Technical Note 67

Instrument Control and Data Acquisition

with Chromeleon

Introduction
Laboratories generally have a combination of chromatography devices from different manufacturers and,
therefore, face several challenges in managing instrument control and data acquisition. These challenges
generally center on the inherent difficulties of using
several different chromatography applications to control
different instruments including higher training and validation costs.
The Chromeleon Chromatography Management
System (CMS) offers a solution to these laboratories.
Chromeleon provides control of more than 250 instruments from over 25 different manufacturers, is easy
to learn and use, and allows instrument methods to be
easily transferred from one instrument to another, even
between those from different manufacturers.
This document describes the problems encountered
with the traditional laboratory environment, the challenges that Dionex overcame in order to provide control
of all these instruments, an overview of how instruments
are controlled with Chromeleon, and a summary of the
benefits Chromeleon offers.
Traditional Environment
The majority of chromatographic instrument manufacturers provide a chromatography software application
that controls their own instruments and processes the
acquired data. Traditionally, laboratories have used the
software application provided by the hardware manufacturer to control these instruments.

This can be a good strategy to adopt if all chromatographic instruments used come from the same
manufacturer, but as soon as a system is required that
this manufacturer cannot provide it becomes necessary
to use a different software application. There are several
disadvantages to using different software applications:
Lack of compatibility it is often very difficult
(and sometimes impossible) to transfer data from one
chromatographic software application to another. This
makes it more difficult to transfer methods from one
instrument to another, or even to compare data generated on one instrument against data generated on
another.
Higher maintenance costs each software package
must be administered separately (e.g., different backup
mechanisms, different operating procedures, etc.).
Higher training costs users have to be trained on
several different software packages.
Higher validation costs each different software
package must be validated.
Complex operation in a mixed system simple operations become complex. For example, to see the status
of all instruments in the laboratory it is necessary to
open several different applications, record the status
of each instrument controlled by that application, and
then collate this information for all applications.

Technical Note 67

Open Environment
All the problems associated with the traditional
environment are solved by adopting an open environment
that allows instruments from different manufacturers to
be controlled by a single application. One of the main
advantages of Chromeleon is that this concept of an open
Chromatography Management System (CMS) was a core
design feature from the beginning. The limitations of the
traditional environment were recognized and the software
designed to eliminate those limitations. Chromeleon can
control more than 250 instruments from over 25 different manufacturers. The main mechanisms for instrument
control are detailed in the following section.

The Chromeleon Server is the only component that

communicates with an instrument. Therefore, to control
it, the computer running the Chromeleon Server needs
to be physically connected to the instrument, either
through a LAN, USB, or other connection protocol. The
other two components can be remote from the server if a
network is available to connect them.
Chromeleon Client
The Chromeleon Client is the User Interface part of
the Chromeleon software. It uses a browser interface to
interact with the Chromeleon Datasource, and a Control
Panel or Panel Tabset to interface with the Chromeleon
Server.

Chromeleon Architecture

For normal operation, there are three components

in Chromeleon that must communicate: Chromeleon
Datasource, Chromeleon Server, and Chromeleon Client.
Any combination of local and network access is supported by Chromeleons three components. All three can
be on the same computer, or all three can be on three
different computers, or any combination in between. It is
also possible for the Chromeleon Client to communicate
with multiple servers and datasources, and for multiple
servers to use a single datasource.
Generally, any Chromeleon components on the same
computer will communicate automatically without the
need for much configuration. When components are installed on different computers they need to be configured
to allow communication. A peer-to-peer or client/server
network is required for this, typically in the form of an
existing Office LAN (usually a domain). Alternatively, a
direct crossover cable connection can be used between
two computers (workgroup).
Chromeleon Datasource
The Chromeleon Datasource is a structured file
system indexed by a database. It is used by Chromeleon
for all data and file storage. Note that Chromeleon does
not need to be installed on the computer that contains a
datasource.
Chromeleon Server
The Chromeleon Server is a background application
that monitors and controls an instrument. It executes
programs, sequences, and batches that are stored on a
datasource, and saves data from an instrument as a channel into the same datasource.

Figure 1. Chromeleon Client showing the browser connected to a

datasource called CM_Data.

Challenges Raised by the Open Environment

Although this open environment removes the limitations associated with the traditional environment, it
raises additional challenges:
How is it possible to have a common interface for different instruments?
How is it possible to ensure the quality of instrument
control provided?
This section first details the basic architecture of the
open Chromeleon environment and then how additional
challenges are overcome by Chromeleon.

Instrument Control and Data Acquisition with Chromeleon

Common Interface for Instruments

In order to provide a common interface for different

instruments from different manufacturers, the concept of
a Chromatography Basic Input/Output System (C-BIOS)
was developed. This concept operates as follows:
Uniform Control Commands
A uniform set of control commands was developed to
meet three main criteria:
Easy to learn
Easy to use
Easy transfer of control commands between
instruments
The basic format of the control commands is:
[module].[command] = [parameter]. Table 1 shows some
examples of control commands.
Table 1. Examples of Control Commands
Module Setting

Control Commands

Set pump flow to 1.0 mL/min

Pump.Flow = 1

Perform sample injection

Sampler.Inject

Set Column oven temperature to

20 C

ColumnOven.Temperature = 20

Set wavelength of detector channel UV_VIS_1.Wavelength = 254

1(UV_VIS_1) to 254 nm

These control commands are fully instrument independent. For example, the control command for pump
flow will work on practically every pump supported by
Chromeleon. As such, these control commands meet all
the development criteria:
Easy to Learn These control commands are intuitive
and can be quickly learned once the basic structure is
understood.
Easy to Use As all control commands are the same,
independent of instrument manufacturer, they are easy
to use. Operators do not need to learn different commands for different instruments.
Easy transfer of control commands between instruments As the control commands are the same for
different instruments, method transfer is effortless. For
example, the pump.flow command will work equally
well on a Dionex Summit HPLC and an Agilent 1100
HPLC.

Communicating Control Commands to Instruments

Once the user has defined the controls they are
sent to the Instrument Control Interface via Remote
Procedure Calls (RPC) to the Chromeleon Server. This
translates the command in to the native control codes for
the instrument.
Execution of Commands
The instrument executes the command as soon as it
receives it. Any errors generated by the execution of the
command (such as a high pressure limit being exceeded
due to an increased flow rate) are then sent back to the user.
Quality of Instrument Control

Dionex takes special care to ensure that all drivers

developed for instruments are fully tested and validated
before release. Rigorous procedures ensure that all drivers made available are of the highest quality. The basic
process is:
1. The testing starts at the control command level. Every
control command, no matter how minor, is tested by
a team of test engineers. For some instruments there
may be literally hundreds of available commands. The
basic test process for each command is to enter three
valid values, a limit(s) value, values that exceed the
limit(s), and invalid values. For example, a pump may
allow flow values between 0 and 10 mL/min. The test
and validation procedure checks that:
Values of, for example, 1, 4, and 8 mL/min are
executed correctly.
Values of, for example, 0 and 10 mL/min are executed correctly.
Values of, for example, 1 and 11 mL/min are not
executed and that an appropriate warning is displayed.
Values of, for example, a or & are not accepted
and that an appropriate warning is displayed.
2. Next, the help text for each command is checked for
accuracy and usefulness.
3. Following this, the error handling is thoroughly checked
by forcing typical errors and checking the response. For
example, check that when the pump pressure exceeds
its limit the flow rate is reduced to 0 mL/min and an
appropriate error message is provided.
4. The drivers are then tested under typical day-to-day
operations where multiple commands are executed
as part of a method. For example, a pump gradient
profile may be created and a check performed to show
that the gradient was generated correctly.
Technical Note 67

5. The driver is also tested to ensure that inappropriate

use is prevented. For example, tests are made to show
that if data acquisition is being performed by a UV
detector it should not be possible to turn off the lamp.
6. Finally, to ensure robust and reliable operation the
instrument is run for a minimum of 24 h to check that
no errors occur, that computer performance is not affected, and that no memory leaks occur.
Additional tests are created that are based on instrument specific tests requirements. Each instrument has its
own test plan and test results, and these can be reviewed
at any time as part of a vendor audit. These plans ensure
that all instrument drivers developed by Dionex are of
the highest quality and validated for laboratory use.
Once a driver is released, a dedicated tracking system ensures that any reported errors (e.g., errors caused
by an unusual series of commands) are investigated and
corrected. Errors found in drivers for third party instruments are treated as seriously as errors found in the drivers for Dionex instrumentation.

Instrument Control with Chromeleon

The Chromeleon CMS provides control for a vast
number of different chromatographic instruments and
has all of the advantages associated with the traditional
laboratory environment. Currently, control is offered for
over 250 instruments from more than 25 different vendors and is extended to instruments other than HPLCs.
Control is also provided for ICs and GCs (a full list
of instruments supported will be supplied on request).
Table 2 shows some of the most common instruments
that can be controlled by Chromeleon.
The next section describes the workflow for setting
up the Chromeleon software to control any of these instruments, and how it is possible to eradicate all the disadvantages associated with the traditional environment.
Timebase Concept

A typical chromatography instrument is a collection

of different modules, therefore a top level instrument
container is needed that is used to store all the different module information. In Chromeleon the name of
that container is a Timebase. This name was chosen
because a collection of different modules must all share
one common characteristic the system time. For
example, pump gradient changes must take place at a
specific time and this is often related to the time that the
autosampler sends the inject command.


Table 2. Common Laboratory Chromatographic

Instruments That Can Be Controlled by Chromeleon
Type

Manufacturer

Instrument

IC

Dionex

All instruments

HPLC

Dionex

All instruments

Agilent

1050, 1100 (including DAD* control)

Waters

Alliance (including DAD* control)

Shimadzu

LC-10 and LC-2010

Merck / Hitachi

LaChrom

Gilson

Most modules. For example:

333, 334 Preparative Pumps
231 Autosampler, 156 Detector

Agilent

5890, 6850, 6890

Perkin Elmer

Autosystem (XL), Clarus

Varian

3400, 3600, 3800

Thermo

FOCUS, TRACE

GC

* DAD: Diode Array Detector

Because the base property that is common among all

modules is time, the name of Timebase was chosen to
define a collection of modules.
Registering an Instrument with Chromeleon

All instruments must be connected to a Chromeleon

Instrument Server. The type of connection is dependant
upon the instrument. For example, Dionex instruments
are generally connected using the more modern USB
interface, whereas an Agilent 1100 can be connected using HPIB or LAN.
Instrument connections are registered through the
Chromeleon Server Configuration application. Step 1 is
to create a timebase the master name for the collection of modules which make up an instrument. Step 2 is
to register the different modules with this timebase. The
Chromeleon Server Configuration application guides a
user through each of these steps (Figure 2).

Instrument Control and Data Acquisition with Chromeleon

Figure 3. Structure of a timebase directory.

Creating a Timebase Directory

A. Create a Timebase

B. Select an Instrument/ Module.

As soon as a timebase is registered in Chromeleon, a

timebase directory is created (Figure 3).
The name of the directory is the same as the timebase name preventing the possibility of duplicate timebase names. The directory contains a sequence named
manual. This is used to store manually acquired data.
The directory also contains a folder named audit
where the daily audit trails are stored. The name of the
daily audit trail always uses the format yyyymmdd,
where yyyy is the year, mm is the month, and dd
is the day. So the file name for audit trail for the 18th
of May, 2005 would be 20050518. The audit trail is extremely comprehensive and stores all instrument events
such as:
Instrument settings current status of the instrument
(pump settings, sampler settings, etc.)
Changes to settings any changes to the instrument
settings such as changes in flow rate, changes to detector wavelength, etc., are logged (along with details of
the user making the change)

C. Define the connection

settings

Warnings and errors all warnings and errors (such

as pump shut down due to pressure limits being exceeded) are logged in the audit trail
Figure 4 shows a typical audit trail. In this example
the audit trail is showing the initial instrument settings.
D. Define the instrument settings

E. Instrument connection completed

Graphical Control Interfaces for a Timebase

Figure 4. Daily audit trail for an Agilent 1100 timebase.

Figure 2. Registering an instrument with Chromeleon.

Technical Note 67

Once a timebase is registered, it is simple to create

a graphical control interface. In Chromeleon these are
called panels, and all Chromeleon installations come
with a prepared library of panels (Figure 5).

Panels show all instrument settings, including an online signal display. If the instrument includes a diode
array detector it is even possible to view the 3-D plot
in real time.
Panels also show the audit trail so it is easy to track
changes or see any warnings/errors.
Connecting a Panel To a Timebase
Once a panel has been chosen it must be connected
to the relevant timebase. Connections can be made either
locally or across a network (Figure 7). As soon as the
connection is made, Chromeleon automatically notifies the user of any problems. For example, if a panel
containing commands for a refractive index detector is
connected to an instrument which has only a UV detector, a warning will automatically be displayed.

Figure 5. Standard Chromeleon panel library.

The library provides a panel for most instrument

configurations, but it is a simple task to create new panels. Figure 6 shows a typical panel for an Agilent 1100
HPLC System.

Figure 6. Panel library for the Agilent 1100.

The panel for the Agilent 1100 demonstrates most of

the main features about Chromeleon panels. That is:
It is possible to have multiple windows to display
module specific information (the pump settings were
activated by clicking on the Settings button).

Figure 7. Different connection options for timebases. Connecting

to a local timebase (top), and connecting to a timebase through
the network (bottom).

Instrument Control and Data Acquisition with Chromeleon

Full Customization Supported

Panels can be designed to fit any laboratory workflow or any specific user requirements. For example, Figure 8 shows a basic panel for any HPLC. It contains no
options for changing any of the instrument parameters.
Instead, it shows users a basic workflow that they must
follow in order to use the instrument.

This feature is one of the major benefits provided by

Chromeleon panels. It means that a single control interface can be designed for all laboratory chromatography
instruments, thus providing lower training coststraining
time is reduced as users need only learn one interface.
Additional Graphical Control Interfaces for
Dionex Instruments

A special class of panels exists for Dionex instrumentation called panel tabsets. Panel tabsets offer some
advanced features that are not available for standard
panels.

Figure 8. Basic instrument interface.

Full customization is mainly used to ensure that the

most important instrument commands and information is
displayed prominently. For example, when an instrument
is used to collect fractions, any commands relating to
starting and stopping fraction collection would be placed
in a prominent position.

Automatic Panel Tabset Creation

Panel tabsets are created automatically based on the
instrument settings in the server configuration. All the
user has to do is specify for which instrument server the
panel tabsets are needed, and Chromeleon will automatically create these for all Dionex instruments that are
connected. Figure 10 shows a tabset containing two automatically created panels for a Dionex Summit HPLC
system and a Dionex ICS-3000 IC system. These can be
expanded or reduced using the buttons next to the timebase name (Figure 11 shows an expanded panel tabset).

Instrument Independence
Panels are designed to be as independent of instrument type as possible. This makes it possible to use
panels designed for one instrument type as an interface
for any other instrument type. For example, if a panel
is designed to show an autosampler sample tray, it will
automatically show the relevant tray design for the
instrument to which it is connected. This can be seen in
Figure 9.

Figure 10. Automatically created panel tabsets.

Figure 9. Rack display changes for the same panel connected to

different instruments: sampler rack for a Dionex Summit HPLC
(left) and sampler rack for a Waters Alliance HPLC (right).

Technical Note 67

Figure 11. Expanded panel tabset.

Working With a Panel Tabset

A panel tabset contains the following tabs:
Home Provides an overview of the system
Sequence control Provides an overview of the currently running sequences
Tab per instrument module (e.g., pump, sampler,
etc.) provides the main instrument settings for each
module
This special type of panel makes it easy to switch
between modules and instruments. It is also possible to
use this panel type with the touch screen technology offered by tablet computers.
Instrument Control Methods

Control panels are used for on-line instrument

control and monitoring. For off-line control, instrument
control methods are used. In Chromeleon, they are called
program files.

Figure 12. Pump Options for the Dionex P680 pump.

In addition, the options offered in individual dialogs

are activated/deactivated based on the instrument server
configuration. Figure 12 shows the Pump Options for
the Dionex P680 pump. A Maximum Flow Acceleration value can be set for this pump, but a Maximum
Flow Deceleration value cannot. To ensure that a user
does not set an invalid value this option is automatically
grayed out.
Editing a Program File
All program files can be viewed as a text display
(Figure 13). This shows all instrument commands that
must be executed as well as the times of the execution.
Any invalid commands are shown in red, making it easy
for users to locate and modify them. Any command can
be modified simply by selecting it and pressing the F8
key. For invalid commands, Chromeleon automatically

Program File Wizard

Program files can be created using a built-in Wizard that guides users through the main steps required to
create a working program file. The Wizard automatically
shows dialogs that are based on the instrument configuration. For example, if the instrument has no column
oven, a column oven screen is not offered.

Figure 13. Program File text display (invalid value highlighted

in red).

Instrument Control and Data Acquisition with Chromeleon

Figure 14. Detailed command options along with value limits.

displays the appropriate command dialog along with the

allowed values for that command (Figure 14).
Simple and intuitive with which to work, this text
display allows easy creation of complex methods. For
example, to create a method that shuts down a system
simply modify a file so that the necessary shutdown
commands are included (Figure 15).

Figure 16. Sampler Device View in the Program Editor.

Transferring a Program File

With Chromeleon, it is easy to transfer a method
from one instrument to another, even if the instruments
are from different manufacturers. Figure 17 shows a
program file for a Dionex Summit system containing
a quaternary pump that has been linked to an Agilent
1100 with a binary pump. In this example, all pump
commands relating to the percent C (%C) and percent
D (%D) values are shown in red. Since there are no C
or D eluent lines in the Agilent 1100, these commands
are irrelevant. Such irrelevant commands are then easily
deleted in order to correct the program file for the particular instrument.

Figure 15. Basic shutdown method for a Dionex Summit

instrument.

Additional editing options are provided for Dionex

instrumentation and selected third party instruments.
These options, called Device views, are displayed on
the left-hand side of the program file editor and make it
simpler to locate and edit device specific commands in the
program file. For example, the user can immediately view
and edit all the major sampler commands by simply clicking on the Sampler device view icon (Figure 16).

Figure 17. Program file for a Dionex instrument that has been
transferred to an Agilent 1100.

Technical Note 67

Sample Lists

Common Data Format

Program files are not used in isolationthey need to

be linked to specific samples. Chromeleon provides this
functionality through sequences. A sequence contains
the list of samples that must be injected, along with the
relevant vial position and injection volume and associated program file(s). Figure 18 shows a typical sequence.

Because all data are now acquired by Chromeleon,

it becomes easy to compare data from different instruments. Chromeleon stores all data in the same format
so there are no tedious import or export procedures. For
example, Figure 19 shows an overlay of two chromatograms. One is of a four-component mixture analyzed by
a Shimadzu LC-2010 and the second is from a similar
mixture (slightly different concentration) analyzed by
a Dionex Summit HPLC. In both cases, the chromatographic instrument method was the same. In this example, the difference in retention times is due to the lower
gradient dwell volume of the Dionex Summit HPLC.

Figure 18. Example sequence.

It is possible to have more than one program file

associated with a sequence. This allows for different
samples to be analyzed under different conditions, and
for the inclusion of specialized program files, such as
shutdown files.

Figure 19. Overlay of two chromatograms from (1) a Dionex

Summit HPLC and, (2) a Shimadzu LC-2010.

On-line Changes to Instrument Parameters

It is possible to change the instrument settings while
the sequence is running. If the program file is modified,
the changes take effect for the next sample in the list, not
the sample currently running.
Changes can be made to the current sample from the
control panel and must be confirmed by the user. These
changes are then logged to the audit trail so they can be
tracked backward.
Sample lists can also be modified during data
acquisition, however details of a currently running
sample cannot be modified. Example modifications
include: (1) adding samples or deleting existing
samples, (2) updating sample names and injection
volumes, and (3) updating sample positions.

10

Instrument Control and Data Acquisition with Chromeleon

Benefits of Chromeleon Instrument Control

The main benefit offered by controlling instruments
with Chromeleon is increased productivity and laboratory efficiency. This is accomplished through:
Increased Data Compatibility All data is stored by
the same application so it is easier to compare data
from different instruments.
Increased Method Compatibility The uniform control commands ensure that transfer of a method from
one instrument to another is simplified.
Reduced Training Costs Instead of training users on
multiple applications in order to control their instruments, they need only be trained on Chromeleon.

With Chromeleon, laboratories are not restricted

to choosing an instrument from Dionex, but are free to
choose instruments best suited to their requirements
from over 25 different manufacturers.
The driver development process used by Dionex ensures that all instrument control drivers released to customers are extensively tested and validated. Laboratories
can use Dionex third party drivers with confidence.
With this range of options available, Chromeleon is
an ideal solution for controlling instruments from a wide
range of different manufacturers.

Reduced Validation Costs Instead of validating

multiple applications, they need only validate
Chromeleon.
Reduced Error Chromeleon panels can be customized so that operators are only shown the information
they need reducing the possibility that they will send
invalid commands to the instruments.

Chromeleon and Summit are registered trademarks of Dionex Corporation.

Clarus is a registered trademark of Perkin Elmer. Alliance is a registered trademark of Waters Corporation.

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LPN 1778 PDF 04/06

2006 Dionex
Technical Note 67
11Corporation