Agilent Technologies BioCel 1200 User manual

Agilent Technologies
BioCel System
User Guide

Notices
© Agilent Technologies, Inc. 2009
No part of this manual may be reproduced
in any form or by any means (including
electronic storage and retrieval or
translation into a foreign language) without
prior agreement and written consent from
Agilent Technologies, Inc. as governed by
United States and international copyright
laws.
User Guide Part Number
G5500-90002
January 2009 rebranded edition
September 2006 fifth edition
Contact Information
Agilent Technologies Inc.
Automation Solutions
5301 Stevens Creek Blvd.
Santa Clara, CA 95051
USA
Technical Support: 1.800.979.4811
or +1.408.345.8011
[email protected]om
Customer Service: 1.866.428.9811
or +1.408.345.8356
[email protected]
European Service: [phone]
[e-mail]
Documentation feedback:
[email protected]
Web:
www.agilent.com/lifesciences/
automation
Acknowledgements
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trademarks of the Microsoft Corporation in
the United States and other countries.
Warranty
The material contained in this docu-
ment is provided “as is,” and is sub-
ject to being changed, without notice,
in future editions. Further, to the max-
imum extent permitted by applicable
law, Agilent disclaims all warranties,
either express or implied, with regard
to this manual and any information
contained herein, including but not
limited to the implied warranties of
merchantability and fitness for a par-
ticular purpose. Agilent shall not be
liable for errors or for incidental or
consequential damages in connection
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mance of this document or of any
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Technology Licenses
The hardware and/or software described in
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Restricted Rights Legend
If software is for use in the performance of
a U.S. Government prime contract or sub-
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(June 1995), or as a “commercial item” as
defined in FAR 2.101(a) or as “Restricted
computer software” as defined in FAR
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agency regulation or contract clause. Use,
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subject to Agilent Technologies’ standard
commercial license terms, and non-DOD
Departments and Agencies of the U.S. Gov-
ernment will receive no greater than
Restricted Rights as defined in FAR 52.227-
19(c)(1-2) (June 1987). U.S. Government
users will receive no greater than Limited
Rights as defined in FAR 52.227-14
(June1987) or DFAR 252.227-7015 (b)(2)
(November 1995), as applicable in any
technical data.
Safety Noticies
A WARNING notice denotes a
hazard. It calls attention to an
operating procedure, practice, or the
like that, if not correctly performed or
adhered to, could result in personal
injury or death. Do not proceed
beyond a WARNING notice until the
indicated conditions are fully
understood and met.
A CAUTION notice denotes a hazard. It
calls attention to an operating procedure,
practice, or the like that, if not correctly
performed or adhered to, could result in
damage to the product or loss of important
data. Do not proceed beyond a CAUTION
notice until the indicated conditions are
fully understood and met.
,

Agilent Technologies, Inc., Automation Solutions, 5301 Stevens Creek Blvd., Santa Clara, CA 95051 USA
Letter to our Customers
Dear Customer,
The Agilent Technologies acquisition of Velocity11 resulted in the following
changes:
•Creation of Agilent Technologies Automation Solutions, formerly Velocity11
•Renaming of some Velocity11 products
•New Customer Service and Technical Support contact information
•New website address for product information
Please make a note of the following changes as they impact this user guide.
Velocity11 product name changes
New contact information
Documentation feedback: [email protected]
Technical Support: 1.800.979.4811 or +1.408.345.8011
[email protected]
Customer Service: 1.866.428.9811 or +1.408.345.8356
[email protected]
European Service: [phone]
euroservice.aut[email protected]
Web: www.agilent.com/lifesciences/automation
Velocity11 product name Changes to …
Access2 Automated Microplate
Loader
Automated Centrifuge Loader
Element Automation System BioCel 900 System
IWorks Device Driver Programming
Interface
VWorks Device Driver Interface
PlatePierce Seal Piercing Station Microplate Seal Piercer
VCode Barcode Print and Apply
Station
Microplate Barcode Labeler
Velocity11 Robot 3- Axis Robot
VHooks Integration Interface VWorks Hooks Interface
VPrep Pipetting System Vertical Pipetting Station
VSpin Microplate Centrifuge Microplate Centrifuge
VStack Labware Stacker Labware Stacker
Agilent Technologies

Letter to our Customers
2Agilent Technologies Inc., Automation Solutions Division

Table of Contents
BioCel User Guide
i
Content
Chapter 1. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Who should read this guide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
What this guide covers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
What is new in this version of the user guide. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
Accessing Velocity11 user guides . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Reporting problems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Safety information about the BioCel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Chapter 2. BioCel overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Basic description. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
BioCel specifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
BioCel 1200 external features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
BioCel 1600 and 1800 external features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Utilities connections . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Power panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Hardware control components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Power system . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Air system . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
Vacuum system. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
Computers and networking. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
Adjusting the keyboard shelf . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Docking the mobile device table to the BioCel . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
BioCel devices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
BioCel accessories . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
Chapter 3. Preparing for a run . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
Workflow for preparing the BioCel for a Run. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
Turning on the BioCel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
Performing a BioCel ready-state check . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
Preparing devices and accessories . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
Placing and removing plate hotel labware . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
Setting up a VSpin counterweight plate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
Aligning and testing auxiliary bar code readers. . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
Setting up the PlateHub . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
Performing pre-run checks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55

Table of Contents
BioCel User Guide
ii
Chapter 4. Performing a run. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
Pausing and stopping a run. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
Comparing interlock and emergency circuits . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
Monitoring the status of a run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
Cleaning up after a run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
Turning Off the BioCel. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
Chapter 5. Diagnostics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
About Diagnostics software. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
Using Bio I/O Diagnostics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
Using Robot Diagnostics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
About fine-tuning robot teachpoints . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
Fine-tuning a robot teachpoint . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
Chapter 6. Maintenance and troubleshooting . . . . . . . . . . . 85
Routine maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
Resolving robot errors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
Overriding the safety interlock . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
Resolving plate placing errors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
Resolving lid removal problems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
Recovering from a power outage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
Index. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95

1
Chapter 1: Introduction
BioCel User Guide
Introduction 1
This chapter contains the following topics:
❑“Who should read this guide” on page 2
❑“What this guide covers” on page 3
❑“What is new in this version of the user guide” on page 4
❑“Accessing Velocity11 user guides” on page 5
❑“Reporting problems” on page 7
❑“Safety information about the BioCel” on page 8

Chapter 1: Introduction
BioCel User Guide
2
Who should read this guide
Job roles This user guide is for people with the following job roles:
Related topics
Job role Responsibilities
Lab manager, administrator, or
technician
Someone who is responsible for:
❑Managing the BioCel
❑Developing the applications that
are run on it
❑Solving the more challenging
problems that might arise
❑Developing training materials and
standard operating procedures for
operators
Operator Someone who performs the daily
production work on the BioCel and
solves routine problems.
Your organization may choose to create
its own procedures for operators
including the procedures in this guide.
For information about... See...
What this guide covers “What this guide covers” on page 3
What uis new in this user guide “What is new in this version of the user
guide” on page 4
Accessing Velocity11 user guides
and online help
“Accessing Velocity11 user guides” on
page 5
Using the BioCel safely “Safety information about the BioCel”
on page 8

3
Chapter 1: Introduction
BioCel User Guide
What this guide covers
What is covered This guide covers a description of the BioCel system, the operation of
the hardware components, and the use of diagnostics.
What is not covered This guide does not cover using VWorks, setting up devices, and
networking the BioCel.
Hardware version This guide covers the hardware for the BioCel 1200, 1600, and 1800. This
includes accessories such as the Weigh Pad and plate hotel.
BioCel
customization
Because the BioCel is a custom product with many options, this guide
describes features that might not be included in your BioCel.
Related topics
For information about... See...
Using VWorks VWorks User Guide
Using diagnostics for a third-party
device
Device Driver User Guide
Operating a Velocity11 device The user guide for that device
Networking the BioCel VWorks User Guide

Chapter 1: Introduction
BioCel User Guide
4
What is new in this version of the user guide
About this topic This topic briefly describes the new features this guide covers.
New Feature
Related topics
Feature Description See...
BioCel 1200 Automation platform that is
smaller than the BioCel 1600 and
1800.
“BioCel 1200 external features”
on page 17
BioCel 1800 Automation platform that is larger
than the BioCel 1200 and 1600.
“BioCel 1600 and 1800 external
features” on page 18
Modifications to the BioCel
1600
❑Changes in the power panel
❑Changes to the air panel
❑“Power panel” on page 21
❑“Hardware control
components” on page 22
Device table Mobile table that locks into the
BioCel
“Docking the mobile device table
to the BioCel” on page 34
New accessories ❑Tra nsl ato r li n ea r ro bot
❑PlateHub
❑“Translator linear robot” on
page 38
❑“PlateHub” on page 37
For information about... See...
Hardware features “BioCel overview” on page 13
What this guide covers “What this guide covers” on page 3
Accessing the online help “Accessing Velocity11 user guides” on
page 5

5
Chapter 1: Introduction
BioCel User Guide
Accessing Velocity11 user guides
About this topic This topic describes the different formats of Velocity11 documentation.
Each Velocity11 user guide is delivered to you as:
❑Online help
❑A PDF file
❑A printed book
The information in each format is the same but each format has different
benefits.
Where to find the
user guides
Online help
The online help is added to your computer with the software
installation.
Velocity11 website
You can download the latest version of any PDF file from our website at
www.velocity11.com.
All Velocity11 user documentation can be searched from the website at
www.velocity11.com.
Online help The online help is the best format to use when you are working at the
computer and when you want to perform fast or advanced searches for
information.
To open the online help:
1. Do one of the following:
Select Help > VWorks Help.
Press F1.
Clicking the question mark icon on the toolbar for context-
sensitive help.
2. Click on the BioCel User Guide link.
Note: If you are not using our software, you can access the help from the
Velocity11 website at http://www.velocity11.com.
Main features
The online help includes a navigation pane, content pane, and
navigation buttons.

Chapter 1: Introduction
BioCel User Guide
6
The navigation pane has four tabs, providing four different ways to
locate information. The content pane displays the online help topics.
Navigation buttons in the content pane allow you to navigate through
the pages.
PDF user guides Computer requirements
To open a user guide in PDF format, you need an Acrobat viewer. You
can either use the viewer that is built into Adobe Acrobat, or you can
download the free Adobe Reader application from
http://www.adobe.com/support/downloads/main.html.
Printing and searching
We provide user guides in PDF format mainly for printing additional
copies. You can use them for simple searches from the Find button,
although these searches are much slower than online help searches:
More information
For more information about using PDF documents, see the Adobe
Acrobat PDF help system that can be accessed from your Acrobat
viewer.
Navigation pane Content pane Navigation buttons

7
Chapter 1: Introduction
BioCel User Guide
Related topics
Reporting problems
About this topic If you have a technical problem that you cannot resolve after reading the
chapter on maintenance and troubleshooting, read the information in
this topic for how to report problems with the BioCel.
Reporting hardware
problems
If you have a problem with a hardware component of the BioCel that
you cannot resolve, let us know by:
❑Sending an email to [e-mail] or
[e-mail]
❑Calling Velocity11 Technical Support at 1-800-979-4811 or
1-650-846-6611
Reporting user guide
problems
If you find a problem with this user guide or have suggestions for
improvement, please use the feedback button in the online help. Your
comments will be reviewed promptly and used to write the next version
of the guide.
You can also send an email directly to [e-mail].
Related topics
For information about... See...
Hardware features “BioCel overview” on page 13
What this guide covers “What this guide covers” on page 3
Contacting Velocity11 “Reporting problems” on page 7
For information about... See...
Reporting software problems VWorks User Guide
Sending files VWorks User Guide

Chapter 1: Introduction
BioCel User Guide
8
Safety information about the BioCel
About this topic This topic gives general information about BioCel safety hazards.
Before using the
BioCel
Before using a BioCel, your organization should make sure that you are
properly trained in:
❑General laboratory safety
❑The correct and safe operation of the BioCel
❑The correct and safe operation of other lab automation systems or
components used in combination with the BioCel
If you are the person in your organization responsible for training others
on the BioCel and you have a safety question, please contact Velocity11
Service Center.
Safety labels Pay attention to any safety labels printed on your BioCel. A safety label,
shown below, consists of a warning symbol. A description of the
warning and information that will help you to avoid the safety hazard
are located in the safety information topic of the user guide.
Chemical hazards Some chemicals used when working with the BioCel might be
hazardous. Make sure you follow the recommendations in the MSDS
(Material Safety Data Sheet) for every chemical that you plan to use. The
manufacturer of the chemical should provide you with the MSDS.
Waste disposal Remember to dispose of chemicals in compliance with all applicable
regulations.
Product use Velocity11’s products must only be used in the manner in which we
intend, as described in our user guides. Any other use might damage the
product or injure you. Velocity11 is not responsible for damages caused,
in whole or part, by unauthorized modifications, or by procedures that
are not explicitly described in our user guides. Any modifications or
changes to products not expressly approved in Velocity11 user guides
could void the warranty.
The BioCel is not intended or approved for diagnosis of disease in
humans or animals.
Overhead door injury
hazards
The overhead door hazards apply only if you have a BioCel 1600 or 1800
that has overhead doors.

9
Chapter 1: Introduction
BioCel User Guide
!! INJURY HAZARD !! Opened overhead doors are
approximately 188 cm (6 ft 2 in) above the floor. To avoid injury, be
aware of the door height and position at all times when working
around the BioCel.
!! INJURY HAZARD !! The pneumatic braces on overhead doors
should be adjusted so you can comfortably open and close the
doors. If you have to strain to open a door, please contact the
Velocity11 Service Center and ask to have the braces adjusted.
Overhead door
damage hazard
The overhead door hazards apply only if you have a BioCel 1600 or 1800
that has overhead doors.
!! DAMAGE HAZARD !! Always open and close overhead doors
using their handles. Opening and closing overhead doors by pulling
and pushing on their corners can crack the glass and damage the
pneumatic braces.
Computer monitor
damage hazard
The computer monitor hazard applies only if you have a BioCel 1600 or
1800 that has overhead doors.
!! DAMAGE HAZARD !! To avoid damage to the computer
monitor, make sure that you move the monitor out of the way as you
close the overhead doors.
00007
6 feet 2 in.
188 cm

Chapter 1: Introduction
BioCel User Guide
10
Lower side door
injury hazard
The lower side door hazards apply only if you have a BioCel 1600 or
1800.
!! INJURY HAZARD !! Always close the lower side doors when
you finish the operation that led you to open them. Leaving side
doors open creates a tripping hazard. It can also block escape routes
in a laboratory.
Interlock override
injury hazard
!! INJURY HAZARD !! Only fully trained BioCel administrators
should have access to, and use of, the safety interlock key. Use the
override only when you know how the robot and devices will move
during the protocol, when the robot speed is slow, and when you
have taken measures to keep away from the areas in which the
robot and device parts will be moving.
With the interlock overridden, it is possible to be hit by the robot when it
is moving. If this happens, the robot will immediately stop, minimizing
injury, and the likely outcome is minor bruising. However, not all
circumstances can be foreseen and more serious injury is possible. It is
the responsibility of every operator to use the built-in BioCel safety
features, follow warnings and safety labels and keep out of the robot’s
radius whenever it is likely to move.
Laser warnings BioCel lasers
Your BioCel contains one or more lasers used to read bar codes. One
bar code reader, attached underneath the robot arm, is used to read
plates as they are picked up. Other bar code readers might be included
on your system, attached to platepads, VPrep shelves, or VCode printers.
!! INJURY HAZARD !! The BioCel bar code readers use class II
lasers. Before using the BioCel, you should be trained in the safe use
of these lasers.
00008

11
Chapter 1: Introduction
BioCel User Guide
The laser beam will not harm your skin so there is no danger in exposing
your arms or hands to the beam. However, you could damage your eyes
if you stare directly into the beam.
Bar code readers emit light for up to 0.5 seconds only when taking a
reading so they are only a hazard during protocol runs. When a plate is
being read, the beam should not pass beyond the plate. If you are
operating the BioCel without plates, and with the overhead doors open,
the risk of exposure is increased.
Before using the BioCel you should identify the locations of all bar code
readers and establish the directions in which they point. All readers
point downwards to minimize the potential exposure at eye level. The
robot bar code reader represents the greatest hazard because of its
height above the table. This bar code reader is angled downwards at 15°
and has a maximum illumination arc of 60°, centered perpendicularly
to the reader. With these measurements you can establish the space that
is illuminated on occasions when there is no plate in the robot gripper.
!! INJURY HAZARD !! Class II laser hazard. Do not look directly
at the laser beam. Looking directly at the laser beam can result in
serious eye injury.
!! INJURY HAZARD !! Do not disassemble bar code reader sensor
heads. Laser emission from the reader is not automatically stopped
if the sensor head is disassembled.
!! INJURY HAZARD !! Unless following a procedure in a
Velocity11 user guide, do not touch the white test button on the side
of the sensor head of an auxiliary bar code reader. This button turns
on the laser creating the possibility of a long exposure to the beam.
Third-party lasers
Your BioCel might also contain lasers built into other third-party devices,
such as Zeiss Multimode readers and Liconic incubators. For
information about laser safety for third-party devices, see the relevant
device’s documentation.
Related topics
For information about... See...
Reporting problems “Reporting problems” on page 7
BioCel features “Basic description” on page 14

Chapter 1: Introduction
BioCel User Guide
12

13
Chapter 2: BioCel overview
BioCel User Guide
BioCel overview 2
This chapter contains the following topics:
❑“Basic description” on page 14
❑“BioCel specifications” on page 15
❑“BioCel 1200 external features” on page 17
❑“BioCel 1600 and 1800 external features” on page 18
❑“Utilities connections” on page 19
❑“Power panel” on page 21
❑“Hardware control components” on page 22
❑“Power system” on page 27
❑“Air system” on page 30
❑“Vacuum system” on page 31
❑“Computers and networking” on page 32
❑“Adjusting the keyboard shelf” on page 33
❑“Docking the mobile device table to the BioCel” on page 34
❑“BioCel devices” on page 35
❑“BioCel accessories” on page 36

Chapter 2: BioCel overview
BioCel User Guide
14
Basic description
About the BioCel The BioCel is a plate-processing automation platform that is used in
combination with devices for applications such as:
❑Compound management
❑Sample preparation
❑Plate replication
❑PCR purification
❑High-throughput screening
To operate the BioCel, you should be familiar with the operating
procedures in this guide as well as the guides for the devices installed
on your BioCel.
Basic BioCel
components
Every BioCel includes:
❑A frame
❑A table
❑A robotic arm
❑A controlling computer, a monitor, a keyboard, and a mouse
❑A main power panel and electrical supply circuits
❑Communication hubs and cables
❑A Bio I/O console for managing sensor information
❑One or more uninterruptible power supplies (UPSs)
❑An AC/DC converter (DC power supply)
❑An air system that includes a main air panel, pressure regulators, an
air filter, and air lines
❑VWorks software
❑Software for each device
Related topics
For information about... See...
BioCel features ❑“BioCel 1200 external features” on
page 17
❑“BioCel 1600 and 1800 external
features” on page 18
BioCel specifications “BioCel specifications” on page 15
VWorks VWorks User Guide