Ettan IPGphor II Control Software

Ettan IPGphor II Control Software
user manual
2-D electrophoresis and first-dimension IEF
Ettan IPGphor II
Control Software
um
80-6500-47/Rev. A0/06-03
Page finder
1. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1
2. Ettan IPGphor II Control Software: . . . . . . . . . . . . . . . . . . . . . . . . . . . . .2
computer requirements and installation
3. Connecting the Ettan IPGphor II to the PC . . . . . . . . . . . . . . . . . . . . . . . .2
4. Ethernet connections and web browser . . . . . . . . . . . . . . . . . . . . . . . . . . 2
for monitoring the Ettan IPGphor II from a remote location.
5. Hardware requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .2
6. Software installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .3
Ettan IPGphor II Control Software
7. Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .6
8. Opening the Ettan IPGphor II
.................................
9. Communication between the Ettan IPGphor II and PC . . . . . . . . . . . . . . . .6
10. The Ettan IPGphor II Control Software . . . . . . . . . . . . . . . . . . . . . . . . . .6
11. IPGphor application window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .6
12. Protocol handling dialog . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .11
13. Creating a new protocol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .13
14. Running a protocol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .19
15. Capturing run data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .22
16. Exiting the software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .23
17. Troubleshooting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .24
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Ettan IPGphor II Control Software
um 80-6500-47
• pii
• introduction
1. Introduction to Ettan IPGphor II
Control Software
The Ettan™ IPGphor™ II Control Software is used to control the Ettan
IPGphor II Isoelectric Focusing Unit from a PC. From the PC, protocols
can be created, stored, and loaded to the Ettan IPGphor II. While isoelectric focusing of the Immobiline™ DryStrip gels progresses, the software
records the isoelectric focusing (IEF) parameters over time. When the IEF
run is completed, graph and log files are produced to document all steps
of the IEF run. The graph and log files can be printed or saved. If desired,
the log file can be exported to programs such as Microsoft® Excel®.
Multiple Ettan IPGphor II units may be controlled from one PC by
using a RS232 expansion module. Expansion modules are available from
National Instruments. Each Ettan IPGphor II unit’s individual IEF parameters are recorded independently. (See hardware requirements and
installation instructions).
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Ettan IPGphor II Control Software
2. Ettan IPGphor II Control Software:
computer requirements and installation
The Ettan IPGphor II Control Software is designed to work with PC’s
that have Windows® 98 SE (Second Edition) or higher, Windows NT® or
Windows 2000.
3. Connecting the Ettan IPGphor II to the PC
Use the serial cable that comes with the Ettan IPGphor II Isoelectric
Focusing Unit to connect the serial port located in back of the Ettan
IPGphor II instrument to the appropriate COM port of the PC or RS232
expansion module.
4. Ethernet connections and web browser
for monitoring the Ettan IPGphor II from a
remote location.
One Ettan IPGphor II instrument can be monitored through a web
browser. This is only true within an internal network setting and cannot
be viewed external to your computer network. Internet Explorer® 5.5
or later is required to monitor the Ettan IPGphor II instrument from
another PC. The web browser must be set for LAN settings and the IP
address of the Ettan IPGphor II instrument must be accessible. Contact
your network administrator for assistance in establishing the connection.
5. Hardware requirements
If multiple Ettan IPGphor II Isoelectric Focusing Units are to be controlled
by the Ettan IPGphor II Control Software the user must add a RS232
expansion box. Such expansion modules are available from National
Instruments. Select the appropriate expansion module to fit with your
computer connections (e.g. USB to RS232, PCMCIA to RS232, Ethernet
to RS232). Up to 4 Ettan IPGphor II units can be controlled from one PC.
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• p2
• software installation
6. Software installation
Insert the Ettan IPGphor II Control Software CD. The installation
procedure will start up automatically. Follow the onscreen instructions.
If the installer does not start up automatically, select “Run…” from the
Windows Start menu and enter “X:\Install.bat” (where “X” designates
the CD drive that contains the Control Software CD).
Installation performs the following actions:
1
National Instruments Program NI-VISA 2.6 “Run time engine” is installed first
[visa260runtime.exe].
2
The uninstall Ettan IPGphor II Control Software program will start first if a
previous version of the Ettan IPGphor II Control Software is already installed
[setup.exe]
3
Install IPGphor [setup.exe].
The default installation of the Ettan IPGphor II Control Software will be on the
local C drive within the folder titled “Amersham Biosciences”.
An additional folder labeled IPGphor will be created on the C drive. This is the
default folder in which saved protocols and saved log files will be stored. The
program also loads a sample file of a protocol and a log file. The sample files will
be loaded in the folders C:\IPGphor\Protocols and C:\IPGphor\Logfiles respectively.
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Ettan IPGphor II Control Software • software installation
Installing and uninstalling the Ettan IPGphor II Control Software
to control multiple Ettan IPGphor II Isoelectric Focusing Units
Although up to 4 Ettan IPGphor II units can be controlled from a single
PC, 4 separate copies of the Control Software must be installed on that
single PC. To carry out the installation of a 2nd copy of the Control Software, select the CD drive containing the Control Software CD, then open
the folder “InstallIPGphor2” and double-click on InstallIPGphor2.bat.
If a 3rd and/or 4th copy needs to be installed, repeat the procedure by
opening the folder InstallIPGphor 3 (or InstallIPGphor 4) and doubleclicking on InstallIPGphor3.bat (or InstallIPGphor4.bat).
The first time the program is started the default port will be COM 1.
Select a different COM path (2 through 8) for each Ettan IPGphor II
Isoelectric Focusing Unit, depending on the COM ports installed on the
computer. Contact your network administrator for more information.
Installing and uninstalling NI-VISA 2.6
Note: The uninstaller application will not
notify you when rebooting is necessary.
If you plan to re-install NI-VISA, you should
always reboot the machine after running
the uninstaller.
Before you install NI-VISA 2.6, we strongly recommend that you uninstall any versions of VISA prior to NI-VISA 2.0.1. NI-VISA 2.6 should
upgrade properly over NI-VISA versions 2.0.1 through 2.5.2.
After uninstalling NI-VISA, some DLLs and executables may remain in
the NI-VISA directories. To complete the uninstall process, you must
restart your machine.
Installing and uninstalling Ettan IPGphor II monitor/embedded
feature on the WEB client
In this feature the monitoring of one Ettan IPGphor II unit is possible.
1
From the server computer go to the Option menu and select “Webserver enable”.
Write down the TCP IP address from the pop-up message. You will need this for
step 2 below. Exit the Ettan IPGphor II Control Software and restart for the
change to take effect.
2
Note: To use the printing feature in Ettan
IPGphor II Control Software, Internet Explorer
5.5 or later must be installed.
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• p4
Go to the client computer. Open the web browser and enter the address
http://xxx/IPGphor#.htm, where xxx is the TCP IP address of the server computer
(obtained in step 1 above), and IPGphor# is the file name that is found on the
window title of the Ettan IPGphor II Control Software that is webserver enabled
(possible alternatives are IPGphor, IPGphor1, IPGphor2, IPGphor3, and
IPGphor4).
• Ettan IPGphor II Control Software
Ettan IPGphor II Control Software
7. Overview
The Ettan IPGphor II Control Software can be used to control up to 4
Ettan IPGphor II units at one time, each running a different set of run
parameters. In addition to creating, saving and editing protocols the software monitors voltage, current and VHrs (volt-hours) of the run and
graphs them as the run proceeds over time. The x and y scale values used
to graph the Log Data change over time and are dependent on the maximum values reached. Contextual help will appear as the mouse is moved
across active buttons, to guide the user in navigating and using the software. More information for several of these functions can be obtained by
right clicking over the active button/hot spot.
8. Opening the Ettan IPGphor II
Control Software
From the Windows Start menu select “Programs”. Select the IPGphor
program from the menu. When controlling multiple Ettan IPGphor II
units off one PC, each individual Ettan IPGphor II Control Software
program (2, 3, or 4) must also be started from the Programs menu.
9. Communication between the
Ettan IPGphor II and PC
When the Ettan IPGphor II Control Software is initiated the software
confirms it is in communication with the Ettan IPGphor II Isoelectric
Focusing Unit. If successful, a window will pop-up indicating communication has been established.
If the software does not recognize connection between it and the Ettan
IPGphor II Isoelectric Focusing Units then an error dialog will appear.
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Ettan IPGphor II Control Software
Note: Check to see that no other program is
trying to access the communication port.
Close all programs that may be accessing the
COM port.
Note: If communication between the PC and
the Ettan IPGphor II Isoelectric Focusing
Unit is broken the software will not recognize
a communication error but will no longer be
collecting the data output from the instrument. Check the connections. Once connection is reestablished, the software will
continue collecting data. Closing the program
is not necessary.
Check that the cable between the Ettan IPGphor II Isoelectric Focusing
Unit and the PC is connected properly. Communication can be confirmed
by selecting “Report” or “ID” from the Run drop-down menu. Communication can also be checked by exiting and then restarting the Ettan
IPGphor II Control Software program. To exit the Ettan IPGphor II
Control Software program, select “Exit” from the Logfile drop-down
menu, use the control keyboard commands Ctrl + Q or press the X
button located in the top right corner of the window. The software will
notify the user that any unsaved protocols that may have been created
will be lost.
Note: In the event of a power failure the software cannot collect data from the Instrument
and the data will not be recoverable.
Click OK to continue to exit as the software must be exited and connection to the instrument established before proceeding.
10. The Ettan IPGphor II Control Software
The Ettan IPGphor II Control Software has two main components; an
IPGphor application window and a Protocol handling dialog. The
IPGphor application window is used when controlling the Ettan
IPGphor II Isoelectric Focusing Unit, viewing the data as the IEF run
progresses and printing or exporting collected data. The second Protocol
handling dialog is visible when Edit Protocol is selected. The Protocol
handling dialog allows for creating, saving and loading protocols. The
IPGphor application window and Protocol handling dialog can be
resized, maximized or minimized.
11. IPGphor application window
Once the Ettan IPGphor II Software Control program is launched the application window will appear. In this main window the Ettan IPGphor II is
controlled and readings taken at selected intervals to be logged and graphed.
This window also allows the user to:
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Open and view stored log files for previous runs
Save, print and export the collected data
Open the Protocol handling dialog to create new protocols
Start, stop and pause the Ettan IPGphor II Isoelectric Focusing Unit
being controlled
Report the status of the Ettan IPGphor II Isoelectric Focusing Unit
(instantaneous report of run conditions when requested)
Capture the ID of the instrument (serial number and firmware version)
Select the default log file directory
Set the baud rate and the communication port
Adjust the graph update interval
Select the protocol to be run
Enable the PC coupled to the Ettan IPGphor II Isoelectric Focusing Unit
to be monitored remotely through a web browser
• IPGphor application window
Fig 4. IPGphor application window.
Description of IPGphor application window (Fig 4)
Instrument Log
The instrument log records data retrieved from the Ettan IPGphor II
Isoelectric Focusing Unit once a run has started.
Edit protocol
The edit protocol button takes the user to the Protocol handling dialog.
Here the user can create, save, load and store new protocols as well as
access previously saved protocols.
Serial #
Indicates the serial number of the Ettan IPGphor II Isoelectric Focusing
Unit that is controlled by the software.
Protocol #
Indicates the Protocol # selected to start from the Control Software.
Step markers
When activated, marks the locations of a step change by placing the
vertical gridlines on the graph at the time of a step change. When inactive
uniformly spaced vertical gridlines are displayed on the graph.
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Ettan IPGphor II Control Software • IPGphor application window
Update interval
Changes the time interval at which the software captures data from the
Ettan IPGphor II Isoelectric Focusing Unit.
Start, Pause and Stop
Controls the Ettan IPGphor II Isoelectric Focusing Unit.
Run and Pause indicators
Indicates the status of the Ettan IPGphor II Isoelectric Focusing Unit as
it is monitored by the Control Software.
Graph
The Ettan IPGphor II Control Software graphs the data (Voltage, Volthours and Current) as it is retrieved from the Ettan IPGphor II Isoelectric
Focusing Unit. The x and y scale values change to the maximum value as
the run progresses. The default colors for the data markers and trendlines
are black for the Voltage, red for the accumulated VHrs and light blue
for the Current in µA.
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• IPGphor application window
Ettan IPGphor II Control Software application window menus
and keyboard commands
Drop-down menus at the top left of the Control Software application
window can be accessed by clicking on the selected header to view the
drop-down menu options or can be accessed though the following
keyboard commands.
menu bar
description
Logfile
Open
Ctrl+O
Opens a log file (from a previously saved text file).
Save
Ctrl+S
Saves captured run data as a text file.
Print
Ctrl+P
Prints the current log data shown in the Instrument
Log window.
Print Graph
Ctrl+G
Prints the graph currently displayed.
Print All
Ctrl+A
Prints the Instrument Log data and the graph currently
displayed.
Export
Ctrl+E
Exports log data to spreadsheet.
Exit
Ctrl+Q
Stops and exits the program.
Protocol
Open Protocol Ctrl+W
Window
Opens the Protocol handling dialog.
Run IPGphor control functions
Start
Ctrl+1
Starts a protocol (indicate no. of IPG strips to be run).
Stop
Ctrl+3
Stops a protocol.
Pause
Ctrl+2
Pauses a protocol.
Report
Retrieves current data from the Ettan IPGphor II instrument
and displays it in the Instrument Log window.
ID
Retrieves the Ettan IPGphor II instrument serial number &
firmware revision.
Options
Folders
Ctrl+F
Allows the user to set the default folders for log files.
Port
Set serial port options and Baud rate.
(Com port number; 1200 or 9600 Baud)
Graph Update Interval
Selectable update rates at 1, 2, 3, 4, 5, 10, 15, 20, 25 or
30 minute intervals.
Webserver Enable
Starts a Webserver.
Monitoring the Ettan IPGphor II Control Software application
window from a Webserver is possible.
To activate the Webserver the Ettan IPGphor II Control
Software program must be exited and restarted.
Webserver Disable
Stops the Webserver.
To deactivate the Webserver, the Ettan IPGphor II Control
Software program must be exited and restarted.
Help
Help
About
Ctrl+F1
Help on use of the software.
Program ID information.
Using the Tab key on the PC can scroll active or editable fields. Shift+Tab
will move the cursor back.
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Ettan IPGphor II Control Software • IPGphor application window
Setting Serial Interface Parameters
The baud rate and the communication port used to communicate with
the Ettan IPGphor II Isoelectric Focusing Unit can be set or checked by
selecting “Port” under the Options drop-down menu. A baud rate of
1200 or 9600 can be used but must match the baud rate set on the unit.
A baud rate of 1200 is the default setting on the Ettan IPGphor II
Isoelectric Focusing Unit.
Setting the default folder
The default location to which log files will be saved is set to
C:\IPGphor\Logfiles. This option can be changed by selecting “Folder”
under the Options drop-down menu. Navigate to the folder or location
you wish for saved data to be stored and click on the
button. Whenever files are saved from the IPGphor application window,
the new default folder will be displayed as the new location for files to
be saved.
Webserver enable
The Ettan IPGphor II Control Software can be used to monitor an Ettan
IPGphor II Isoelectric Focusing Unit from another PC. In order to monitor the Ettan IPGphor II Isoelectric Focusing Unit the Webserver must be
enabled and the Ettan IPGphor Control Software program closed and
restarted. Internet Explorer 5.5 or later is required.
On the server computer select “Webserver Enable” from the Options
drop-down menu. Record the http:// (TCP IP) address as indicated on the
pop-up window. Close the Ettan IPGphor II Control Software. The Ettan
IPGphor II Control Software program should now be restarted.
In the remote PC, open the web browser. For Internet Explorer select
“Internet Options” under the Tools menu bar and select the Connections
tab. Select LAN settings. Mark bypass proxy server for local addresses.
Enter the web address http://xxx/IPGphor#.htm where xxx is the TCP IP
address of the server computer and IPGphor # is the Ettan IPGphor II
software installed file (IPGphor, IPGphor 1, IPGphor 2, IPGphor 3 or
IPGphor 4).
If established properly, the Ettan IPGphor II Control Software application
window should be displayed and the Ettan IPGphor II Isoelectric Focusing Unit run can be monitored from a remote location.
Webserver disable
Selecting “Webserver Disable” from the Options drop-down menu disables
Webserver. The program needs to be closed and restarted for the change
to take effect.
ID
Selecting “ID” from the Run drop-down menu can capture the serial
number of the Ettan IPGphor II Isoelectric Focusing Unit currently
controlled by the software. The ID of the instrument controlled will be
displayed in the Instrument Log window. This is helpful when multiple
Ettan IPGphor II units are controlled from one PC.
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• p10
• protocol handling dialog
12. Protocol handling dialog
To create a protocol click the
button in the top
lefthand corner of the Ettan IPGphor II Control Software application
window or select “Open Protocol Window” from the Protocol dropdown menu.
The Protocol handling dialog will open to allow the user to create an
IEF protocol (Fig 5).
The window will appear with default values of 0 for the rehydration
time, gradient steps, 20 °C for the rehydration and IEF set temperature.
100 Volts, 50 µA and 5 minutes run time are the default settings for step 1.
The values for these parameters can be changed by either using the up
and down buttons
for the field.
to the left of each field or by inserting a new value
To change the time of the step it frequently is quicker to highlight and
enter the desired value by using your keyboard than it is to use the up
and down arrows to change the value.
Fig 5. The Protocol handling dialog.
• p11
Ettan IPGphor II Control Software • protocol handling dialog
Protocol handling dialog: menus and keyboard commands
Drop-down menus at the top left of the Protocol handling dialog can be
accessed by clicking on the selected header to view the drop-down menu
options or can be accessed though the following keyboard commands.
menu bar
Protocol
description
New
Ctrl+N
Creates an “empty” protocol.
Open
Ctrl+O
Opens a protocol from file.
Save
Ctrl+S
Saves captured run data.
Print
Ctrl+P
Prints the current protocol.
Load
Ctrl+L
Loads the current protocol displayed to the Ettan IPGphor II
Isoelectric Focusing Unit.
Load All
Loads retrieved protocols (files 1–10) to the Ettan IPGphor II
Isoelectric Focusing Unit (batch).
Retrieve All
Retrieves all stored protocols (files 1–10) from Ettan
IPGphor II Isoelectric Focusing Unit (batch).
Hide Window
Ctrl+W
Stops and exits the dialog.
Cut
Ctrl+X
Cuts selected text.
Copy
Ctrl+C
Copies selected text.
Paste
Ctrl+V
Pastes text.
Ctrl+F
Allows the user to set the default folder for saved
protocol files.
Edit
Options
Folders
Help
Help
About
Ctrl+F1
Help on use of the software.
Program ID information.
Using the Tab key on the PC allows the cursor to scroll through active or
editable fields. In the Protocol handling dialog, Ctrl+↓ will move the
cursor down into the editable fields then Tab will allow scrolling through
those fields. Ctrl+↑ will move the cursor out of the individual step lines.
Shift+Tab allows the cursor to scroll backwards.
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• creating a new protocol
13. Creating a new protocol
Protocol name
To name a protocol, highlight and delete the words “New protocol” and
then enter the name you wish to identify the file by.
The filename can contain an indefinite number of characters but only the
first 16 characters will be displayed on the Ettan IPGphor II Isoelectric
Focusing Unit display.
For example, the protocol could be identified with the length of the IPG
strip and the pH range that is being run.
Range of parameters allowed for each step
Rehydration time:
Rehydration time can be set from 1 minute to 99 hrs:59 minutes.
Temperature during rehydration:
Temperature during rehydration can be set between 15 °C and 30 °C.
This value can be controlled in 1 °C increments.
µA:
The µA limit of the IEF run can be set from 1 to 200 µA/strip. 50 µA/strip
is the recommended value for IEF for all IPG strips. This value can be
changed from 1–200 µA in 1 µA increments.
Temperature of the run:
Temperature during IEF can be set between 15 °C and 30 °C. This
value can be controlled in 1 °C increments. Since strips are run in high
concentrations of urea, colder temperatures can lead to formation of urea
crystals that block proper focusing. Ideally, IPG strips should be run at
temperatures between 20 °C and 25 °C.
Step/Grad
The two options for the voltage change pattern are “Step”, which sets the
voltage at the selected value for the new step and then holds the voltage
constant for the step duration; and “Gradient,” which increases the voltage linearly with respect to time from the value set in the previous step to
the value set for the current step. If the first step is set in gradient mode,
the voltage will increase starting from 0 Volts.
• p13
Ettan IPGphor II Control Software • creating a new protocol
Voltage:
Note: Depending on the µA limit of the
IEF run, the conductivity of the IPG strip,
rehydration solution and the sample Ettan
IPGphor II Isoelectric Focusing Unit may
not operate at the set maximum voltage.
The voltage of any step may be set from 1–8000 Volts. A value of 0 in
this field will cause the program to end regardless of what values are set
for any subsequent steps.
Hrs/VHrs:
Each step of the protocol can be programmed to run for a specified
number of hours (in hours and minutes) or for a specific number of
VHrs. Volt-hours is the product of the voltage multiplied by the number
of hours for each step.
Each VHrs step may be set from 1–99,999 VHrs. If more than 100,000
VHrs is desired it will have to be split between two steps.
The maximum value for Hours and minutes is 99 hours and 59 minutes.
At least 1 minute or 1 VHr must be programmed for a step or the
program will end at that step regardless of what values are set for any
subsequent steps.
Editing fields
Editing modes for Hrs/VHrs and Step/Gradient
The Hrs/VHrs and Step/Gradient fields each have two options which can
be selected by using the up/down
arrows located to the left of each
field. Alternatively, clicking on one of these fields produces a pop-up
menu, allowing you to select one of the options.
For example: To change the voltage transition mode from gradient to
step-n-hold mode, click in the Step/Grad field you wish to change. A
pop-up menu will appear with the two modes allowed. Select a mode by
holding down the mouse and highlighting the mode desired. Unclick the
mouse and the selected mode will appear in the window.
In the VHrs mode, the dialog will change slightly as the two fields (hrs
and minutes) are not required to program this step. Only the total VHrs
for that step will be entered.
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• creating a new protocol
Editing numbers in the Voltage, Hrs, VHrs and minutes fields.
For fields that require a time or number to be entered, use the up and
down
buttons to the left of the field to change the value 1 digit at a
time. Alternatively, you can highlight and use the keyboard to enter the
desired value.
Saving protocols
Once a protocol is created it can be saved for future reference. To save
a file either click on the
button, use the keyboard shortcut
Ctrl + S or select “Save” from the Protocol drop-down menu. The
default location for the saved files is in the local C directory under
C:\IPGphor\Protocols. The file will be specified by the protocol name
and saved as a custom pattern Excel file (.xls).
If desired, the user can change the default directory by selecting “Folder”
under the Options drop-down menu. The default protocols folder will be
shown. If desired, navigate to the location where files are to be stored
and click on the
button.
Printing Protocols
A protocol may be printed from the Protocol handling dialog. To print a
protocol, either use the keyboard command Ctrl + P or select “Print”
from the Protocol drop-down menu.
A dialog box will appear. Select the printer, the print orientation (Portrait
or Landscape), and the number of copies.
Printer and print orientation selections can be made either by clicking on
the up/down buttons located to the left of the respective fields to scroll
through the available choices, or by clicking in the field to produce a
pop-up menu. Select the number of copies by using the up/down buttons
located to the left of that field.
• p15
Ettan IPGphor II Control Software • creating a new protocol
Opening previously saved protocols
Multiple numbers of protocols can be saved. Once saved protocols can
be recalled either by clicking the
button, by using the keyboard
command Ctrl + O or by selecting “Open” from the Protocol dropdown menu.
Any steps programmed in the current protocol file will be deleted and
the software prompt notifies the user of this action.
If changes to the current protocol do not need to be saved click
and continue. To save any changes to the current protocol,
click
to abort opening the stored protocol. Save the current
protocol before attempting to reopen the stored protocol.
To continue opening a stored protocol select the saved file from the
Protocols folder and click the
button. The stored protocol will
now be displayed in the Protocol handling dialog.
If necessary, make any adjustments to the values in the fields before
proceeding to load the protocol.
Loading protocols
To load the protocol displayed in the Protocol handling dialog first select
a Protocol #. The Protocol # (1–10) chosen here designates the protocol
number on the Ettan IPGphor II Isoelectric Focusing Unit which will be
overwritten by your loaded protocol. Select the Protocol # by using the
up/down buttons located to the left of the field.
To load a protocol, either click the
button select “Load” from the
Protocol drop-down menu or use the keyboard command Ctrl + L. The
software will prompt the user that the protocol occupying that protocol
number on the Ettan IPGphor II Isoelectric Focusing Unit itself will be
overwritten. If this is acceptable, click
to continue.
um 80-6500-47
• p16
• creating a new protocol
A yellow highlighting of the Writing icon indicates the protocol is
being loaded. The IPGphor application window is updated with the
loaded protocol.
If the PC and Ettan IPGphor II Isoelectric Focusing Unit are in communication the protocol will be loaded into the designated protocol number
on the instrument. The display on the Ettan IPGphor II will indicate the
new file name and save the protocol into the protocol number that was
designated when loading.
If the PC and Ettan IPGphor II Isoelectric Focusing Unit are not in proper
communication an error message will appear. Check that the cable
between the Ettan IPGphor II Isoelectric Focusing Unit and the PC is
connected properly. Communication can be confirmed by selecting
“Report” or “ID” from the Run drop-down menu.
Retrieving all preprogrammed IPGphor protocols
Files that exist within the Ettan IPGphor II Isoelectric Focusing Units
memory can be captured to the PC. This allows the archiving of protocols that are no longer frequently used and frees up needed file space on
the Ettan IPGphor II Isoelectric Focusing Unit.
Under the Protocol drop-down menu select “Retrieve all”. A communication window will appear to confirm the action.
Click
to continue to retrieve the files.
The software will indicate it is reading protocols (1–10) by displaying a
message in the top portion of the dialog.
• p17
Ettan IPGphor II Control Software • creating a new protocol
Files are saved under the default protocol folder with the default name:
Instrument protocols, date and time.
A message displayed in the dialog box indicates protocols (1–10) on the
Ettan IPGphor II Isoelectric Focusing Unit are being retrieved.
Once retrieved the user is prompted to save the protocols to disk with a
“Save As…” dialog box. Files are saved within the default protocol folder
with a default name: Instrument protocols date time. The files are stored
as a custom pattern (Excel) text file.
Null protocols retrieved from the Ettan IPGphor II Isoelectric Focusing
Unit (i.e., those lacking any steps) are not saved. In order to be saved to
disk a protocol must contain programmed steps.
If the Ettan IPGphor II Isoelectric Focusing Unit is not in proper communication with the computer, an error message will appear.
Check that the cable between the Ettan IPGphor II Isoelectric Focusing
Unit and the PC is connected properly. Communication can be confirmed
by selecting “Report” or “ID” from the Run drop-down menu.
Loading retrieved Ettan IPGphor II protocols
“Load all” allows the user to reload stored protocols (1–10) to the Ettan
IPGphor II Isoelectric Focusing Unit that have been retrieved as indicated
in the section above. When “Load all” is selected from the Protocol dropdown menu (Protocol handling dialog), the software opens the Protocols
folder on the C drive. Select the instrument protocol set you wish to load.
A message in the top portion of the window indicates the protocols
(1–10) are being loaded and displays the number of lines written to the
Ettan IPGphor II Isoelectric Focusing Unit.
Closing the Protocol handling window
Once a protocol has been loaded, click on the
to close the Protocol handling dialog.
um 80-6500-47
• p18
button
• running a protocol
14. Running a protocol
Once a file has been created and loaded to the Ettan IPGphor II
Isoelectric Focusing Unit the instrument can be controlled by either
using the software or by manually starting the instrument using the
IPGphor keypad.
Prior to starting the software confirm the protocol to be run. The software automatically prepares to run the last protocol loaded (written) to
the instrument. Select the correct protocol # to run by confirming the
protocol on the Ettan IPGphor II Isoelectric Focusing Unit display. If the
correct protocol is not on the display, use the Ettan IPGphor II Isoelectric
Focusing Unit keypad or use the up/down button located to the left of the
# field to select the desired protocol.
Adjusting the log file data capture time
The time interval that data is captured from the Ettan IPGphor II Isoelectric Focusing Unit can be adjusted by changing the Update interval on the
IPGphor application window. Use the up/down button to adjust the interval or click on the time field and select one of the time options with the
pop-up menu.
You can also adjust the interval by selecting
“Graph update interval” from the Options
drop-down menu. Allowed intervals are 1,
2, 3, 4, 5, 10, 15, 20, 25 and 30 minutes.
For long runs it is recommended to set the
interval for at least 10 minutes to avoid
Instrument log data printouts that are many
pages long.
Once everything has been properly set, the
software can be used to control the Ettan
IPGphor II Isoelectric Focusing Unit.
Note: Pressing Start on the Ettan IPGphor II
Isoelectric Focusing Unit causes the software
to automatically save the data displayed in
the application window. The file is saved in
the default directory with the name of the
protocol, the date and the time the file was
saved. For example:
Starting a run
To start the Ettan IPGphor II Isoelectric Focusing Unit either click the
button in the application window, select “Start” from the Run
drop-down menu, use the keyboard command Ctrl + 1 or press Start on
the Ettan IPGphor II Isoelectric Focusing Unit.
18 cm 6–11 05.15.2003 03.54.59 PM.txt).
To avoid autosaving the data, start the Ettan
IPGphor II Isoelectric Focusing Unit using
the software. The software prompts the user
to select whether the displayed data should
be deleted.
• p19
Ettan IPGphor II Control Software • running a protocol
Old file logs from the last run are deleted prior to the instrument
starting the run. The software notifies the user of this action.
The instrument prompts the user to indicate how many IPG
strips will be run.
The indicator icon for Run changes to green when the run has
been started.
Note: If communication between the PC and
the Ettan IPGphor II Isoelectric Focusing Unit
is broken the software will not recognize
communication error but will no longer be
collecting the data output from the instrument. Check the connections. Once connection is reestablished, the software will
continue collecting data. Closing the program
is not necessary.
Note: In the event of a power failure the software cannot collect data from the Instrument
and the data will not be recoverable.
um 80-6500-47
• p20
The Ettan IPGphor II Isoelectric Focusing Unit display shows the run has
started and the red HV light turns on.
While the run is starting the Instrument Log displays the instrument ID,
the firmware version, the name of the protocol, and the programmed
steps of the protocol. Data is collected at time 0, at the occurrence of a
step change, and at the desired time interval that has been set prior to the
run. The update interval can be adjusted during the run but previous data
points cannot be deleted or added.
The graph will be updated as data points are collected and the x and y
axis scale will change as the run progresses.
• running a protocol
To pause the protocol either click the
button on the application
window, select “Pause” from the Run drop-down menu, use the keyboard command Ctrl + 2 or press the Stop button on the Ettan IPGphor
II Isoelectric Focusing Unit control panel. The indicator icon for Pause
changes to green while the Ettan IPGphor II Isoelectric Focusing Unit is
in pause mode and the red HV light on the Ettan IPGphor II Isoelectric
Focusing Unit turns off.
To stop the protocol either click the
button on the application
window, select “Stop” from the Run drop-down menu, use the keyboard
command Ctrl + 3 or press the Stop button twice on the Ettan IPGphor II
Isoelectric Focusing Unit control panel. Both the Run and Pause indicator
icons darken and the red HV light on the Ettan IPGphor II Isoelectric
Focusing Unit turns off.
Monitoring the run
Note: Additional data points can be collected
while the unit is running by selecting the
“Report” from the drop-down menu. However
collecting multiple data points over a 1 minute
interval may result in multiple y values on the
same plot.
As the run progresses, the Ettan IPGphor II Isoelectric Focusing Unit
conditions are recorded in the Instrument log window and the data
points graphed in real time. The user may scroll through the log file
values by using the scroll bar to the right of the log window.
Step markers
The Step markers button functions to indicate where a step transition has
occurred (e.g. changing from step 1 to step 2, etc.). To mark where the
steps have occurred, click the button so that the green indicator is on.
To return to uniform vertical gridline marks along the x axis click the
button so that the indicator is darkened .
• p21
Ettan IPGphor II Control Software • capturing run data
15. Capturing run data
Storing log files
The log of a file can be stored and recalled for future reference. To store a
log file, select “Save” from the Logfile drop-down menu. The default filename is the date and time (e.g. 05.02.2003 01.59.43 PM) but this can be
edited. The default location for the saved file is C:\IPGphor\Logfiles. These
files can be reloaded into the software at any time to view data and graphs.
Printing log files and graphs
To print the log file only, select “Print” from the Logfile drop-down menu
or use the keyboard command Ctrl + P.
To print the graph only, select “Print Graph” from the Logfile drop-down
menu or use the keyboard command Ctrl + G*.
To print the log file and the graph, select “Print All” from the Logfile
drop-down menu or use the keyboard command Ctrl + A*.
A dialog box will appear. Select the printer, the print orientation (Portrait
or Landscape), and the number of copies.
Printer and print orientation selections can be made either by clicking on
the up/down buttons
located to the left of the respective fields to
scroll through the available choices, or by clicking in the field to produce
a pop-up menu. Select the number of copies by using the up/down
buttons located to the left of that field.
Exporting the log files to Excel
To export the log files to Excel either select “Export” from the Logfile
drop-down menu or use the keyboard command Ctrl + E.
When opening in Excel, keep the default values (Delimited, Delimiters =
Tab, Text Qualifier = “ and Column data = General).
*The size of the graph printed is dependent on the size the
graph is viewed onscreen. To enlarge the graph either
expand or maximize the Logfile window.
um 80-6500-47
• p22
• exiting the software
16. Exiting the software
Note: Before exiting the Ettan IPGphor II
Control Software make sure that all data
collected has been saved, printed or exported.
Closing the software will result in the loss of
unsaved data.
To close the program, either select “Exit” from the Logfile drop-down
menu, use the keyboard command Ctrl + Q or press the X button in the
top right corner of the window. When the software is closed a dialog box
appears to confirm whether the program should be exited.
If the instrument is in run mode a different dialog box will appear.
When OK is clicked, a second dialog box requesting the user to stop the
Ettan IPGphor Isoelectric Focusing Unit appears. Click
to
stop the unit and continue exiting.
• p23
Ettan IPGphor II Control Software • troubleshooting
17. Troubleshooting
Note: If communication between the PC and
the Ettan IPGphor II Isoelectric Focusing Unit
is broken the software will not recognize a
communication error but will no longer be
collecting the data output from the instrument. Check the connections. Once connection is reestablished, the software will
continue collecting data. Closing the program
is not necessary.
Note: In the event of a power failure the software cannot collect data from the Instrument
and the data will not be recoverable.
Printing seems to hang when using the control software:
• Network printer was selected and the computer is not logged into the network.
Log in, or if printing is no longer required press Cancel until the login dialog
box disappears.
Cannot monitor through a web browser
• Only one Ettan IPGphor II Control Software copy can be monitored from a
remote web browser. From the server computer go to the Option menu and
Enable or Disable the Webserver as necessary. Restart the correct Ettan II
IPGphor Software copy that correlates to the Ettan IPGphor II Isoelectric Focusing Unit to be monitored. Software copies are denoted by IPGphor(x) where (x)
is the number (1– 4) assigned to the Ettan IPGphor II Isoelectric Focusing Units
being monitored.
• If a proxy server is used right click on Internet Explorer and select “Internet
Options” under the Tools drop-down menu. Select the Connection tab. Select
LAN settings. Mark bypass proxy server for local addresses or contact your
network administrator. The viewer will only work within a firewall.
Communication error:
• Check that the Ettan IPGphor II Isoelectric Focusing Unit is switched on.
• Check that the serial cable is properly connected to the PC and the Ettan
IPGphor II Isoelectric Focusing Unit.
• Check to see that no other program is trying to access the communication port.
Close all programs that may be accessing the COM port.
um 80-6500-47
• p24
• ordering information
Ordering information
product
quantity
code number
Ettan IPGphor II Isoelectric Focusing Unit
Basic unit. Order strip holders separately
1
80-6505-03
Fuses, 1.6 A, 250V, 5 × 20 mm
5
80-6108-69
Cable Serial 9 Pin F/F with Null Modem Adapter
1
80-6506-36
Ettan IPGphor II Control software
1
80-6506-55
7 cm
2
80-6455-44
11 cm
2
80-6455-63
13 cm
2
80-6455-82
18 cm
2
80-6456-01
24 cm
2
80-6479-76
7 cm, complete
6
80-6416-11
11 cm, complete
6
80-6416-30
13 cm, complete
6
80-6416-49
18 cm, complete
6
80-6416-68
24 cm, complete
6
80-6469-88
7 cm, complete
1
80-6416-87
11 cm, complete
1
80-6417-06
13 cm, complete
1
80-6417-25
18 cm, complete
1
80-6417-44
24 cm, complete
1
80-6470-07
Manifold Kit
1
80-6498-38
7–18 cm
1
80-6371-84
7–24 cm
1
80-6465-32
Strip Holder Covers
Strip Holders for use with Immobiline DryStrip gels
Immobiline DryStrip Reswelling Trays
IPG Buffer
pH 4–7
1 ml
17-6000-86
pH 3–10 L
1 ml
17-6000-87
pH 3–10 NL
1 ml
17-6000-88
pH 3.5–5.0
1 ml
17-6002-02
pH 4.5–5.5
1 ml
17-6002-04
pH 5.0–6.7
1 ml
17-6002-05
pH 5.5–6.7
1 ml
17-6002-06
pH 6–11
1 ml
17-6001-78
Rehydration Solutions
DeStreak Rehydration Solution
1 ml
17-6003-19
DeStreak Reagent
5 × 3 ml
17-6003-18
• p25
Ettan IPGphor II Control Software • ordering information
product
quantity
code number
Ettan preparation kits and reagents
2-D Fractionation Kit
10 preps
80-6501-04
Albumin and 1gG Removal Kit
10 preps
RPN6300
Protease Inhibitor
1 ml
80-6501-23
Nuclease Mix
0.5 ml
80-6501-42
Thiourea
100 g
RPN6301
Iodoacetamide
25 g
RPN6302
Sample Grinding Kit
50 samples
80-6483-37
2-D Clean-Up Kit
50 samples
80-6484-51
SDS-PAGE Clean-Up Kit
50 samples
80-6484-70
2-D Quant Kit
500 assays
80-6483-56
Mini Dialysis Kit, 1 kDa cut-off, 250 µl
1
80-6483-75
Mini Dialysis Kit, 1 kDa cut-off, 2 ml
1
80-6483-94
Mini Dialysis Kit, 8 kDa cut-off, 250 µl
1
80-6484-13
Mini Dialysis Kit, 8 kDa cut-off, 2 ml
1
80-6484-32
500 g
1g
17-1319-01
17-1314-01
PlusOne™ reagents
Urea
CHAPS
Triton™ X-100
500 ml
17-1315-01
Dithiothreitol (DTT)
1g
17-1318-01
Bromophenol Blue
10 g
17-1329-01
Immobiline DryStrip Cover Fluid
1000 ml
17-1335-01
Immobiline DryStrip gels
7 cm
pH 4–7
12
17-6001-10
pH 3–10
12
17-6001-11
pH 3–10NL
12
17-6001-12
pH 6–11
12
17-6001-94
11 cm
pH 4–7
12
18-1016-60
pH 3–10
12
18-1016-61
pH 6–11
12
17-6001-95
13 cm
pH 4–7
12
17-6001-13
pH 3–10
12
17-6001-14
pH 3–10NL
12
17-6001-15
pH 6–11
12
17-6001-96
18 cm
um 80-6500-47
• p26
pH 4–7
12
17-1233-01
pH 3–10
12
17-1234-01
pH 3–10NL
12
17-1235-01
pH 3.5–4.5
12
17-6001-83
pH 4.0–5.0
12
17-6001-84
pH 4.5–5.5
12
17-6001-85
pH 5.0–6.0
12
17-6001-86
pH 5.5–6.7
12
17-6001-87
pH 6–9
12
17-6001-88
pH 6–11
12
17-6001-97
• ordering information
product
quantity
code number
pH 3.5–4.5
12
17-6002-38
pH 4.0–5.0
12
17-6002-39
pH 4.5–5.5
12
17-6002-40
pH 5.0–6.0
12
17-6002-41
pH 5.5–6.7
12
17-6002-42
pH 3–7 NL
12
17-6002-43
pH 3–10
12
17-6002-44
pH 3–10 NL
12
17-6002-45
pH 4–7
12
17-6002-46
pH 6–9
12
17-6002-47
Cleaning solution, IPGphor Strip Holder
950 ml
80-6452-78
2-D Electrophoresis Principles and Methods
1
80-6429-60
24 cm
Equilibration tube set for 24 cm IPG Strips
12
80-6467-79
IEF electrode strips
100
18-1004-40
• p27
Ettan, Immobiline, IPGphor, and PlusOne are
trademarks of Amersham Biosciences Limited.
Amersham and Amersham Biosciences are trademarks
of Amersham plc.
MicroSoft, Windows SE, Excel, Windows NT, and
Internet Explorer are either registered trademarks or
trademarks of Microsoft Corporation in the United
States and/or other counties.
Triton is a trademark of Union Chemicals and
Plastics Co.
© Amersham Biosciences Corp. 2003—
All rights reserved.
All goods and services are sold subject to the terms
and conditions of sale of the company within the
Amersham Biosciences group that supplies them.
A copy of these terms and conditions is available
on request.
Printed in the USA
www.amershambiosciences.com
Amersham Biosciences UK Limited
Amersham Place, Little Chalfont,
Buckinghamshire, England HP7 9NA
Amersham Biosciences AB
SE-751, 84 Uppsala, Sweden
Amersham Biosciences Corp.
800 Centennial Avenue, PO Box 1327,
Piscataway, NJ 08855 USA
Amersham Biosciences Europe GmbH
Munzinger Strasse 9, D-79111, Freiburg, Germany
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