insert the Lid Adapter Probe near the center of the sample block between four center
wells. See Figure 4-33.
Figure 4-33:
2. Insert the probe in the hole of the Lid Adapter Probe as shown in Figure 4-33.
3. Close and latch the sample compartment. Be careful not to snag and unseat the probe cable.
4. At the home screen, select Protocol Library (F1)
5. Select BIO-RAD/Service Validation/SVC STANDARD or SVC Dual (2 x 48 Well) protocol and press Enter
7. Press Enter and select temperature mode to Algorithum Measurement Mode.
8. Press the Begin Run (F5).
9. After about 3 minutes, verify that the lid heater temperature maintains a stable temperature of 105°C ± 3.0°C for 96,
60, or 2 x 48 well block.
10. Press the End Run (F3).
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4.11 384 Well Lid Heater Test

This section tests for the temperature of the 384 well lid heater at the default setting of 90°C.
1. Disassemble and remove the spacer and screw of the Lid Adapter Probe. See Figure 4-34.
Probe Hole
Screw
Spacer
Lid Probe
Figure 4-34: Lid Probe Adaptor Diassembly

2. Insert a blank 384 well plate in the 384 well sample block. See Figure 4-35.
Figure 4-35: 384 Well Measurement

3. Place the disassembled Lid Adapter Probe adaptor on the center of the plate as shown in Figure 4-35.
4. Insert the probe in the hole of the Lid Adapter Probeas shown in Figure 4-35.
5. Close and hold down the sample compartment lid as shown in Figure 4-36. Be careful not to snag and unseat the
probe cable.
100-1862E 02/06 4-21

System Checkout
Figure 4-36: Holding Lid for 384 Well Lid Test
Note: When testing only for the 384 Well Reaction Module, the 384 Well Algorithm Defeat function must be
defeated to allow the unit to run from “Algorithm Measurement Mode” to “Block Measurement Mode” in the
“Run Setup” screen.The 384 Well Algorithm Defeat function can be accessed by selecting “Utilities” >
“Device Configuration” > “Calibration Mode Only” > “Yes” at the “384 Well Algorithm Defeat” pop-up
screen.To prevent any possible application problems by the customer, the 384 Well Algorithm Defeat.The
iCycler unit must be reset from the “Block Measurement Mode” to the customer’s original “Algorithm
Measurement Mode” setting in the “Run Setup” screen. When testing the 384 Well Reaction Module, the 384
Well Algorithm Defeat function must be used to reset from block mode to the customer’s original algorithm
mode after all external block and lid temperature measurements have been performed. function must be used
to reset from block mode to the customer’s original algorithm mode after all external block and lid temperature
measurements have been performed. Reference to ISA # 019A for additional information.
6. At the home screen, select Protocol Library (F1)

7. Select BIO-RAD/Service Validation/SVC STANDARD or SVC Dual (2 x 48 Well) protocol and press Enter
9. Press Enter and select temperature mode to Algorithum Measurement Mode.
10. Press the Begin Run (F5).
11. After about 3 minutes, verify that the lid heater temperature maintains a stable temperature of 90°C ± 3.0°C.
12. Press the End Run (F3).
4-22 100-1862E 02/06

Preventative Maintenance
Section 5
5.1 Introduction
This section provides the preventative maintenance procedure for the iCycler Thermal Cycler. Preventative
maintenance is recommended at least once a year.
5.2 Tools and Materials

• Small Hand Tools
• Cleaning Materials:
• IPA (Rubbing Alcohol)
• Cotton swabs (Q-Tip)
• Soapy water (Liquid dishwashing agent)
• Soft cloth
5.3 Preventative Maintenance
5.3.1 Firmware
2. The LCD will display the version number of the firmware.
3. Record firmware version.
4. Turn OFF instrument.
5. Update to latest firmware of v4.006 or above as applicable.
5.3.2 Inspection of iCycler Chassis

1. Remove top cover.
2. Visually inspect for dirt or dust buildup around fans. Clean as required with soapy water and soft cloth.
3. Reassemble instrument.
5.3.3 Inspection of Reaction Module

1. Slide lid heater open.
2. Visually inspect sample block wells for dirt or residue spills. Clean as required with IPA and cotton swabs.
3. Wipe off surrounding areas with soft cloth and IPA.
5.3.4 Perform System Checkout

1. Perform the System Checkout section of this Service Manual.
1001862E 02/06 5-1

iCycler Thermal Cycler

Preventative Maintenance Report
Customer: Case Number:
Performed by: Serial #: Date:
Component Checked Replaced Cleaned

Firmware version #
Chassis Inspection
Reaction Module Inspection
System Checkout
Display Function
Power-On Test
Keypad
Comments:
The iCycler has been serviced for preventative maintenance and meets all of the PM requirements for the iCy-
cler Thermal Cycler.
Performed by____________________________________________ Date__________________________

Bio-Rad Service Engineer
5-2 1001862E 02/06

Removal and Replacement
Section 6
6.1 Introduction
This section of the manual provides instructions on the proper way to remove and replace parts and assem-
blies. Alignment procedures that should be performed when an assembly is replaced are listed in this section
in the Replacement /Adjustment Matrix. The procedures indicated should be performed in the order they are
listed in the matrix.
Note: Removal and replacement procedures which are obvious from the
appearance of the unit are not included. Unless otherwide specified, following
the removal instructions in reverse order will provide the correct procedure for
replacing the assembly.
6.2 Replacement/Adjustment Matrix

The following table shows what adjustment or checkout procedures must be performed after an assembly is
replaced. The calibration procedures must be performed even if the original assembly is being reinstalled in the
same unit. They must be performed in the order specified.
R ep l acea ble Assy. C hecko ut / Adju stme nt / Ca libr at io n Sect ion

F i r mw ar e dow nlo ad 7
C on tr as t ad j us tm en t ( di s p l ay ) 7
C P U P CB S ett ing da te an d time 7
B l o c k S a m pl e Wel l Val i d a t i o n Te s t 4
B l oc k L i d H ea te r Tes t 4
L CD D i s pl ay B l o c k S a m pl e Wel l Val i d a t i o n Te s t 4
S ett ing da te an d time 7
Main PC B B l o c k S a m pl e Wel l Val i d a t i o n Te s t 4
Main PCB Chassis Calibration 7
C P U P CB C ha s s i s C al i br at i on 7
Stand ar d Lid
Sam ple Block
Lid H eat er H ar ne s s
Ba tt er y S e tt in g da te an d t i me. 7
1001862E 02/06 6-1

6.3 Safety
Electrical
High Voltage Circuits: The MyCycler contains high voltage circuits. Instrument must have power discon-
Thermal

6-2 1001862E 02/06

6.4 Removal and Replacement Procedures
6.4.1 Tools Required

• Phillips head screwdriver
• Small flat blade screwdriver
• 1/16” Hex driver wrench (2 x 48 Well)
6.4.2 Reaction Module

This section describes removal of Reaction Module from iCycler chassis.
Lid Handle
Lever
Figure 6-1:
1. Raise the lid handle and slide the lid cover towards the back.
2. Lift both left and right levers and slide the heating block forward and out.
3. Remove the Reaction Module from the Chassis Assembly.
4. Install the Reaction Module in the reverse order of the above steps.
6.4.3 Top Case

This section describes removal and replacement of Top Case.
1001862E 02/06 6-3

1. Invert the iCycler so that the legs are pointing upward. See Figure 6-2.
Figure 6-2: Figure 6-3:

2. Remove the four screws and green rubber feet from the unit.
3. Remove the four rear 8-32 X 5/8” Phillips head screws from the bottom case. See Figure 6-3.
4. Turn the unit over.
5. Pull the front display case towards you and remove the two 8-32 X 5/8” Phillips head screws from the top case.
See Figure 6-4.
6. Install the Top Case in the reverse order of the above steps.
7. Lift and remove the top case from the bottom case. See Figure 6-5.
Remove
Remove
Figure 6-4:
Figure 6-5:
6-4 1001862E 02/06

Note: The following procedures assume that the Top Case has already been removed.
6.4.4 CPU Board

This section describes removal and replacement of CPU Board.
1. Lift the Front Case Assembly off from the Chassis.
2. Disconnect the cables at J4, J5, J6, J7, J8 and J10 from the CPU Board (10001672). See Figure 6-6.
J8
J5
J9
J6
J4
J10
J7
J10
Figure 6-6: CPU Board
3. Remove the 4-40 X 5/8” Phillips head screw and 4-40 X 5/8” spacer from the CPU Board.
4. Remove the three remaining 6-32 X 1/4” Phillips head screws at the corners of the CPU Board.
5. Remove the three shield clips to remove the CPU Board.
6. Install the CPU board in the reverse order of the above steps.
6.4.5 LCD Backlit Display (9206089)

This section describes removal and replacement of LCD Display Board.
1. Remove the two screws of the Image Plane Shield (10003310) from the LCD Backlit Display Board.
2. Remove the three 4-24 X 3/8” Self Tap screws from the front case panel.
3. Install the LCD Backlit Display in the reverse order of the above steps.
1001862E 02/06 6-5

6.4.6 Main Assembly ( 8008650-01 )

This section describes removal and replacement of Main Board.
1. Remove the four 8-32 X 1/4” Phillips head screws from the Air Baffle cover. See Figure 6-7.
2. Remove the Air Baffle cover.
3. Remove the four 8-32 X 3/8” Phillips head screws from the Fan Bracket assembly
Remove
Screws
Air Baffle
Cover
Figure 6-7: Figure 6-8: Fan Bracket

4. Lift the Fan Bracket assembly until it is restrained by the cabling.
5. Disconnect the cables at J4, J6, J8, J10, J13, J16, J17, J20, J21 from the Main PCB assembly. See Figure 6-8.
6. Remove the Fan Bracket assembly.
7. Remove the two 4-40 jacknuts from the Rear Panel.
8. Use a small flat blade screwdriver to press both clips in and push out the Power Entry Module from the Rear Panel.
9. Disconnect the cable and connectors at J10, J16, J21 from the main PCB assembly.
10. Remove the Rear Panel assembly by sliding it out.
11. Remove the eight 6-32 X 1/4” Phillips head screws from the Main PCB assembly.
12. Install the Main Board in the reverse order of the above steps.
6.4.7 Fan Bracket Assembly ( 8008127 )

This section describes removal and replacement of Fan Bracket Assembly.
1. Remove the Reaction Module.
2. Remove the Top Case.
3. Remove the Front Case.
6-6 1001862E 02/06

4. Remove the four 8-32 X 1/4” Phillips head screws from the Air Baffle cover.
5. Remove the Air Baffle cover.
6. Remove the four 8-32 X 3/8” Phillips head screws from the Fan Bracket assembly.
7. Lift the Fan Bracket assembly until it is restrained by the cabling.
8. Disconnect the cables at J4, J6, J8, J10, J13, J16, J17, J20, J21 from the Main PCB assembly.
9. Install the Fan Bracket assembly in the reverse order of the above steps.
6.4.8 Standard Lid Assembly

This section describes removal and replacement of the Standard Lid Assembly.
2. Slide the Lid forward and remove both Phillips screws with spacer before disconnecting the two cables from the
rear of the Sample Block Assembly. Note: The 384 Well Lid requires removing the cable ties, then removing
the Phillips screws.
3. Gently remove the two ribbon cables from the cable clips. Note: The 384 Well Lid does not have any cable clips
but cable tie anchor mounts to provide strain relief and hold down of the two ribbon cables.
4. Slide the Lid back and remove the Light Baffle by pulling up.
5. Raise the Lid handle.
6. Hold the handle and ribbon cables while sliding the Lid Assembly forward from the Sample Block rails.
7. Install the standard lid assembly in the reverse order of the above steps.
6.4.9 Sample Block Assembly ( 96/60/384 Well )

This section describes removal and replacement of the Sample Block Assembly for 96, 60, or 384 Well.
2. Remove the Standard Lid assembly.
3. Remove the two allen head screws from the heatsink baffle cover.
4. Install the sample block assembly in the reverse order of the above steps.
6.4.10 2 x 48 Well Lid Assembly (800-5960 per pair)

This section describes removal and replacement of the Lid Assembly for 2 x 48 Well.
2. Turn the module over so the heatsink is facing up.
3. Loosen the two 1/16” hex screw stops. See Figure 6-9.
4. Turn the module back over so both lid heater housings are facing up.
5. Slide both the lids forward and remove both Phillips screws with spacer before disconnecting the two ribbon
cables from the rear of the Sample Block Assembly.
6. Gently remove the two ribbon cables from the cable clips.
1001862E 02/06 6-7

7. While holding the cable and lid handle to prevent snagging, gently slide both of the lid assembly backwards from
the sample block rails.
Loosen both 1/16” hex screw stops
Figure 6-9: Hex Screw Stops
8. Install the 2 x 48 well lid in the reverse order of the above steps.
6.4.11 2 x 48 Well Sample Block Assembly (100-3561)

This section describes removal and replacement of the Sample Block Assembly for 2 x 48 Well.
2. Remove both of the 2 x 48 Well Lid Assemblies from the sample block assembly. See Figures 6-9 and 6-10.
Figure 6-10: Dual 48 Well Sample Block Assembly
3. Install the 2 x 48 Well Sample Block assembly in the reverse order of the above steps.
6-8 1001862E 02/06

6.4.12 2 x 48 Well Lid Heater Assembly ( 800-5963 per pair )

2. Remove the 2 x 48 Well Lid Assembly.
3. Invert the lid assembly so that the heater plate is pointing upward.
4. Remove the four hex screws. See Figure 6-11.
Remove Remove
Screws Screws
Figure 6-11: Dual 48 Well Lid Heater Assembly
5. Install the Dual 48 Well Lid Heater assembly in the reverse order of the above steps.
6.4.13 96/60/384 Well Lid Heater Harness Assembly ( 8005833/8008133/8008136 )

2. Remove the Standard Lid assembly.
3. Invert the Lid assembly so that the heater plate is pointing upward.
4. Disconnect the two wire cable connector.
5. Remove the four 8-32 X .25” Flat Button Head screws.
6. Install the lid heater harness assembly in the reverse order of the above steps.
6.4.14 Battery Replacement( 9006020 )

Refer to Figures 6-12 and 6-13 for the following procedure:
1. Invert the iCycler so that the legs are pointing upward.
2. Remove the 8-32 X 3/8” screw and battery cover.
3. Slide the battery out by lifting the bracket.
1001862E 02/06 6-9

4. The battery is installed with the ( + ) side touching the bracket.
Figure 6-12: Battery Cover Figure 6-13: Battery

5. Install the clock battery in the reverse order of the above steps. All user protocols will be lost upon removal of the
clock battery. Replacement of the clock battery with the chassis power on will not lose user protocols.
Note: Typically, replace the clock battery if voltage drops below 2.5 volts.
6.5 CPU Board Kit (10005213)

This section describes installing CPU Board Kit (10005213) for current production CPU Board and Image
Plane Shield with extra Grommet Clip from earlier production CPU Board. The earlier type CPU Board
(8008651-01) is obsolete, but currently available on limited supply. When future ISA 0104A is released, refer
for more detailed information.
Note: This section is performed ONLY if replacing a faulty earlier version CPU Board (8008651-01) with the
current production CPU Board. Installation of an updated Image Plane Shield with 3rd Grommet Clip meets
EMC requirements.
1. With the unit power off, invert the iCycler so that the feet are pointing upward.
2. Remove the two front screws and green rubber feet from the unit.
3. Remove the two Phillips screws from the front of the bottom case.
4. Turn the unit over.
5. Pull the front panel case forward being careful not to damage the cables attached to the CPU Board.
6. Disconnect the seven cables from the CPU Board at J7, J4, J8, J9, J5, J6, J10 and J9 connector on Main Board.
7. Remove the 4-40 X 5/8” Phillips head screw and 4-40 X 5/8” spacer from the CPU Board.
8. Remove the three remaining 6-32 X 1/4” Phillips head screws at the corners of the CPU Board.
9. Remove the 2 clips from the CPU Board and Image Plane Shield.
10. Remove the 2 screws from the Image Plane Shield.
11. Remove the Image Plane shield from the LCD Board.
6-10 1001862E 02/06

12. From the kit, cut the long piece of the clip into 3 each of 0.75 inch (1.90 mm) pieces using a diagonal cutter. See Fig-
ure 6-14.
CPU Board
Image Plane
Shield
Grommet Clip
Figure 6-14:
13. From the kit, install the replacement Image Plane Shield by first folding the 3 tabs inward and securing it to the LCD
display with the 2 screws as shown in Figure 6-15.
Image Plane
Shield
Figure 6-15:
14. Slip on the 3 new clips to secure the Image Plane Shield to the CPU Board as shown in Figure 6-16.
15. Secure the CPU Board with the screws and spacer onto the Front Panel as shown in Figure 6-16.
1001862E 02/06 6-11

Figure 6-16:
16. Reconnect all of the seven cables to the CPU Board and and J9 connector on Main Board.
17. Attach the front panel to the chassis.
18. Re-install the chassis screws.
19. Install the front rubber feet and install the screws.
20. Turn on the iCycler power.
21. Verify the unit passes power-up self test without any fault errors.
6-12 1001862E 02/06

Adjustment and Calibration
Section 7
7.1 Introduction
This section of the manual provides instructions for adjusting, calibrating, and maintaining the iCycler Thermal
Cycler. Each procedure also has a short introduction explaining its purpose.
7.2 Safety
Hazardous voltages and hot surfaces are present inside the iCycler. Care should be exercised to prevent injury
whenever the cover is removed. The procedures in this section should be performed by qualified technicians
only.
7.3 Test Equipment

• RS-232, DB9 Serial Cable 930-1522
• WPCRTEST Utility Software, v1.227 or higher (located in Global Service Support on Bio-Rad Desktop)
• iCycler Chassis Calibration Fixtures (4°C and 105° C Set) 100-2453
7.4 Firmware Download

This section provides a procedure to update and download the firmware.
1. Turn off the iCycler power and connect the 9 pin male end of the PC cable to the 9 pin port located on the rear panel
of the iCycler.
2. Connect the other end of the 9 pin cable to Com 1 or Com 2 RS-232 serial port of the PC.
3. Turn on the PC power.
4. Turn on the iCycler power and wait for unit to complete the self-test
5. Drag the firmware folder on the desktop.
6. Launch the firmware file called Update.EXE.
7. At the window Old Version, New Version - Proceed to Download: Y/N ?, enter Y for yes and press Enter.
8. The files will start downloading for about 3 minutes.
9. After download completion, a window will appear : Upgrade Complete - Cycle Instrument Power to Activate -
Press a Key. Press any key on the keyboard.
10. Usually, the unit will recycle its power automatically. If not, turn off the iCycler power and wait 10 seconds.
11. Turn on the iCycler power and verify the firmware version number which is v4.006 or higher.
7.5 Display Contrast Setting

This section provides a procedure to adjust the display contrast of the LCD
1. At the home screen, press F4 key to enter the Utilities screen.
2. Press the down arrow key to select to the Device Configuration option.
1001862E 02/06 7-1

3. Press Enter to continue.

4. Press the Enter key to enter the Set Display Contrast option.
5. Press the down arrow or up arrow key to adjust the screen contrast to a range of 150-250 for the display. Adjust the
contrast so that the alphanumeric characters appear purple with a white background.
7.6 Date and Time Setting

This section provides a procedure to set the date and time
2. Press the down arrow key to select to the Set Date and Time option.
3. Press Enter to continue.
4. Press the arrow keys to select the date for the month, day, and year.
5. Press Enter to save the date settings.
6. Press the arrow keys to select the time for the hour, minutes, and seconds.
7. Press Enter to save the time settings.
7.7 Instrument Check Diagnostics

This section provides a procedure to run the internal diagnostics in checking functionality of the instrument
Note: The Instrument Check function in the firmware for the 2 x 48 Well Reaction Module is deactivated and
NOT in use. The 96, 60, and 384 well modules remain functional for Instrument Check.
1. At the home screen, press the F4 key to enter the Utilities screen.
2. Select Instrument Check to automatically run a 10 stage diagnostic routine. This diagnostic will run a 5 stage block
test, Lid Test, and Edge Heater Test for approximately 6 minutes.
3. At the completion of Instrument Check run, reference to the iCycler Instrument Check Flow Chart for condi-
tions and actions taken in the Section 10 Drawings.
7.8 Chassis Calibration

This section provides a procedure to perform the calibration of the chassis unit
Note: Base calibration uses a table of offsets and scales stored in the chassis unit to be applied to all A/D
readings. Both 4 ° C and 105 ° C precision resistor calibration fixtures will be required of the iCycler chassis
unit electronics. The results of this calibration will be stored in the nonvolatile memory of the base unit. This
calibration will be made using precision fixed resistors in place of thermistor sensors, and will be used to
adjust corresponding A/D values. Both 4 ° C and 105 ° C precision resistor calibration fixtures will be used to
provide precision resistors to the inputs of the A/D channels. All sensor A/D channels will be simultaneously
provided with resistances corresponding to a given setpoint, which can then be switched to the other setpoint,
again providing all channels with the resistances for that setpoint. Chassis calibration provides marginal
temperature corrections and does not correct wide temperature tolerances.
1. Remove the Reaction Module from the chassis unit with the power turned off.
7-2 1001862E 02/06

2. Install the 4 °C - iCycler Chassis Calibration Fixture (100-2453) in the chassis connectors. See Figure 7-1.
Figure 7-1: : 4 ° C - Dual 48 Well Calibrator Fixture

3. Verify that the RS-232 cable is connected to the serial port of the rear chassis and to the serial port of the rear com-
puter PC.
4. Turn on the chassis unit power.
5. The chassis screen will display No Reaction Block Detected, Operation Not Possible. Disregard this message.
6. Drag the WPCRTEST (Version 1.227 or higher) software folder on the PC desktop.
7. Select the <s>Manufacturing Settings Menu.
8. Select <b>Base Unit Calibration and a prompt will be displayed:
This operation requires the iCycler base calibration block.

Press <enter> to proceed or any other key to abort...
9. Press Enter and a prompt will be displayed:
Select 4 degree calibrators, then press enter.
10. Press Enter and a display will read calibrating, please wait .... A/D values will be generated from the precision
resistors corresponding to the resistance equivalent to 4 degrees and all values will be stored within the program.
After 4 degree calibration, a prompt will be displayed:
Select 105 degree calibrators, then press enter.
11. Without turning off the power, gently remove the 4 ° C - iCycler Chassis Calibration Fixture (100-2453) from the
chassis connectors. There is no damage to the test fixture on Hot Starts.
1001862E 02/06 7-3

12. Install the 105 ° C - iCycler Chassis Calibration Fixture (100-2453) in the chassis connectors. There is no damage to
the test fixture on Hot Starts. See Figure 7-2.
Figure 7-2: : 105 °C - Dual 48 Well Calibrator Fixture

13. Press Enter and A/D values will be generated from the precision resistors corresponding to the resistance equivalent
to 105 degrees and all values will be stored within the program. A prompt will be displayed:
calibrating, please wait ...

14. During the calibration wait, the program queries the iCycler chassis for the associated A/D values and will check that
these fall within a reasonable range (exact value TBD). If the A/D values fall within a reasonable range, a successful
prompt will be displayed:
Press Enter to commit values to flash. Press any other key to abort. Press Enter
Store base calibration to flash. Are you sure? Y/N

15. Press Enter, then Y and the program will compute the correct offsets and scales, then command the iCycler chassis to
store the new values. The program will display updating instrument during calibration.
16. When this message disappears, calibration is completed and the results have been stored.
17. The program cannot calibrate if a hardware problem exists in the chassis unit.
7.9 Chassis Calibration Verification

This section provides a procedure to verify calibration of the chassis instrument
1. Return to the Maufacturing Settings menu of WCRTEST.
2. Select lower case <L>- Low level calibration functions menu.
3. Select <7> View current base calibration settings to display a report showing the current stored calibration settings
consisting of offset and scale values for each A/D channel.
7-4 1001862E 02/06

4. Observe the values in the OFFSET column and verify that each A/D channel is within -5 through + 5. If the offsets
values are outside these specifications, the chassis calibration must be performed again.
Warning: If all A/D channels have values of 0 in the OFFSET column, and all A/D channel have values of
32768 in the SCALE column, then the calibration data did not get saved into the flash memory of the chassis
unit. The chassis calibration must be performed again.
7.10 Calibration Fixture Verification

This section provides a procedure to check for proper function of the fixture used for chassis calibration
1. Return to the top level menu of WPCRTEST.
2. Select <h> Heat/Cool Test Menu.
3. Select <t> Thermistor Monitor and WPCRTEST will display each thermistor channel (CH0 to CH7) with an A/D
value and the corresponding temperature.
4. With the 105 ° C - iCycler Chassis Calibration Fixture (100-2453) still connected to the chassis unit, verify the A/D
values are 332 +/- 3 counts for each channel from CH0 to CH7. Disregard the temperature values.
5. Without turning off the power, gently remove the 105 ° C - iCycler Chassis Calibration Fixture and carefully install
the 4 ° C -iCycler Chassis Calibration Fixture to the chassis unit. There is no damage to the test fixture on Hot Starts.
6. Verify the A/D values are 3960 +/- 3 counts for each channel from CH0 to CH7. Disregard the temperature values.
7. If any of the A/D specifications are not met, chassis calibration must be performed again.
8. Exit WPCRTEST, turn off the chassis power and remove the calibrator fixture.
9. Reinstall Reaction Module to Chassis.
7.11 Displaying Temperature

This section provides a procedure to display the condition of the thermistor channels for SERVICE ONLY.
Note: The temperature may be displayed below the “Run Screen” through Service Options. This option
displays current temperature readouts for the reaction module and lid heater. The option should be disabled
after completion of servicing BEFORE returing the instrument to the customer.

2. Press the down arrow key to select Service Options. Enter password 94547 and press Enter to display the menu.
3. Select Run Display Options and press Enter.
4. Select Yes and press Enter.
5. Press F5 to return to the home screen.
6. Press F2 key to create a protocol.
7. Run a protocol.
1001862E 02/06 7-5

8. The current temperature sensor readouts for the 96, 60 and 384 well modules and lid heater will be displayed in Fig-
ure 7-3. For 2 x 48 well, see Figures 7-4 and 7-5.
Figure 7-3:
Block Sensors
T0 T1 T2 T3
Lid Sennsor
Reaction Module Thermistors Reaction Module Thermistors
Lid Temperature Lid Temperature
Figure 7-4: Left Block Run Screen Figure 7-5: Right Block Run Screen
Note: Thermistor readings can also be monitored externally using the WPCRTEST program and the serial
connection to the PC by selecting <h>, then <t> in the utility.
9. Revert the Run Display Options to customer setting before returning instrument to the customer.
7-6 1001862E 02/06

7.12 Chassis Serial Number Setting

This section describes setting the serial number of the Chassis to the CPU.
1. Using the WPCREST program from previous Chassis Calibration sections, select <s>Manufacturing Settings
Menu. See Figure 7-6.
Figure 7-6:
2. Select <2> Set Instrument Serial Number. See Figure 7-7.
Figure 7-7:
1001862E 02/06 7-7

3. Enter complete serial number taken from the rear chassis panel serial number label and press Enter. Exam-
ple:582BR00xxxx as shown in Figure 7-8.
Figure 7-8:
7-8 1001862E 02/06

Troubleshooting
Section 8
Troubleshooting
8.1 Introduction
The troubleshooting information is this section will help to identify and diagnose operating difficulties and com-
ponent failures in the iCycler, thermal cycler. This section may be expanded to include additional troubleshoot-
ing aids as service center experience identifies recurrent problems and appropriate diagnostic processes.
If after reading through this manual, you find that you need additional assistance in resolving a problem, you
may contact our Technical Service Department by phone at 800-424-6723, or by FAX at 510-741-5802
8.2 Troubleshooting the iCycler

The troubleshooting guide below is intended to be used as an aid for troubleshooting the iCycler Thermal
Cycler.
Troubleshooting Guide
Problem Cause Solution
Lack of uniformity • Failed main board edge heater • Repair or replace main board;
regulator (Q32, Q40, D26, D33) check reaction module for con-
or Peltier regulator (Q13, Q26, tinuity between connector ter-
D13, D20) or H-bridge (Q3, Q4, minals and heat sink, only pin 4
Q8, Q9, Q14, Q15, Q20, Q21) should show continuity
• Loose or misplaced harness • Check harness to main board
connector, CPU-main PCB connectors J8, J10 (Peltier),
cables J16, J17 (edge heater), CPU-
main
• Failed sample block edge • Calibrate chassis
heater
• Replace or repair reaction
• Defective CPU A/D module
• Defective main board ther- • Replace or repair CPU
mistor amplifier(s) (U3, U6,
• Replace or repair main board
U27, U32)
Temperature non-uniformity • Transients during power-on • Calibrate chassis
condition of the FET transistors
• Reference to ISA # 022A
Q32 and Q40
Lid heater does not reach temper- • Loose or misplaced harness • Check harness to main board
ature connector or lid connector connectors J13, J20. Check
connectors between heat sink
assembly and lid assembly.
• Lid heater thermal fuse cutoff at • Replace lid or replace lid heater
145 degrees C assembly
• Shorted or open lid assembly • Replace or repair lid assembly
wiring
• Failed main board lid heater • Repair or replace main board
regulator (Q27, Q41, D22, D32)
1001862E 02/06 8-1

Troubleshooting

Lid heater temperature rises • Lid heater thermal runaway • Repair or replace main board
above setpoint; unit may shut due to failed main board lid
• Replace lid or replace lid heater
down and LCD display may flicker heater regulator
assembly
• Lid heater thermal fuse cutoff at
• Check and replace sample
145 degrees C
block
• Thermal runaway of heater
block
LCD display blank, but fan runs • Loose connector (CPU board) • Reseat connector
• CPU-main board cables not • Reseat connectors
connected
• +5V shorted in CPU or main • Isolate short, repair or replace
board cpu or main board
• Failed main board control • Repair or replace main board
power regulator (Q5, D1, D4,
• Reference to ISA # 003B
U20)
• Failed U19
LCD too light or too dark • Failed main board LCD con- • Repair or replace main board
trast regulator (U19)
LCD backlight not working • Loose connector • Reseat J9 at main board
• Failed main board LCD back- • Repair or replace main board
light inverter
Faint or bluish LCD display • Backlight is overdriven by U18 • Reference to ISA#011A
inverter circuit
• Replace LCD display
Unit stops cycling and display • Reaction module temperature • Allow unit to cool and restart; if
backlight flickers exceeds 130° C problem repeats, replace or
repair main board (failed main
board lid heater or Peltier regu-
lator) or CPU board (failed
DAC)
No power • Open fuse(s) in power entry • Replace fuses
module
• Replace power cord
• Bad power cord
• Replace F2 fuse
• Open main PCB fuse (f2)
• Replace switch
• Bad power switch
• Check connectors from har-
• Harness wiring loose ness to main board
• Main board Peltier regulator • Repair or replace main board
(Q13, Q26, D13, D20), H-
Bridge failure (Q13, Q4, Q8,
Q9, Q14, Q15, Q20, Q21)
• Main board RT1 open
8-2 1001862E 02/06

Troubleshooting

PEM fuse blows repeatedly • Failed main board mains power • Repair or replace main board
components (BR1, MOV1,
• Set voltage select switch to
C35, C45, C63, C79)
230V, replace PEM fuses
• Main voltage is 220/240V and
voltage and fuses set to 120V
• Bad memory backup battery • Remove access panel at unit

bottom and replace battery
Flashing LCD bluish display • Shorting thermistors of Sample • Check that each thermistor
Block Assembly or Lid Heater measures 10K ohms at 25
Assembly degrees C
• Replace lid heater or sample
block
Erratic temperature accuracy and • Bad U28 (A/D) of CPU board • Calibrate chassis
uniformity
• Defective main board ther- • Replace U28 of CPU board
mistor amplifier(s) (U3, U6,
• Replace or repair main board
U27, U32)
• Reference to ISA # 022
• Failed sample block edge
heater • Failed sample block edge
heater
LCD display blank, fan runs, yel- • Bad U19 of main board • Replace U19 of main board
low LED lights, backlit lights
• Bad D10, D11, Z5, Z6, C27, • Replace components or main
R19 for Rev ZB-ZF main board board
• Bad D11, D12, Z5, Z6, • Replace components or main
C31,R19 for Rev A main board board
LCD is dark with no backlit • Main board overtemp shutdown • Repair or replace sample block
is being triggered from appar- or main board
ent thermistor reading over
120C or from main board
defect. • Replace VGA display assembly
• Bad backlit • Replace U18 of main board
• Bad U18
No Power from line surge or • Open main board and power • Replace F2 Main PCB , power
incorrect voltage selector switch entry module fuse(s) and entry module fuse(s) and CR1
setting shorted Transorb Lambda Conv PCB
Heat/Cool Test Fault • If first two thermistors of top • Replace FET transistors
row channel reads 0.5C higher
than last two, MOSFET transis-
tors Q3, Q4, Q8, Q9, Q14, • Upgrade firmware version
Q15, Q20, or/and Q21 failed
Intermittent or multiple lid preheat • A protocol run was initiated • Allow the unit to warm up for at
messages during protocol run before the 3-5 minutes required least 5 minutes for the lid tem-
at power on to preheat the lid perature to reach 105°C before
temperature to 105°C starting a protocol run.
1001862E 02/06 8-3

Troubleshooting

Reaction Module Sensor Fault • Replace sample block
• Bad themistor on sample block • Reference to WPCRTEST- ISA
# 019A
• Moisture build-up from high
humidity and low cooling runs • Check lid heater
on non-conformal coating
• Replace sample block with
design
conformal coating design - ISA
083A and 084A
Edge Balance Fault • Repair Q32, Q40 circuits and
perform ISA#022A
• Failed sample block edge
heater on sample block and • Run Instrument Check Diag-
shorted Q32, Q40 FET transis- nostics to determine course of
tor circuit action
• Moisture build-up from high • Replace sample block if
humidity and low cooling runs required by the Instrument
on non-conformal coating Check Diagnostics
design
• Replace sample block with
• Bug in firmware v3.032 conformal coating design - ISA
083A and 084A
• Update to latest firmware
Lid Heating Fault on 2 x 48 Well • Moisture build-up from high • Replace sample block with
humidity and low cooling runs conformal coating design - ISA
on non-conformal coating 084A
design
Reaction Block Not Detected • Broken lid heater right ribbon • Check LED cable assembly
Error cable connection or internal
• Check for broken contact con-
connection breakage in sam-
nections on white connectors of
ple block
fan bracket
• Faulty LED or cabling
• Check for broken or bent pins
• Bad white connector connec- on sample block white connec-
tions from fan assembly to tors
block
• Replace lid heater assembly
• Broken sample block pins
• Replace sample block
No power with fuses fine • Shorted Lamda image plane • Install longer Lambda shield
shield across secondary trans- rev B or insulate edge of shield
former pins on Lambda board with Kapton tape.
• Regulator to fan compatibility • Check regulator component
compatibility on main board to
EBM or NIDEK fan per ISA #
050A
8-4 1001862E 02/06

Troubleshooting

Solid blue, non-flashing display • Connection problem of the LCD
Blank, white display controller, U17
• Replace CPU board assembly.
Distorted display
• Defective LCD Controller IC Reference to ISA # 049A, #
Vertical display lines
036A, and #037A
• Flash memory corruption dur-
ing download
External sample probe does not • Function removed on firmware
function for either 96, 60, or 384 versions 2.033, 2.038, and
• Install latest firmware
well 2.039
• Check and replace sample
• Correction made on version
probe and pin connections
3.021 or higher for 96, 60, and
384 well blocks. The external
sample probe feature for dual
48 well block is inactive.
Fails temperature accuracy or • Reseat probe in test well and
uniformity tests repeat tests
• Poor temperature probe setup
• Dip probe in mineral oil
• Mineral oil was not used
• Reseat Reaction Module to
• Poor connection from Reaction
chassis connectors
Module to Chassis connectors
• If accuracy or uniformity is mar-
• Bad peltier or thermistors
ginal, calibrate chassis
• Chassis out of calibration
• Replace sample block
• Bad MOSFET H-Bridge Drivers
• Replace main board or check
• Bad test probe and replace all eight driver tran-
sistors
• Replace test probe
Fails lid heater temperature accu- • Probe dislodged from lid adap- • Reseat probe in lid adaptor and
racy test tor hole repeat test
• Poor ribbon cable connection • Reseat lid heater ribbon cables
from lid to sample block to sample block
• Poor connection from Reaction • Reseat Reaction Module to
Module to Chassis connectors chassis connectors
• Bad lid heater assembly • Replace lid heater assembly
• Bad main board or driver tran- • Replace lid driver transistor
sistor
• Replace main board
Block format not supported mes- • Both J8 and J9 cable connec- • Switch both J8 and J9 cable
sage at power-up tors to the CPU Board are connectors on the CPU Board
switched due to vendor assem-
• Replace Main Board
bly problem
• Bad channel amplifier compo-
nents, U32,R100,J15,J19 on
Main Board
1001862E 02/06 8-5

Troubleshooting

Keypad fault error • Sticky key(s) causing contact • Replace with Front Panel
activation on power-up Assembly with Keypad
(10005070)
• Bad keypad
Lid opening scrapping sample • Manufacturing problem with • Replace sample block
block railing countersunk screw causing
interference. Correction made
with setscrew
Lid Heater Fault • Shorted lid heater sensor or • Replace lid heater
shorting lid heater ribbon
cables
Dwell Settling Error • Default Dwell time is 30 sec- • Increase Dwell time in Service
onds when unit is powered-off Options
Missing serial number of Chassis • Serial number was not pro- • Set the serial number using
in Validation Report grammed into CPU WPCRTEST. Refer to Section
7
Binding problem when opening lid • Poor mechanical fit with dust • Check and replace sample
of 2 x 48 Well Reaction Module cover and tracks of lid and block
sample block rails
• Check and replace 2 x 48 Well
Lids
Overheated 2 x 48 Well lids and • Failure of sample block over- • Replace sample block
cracks from binding problem heating most likely caused by
• Replace Lid(s)
bad Main Board drivers
• Replace Main Board
Cracks on bosses of front panel • Bad batch of panels manufac- • Replace with Front Panel
tured by vendor sometime in Assembly with Keypad
2003/2004 (10005070)
8.3 Chassis Test Points

This section provides test point measurements of the Chassis connectors on the Fan Bracket Assembly used
to aid in general troubleshooting Chassis problems.
1. Using a digital multimeter (DVDM), follow Figure 8-1 and Table 8-1 below for test point measurements:
8-6 1001862E 02/06

Troubleshooting
LEFT P1 RIGHT P1
1 13 24 12
12 24 13 1
FRONT
Figure 8-1:
Table 8-1
Connector Test Point Good Bad
Left P1 Connector Edge Heater 0 - 10 VDC Exceeding 10.0 VDC
Pins 21 and 22
Right P1 Connector Edge Heater 0 - 10 VDC Exceeding 10.0 VDC
Pins 21 and 22
Left P1 Connector Sensor Detection 25°C ±0.5C Below 24.5°C or above
25.5°C
1 and 10 with 10K ohm
dummy
25.5°C
dummy
25.5°C
dummy
Right P1 Connector Sensor Detection 25°C ±0.5C Below 24.5°C or above
25.5°C
dummy
25.5°C
dummy
25.5°C
dummy
1001862E 02/06 8-7

Troubleshooting
2. In reference to the test point table, measure edge heater voltage conditions on the specified connectors with the
Chassis turned on without the Reaction Module.
3. In reference to the test point table, install a 10K ohm (1%) resistor on the specified connectors with the Chassis
turned on without the Reaction Module and observe the temperature sensor display as shown in Figure 8-2. From Fig-
ure 8-2, sensors T1,T2, T3 are wired to the Left P1 Connector of the block and sensors T4,T5, T6 are wired to the
Right P1 Connector of the block.
T1 T2 T5 T6
T3 T4
Figure 8-2:
8.4 Sample Block Test Points

This section provides test point measurements of the sample block connectors on the used to aid in general
troubleshooting Reaction Module problems.
1. Using a digital multimeter (DVDM), follow Figure 8-3 and Table 8-2 below for test point measurements:
LEFT P2 RIGHT P1
12 24 13 1
1 13 24 12
FRONT
Figure 8-3:
Table 8-2
Connector Test Point Good Bad
Left P2 Connector Edge Heater 2.0 to 2.6 ohm Below 2.0 or above 2.6 ohm
Pins 21 and 22
8-8 1001862E 02/06

Troubleshooting
Left P2 Connector Ground Isolation OPEN resistance or infinite Any resistance that is
Pins 4 and 21 NOT OPEN
Left P2 Connector Ground Isolation OPEN resistance or infinite Any resistance that is
Right P1 Connector Edge Heater 2.0 to 2.6 ohm Below 2.0 or above 2.6 ohm
Pins 21 and 22
Right P1 Connector Ground Isolation OPEN resistance or infinite Any resistance that is
Right P1 Connector Ground Isolation OPEN resistance or infinite Any resistance that is
Left P2 Connector Block Thermistor 10K ohm ±0.5 ohm@ 25°C Below 9.5K ohm or above
10.5K ohm@ 25°C
7 and 10 or
or
about 10.5K ohm ±0.5 ohm
@ room temperature Below 10.5K ohm or above
11K ohm @ room tempera-
ture
Left P2 Connector Block Thermistor 10K ohm ±0.5 ohm@ 25°C Below 9.5K ohm or above
10.5K ohm@ 25°C
8 and 10 or
or
ture
Right P1 Connector External Thermistor 10K ohm ±0.5 ohm@ 25°C Below 9.5K ohm or above
10.5K ohm@ 25°C
9 and 10 or
or
ture
Right P1 Connector Block Thermistor 10K ohm ±0.5 ohm@ 25°C Below 9.5K ohm or above
10.5K ohm@ 25°C
7 and 10 or
or
ture
Right P1 Connector Block Thermistor 10K ohm ±0.5 ohm@ 25°C Below 9.5K ohm or above
10.5K ohm@ 25°C
8 and 10 or
or
ture
1001862E 02/06 8-9

Troubleshooting
Right P1 Connector Lid Thermistor 10K ohm ±0.5 ohm@ 25°C Below 9.5K ohm or above
10.5K ohm@ 25°C
1 and 10 or
or
ture
2. In reference to the test point table, measure edge heater and ground isolation resistance conditions on the specified
connectors of the sample block.
3. In reference to the test point table, measure thermistor sensor conditions on the specified connectors of the sample
block. Resistance measurements will vary depending on the block or room temperature. Generally, measurement at
room temperature of a cold block will measure about 0.5 ohm higher.
8-10 1001862E 02/06

Parts Information
Section 9
Parts Information
9.1 Introduction
This section contains parts lists and associated information. It provides instructions for ordering and returning
defective parts. This section also identifies parts that are field replaceable.
9.2 Parts Orders - US Domestic Operations

Parts may be ordered through our Customer Service department. You can reach the Customer Service depart-
ment during regular office hours by calling 1-800-4BIO-RAD (1-800-424-6723), and selecting “1” for customer
service. If you do not have a touch tone phone, please stay on the line and an attendant will connect you. You
can help to make processing your order more efficient by having the following information before you call:
• The part number(s) or catalog number(s) of the parts you want to order
• Your company’s purchase order number
• Your customer account number
9.3 Parts Orders - International Subsidiaries

The procedures for ordering parts vary from region to region outside the United States. Please contact your
Bio-Rad Export Sales Representative through your regular sales and service channels.
9.4 Returning Defective Parts

Defective assemblies returned for repair are an important part of the service logistics and inventory control pro-
cess. Returned assemblies are refurbished, tested, and returned to service stock. Maintaining the effective-
ness and efficiency for this process enables us to deliver the high standard of service that our customers
expect, at reasonable cost that allows us to remain competitive.
You are an integral part of our inventory process. When you return parts or assemblies to Bio-Rad to be
repaired, please attach a tag to each assembly. The tag should contain the following information:
• Model and serial number of the unit from which the part was removed
• The date of removal
• A description of the problem or symptoms exhibited (if you could not find the problem, describe what the
user reported and specify “CND - Can Not Duplicate”)
• The part number or catalog number of the part being returned
• Your name and other identification information
100-1862E 02/06 9-1

Parts Information
This information will help our service centers to make repairs efficiently. When you receive replacement parts,
save the packaging material for returning the defective part for repair. Many of the parts are delicate and
expensive; extra attention to packaging will pay off in less damage to parts during shipment.
Note: Additional procedures and information may be needed for the return of
defective parts from international operations. These procedures vary depending
on your location
9.5 iCycler Thermal Cycler Spare Parts

The appropriate quantity for each of the iCycler spares will vary depending on the total quantity of instruments
in your installed base. A quantity of 1 for each field replaceable part is a good starting point. The spare parts
below provides a list of spare parts that are available to order, but not commonly used.
Spare Parts List

P ar t Nu m be r D esc r ip t io n Ph o to
900-8933 8.0A, 250V, 5X20MM SLOW BLOW
900-0234 4.0A, 250V, TYPE T TIME LAG, 5X20MM
8008250 CASE KIT, COMPLETE
920-8290 SWITCHPANEL
9-2 100-1862E 02/06

Parts Information
Spare Parts List

Part Number Description Photo
920-8280 CPU IMAGE PLANE
*Old Type
920-8322 LAMBDA IMAGE PLANE, REV B
920-8294 FOOT, LEFT, FRONT, CHASSIS
920-8295 FOOT, RIGHT FRONT, CHASSIS
920-8296 FOOT, BACK, CHASSIS
800-8252 CABLE, LPT CONNECTOR (CHASSIS TO

CPU)
100-1862E 02/06 9-3

Parts Information
Spare Parts List

800-8261 ASSY, CABLE, CPU- MAIN BOARD
920-6089 DISPLAY, QVGA LCD, BACKLIT
900-5169 SWITCH, DPDT, POWER, 15a/250v
900-5048 FUSE DRAWER, 2 POLE, 5X20MM, BLK
900-8795 PWR ENTRY MOD, SCHURTER 4301.0502
900-6020 BATTERY, LITHIUM, 3V, 2032
9-4 100-1862E 02/06

Parts Information
Spare Parts List

800-5829 96 WELL LID HEATER ASSEMBLY
900-6560 LF347 Q JFET OP AMP, U19
100-1944 NOISE REDUCTION KIT
900-1599 12 BIT A/D CONVERTER
900-8927 4A/250V PIGTAIL FUSE, 5X20MM, F2
900-6350 DIODE, TRANSORB, 1.5KE400CE, CR1
100-1862E 02/06 9-5

Parts Information
Spare Parts List

800-8126 U12,CPU, FLASH MEMORY IC
170-8731 96 WELL SEALING RING
100-2124 60 WELL SAMPLE BLOCK ASSEMBLY
100-2125 384 WELL SAMPLE BLOCK ASSEMBLY
920-8592 384 WELL PRESSURE PAD
9-6 100-1862E 02/06

Parts Information
Spare Parts List

910-9243 60/96 WELL LID HEATER SPRING
910-1724 384 WELL LID HEATER SPRING
910-9244 LID HANDLE SPRING
100-3561 DUAL 48 WELL SAMPLE BLOCK ASSEMBLY,

CALIBRATED
800-5963 DUAL 48 WELL HEATER ASSEMBLY, PAIR
100-1862E 02/06 9-7

Parts Information
Spare Parts List

800-5960 DUAL 48 WELL LID ASSEMBLY, PAIR
910-9245 DUAL 48 WELL LID HEATER SPRING
800-5968 DUAL 48 WELL BLOCK SHIELD SEALING

RING
900-6650 POWER FET TO220 TRANSISTOR
910-0855 # 4 NYLON FET SHOULDER WASHER
940-0626 8.25”, .20”H x .27”W BLACK ADHESIVE PILE
9-8 100-1862E 02/06

Parts Information
Spare Parts List

800-8250 PAINTED CHASSIS ENCLOSURE ASSEMBLY
KIT
920-8298-1 PAINTED SLIDING DUST COVER, STAN-

DARD
800-6471 PAINTED SLIDING DUST COVER, DUAL 48

WELL, PAIR
100-2126 96 WELL SAMPLE BLOCK, TESTED
800-8650-01 MAIN BOARD ASSEMBLY, TESTED
800-8651-01 CPU BOARD ASSEMBLY, TESTED

*OLD TYPE - OBSOLETE
100-1862E 02/06 9-9

Parts Information
Spare Parts List

10005213 iCYCLER CPU BOARD KIT, TESTED
*NEW TYPE - ABOVE S/N582BR014381
(PROJECTED AVAILABLILITY Q2)
800-8127 FAN BRACKET ASSEMBLY
10005070 FRONT PANEL ASSEMBLY WITH SWITCH-

PANEL
9.6 Tools
The following list of tools are required to perform the System Checkout and/or Adjustment and Calibration sec-
tions.
Tools List
100-6494 THERMAL VALIDATION KIT
9-10 100-1862E 02/06

Drawings
Section 10
Drawings

This section contains schematics and assembly drawings for the iCycler Thermal Cycler. These drawings are intended to
be used as aids for troubleshooting and parts identification.
10.2 Drawings
10.2.1 Instrument Check Flow Chart
10.2.2 Schematics
• Interconnect 96 Well Block Schematic E8260
• Interconnect 60/384 Well Block Schematic E8662
• Electronic Dual 48 Well Block Schematic E8664
• Main PCB Schematic E8650
• CPU Board Schematic D009467
10.2.3 Assembly Drawings

• Main PCB 8008650
• CPU Board 10001672
• Fan Bracket Assembly 8008127
• Main-RB,L,Chassis Cable 8008254
• Main-RB,R,Chassis Cable 8008255
• 96 Well Heater Harness Assembly 8005833
• 60/384 Well Heater Harness Assembly 8008135
• 2 x 48 Well Heater Assembly 8005958
1001862E 02/06 10-1

iCycler Instrument Check
Marginal sensor accuracy,

Test 4 #1
swap module if possible and
300 to 400?
repair or replace module soon
Yes
No
Failed sensor, swap module if

Test 4 #1
possible to confirm and
above 400?
Yes repair or replace
No
Test 1 #1 Test 1 #1
No
above 400? above 1000?
Yes Yes
No No
Test 1 #3
below -150 or
above +150? Yes
No
Replace Reaction Module
Diagnose further with
soon, operate temporarily
heat/cool tests
if other tests pass
Heat/Cool Tests
DO NOT swap module,

Test 2 #3
Test 2 #1 above 800? recheck for edge
-200 to +200?
heater balance fault
Yes Yes
No No
Power-on
Test 2 #3 self-tests
below -200?
Yes
No
Test 5 #1
Return module for repair
above 500?
Yes
No
DO NOT swap module,

Test 3 #3
Normal Block recheck for edge
-200 to +200?
Yes heater balance fault
No
Power-on
Return chassis for repair
self-tests
Lid Heater Tests
Lid Test Lid Test

#2 below 400? #4 below 500?
Yes Yes
No No
Return lid for repair
or replacement
Return chassis for repair

or replacement
Lid Test Return chassis for repair

#4 below 0? or replacement
Yes
No
Continue instrument usage
5 4 3 2 1
R_LIDHTR-
R_LIDHTR+
L_LIDHTR+
L_LIDHTR-
(T7)
(T11)
REVISIONS
L_TRET
L_TLID
CHANGED CHECKED APPROVED
REV P.C.O.# DESCRIPTION OF CHANGE
R_TRET
R_TLID
BY/DATE BY/DATE BY/DATE
RT13-A
RT13-B
ZA L010696 RELEASE CB 12/28/01 CB 1-16-02 RP 1-17-02
X
X
X
X
ZB L010175
L010 CLARIFY C10,U7 VALUES CB 3-19-02 CR
.. - -4-5-02 .. - 4-8-02
RP -
J3 J7
CON10 CON10
1
10
10
1
2
3
4
5
6
7
8
9
1
2
3
4
5
6
7
8
9
D D
RTL_LIDB RTR_LIDB
RTL_LIDB pg2 RTR_LIDB pg2
RTL_LID RTR_LID
RTL_LID pg2 RTR_LID pg2
P1 P2
L_TLID 1 L_TLID
L_TLID pg2 R_TLID 1 R_TLID
R_TLID pg2
L+ 2 L+
L+ pg2,3 R+ 2 R+
R+ pg2,3
L_LED 3 L_LED
L_LED pg2 R_LED 3 R_LED
R_LED pg2
L_BLKGND 4 L_BLKGND
L_BLKGND pg2,3 R_BLKGND 4 R_BLKGND
R_BLKGND pg2
THSINK 5 5
THSRET 6 6
TBLK1 7 TBLK1 TBLK3 7 TBLK3
TBLK2 8 TBLK2 TBLK4 8 TBLK4
L_TVIAL 9 L_TVIAL
L_TVIAL pg2 R_TVIAL 9 R_TVIAL
R_TVIAL pg2
L_TRET 10 L_TRET
L_TRET pg2 R_RET 10 R_TRET
R_TRET pg2
L_LIDHTR+ 11 R_LIDHTR+ 11
L_LIDHTR- 12 R_LIDHTR- 12
13 L_TE+ 13 R_TE+
L_TE+ pg3 R_TE+ pg3
L_TE+ 14 R_TE+ 14
15 15
16 L_TE- 16 R_TE-
L_TE- pg3 R_TE- pg3
L_TE- 17 R_TE- 17
18 18
19 L_BLKHTR- 19 R_BLKHTR-
L_BLKHTR- pg3 R_BLKHTR- pg3
L_BLKHTR- 20 R_BLKHTR- 20
21 21
22 L_BLKHTR+ 22 R_BLKHTR+
L_BLKHTR+ pg3 R_BLKHTR+ pg3
L_BLKHTR+ 23 R_BLKHTR+ 23
24 L_BLKHTRC 24 R_BLKHTRC
L_BLKHTRC pg3 R_BLKHTRC pg3
CON24 CON24
RT2A
RT2B
RT4A
RT4B
L_TRET R_TRET
H1B
H2A
H3B
H4A
TE2A
TE2B
TE4A
TE4B
C C
1
1
J1 RED (T1) BLK J6 RED (T3) BLK
(T4) (T0) (T5) (T8) (T2) (T9)

BLK RED BLK RED
B B
H1A
H2B
H3A
H4B
TE1B
TE1A
TE3B
TE3A
RT5A
RT5B
RT1A
RT1B
RT6A
RT6B
RT9A
RT9B
RT3A
RT3B
RT10A
RT10B
L_TRET R_TRET
L_TEC R_TEC
L_TEC pg3 R_TEC pg3
RT6B pg2 RT10B pg2
J4 RT6 pg2 J8 RT10 pg2

(T6) RT5B pg2 (T10) RT9B pg2
RT5 pg2 RT9 pg2

1
2
1
2
RTL_VIAL pg2 RTR_VIAL pg2
RTL_VIALB pg2 RTR_VIALB pg2

(Tn ARE FIRMWARE REF)
THE INFORMATION CONTAINED IN

THIS DOCUMENT IS PROPRIETARY BIO-RAD Laboratories
CONFIDENTIAL. THIS DOCUMENT MAY
NOT BE COPIED OR REPRODUCED
Life Science Group, Lab Devices Division
A WITHOUT WRITTEN PERMISSION 2000 Alfred Nobel Drive A
FROM BIO-RAD. Hercules, CA 94547 USA

DRAWN BY DATE Title
C.Baldwin Jul. 11 '01
CHECKED BY DATE
Elec Schem, Dual Block
Interconnections
ENGINEER APPRV'D DATE Document Number
E8664
MANAGER APPRV'D DATE Size Rev
C Sheet 1 of 3 ZB
5 4 3 2 1
5 4 3 2 1
pg1 L_TLID
pg1 L_TVIAL (Tn ARE FIRMWARE REF)
pg1 RTL_LIDB L (T7)

pg1 RTL_LID
pg1 RTR_LIDB R (T11)

pg1 RTR_LID
pg1 RTL_VIALB L (T6)

pg1 RTL_VIAL
pg1 RTR_VIALB R (T10)

pg1 RTR_VIAL
D D
Q6 Q7 Q8 Q9
MMFT3055V MMFT3055V MMFT3055V MMFT3055V
pg1 L_TRET
pg1 R_TLID
pg1 R_TVIAL
pg1 RT5B L (T4)

pg1 RT5
pg1 RT9B R (T8)

pg1 RT9
pg1 RT6B L (T5)

pg1 RT6
pg1 RT10B R (T9)

pg1 RT10
Q10 Q11 Q12 Q13

MMFT3055V MMFT3055V MMFT3055V MMFT3055V
pg1 R_TRET
VCC
C U6A U6B U6C U6D C
C14 1 2 3 4 5 6 9 8
0.1
74AC14 74AC14 74AC14 74AC14

VCC VCC VCC VCC VCC
VCC
8
RN1 RN2 RN3 U4 RN4 RN5
8
7
6
5
8
7
6
5
8
7
6
5
8
7
6
5
8
7
6
5
3 4
VCC
DI DO
2
CLK
GND
1
100K 100K 100K CS 100K 100K
1
2
3
4
1
2
3
4
1
2
3
4
1
2
3
4
1
2
3
4
93C46/SO
5
U7
43 24 PWM1 pg3
P0.0/AD0 P2.0/A8
42 25 PWM2 pg3
P0.1/AD1 P2.1/A9
41 26 PWM3 pg3
P0.2/AD2 P2.2/A10
40 27 PWM4 pg3
P0.3/AD3 P2.3/A11
39 28 PWM5 pg3
P0.4/AD4 P2.4/A12
38 29 PWM6 pg3
P0.5/AD5 P2.5/A13
37 30 PWM7 pg3
P0.6/AD6 P2.6/A14
36 31 PWM8 pg3
P0.7/AD7 P2.7/A15
2 11
VLEDS VCC VLEDS U3 3.3V P1.0/T2 P3.0/RXD
3 13
P1.1/T2EX P3.1/TXD
4 14
U6F P1.2/ECI P3.2/INT0
1 5 5 15
B IN OUT P1.3/CEX0 P3.3/INT1 B
pg1,3 L+ 6 16 CPCLK1 pg3
P1.4/CEX1 P3.4/T0
4 12 13 7 17 CPCLK2 pg3
VLEDS + C13 BP + C9 P1.5/CEX2 P3.5/T1
8 18
GND
P1.6/CEX3 P3.6/WR
pg1,3 R+ 3 9 19
10 SHDN 10 P1.7/CEX4 P3.7/RD J9
MAX8878/SOT 74AC14 Y1 C16 X1 21 32
+ C19 X2 X1 PSEN
2
20 2 1
X2
33 4 3
100 C10 11.0592MHz 22PF ALE/PROG
35 6 5
6.3V 0.01 EA/VPP
10 8 7
GND C15 RST
10 9
GND
pg1,3 L_BLKGND VCC
GND2 44
VCC
22PF
22
87LV52/87C54 HEADER 5x2/SM
pg1 R_BLKGND
VCC VCC
U5
GND2 3.3V 3 2
VCC VCC RESET
GND
VCC
3.3V R15 C26 C11 C12
R5 0.1 0.1 MAX810 0.1
1.2K GND2 R18
1
U2A 750K U2B 22K
3
C7
7 + 0.1 R9 R16 5 +
pg1 L_LED /INT0
1 2
3.3V 6 - 4 -
LM339/SO 19.1K 10K
Q2 + C8
12
PNP50V1A C5 LM339/SO
R3 1.0 0.1
9001094
R8 35V
1.2K GND2 GND2 GND2
4.7K
A A
pg1 R_LED
VCC
3.3V R12 C27

0.1
GND2 R17
U2C 750K U2D 22K
9 + R4 R7 11 + Control Core
14 13 /INT1
U6E 8 - 10 -
19.1K 10K Title
11 10 + C2
LM339/SO C4 LM339/SO Elec Schem, Dual Block, iCycler
1.0 0.1 Size Document Number Rev
35V
74AC14 GND2 GND2 C E8664 ZB
Date: Tuesday, March 19, 2002 Sheet 2 of 3
5 4 3 2 1
5 4 3 2 1
VLEDS
D1 D2
V_BST 7V
B120/B B120/B
+ C3 + C6
+ C1 10 22 R14 Q5
10 10K
PNP50V1A
U1A
9001094
1 2 CP1A/ R11 R10
pg2 CPCLK1
U1C
74AC14 5 6 19.1K 10
U1B R6 R2
74AC14 R13 10K
D D
3 4 CP1B/ Q4
U1D MMBT3904/SOT 10
15K Q3
9 8 74AC14 MMFT3055V
U1F U1E
74AC14 R1
13 12 CP2A/ 11 10 CP2A Q1
pg2 CPCLK2
MMBT3904/SOT
15K
74AC14 74AC14
V_CP
D7 D10
D9 B120/B D8 B120/B
B120/B B120/B
+ C24 + C20
+ C22 22 + C23 22
1.0 25V 1.0 25V
50V 50V
7+VD2 7+VD6
pg1 L_TE+ pg1 R_TE+
C VLEDS VLEDS Q25 C

R27 U13 Q24 R20 U8
IRF3205/TO IRF3205/TO
1 6 1 6
5 5
4.7K 4.7K
2 4 VS1 2 4 VS5
pg2 PWM1 pg2 PWM5
H11AG1 H11AG1
Q23 Q22
R34 R33
27K IRF3205/TO 27K IRF3205/TO
pg1 L_TEC pg1 R_TEC
Q15 Q16
R28 U14 R19 U9
1 6 1 6
5 5
4.7K 4.7K
2 4 VS2 2 4 VS6
pg2 PWM2 pg2 PWM6
H11AG1 H11AG1
Q18 Q19
R24 R26
27K IRF3205/TO 27K IRF3205/TO
pg1 L_TE- pg1 R_TE-
D4 D5
D3 B120/B D6 B120/B
B B
B120/B B120/B
+ C18 + C25
+ C17 22 + C21 22
1.0 25V 1.0 25V
50V 50V
7+VS3 7+VS7
pg1 L_BLKHTR+ pg1 R_BLKHTR+

VLEDS VLEDS
R22 U11 R25 U12
1 6 1 6
5 Q21 5 Q20
4.7K 4.7K
pg2 PWM3 2 4 pg2 PWM7 2 4
H11AG1 H11AG1
R32 R31
27K 27K
pg1 L_BLKHTRC R21 pg1 R_BLKHTRC R29

U10 U15
1 6 1 6
5 Q14 5 Q17
4.7K 4.7K
pg2 PWM4 2 4 pg2 PWM8 2 4
H11AG1 H11AG1
R23 R30
27K 27K
A A
pg1 L_BLKHTR- pg1 R_BLKHTR-
Balance Drivers
Title
Elec Schem, Dual Block, iCycler
Size Document Number Rev
C E8664 ZB
Date: Tuesday, March 19, 2002 Sheet 3 of 3
5 4 3 2 1
REVISIONS CHANGED CHECKED APPROVED
REV BP# DESCRIPTION OF CHANGE BY/DATE BY/DATE BY/DATE
A 003990 New RELEASE (Modify From E8651 TC/4-21-05 GS/10-20-05 CB/10-21-05
Schematics)
CPU, Flash & I/O Select DRAM & Support Logic
Page 2 Page 3 ICYCLER - CPU Board

This Schematic Consists of 7 Pages:
1. Cover Sheet (This Page)
Microprocessor Core Memory, Refresh Control & Interface 2. CPU (386EX), Flash Memory, & I/O Select
3. DRAM, SRAM & Support Logic
4. LCD Controller
5. Data Acquisition and Timekeeper
LCD Controller Data Acq & Timekeeper 6. External Interface
7. Keyboard & Printer Interface
Related Part #'s:

PCB # 920-8651 Up to Reversion D Reference to E8651 Schematics.
Page 4 Page 5 ASSY# 800-8651 Up to Reversion D Reference to E8651 Schematics.
PCB # 10001671
ASSY# 10001672
Display Interface
Miscellaneous I/O
External Interface Keyboard & Printer
Page 6 Page 7 THE INFORMATION CONTAINED IN

CONFIDENTIAL. THIS DOCUMENT MAY
Life Science Group, Gene Expression Division
WITHOUT WRITTEN PERMISSION 2000 Alfred Nobel Drive
DRAWN BY DATE Title
TC/4-21-05
CHECKED BY DATE
ICYCLER CPU
GS/10-20-05 Cover Sheet
Buffer & Interconnect Input/ Output Interface ENGINEER APPRV'D DATE Document Number
TC/10-20-05 D009467
CB/10-21-05
Custom
Sheet 1 of 7 A
VCC TP284 VCCU5 CLK2_A
U30 TP26
RESET
CLK2_A pg3
RESET pg4,7
1 5 TP285 RESET_L
Vin Vout RESET_L pg3,5,6,7
TCLK
TCLK pg3
C152 3 on/off C153 A[25..1]
A[25:1] pg3,4,7
VCCU5 1UF 2 TP187 A1
TP16 TP286 GND 1UF A2 ZA[16..1]
4 ByPass TP115 ZA[16:1] pg3,4,5
R64 TP188 A3
LP2985/SOT23 C18 0.0022 TP274 A4
C151 1 2 TP276 A5
0.01UF PLDTCK pg3,6
10K VCCU5 TP114 A6
PLD2TDI pg3
U5 TP275 A7 TP6 VCC
PLDTDO pg6
1
C11 C12 TP277 A8 256K x 16 FLASH MEMORY RN1O 10K
40MHZ VCC PLDTMS pg3,6
TP278 A9 VCC 15 16
TP256 C10
PUI1
1 4 0.0022 1UF C19 1UF TP113 A10 23 VCC
EN VCC VCCU5 C52 VCC TP280 A11 U12 VCC PPSR_L
2
TP186 PPSR_L pg7
2 GND OUT 3 U6 L1 0.01UF TP281 A12 FLASHBANK
29F400 TP163 PPDW_L
PPDW_L pg7
5 2 TP259 1 2 TP282 A13 3 C15 0.01UF
L2 VCC O0 A14 A17 NC_A17 0.01UF
44
43
42
41
40
O1 3 TP258 1 2 TP112 34 A16
6
5
4
3
2
1
1 2 40M_F TP22 1 6 L3 ZA16 35 13
GND
TP257 CLK O2 A15 VSS
33 4 7 100 L4 TP279 A16 ZA15 36 32 TP27
GND
VCC
IO4
IO3
IO2
IO1
IO0
IO31
IO30
IO29
IO28
GND O3 A14 VSS
109
121
127
RES RES 100 ZA14
15
28
38
47
60
71
81
88
VCC TP20 37 A13
9
CGS74CT2524M RES ZA13 38
A25 ZA12 A12 ZD15
1
72 TP90 39 31 TP65 7 39
VCC
VCC
VCC
VCC
VCC
VCC
VCC
VCC
VCC
VCC
VCC
VCC
R17 CLK2 A25 A24 ZA11 A11 DQ15 ZD14 IO5 IO27
115 CLK2 A24 70
68 A23
TP111
TP165 ZA10
40
41
A10 DQ14 29
27 ZD13
TP61
TP64
8
9
IO6 U4 IO26 38
37
pg6 PWRGOOD_C A23 A9 DQ13 IO7 IO25
VCC CLKOUT 67 A22 TP146 ZA9 42 25 ZD12 TP60 10 M4_32/32_J 36
7.5K PWRTH1_25 A22 A21 ZA8 A8 DQ12 ZD11 TDI IO24
103 CLKOUT 66 TP155 4 22 TP63 11 35
pg6 PWRGOOD_E U8 A21 A7 DQ11 CLK0/I0 TDO
T190_AREG
1.42V NORM TP94 65 A20 ZA7 5 20 ZD10 12 34
T192_DWR_L
A20 TP57 A6 DQ10 TP59 GND GND
SW1 A19 ZA6 ZD9
2 63 TP148 6 18 TP62 13 33
T192_DRD_L
X488 VCC A19 A5 DQ9 TCK CLK1/I1
4 3 RST_PB TP8 1 8 TP1 110 62 A18 TP55 ZA5 7 16 ZD8 TP45 14 32
CS_TIMEK_L
MR RSTH RESET CAS2/A18 A17 ZA4 A4 DQ8 ZD7 IO8 TMS KB120R_L
CAS1/A17 61 TP153 8 A3 DQ7 30 TP67 15 IO9 IO23 31 TP208 KB120R_L pg7
CTL130W_L
7 59 A16 1 8 ZA16 R32A 33 ZA3 9 28 ZD6 16 I/O SELECT PLD 30 KB120W_L
RESET RSTL TP3
TP92 114
CAS0/A16
58 A15 2 7 ZA15
TP136
TP137 R32B 33 ZA2 10
A2 DQ6
26 ZD5
TP66
TP70 17
IO10 IO22
29
TP204 KB120W_L pg7
AD180R_L
WDTOUT A15 A1 DQ5 IO11 IO21
SWITCH TP7 4 5 57 A14 3 6 ZA14 TP75 R32C 33 ZA1 11 24 ZD4 TP69
AD180W_L
PFI PFO A14 A0 DQ4
AD180CS_L
1 2 X487 3 RN2B 56 A13 4 5 ZA13 TP152 R32D 33 21 ZD3 TP73
GND
IO12
IO13
IO14
IO15
IO16
IO17
IO18
IO19
IO20
VCC
R6 GND A13 A12 ZA12 R31A 33 DQ3 ZD2
16 2 73 55 1 8 14 19
DA100W_L
TP87 TP154 TP119
3.57K MAX708
VCC SMI U14 A12
54 A11 2 7 ZA11 TP149 R31B 33 43
OE DQ2
17 ZD1 TP120
RESET_L
SW PB 10K A11 A10 ZA10 R31C 33 WE DQ1 ZD0
120 53 3 6 TP121 12 15 TP72
18
19
20
21
22
23
24
25
26
27
28
PF_L SMIACT A10 A9 ZA9 R31D 33 CE DQ0
A9 52 4 5 TP58
A8 ZA8 R30A 33 VCC C14
TP2 99 51 1 8 TP129 33
FLASHBANK
FLT A8 BYTE
ZWR_STB_L
ZRD_STB_L
50 A7 2 7 ZA7 TP142 R30B 33 1 2 ZA5
A7 NC RY/BY
CS5_IO_L
CS4_IO_L
CS3_IO_L
3
Q1 R8 A6 ZA6 R30C 33 ZA4

386EX-25 49 3 6 TP141
ZADS_L
A6
ZBLE_L
1 TP91 WDTOUT 48 A5 4 5 ZA5 TP117 R30D 33 44 ZA3 0.01UF
TP269 A5 RESET
U15C 45 A4 1 8 ZA4 TP118 R29A 33
10K RN2C A4 A3 ZA3 TP180 R29B 33 ZA1 VCC
A3 44 2 7
MMBT3904 NMI A2 ZA2 R29C 33 ZD[15..0]
2
VCC 16 3 5 6 TP86 90 NMI A2 43 3 6 TP179 ZD[15:0] pg3,4,5,6

VCC 42 A1 4 5 ZA1 TP139 R29D 33
X6 10K X7 A1 D[15..0]
D[15:0] pg7
74HC14
PAD PAD 23 D15 TP110 1 8 R21A 33 ZD15
TP104 INT0 D15 D14 R21B 33 ZD14 TP37 DA108W_L
80 INT0/P3.2 D14 22 TP126 2 7 DA108W_L pg5
RN2A 10K 16 1 TP85 LED1 82 21 D13 TP108 3 6 R21C 33 ZD13 TP35
LED2 INT1/P3.3 D13 D12 R21D 33 ZD12 TP36 DA100W_L pg5
RN2K 10K 16 11 TP81 84 INT2/P3.4 D12 20 TP125 4 5 AD180CS_L pg5
RN2G 10K 16 7 TP82 LID1 85 19 D11 TP105 1 8 R20A 33 ZD11 TP244
INT3/P3.5 D11 D10 R20B 33 ZD10 TP33 AD180W_L pg5
pg4 LCD_V_INT TP98 93 INT4/TMRCLK0 D10 18 TP124 2 7 AD180R_L pg5
RN2L 10K 16 12 TP93 FLASHRY 94 16 D9 TP103 3 6 R20C 33 ZD9 TP28
LID2 INT5/TMRGATE0 D9 D8 R20D 33 ZD8 VCC VCC VCC VCC VCC VCC VCC VCC TP78 CTL130W_L pg6
RN2F 10K 16 6 TP96 95 INT6/TMRCLK1 D8 14 TP123 4 5 CS_TIMEK_L pg5
TP84 96 13 D7 TP122 1 8 R19A 33 ZD7 TP24
pg5 TIMEK_INT INT7/TMRGATE1 D7 T192_DRD_L pg5
D6 R19B 33 ZD6 TP68
16
16
16
16
16
16
16
16
pg6 BEEPER TP183 74 INT8/TMROUT0/P3.0 D6 12 TP196 2 7 T192_DWR_L pg5
TP106 PWM1 75 11 D5 TP195 3 6 R19C 33 ZD5 TP79
INT9/TMROUT1/P3.1 D5 T190_AREG pg5
TP100 PWM2 10 D4 TP198 4 5 R19D 33 ZD4 RN1A RN1H RN1G RN1F RN1E RN1D RN1C RN1B
R27 D4 D3 R18A 33 ZD3 10K 10K 10K 10K 10K 10K 10K 10K
D3 8 TP197 1 8
X8 7 D2 TP200 2 7 R18B 33 ZD2
10K PAD D2 D1 R18C 33 ZD1
D1 6 TP199 3 6
D0 R18D 33 ZD0
2
RN2N 10K 16 14 TP97 89 TMRCLK2/PEREQ D0 5 TP201 4 5
RN2M 10K 16 13 TP95 92 TMRGATE2/BUSY
91 41 TP159 4 16 RN2D 10K
TMROUT2/ERROR NA VCC
40 ADS_L TP13
ADS
D/C 29 1 8 R22A 33 ZADS_L TP32 ZADS_L pg3,4
30 W_R_L TP30
W/R W_R_L pg3
27 M_IO_L TP31
M/IO M_IO_L pg3
4 5 R22D 33 ZRD_STB_L TP132 ZRD_STB_L pg3,4
RN2H 10K 16 8 P1_0 101 34 RD_STB_L TP167
P1.0/DCD0 RD WR_STB_L TP166
WR 35
RN2I 10K 16 9 P1_2 104 2 REFRESH_L TP101
P1.2/DTR0 CS6/RFSH REFRESH_L pg3,4
RN2J 10K 16 10 P1_3 105 3 6 R22C 33 ZWR_STB_L TP140
P1.3/DSR0 ZWR_STB_L pg3,4
TP251 106 39 BHE_L TP39
pg5 SEL_LIDL P1.4/RI0 BHE BHE_L pg3,4
TP250 107 37 BLE_L TP185
pg5 SEL_VIALL P1.5/LOCK BLE BLE_L pg7
pg5 SEL_VIALR TP236 108 P1.6/HOLD 2 7 R22B 33 ZBLE_L TP127 ZBLE_L pg3,4
TP235 111 4 LOCAL_L TP29
pg5 SEL_LIDR P1.7/HLDA LBA LOCAL_L pg3
32 READY_L TP38
READY READY_L pg3
U15A 33 TP83 BS8_L 5 16 RN2E R4 1K
BS8 VCC VCC
8
6
4
2
2 1 LED1 10K
pg7 LEDLEFT
J2
+
+
+
+
U15F 1 CS_FLASH_L TP34

UCS CS_FLASH_L pg3
+
+
+
+
74HC14 12 13 LED2 CON8AP 122 CS_DRAM_L TP10

pg7 LEDRIGHT P2.0/CS0 CS_DRAM_L pg3
123 CS_SRAM_L TP40
P2.1/CS1 CS_SRAM_L pg3,5
FLASHBANK
7
5
3
1
P2.2/CS2 124 TP25

74HC14 125 CS3_IO_L TP12
P2.3/CS3 CS4_IO_L
P2.4/CS4 126 TP11
CS5_IO_L
pg6 FANADV_L TP181 86 P3.6/PWRDOWN VCC J3
TP102 87 P3.7/COMCLK U7
R26
P2.5/RxD0 129 TP18 16 VCC VDD 1 +12V
1
2
RS232 DEBUG
10K
113 EOP/CTS1 P2.6/TxD0 131 TP19
CTS0
TXD0_L
TSTI 3
TXD0
TSTI
PORT
15 DO1 RX1 2 4
132 TP21 RXD0_L RXD0
TXD1 P2.7/CTS0 TXD0 TSTO 5 TSTO
VCC TP17 112 DACK1/TxD1 P1.1/RTS0 102 TP15 14 DI1 TX1 3 6
TP89 RXD1_TRT 118 DRQ1/RxD1 X9 X10 X11 RXD0 7
13 DO2 RX2 4 8
TP14 CS5_IO_L 128 DACK0/CS5 U15B U15E TXD1 9
117 DRQ0/DCD1 12 DI2 TX2 5 10
VCC PAD PAD PAD
TP116 24 79 4 3 R_L_TRT 10 11 RXD1 11 6 CON10
RN1I 10K X419 TDO RTS1/SSIOTx DO3 RX3
16 9 RI1/SSIORx 78
RN1J 10K 16 10 X420 TP107 25 RTS0 10 7
RN1K 10K TDI DI3 TX3
16 11 X421 DTR1/SRxCLK 77 TP261 TP260
RN1L 10K 16 12 X422 TP109 26 98 X431 74HC14 74HC14 9 8
TMS DSR1/STxCLK GND VSS -5V RS232 COMPUTER PORT
TP99 119 TXD1_L
TRST VCC 1406 C21
COMP_RX pg6
VCC TP88 76 0.1UF RXD1_L
GND
GND
GND
GND
GND
GND
GND
GND
GND
GND
GND
GND
TCK VCC VCC VCC COMP_TX pg6

C20
0.1UF
C23 C59 C51 C17
100
116
130
17
31
36
46
64
69
83
97
RN3A 4.7K 0.01UF 0.01UF 0.01UF 0.1UF

3
16 1
RN3L 4.7K 16 12
RN3M 4.7K 16 13
RN3N 4.7K 16 14
RN3O 4.7K 16 15
CONFIDENTIAL. THIS DOCUMENT MAY Life Science Group, Gene Expression Division
WITHOUT WRITTEN PERMISSION
+15V
R7
TP5 FROM BIO-RAD. Hercules, CA 94547 USA
+12V
DRAWN BY DATE Title
510 3
pg5,6 +15V
pg5,6 -5V
+15V
-5V
D1
MMBZ5242
TC/4-21-05 ICYCLER CPU
12V CHECKED BY DATE
pg3,4,5,6,7 VCC VCC
CPU, Flash, & I/O Select
1
GS/10-20-05
+ C16
10 C150 C27
0.1UF 0.1UF
TC/10-20-05 D009467
pg3,4,5,6,7 DGND MANAGER APPRV'D DATE Size Rev
GND
CB/10-21-05 Custom Sheet 2 of 7 A
VCC
pg2,4,5 ZA[16:1] U9
MA[10..0] U2
22
35
50
VCC 1 VCC
7
ZA1 23 53
4C1M16C3 VCC 6
21
VCC
VCC
VCC
VCC
pg2,4,7 A[25:1] 1B1 GND VCC VCC
ZA2 24 46 MA10 TP54 16
ZA3 1B2 GND MA9 NC_A10
26 1B3 GND 39 TP48 28 A9
ZA4 31 32 MA8 TP43 27 22 C1 C2 C5
ZA5 1B4 GND MA7 A8 VSS 0.01UF 0.01UF 0.1UF
33 1B5 TP47 26 A7 VSS 37
ZA6 34 MA6 TP42 25 42
ZA7 1B6 MA0 MA5 A6 VSS
36 1B7 A1 8 TP46 24 A5
ZA8 37 9 MA1 MA4 TP41 23
ZA9 1B8 A2 MA2 MA3 A4 ZD15
38 1B9 A3 10 TP138 20 A3 DQ16 41
ZA10 40 12 MA3 MA2 TP134 19 40 ZD14
A21 1B10 A4 MA4 MA1 A2 DQ15 ZD13
41 1B11 A5 13 TP53 18 A1 DQ14 39
42 14 MA5 MA0 TP131 17 38 ZD12
ZA11 1B12 A6 MA6 A0 DQ13 ZD11
6 2B1 A7 15 DQ12 36
ZA12 5 16 MA7 RD_DRAM_L TP44 29 35 ZD10
ZA13 2B2 A8 MA8 ZWR_STB_L OE DQ11 ZD9
3 2B3 A9 17 13 WE DQ10 34
ZA14 54 19 MA9 33 ZD8
ZA15 2B4 A10 MA10 RAS_L DQ9 ZD7
52 2B5 A11 20 TP51 14 RAS DQ8 10
ZA16 51 21 UCAS_L TP50 30 9 ZD6
A17 2B6 A12 LCAS_L TP49 CASH DQ7 ZD5
49 2B7 31 CASL DQ6 8
A18 48 7 ZD4
A19 2B8 DQ5 ZD3
47 2B9 GND 25 11 NC DQ4 5
A20 45 18 12 4 ZD2
A22 2B10 GND NC DQ3 ZD1
44 2B11 GND 11 15 NC DQ2 3
43 4 32 2 ZD0
2B12 GND 0 OHM NC DQ1
TP77 R3
29 OE1B OEA 1 TP145
56 28 TP52
2
OE2B
LE1B
SEL
LEA1B 30 TP76 1M x 16 DRAM
27 LE2B LEA2B 55
R1
74ABT162260 R2
10K VCC VCC 0 OHM
C8 C26
0.01UF 0.01UF
VCC
PLDTCK
PLDTCK pg2,6
PLDTDI
PLDTDI pg6
PLD2TDI
PLD2TDI pg2
VCC PLDTMS
PLDTMS pg2,6
RESET_L
pg2,5,6,7 RESET_L C9
CS_SRAM_L
pg2,5 CS_SRAM_L
0.01UF CS_DRAM_L
CS_DRAM_L pg2
RD_DRAM_L
LCAS_L
UCAS_L
44
43
42
41
40
6
5
4
3
2
1
RAS_L
GND
VCC
IO4
IO3
IO2
IO1
IO0
IO31
IO30
IO29
IO28
SEL_CA_L
7 39 CS_FLASH_L
IO5 IO27 CS_FLASH_L pg2
REFRESH_L
8
9
IO6 U3 IO26 38
37 LOCAL_L
REFRESH_L pg2,4
IO7 IO25 LOCAL_L pg2
10 M4_32/32_J 36 TCLK
TDI IO24 TCLK pg2
VCC RN1N 10K 16 14 PUI0 TP4 11 35
CLK0/I0 TDO
12 GND GND 34
13 33 CLK2_A
TCK CLK1/I1 CLK2_A pg2
14 IO8 TMS 32
15 RAM PLD 31 M_IO_L
IO9 IO23 W_R_L M_IO_L pg2
16 IO10 IO22 30 W_R_L pg2
VGA_READY 17 29 READY_L
pg4 VGA_READY IO11 IO21 READY_L pg2
GND
IO12
IO13
IO14
IO15
IO16
IO17
IO18
IO19
IO20
VCC
18
19
20
21
22
23
24
25
26
27
28
VGAMEM_L C13 ZADS_L
pg4 MEMCS16_L ZADS_L pg2,4
IOWR_L
pg4 IOWR_L
IORD_L BHE_L
pg4 IORD_L BHE_L pg2,4
ZBLE_L
ZBLE_L pg2,4
0.01UF
VCC
ZWR_STB_L
pg2,4 ZWR_STB_L
ZRD_STB_L
pg2,4 ZRD_STB_L
ZD[15..0]
pg2,4,5,6 ZD[15:0]
C50
pg5 V_CMOS
0.01UF
28 VB
pg2,4 ZBLE_L
U13
10 11 ZD0
ZA1 A0 D0 ZD1
9 12
A1 D1
ZA2
ZA3
ZA4
8
7
6
A2
A3
D2
D3
13
15
16
ZD2
ZD3
ZD4 THIS DOCUMENT IS PROPRIETARY BIO-RAD Laboratories
ZA5 5
A4
A5
D4
D5 17 ZD5 CONFIDENTIAL. THIS DOCUMENT MAY Life Science Group, Gene Expression Division
ZA6 ZD6
4 A6 D6 18
ZA7 3 A7 D7 19 ZD7 2000 Alfred Nobel Drive
ZA8 25 A8 WITHOUT WRITTEN PERMISSION
ZA9
ZA10
24
21
A9 FROM BIO-RAD. Hercules, CA 94547 USA
ZA11 A10
ZA12
23 A11 DRAWN BY DATE Title
2 A12
ZA13
ZA14
26
1
A13
A14
TC/4-21-05
CHECKED BY DATE
ICYCLER CPU
20
pg5 CS_CMOS_L
TP130
ZRD_STB_L
LSRAM_WR_L
22
27
CS
OE GS/10-20-05 DRAM & SRAM
WE
32K x 8 SRAM D009467
GND
pg2,4,5,6,7 VCC VCC

TC/10-20-05
pg2,4,5,6,7 DGND
UPD43256BGU-70LL MANAGER APPRV'D DATE Size Rev
14
GND
VCC
C97
VCC 0.01UF VCC

VCC C103
VCC
1
VCC VCC 0.01UF VCC
R24 C104
1
4.7K
C98 C96
0.0022 0.01UF VCC VCC 0.01UF
U18 C101 C53
2
TP220
1 EN VCC 8
4 5 1 2 25MHZ VCC 0.1UF VCC 0.01UF

GND OUT L6 C55 C54
25.175MHz 68
RES X466
0.01UF 0.1UF
pg2,3 ZBLE_L
109
108
124
123
144
90
91
86
87
14
37
85
92
89
88
36
11
50
73
72
49
1
pg2,3,5 ZA[16:1] ZA[16..1]
VCC VCC
COREVDD
COREVDD
COREVDD
COREVDD
COREVDD
IOVDD
IOVDD
IOVDD
IOVDD
VSS
VSS
VSS
VSS
VSS
IOVSS
IOVSS
IOVSS
IOVSS
CLKI1
CLKO1
CLKI2
CLKO2
ZBLE_L 104
A[25..1] ZA1 A0
pg2,3,7 A[25:1] 105 A1
ZA2 106
ZA3 A2 TP262 R59
107 A3 YD 10 1 2
ZA4 110 13 TP267 1 2 L11 33 10K
ZA5 A4 LP L12 33 RES C130
111 A5 WF 15 TP231
ZA6 TP268 0.1UF
ZA7
112 A6 XSCL 12 1
L5
2
100 RES
J7
113 A7
ZA8 114 22 TP265 1 2 LCD_D0
ZA9 A8 UD0 TP264 L7 LCD_D1 1
115 A9 UD1 23 1 2 2
ZA10 116 24 TP266 1 2 L8 LCD_D2
ZA11 A10 UD2 TP263 L9 LCD_D3 3
117 25 1 2
ZA12
ZA13
ZA14
118
119
120
A11
A12
A13
A14
U17 UD3
LD0
LD1
16
17
L10 100
RES
LCD_OFF_L
FLM
4
5
6
7
ZA15 121 18 R48 LP To LCD Display
ZA16 122
A15
A16 SPC8106/SPC8108 LD2
LD3 19 47K CP 8
9
10
1
A17 2 21 X441
A18 LA17 LCDPWR# C132 11
A19
3
4
LA18 LCD CONTROLLER, LOAD PER TABLE XSCL2 9 TP232
0.0022 12
A20 LA19 13
2
5 LA20 14
A21 6 R49
A22 LA21 47K
7 CON14
LA22
1
pg2,3,5,6 ZD[15:0] ZD[15..0] A23 8 LA23 C131
ZD0 125 0.0022
ZD1 D0
2
126 D1
ZD2 127 R61
D2
1
ZD3 128 ZERO OHM
ZD4 D3 OPT LOAD PER TABLE
129
T
D4
1
ZD5 130 D5
1
ZD6 131 X5
T
ZD7 D6 C106 GNDBUS
132 D7 IREFEN# 47
ZD8 133 0.0022 X4 EXPOSE TRACE
ZD9 D8 MOUNTPAD
2
134 D9 P0 26
ZD10 135 27
ZD11 D10 P1
136 D11 P2 28
ZD12 137 29
ZD13 D12 P3
138 D13 P4 30
ZD14 139 31 LOAD OPTION TABLE PER LCD CONTROLLER
ZD15 D14 P5
140 D15 P6 32
P7 33
PCLK 34 U17 TYPE INSTALL R61 INSTALL R62
pg2,3 BHE_L 101 BHE# DACRD# 43
pg2,3 ZADS_L 102 ALE DACWR# 45
OL(0) 39 X453 SPC8106 NOT INSTALLED YES
pg2,3 REFRESH_L 97 MEMEN OL(1) 38 X452
TP177 93 IOEN# OL23 35
R42 4.7K
94 IOR# RS2 46 X460 SPC8108 YES NOT INSTALLED
95 IOW# D477 40
pg2,3 ZRD_STB_L 96 MEMR# BLANK# 44 X458
pg2,3 ZWR_STB_L 98 MEMW# HSYNC# 41 X455
R5 1K 42 X456
VCC VSYNC#
pg3 VGA_READY TP128 142 READY MS2 83
pg2,7 RESET 141 RESET MS1 82
MS0 71
R62 OPT PER TABLE TP23
pg2 LCD_V_INT
103 IRQ
ZERO OHM TP56 99
pg3 MEMCS16_L IOCS16STS 100 MEMCS16#
TP176 IOCS16#
R23 VCC
R41
VCC
TP219 84 SUSPEND#
1K
10K 143
UCAS#
LCAS#
PDCLK
MD10
MD11
MD12
MD13
MD14
MD15
RAS#
WE#
MD0
MD1
MD2
MD3
MD4
MD5
MD6
MD7
MD8
MD9
MA0
MA1
MA2
MA3
MA4
MA5
MA6
MA7
MA8
MA9
IORD_L TP135 R63

pg3 IORD_L
81
79
77
75
70
68
66
64
63
65
67
69
74
76
78
80
62
60
59
61
57
55
53
51
48
52
54
56
58
20
47K
VCASH_L
X440
VCASL_L
VRAS_L
VWE_L
VD10
VD11
VD12
VD13
VD14
VD15
VA0
VA1
VA2
VA3
VA4
VA6
VA7
VA8
VA5
VD0
VD1
VD2
VD3
VD4
VD5
VD6
VD7
VD8
VD9
IOWR_L TP133
pg3 IOWR_L
VOE
TP194
TP193
TP213
TP207
TP172
TP206
TP212
TP205
TP211
TP190
TP189
TP191
TP171
TP192
VA9 TP215
R47
R55 NOT LOADED Aux Reg b0 R55 15K VD0 R50 47K
Aux Reg b1 R56 15K VD1 47K
Aux Reg b2 R57 15K VD2
32
15
12
11
31
30
14
13
29
17
18
19
20
23
24
25
26
27
28
16

NC
NC
NC
NC
CASH
RAS
WE
OE
CASL
A0
A1
A2
A3
A4
A5
A6
A7
A8
A9
NC_A10
U19
4C1M16C3
DQ10
DQ11
DQ12
DQ13
DQ14
DQ15
DQ16
VCC
VCC
VCC
DQ1
DQ2
DQ3
DQ4
DQ5
DQ6
DQ7
DQ8
DQ9
VSS
VSS
VSS
1M x 16 DISPLAY RAM

10
33
34
35
36
38
39
40
41
42
37
22
21
BIO-RAD Laboratories
2
3
4
5
7
8
9
6
1
C119 THIS DOCUMENT IS PROPRIETARY

VCC
TP230
TP229
TP228
TP227
TP224
TP226
TP223
TP225
TP217
TP173
TP174
TP175
TP178
TP222
TP221
TP218
0.01UF 2000 Alfred Nobel Drive

C105 WITHOUT WRITTEN PERMISSION
VD10
VD11
VD12
VD13
VD14
VD15
VD0
VD1
VD2
VD3
VD4
VD5
VD6
VD7
VD8
VD9
VCC
0.1UF
DRAWN BY DATE Title
g2,3,5,6,7 VCC
g2,3,5,6,7 DGND
VCC
VD[15..0]
C102
VCC
0.01UF CHECKED BY DATE
GND
GS/10-20-05
LCD Controller
pg6 LCD_VEE
pg6 LCD_VADJ
-18.2V to -22.6V TC/10-20-05 D009467
+15V +15V
R51
TP252 1 2
X483
470 U27
1/2W OP07CS C94
1
7
Q2 0.01UF
U26
3
R53 3 TP254
+
1 TP272 1 2 6 18
4_096VR ZD0 VDD
- 2 TP255 14 D0 VOUTA 2 CVLID1 pg6
1
200 + C123 R54 ZD1 13 1
10 D1 VOUTB CVLID2 pg6
MMBT3904 C124 ZD2
2
12 20 CVLCD pg6
0.22 VCC ZD3 D2 VOUTC
8
4
pg6 4_096VR 11 D3 VOUTD 19 CVBEEP pg6
X485 C127 0 OHM TP283 ZD4
2
10 D4
1
TP253 2 1 ZD5 9
+ C122 + C128 ZD6 D5 C92 C91
8 D6
10 C129 10 ZD7 7 0.0022 0.0022
150pF 0.01UF D7
2
pg6 VR_RET
1
R52 ZA1 17
ZA2 A0 C75 C90
1 2 27 16 A1
U28 0.0022 0.0022
200
2
VCC pg2 DA108W_L 15 WR
4_096VR 4
VREF VREF
R40 33
MAX196 VREF 23
5 AGND
TP240 ADIN1 16 3 ZD11 6
pg6 T_BLOK1 CH0 D11 DGND
R39 33 4 ZD10 3
pg6 A_RET D10 VSS
TP241 ADIN2 17 5 ZD9
pg6 T_BLOK2 CH1 D9
R38 33 6 ZD8 C95 AD7226
pg6 A_RET2 D8 0.01UF
pg6 T_BLOK3 CH2 D7
R37 33 8 ZD6
pg6 A_RET3 D6
pg6 T_BLOK4 CH3 D5
10 ZD4 -5V
pg6 A_RET4 D4
ADCH5 TP238 20 11 ZD3
C87 C85 +15V CH4 D3 ZD2
D2 12
0.1UF C86 0.1UF C84 ADCH6 TP233 21 13 ZD1
0.1UF 0.1UF CH5 D1 ZD0
D0 14
6
U25A
C125 +15V
1 +
U24 7 2 1 TP245 22
R34 33 REFADJ
8 -
ADIN5 TP248 3 2 ADHZ4 1013D 0.01UF 24 X486
pg6 T_LIDL S1 D1 NC
pg6 A_RET5 1 IN1
R35 33 -5V C78
2
25 RD
ADIN6 0.01UF
pg6 T_VIALR TP249 14 S2 D2 15 TP247 U16
pg6 A_RET6 16 IN2 26 WR CLK 1 TP246
R36 33 U25B 18 VDD
1
ADIN7 TP234 11 10 ADHZ5 3 2 ZD0 14 2
pg6 T_VIALL S3 D3 + CS D0 VOUTA CVCR1 pg6
9 5 C133 ZD1 13 1
pg6 A_RET7 IN3 150pF D1 VOUTB CVCR2 pg6
R33 33 4 ZD2 12 20
- AGND DGND D2 VOUTC CVVR1 pg6
ADIN8 1013D ZD3
2
pg6 T_LIDR TP239 6 S4 D4 7 TP237 11 D3 VOUTD 19 CVVR2 pg6
8 ZD4 10
pg6 A_RET8 IN4 D4 CVGND pg6
1
15 28 ZD5 9 D5
+15V 13 ZD6 8 C89 C74
C81 C83 -5V V+ ZD7 D6 0.0022 0.0022
4 V- 7 D7
0.1UF 0.1UF
2
5 GND
1
ZA1 17
C82 C80 ZA2 A0 C88 C73
DG201ADY 16 A1
0.1UF 0.1UF 0.0022 0.0022
ARET PLANE IN JOIN ARET
2
pg2 DA100W_L 15 WR
4_096VR 4
PLACE OF VCC WITH 12 VIAS VREF
pg2 SEL_LIDL 1 2
UNDER U19 5
C136 0.0022 AGND
pg2 SEL_VIALL 1 2 6 DGND
3 VSS
1 2 C135 0.0022
pg2 SEL_VIALR
C93 AD7226
C28 0.0022 1 2 0.01UF
pg2 SEL_LIDR
C134 0.0022
-5V
pg2 AD180R_L
pg2 AD180W_L
pg2 AD180CS_L
pg2,3,4,6 ZD[15:0]
pg2,3,4 ZA[16:1]
VCC
VCC
RN2O 10K 16 15 U15D
C6 TP80 9 8
0.01UF TIMEK_INT pg2
VCC
74HC14
pg2 T192_DWR_L
U1
24
TP143 V_CMOS pg3
TP158 CS_CMOS_L pg3
VCC
ZD0 4
ZD1 AD0
5 AD1
ZD2 6
ZD3 AD2
7 AD3
ZD4 8
pg2 T192_DRD_L AD4
ZD5 9
ZD6 AD5
10 AD6
ZD7 11 AD7
pg2 CS_TIMEK_L 13 CS IRQ 19

pg2 T190_AREG 14 AS SQW 23 TP156
TKWR_L 15
TKRD_L R/W
17 DS
pg2,3,6,7 RESET_L 18 RST
pg6 VBAT 20 VBAT VCCO 1

TP144 2 X1
Y1 TP74 3 X2
TP287 1 2
Bio-Rad Laboratories
1
C3 21 22
BT1 0.01UF CEI CEO
32768
THIS DOCUMENT IS PROPRIETARY
GND
GND
1
BATTERY C7 C4 CONFIDENTIAL. THIS DOCUMENT MAY Life Science Group, Gene Expression Division
12PF 12PF
2
DS14285 NOT BE COPIED OR REPRODUCED

12
16
2
ALT bq4285 WITHOUT WRITTEN PERMISSION 2000 Alfred Nobel Drive

pg2,3 CS_SRAM_L
DRAWN BY DATE Title
pg2,6 +15V +15V

CHECKED BY DATE
pg2,6 -5V
pg2,3,4,6,7 VCC VCC

C126 C121
-5V
GS/10-20-05 Data Acq & Timekeeper
0.01UF 0.01UF ENGINEER APPRV'D DATE Document Number
pg2,3,4,6,7 DGND
GND TC/10-20-05
MANAGER APPRV'D DATE
D009467
Size Rev
CB/10-21-05 Sheet 5 of 7 A
Custom
RXD1_L
pg2 COMP_TX TXD1_L
pg2 COMP_RX
PWRGOOD_C
pg2 PWRGOOD_C PWRGOOD_E
pg2 PWRGOOD_E
1
C46 C45
pg2,3,4,5 ZD[15:0] 0.0022 0.0022
2
U11
ZD0 3 2
ZD1 D1 Q1
4 D2 Q2 5
ZD2 7 6
ZD3 D3 Q3
8 D4 Q4 9
ZD4 13 12
ZD5 D5 Q5
14 D6 Q6 15
ZD6 17 16
ZD7 D7 Q7
18 D8 Q8 19
pg2 CTL130W_L 11 CLK
1
pg2,3,5,7 RESET_L 1 CLR C43 C44 C41 C42 C39 C40 C38 C37
R11 10K 74HCT273 0.0022 0.0022 0.0022 0.0022 0.0022 0.0022 0.0022 0.0022
2
VCC
X12
R15 10K
PAD
R14 10K
R13 10K
U10
2 1A1 1Y1 18
C48
pg2 BEEPER 4 1A2 1Y2 16
pg2 FANADV_L 6 1A3 1Y3 14 2 1
J5
J1 8 1A4 1Y4 12
1
XTCK 11 9 TP151
2 1 XTMS 2A1 2Y1 C33 C36 C34 0.0022 1
4 3 13 2A2 2Y2 7 2
XTDI 15 5 PAD 0.0022 0.0022 0.0022
VCC 6 5 2A3 2Y3 3
XTDO
2
8 7 17 2A4 2Y4 3 X13 4
R16
10 9 5
1 1G 6
JTAG TAP 19 ENCR1
CON10A 330 2G ENCR2 7
PLD PROG ENVR1 8
TP273 9
74HCT244 ENVR2
ENVR3 10
pg2 PLDTDO TP182 11
TP184 ENVR4
pg3 PLDTDI H/C1 12
pg2,3 PLDTMS TP147 13
TP150 X14 X15 X16 H/C2
pg2,3 PLDTCK 14
2
R12 68 XBEEPER
PAD PAD PAD C30 C31 C32 XFANADV_L 15
XRESET_L 16
0.0022 0.0022 0.0022 17
1
18
19
20
21
C29 2 22
1 23
T_VIALL 0.0022
pg5 T_VIALL 24
T_VIALR 25
pg5 T_VIALR 26
T_LIDL 27
pg5 T_LIDL 28
T_LIDR 29
pg5 T_LIDR 30
4_096VR 31
pg5 4_096VR 32
33
34
2 1
C69
0.0022 CON34
pg5 A_RET
ARET PLANE
C70
CONNECTIONS
1 2
J6
0.0022
34
T_BLOK4 33
pg5 T_BLOK4 32
T_BLOK3 31
pg5 T_BLOK3 30
T_BLOK2 29
pg5 T_BLOK2 28
T_BLOK1 27
pg5 T_BLOK1 26
CVVR2 25
pg5 CVVR2 24
CVCR2
pg5 CVCR2 23
CVVR1
pg5 CVVR1 22
CVCR1
pg5 CVCR1 21
CVBEEP
pg5 CVBEEP 20
CVLCD
pg5 CVLCD 19
CVLID2
pg5 CVLID2 18
CVLID1
pg5 CVLID1 17
2 1 16
C35 2 1
0.0022 C76 0.0022 15
VBAT 14
pg5 VBAT LCD_VEE 13
pg4 LCD_VEE LCD_VADJ 12
pg4 LCD_VADJ +15V 11
+15V -5V 10
pg2,5 +15V 9
-5V 8
1
pg2,5 -5V C99 C100 7
0.0022 0.0022 6
5
2
2
VCC 4
pg2,3,4,5,7 VCC 3
+ C49 C71 + C79 2
10 C72
+
C47 10 C77 1
0.01UF 10 0.01UF 0.01UF
CON34
DGND
pg2,3,4,5,7 DGND
Bio-Rad Laboratories
1
1
GND
THIS DOCUMENT IS PROPRIETARY
T
T
X1 X2 X3
MOUNTPAD MOUNTPAD MOUNTPAD NOT BE COPIED OR REPRODUCED
DRAWN BY DATE Title
CHECKED BY DATE
External Interface
GS/10-20-05
TC/10-20-05
D009467
Size Rev
CB/10-21-05 Custom
Sheet 6 of 7 A
VCC
U29D
TP209 9 8 COL0
C120 KEYBOARD
1
0.1UF
74ALS1035 C149 COL1
0.0022
U29C J10
2
COL2 ROW0 COL0
ROW1 1 9 COL1
TP214 5 6 2 10
ROW2 COL2
3 11
1
COL3 ROW3 COL3
C147 ROW4 4 12 COL4
74ALS1035
0.0022 ROW5 5 13 FPLED-
COL4 6 14 FPLED+
U29E
2
7 15
2 1 8 16
TP202 11 10 C140 0.0022
ROW0 CON16B
1
2 1
74ALS1035 C145 C148 0.0022
0.0022 ROW1
4.7K
4.7K
4.7K
4.7K
4.7K
4.7K
4.7K
4.7K
4.7K
4.7K
U29B
2
2 1
C146 0.0022
TP210 3 4 ROW2
16 RN3G
16 RN3D
16 RN3C
16 RN3H
RN3I
16 RN3J
16 RN3E
16 RN3B
16 RN3K
16 RN3F
2 1
1
C144 0.0022
VCC 74ALS1035 C143 ROW3
0.0022
16
2 1
U29F C142 0.0022
2
ROW4
TP203 13 12 2 1
VCC C141 0.0022
U20 ROW5
pg2 D[15:0]
10
11
74ALS1035
9
29 VCC 2 1
R60 C139 0.0022
D0 38 5 VCC 1 2 FPLED+
D1 D0 PA0
37 4 U29A 2 1
D2 D1 PA1 330 C137 0.0022
36 D2 PA2 3
D3 35 2 TP216 1 2 FPLED-
D4 D3 PA3
33 D4 PA4 44 2 1
D5 32 43 TP271 C138 0.0022
D6 D5 PA5 TP270
31 42 74ALS1035
D7 D6 PA6
30 D7 PA7 41
pg2 KB120R_L 6 RD PB0 20

pg2 KB120W_L 40 WR PB1 21
pg2 BLE_L 10 A0 PB2 22
A1 9 24
A1 PB3
39 RESET PB4 25
A3 7 26
CS PB5 BKINL_H
PB6 27
BKINR_H
PRINTER PORT
28 U21A
PB7
pg2,3,4 A[25:1]
16 TP164 1 2 DSTB_L J4
PC0 DSTB_L
pg2,4 RESET 1 NC1 PC1 17 TP168 2 1 1
12 18 TP169 C60 0.0022 AUTOLF_L
NC2 PC2 AUTOLF_L PTRD0 2
34 19 TP170 74ALS1035 TP160 LEDRIGHT pg2
NC3 PC3 ERROR_L 3
23 NC4 PC4 15 2 1 4
C110 14 U21D C58 0.0022 PTRD1 TP161
0.01UF PC5 5 LEDLEFT pg2
13 INIT_L INIT_L
PC6 PTRD2 6
8 GND PC7 11 9 8 2 1 7
C61 0.0022 SEL_L
SEL_L PTRD3 8
PD71055 74ALS1035
9
2 1 10
C66 0.0022 PTRD4
BUSY 11
U21E
PTRD5 12 BKINL_H
2 1 13 TP9
11 10 C114 0.0022
ACK_L PTRD6 14 R9
15 VCC XLEDL+
J8 LEFT LID CON, KEY 2
2 1 16
74ALS1035 C113 0.0022 PTRD7 U21B LED +
PAPER 17 R10 47 1/4W 1
VCC ACK_L 18 XLEDL- 2
U21F 2 1 19 3 4 3 LED -
C115 0.0022
ONLINE BUSY 20 330 4
13 12 21
2 1 74ALS1035 CON4
C108 C116 0.0022 PAPER 22
0.1UF ERROR_L 23
74ALS1035
24
1
2 1 ONLINE
C117 0.0022 25 C24 C25
PTRD7 26 0.0022 0.0022
CON26
2
2 1
C112 0.0022
PTRD0
2 1 TP162 BKINR_H
VCC C64 0.0022
PTRD1 R25 J9 RIGHT LID CON, KEY 4
2 1 VCC XLEDR+
C63 0.0022 U21C LED +
C118 PTRD2 R28 47 1/4W 1
0.01UF XLEDR- 2
2 1 5 6 3 LED -
C65 0.0022
PTRD3 330 4
2 1 74ALS1035 CON4
C67 0.0022
U23 PTRD4
1
D3 18 2 2 1
D4 1Y1 1A1 C68 0.0022 + C22 + C62 C56 C57
16 1Y2 1A2 4
D5 14 6 PTRD5 10 10 0.0022 0.0022
D6 1Y3 1A3
2
12 1Y4 1A4 8 2 1
D7 9 11 C107 0.0022
x481 2Y1 2A1 PTRD6
7 2Y2 2A2 13
x480 5 15 2 1
x479 2Y3 2A3 C109 0.0022
3 2Y4 2A4 17
1G 1
2G 19
74HCT244
pg2 PPSR_L
U22
D7 3 2
D0 D1 Q1
4 D2 Q2 5
D1 7 6
D2 D3 Q3
8 D4 Q4 9
D3 13 12
D4
D5
D6
14
17
18
D5
D6
D7
Q5
Q6
Q7
15
16
19
THIS DOCUMENT IS PROPRIETARY Bio-Rad Laboratories
D8 Q8
VCC
pg2 PPDW_L 11 CLK NOT BE COPIED OR REPRODUCED
pg2,3,5,6 RESET_L 1 CLR
74HCT273
C111 FROM BIO-RAD. Hercules, CA 94547 USA
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DRAWN BY DATE Title
CHECKED BY DATE
Keyboard & Printer
GS/10-20-05
pg2,3,4,5,6 VCC VCC ENGINEER APPRV'D DATE Document Number
pg2,3,4,5,6 DGND
TC/10-20-05
D009467
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CB/10-21-05 Sheet 7 of 7 A
Custom
Appendix
Section 11
Appendix
11.1 Installation Qualification Report

This section is the Installation Qualification as performed in the Installation section with additional recording of
information on the report. Successful completion of the Installation section represents the verification of instru-
ment installation to meet IQ Installation Qualification requirements.This report should be filed for record keep-
ing.
1001862E 02/06 11-1

Appendix

Installation Qualification Report
Customer: Instrument Model

Case Number: Instument Serial Number
Test Specification Results

Visual Inspection
No signs of damage Pass Fail
All contents and accessories received: Pass Fail
iCycler Chassis Pass Fail
iCycler Reaction Module: Record Sample Well Type:___________ Pass Fail
Power Cord Pass Fail
Fuses Pass Fail
Operating Manual Pass Fail
Warranty Card Pass Fail
Voltage Setting iCycler Chassis: Voltage Setting_____________ Pass Fail
Power Line Requirements Line Voltage Check: Record AC line voltage_______________ Pass Fail
Serial Number Instrument Serial Number:
iCycler Chassis S/N________________________ Pass Fail

Pass Fail
Reaction Module S/N________________________
Instrument Software Firmware Version:
iCycler Chassis Firmware Version ______________________ Pass Fail
Start Up Power-up self-test Pass Fail

Display Check Pass Fail
Fan Check Pass Fail
Installation Qualification IQ/OQ Protocol Not Applicable

Yes No N/A Pass Fail
11-2 1001862E 02/06

Appendix
Instrument Check Record all threshold values:
Test #1 Range #2 Balance #3 Error to Setpoint

1
2
3 Pass Fail
4
5
Lid
Edge Heater
The above referenced instrument has been installed and meets all Installation Qualification or IQ requirements.
Comments:
Bio–Rad Labs Service Date
1001862E 02/06 11-3

Appendix
11.2 Operational Qualification Report

This section is the Operational Qualification as performed in the System Checkout section. Successful comple-
tion of the tests in the System Checkout section represents a complete functional check of all system compo-
nents from software through hardware control of advertised specifications to meet Operational Qualification or
OQ requirements.
11-4 1001862E 02/06

Appendix

Operational Qualification Report
Customer Instrument Serial Number:
Case Number: AC Input Voltage: 100v 120v 220v 240v
Test Specification Results
Instrument Condition Sample Block Cleanliness Pass Fail

LCD Display Function Pass Fail
Power-on Self-Test Pass Fail
Firmware Version Record version______________ Pass Fail
________
Instrument Check Record all threshold value results:
Test #1 Range #2 Balance #3 Error to Setpoint

1
2 Pass Fail
3
4
5
Lid
Edge Heater
Operational Test Protocol : Standard-2 protocol, edited to (5x) for Cycle 2

Record Run Display Temperatures at:
95°C Run_______________°C ±0.5°C Pass Fail

65°C Run_______________°C ±0.5°C Pass Fail
72°C Run_______________°C ±0.5°C Pass Fail
4°C Run_______________°C- 3.0°C to 5.0°C in 2 - 2.5 minutes @ Pass Fail

room temperature (21-23°C)
105°C Lid Run____________°C ±3.0°C Pass Fail
1001862E 02/06 11-5

Appendix
Lid Heater Test

(OPTIONAL) Record Lid Temperature ________°C
Record Lid Temperature ______ °C (L)______ °C (R) for 2 x 48W
Specification: Pass Fail
105°C ±3.0°C
90°C ±3.0°C for 384 Well Block
Reaction Module Thermal Test Validation Result Printout Attachment Not Applicable
(OPTIONAL) Yes No N/A
iCycler Certificate Printout Completed Not Applicable
Yes No N/A
Thermal Validation Contract Not Applicable
Yes No N/A
IQ/OQ Protocol Not Applicable
Yes No N/A
Record Temperature Data:

90°C: Accuracy____________°C Uniformity____________°C
55°C: Accuracy____________°C Uniformity____________°C Pass Fail
72°C: Accuracy____________°C Uniformity____________°C Pass Fail
Pass Fail
Record 2 x 48 Well Temperature Data:
90°C: Accuracy_____(L)_____(R)Uniformity_____(L)_____(R)
Specification:
Accuracy is ±0.3°C
Uniformity is ±0.4°C or 0.8°C
Test Equipment Standards
Calibration Model Description Serial Number Cal Date Cal Due

Date
Control Number
The above referenced instrument meets all performance specifications and Operational Qualification or OQ
requirements.
Comments:
Bio-Rad Labs Service Date
11-6 1001862E 02/06

Appendix
11.3 Save/Restore Protocol Procedure

This section provides instructions to save and restore user protocols using upgrade.exe. This procedure
requires a strong computer software background in the DOS environment.
HOW TO SAVE/RESTORE PROTOCOLS ON THE ICYCLER WITH UPGRADE.EXE?

-------------------------------------------------------------
1) Write down the firmware version of the base unit on which protocols need to be saved
(information available in Utilities->Display Firmware version)
2) Retrieve the UPGRADE.EXE utility corresponding to the loaded firmware.

Each firmware released is bundled with it's own version of UPGRADE.EXE.
For instance:
- firmware v2.039 is bundled with Upgrade.exe v2.017
- firmware v3.021 is bundled with upgrade.exe v2.020
3) Create a new folder on the PC and copy UPGRADE.EXE to this folder

(for instance C:\upgrade)
4) Connect the icycler base unit to the PC using the standard serial cable
(the same way an upgrade would be performed)
5) Backup protocols from the base unit

Open a DOS command line in Windows.
Type:
cd c:\upgrade <ENTER> (assuming the folder is c:\upgrade)
UPGRADE.EXE -v -s <ENTER>
-> all the protocols are saved to a file called OLDPROTS.BIN
6) Reset NVRAM* on the base unit then turn it OFF/ON

-> all the protocols on the base are now erased
* Assuming the backup succeeded
7) Restore protocols
Now from the same command line on the PC, type:
UPGRADE.EXE -r -v <ENTER>
-> Protocols are restored to the base.
WARNING:
a) It is very important to reset NVRAM before restoring protocols.
Restore will fail if a protocol that needs to be restored from OLDPROTS.BIN
is still defined in the base unit.
b) OLDPROTS.BIN is erased each time a new save operation (UPGRADE.EXE -v -s) is performed.
If several base units need to be saved, make sure to backup the file OLDPROTS.BIN after
each save operation.
(For instance OLDPROTS.BIN can be renamed with the customer's name or the base unit's
serial number)
Then when it's finally time to restore the customer's data:

- Copy the corresponding saved .BIN file back to the folder where UPGRADE.EXE is used
- Rename this .BIN file to OLDPROTS.BIN
- Type: UPGRADE.EXE -r -v <ENTER> to restore the customer's data
1001862E 02/06 11-7

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Life Science Group

Part Number 1001862E

Copyright 2006 by Bio-Rad Laboratories, Incorporated. All rights reserved.

Technical Editor, Global Service Support Dept.

Document: iCycler Service Manual

100-1862E 02/06 III

Section 2. System Overview

Section 4. System Checkout

Section 5. Preventative Maintenance

Section 6. Removal and Replacement

Section 7. Adjustment and Calibration

Section 9. Parts Information

Section 10. Drawings

1001862E 02/06 VII

Section 11. Appendix

VIII 1001862E 02/06

1.1 General Information

1.2 Service Philosophy

1.3 Safety Precautions

100-1862A 03/00 1-1

2.1 About this Section

2.2 Product Description

2.2.1 General Description

2.2.2 Technical Description

Figure 2-1: iCycler Thermal Cycler

100-1862B 05/01 2-1

iCycler Reaction Module

Figure 2-2: iCycler Thermal Cycler

2.3 Theory of Operation

2.3.1 Operating Principles

2-2 100-1862B 05/01

2.3.2 Control Circuits

100-1862B 05/01 2-3

3.2 Customer Catalog Items

1001862E 02/06 3-1

Electro Static Discharge (ESD)

3.4 Visual Check

3-2 1001862E 02/06

3.5 Fuse Installation

3.6 Installation Procedure

3.6.1 Instrument Installation

1001862E 02/06 3-3

Figure 3-2: Figure 3-3:

3-4 1001862E 02/06

3.6.2 System Checkout

1001862E 02/06 3-5

4.1 About this Section

4.2 System Verification

100-1862E 02/06 4-1

Electro Static Discharge (ESD)

4.4 Tools and Materials

4.5 Startup and Preliminary Checks

4-2 100-1862E 02/06

4.6 Instrument Check Diagnostic

1. At the home screen, select Utilities (F4).

100-1862E 02/06 4-3

4.7 Operational Test

4.7.1 Run Display Options - Debug Menu

6. Press Done (F5) twice to return to home screen.

4.7.2 Setup and Run Protocol

4-4 100-1862E 02/06

Table 4-1 Edit Standard Protocol

4 Sensor Block Readings

Performed by__________________ Date