Bio-Plex Manager MP Software Getting Started Guide Version 1.0

Bio-Plex Manager MP Software Getting Started Guide Version 1.0
Bio-Plex Manager™ MP Software
Getting Started Guide
Version 1.0
Bio-Plex Manager™ MP
Software
Getting Started Guide
Version 1.0
10032064 Rev A
Bio-Rad Technical Support Department
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Fax:
1-510-741-5802
Email:
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Web:
www.consult.bio-rad.com
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without notice. Although prepared to ensure accuracy, Bio-Rad assumes no liability for errors or omissions, or for
any damage resulting from the application or use of this information.
Luminex, MAGPIX, and xPONENT are trademarks of Luminex Corporation. Windows and Excel are trademarks of
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The Bio-Plex suspension array system includes fluorescently labeled microspheres and instrumentation licensed to
Bio-Rad Laboratories, Inc. by the Luminex Corporation.
Copyright © 2013 by Bio-Rad Laboratories. All rights reserved.
Table of Contents
Chapter 1 Installing and Preparing Your System . . . . . . . . . . . . . . . . .5
Required Materials . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Setting up your MAGPIX Instrument and Computer. . . . . . . . . . . . . . . . . . . . . . . . 6
Differences Between Bio-Plex Manager MP and xPONENT . . . . . . . . . . . . . . . . . 7
Next Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Chapter 2 An Overview of Bio-Plex Manager MP . . . . . . . . . . . . . . . . .9
Run the Daily Start Up Routine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Create the Protocol. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Run the Protocol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Analyze Your Data in Bio-Plex Manager 6.x . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Run the Shut Down Routine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Chapter 3 Analyzing Your Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .27
Exporting Your Data from the Analyze/Export View . . . . . . . . . . . . . . . . . . . . . . . 27
Optimizing the Standard Curve in Bio-Plex Manager 6.x . . . . . . . . . . . . . . . . . . . 29
Analyzing Your Data Using Other Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
Chapter 4 Maintaining the MAGPIX Instrument . . . . . . . . . . . . . . . . .33
Daily Maintenance. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Weekly Maintenance. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Cleaning the Sample Probe . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
MAGPIX Maintenance. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
Getting Started Guide | iii
Table of Contents
Appendix A License Activation . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
Activating the Bio-Plex Manager MP License . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
Activating the License Online . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
Activating the License through Technical Support . . . . . . . . . . . . . . . . . . . . . . . . 39
Generating the Credentials File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
Activating the Software with a License File . . . . . . . . . . . . . . . . . . . . . . . . . . 42
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1 Installing and Preparing
Your System
This chapter gives you an overview of how to get your MAGPIX instrument and your
computer installed and prepared for use.
Required Materials
You will need the following materials to complete setting up the MAGPIX instrument.
Material
Where to find it
Probe height adjustment plate
Bio-Plex Manager™ MP software box
Well strip
Calibration kit or performance verification
kit
Reagent block
Accessory tray in the MAGPIX shipping
crate
Calibration kit
(catalog #171-213001)
These two kits are shipped separately.
Performance verification kit
(catalog #171-213002)
Note: The location for the materials applies to the new MAGPIX users.
You will also need the following materials for daily maintenance of the MAGPIX
instrument:

70% ethanol or isopropanol

10% bleach

Distilled or deionized water

0.1N NaOH
Getting Started Guide
|
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1 |
Installing and Preparing Your System
Setting up your MAGPIX Instrument and Computer
To set up your MAGPIX instrument and computer
1.
Follow the instructions for your situation:

You just purchased the MAGPIX instrument from Bio-Rad.
Follow the instructions in the Computer and MAGPIX Assembly
Instructions (part #10020326) that are included in the MAGPIX shipping
crate.

You were using the xPONENT software to run the MAGPIX instrument
and you now want to use the Bio-Plex Manager MP software.
Follow the instructions on the Bio-Plex Manager MP software folder to
install the software. Next, follow the instructions in Appendix A to activate
your software.
2.
Start Bio-Plex Manager MP and complete the steps in the Setup MAGPIX
wizard.
When you start the software for the first time, the Setup MAGPIX wizard is
automatically launched. The wizard walks you through the steps of completing
the preparation of your instrument, including adjusting the probe height,
importing the calibration and verification kits, and running the maintenance
routines.
Adjusting the Probe Height — Bio-Plex Manager MP simplifies and
automates this procedure. With the push of a single button, the routine sets the
probe for the most common plate types.
Complete the steps in this wizard before you use Bio-Plex Manager MP to run
the instrument.
Note: You can always return to the wizard at a later time to complete the
setup. You launch the wizard from the Instrument menu by clicking Setup
MAGPIX.
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Bio-Plex Manager MP Software
Differences Between Bio-Plex Manager MP and xPONENT
Differences Between Bio-Plex Manager MP and
xPONENT
If you have used xPONENT software with MAGPIX, there are some differences in
how Bio-Plex Manager MP software works that you should be aware of:

Adjusting probe height — adjusting the probe height is simple and
reproducible. The software uses the probe height adjustment plate to set
the probe height for the two locations in the off-plate reagent area and four
heights for consumables. These settings cover most consumables. The
height used in the four settings is indicated on the probe height adjustment
plate and in the Bio-Plex Manager MP User Guide.

Start-of-day maintenance — run the Daily Start Up routine at the
beginning of each day. With Bio-Plex Manager MP, you do not have to
keep track of whether the instrument requires calibration and verification or
only verification on any given day. The software ensures that the correct
routines are run each day. The Daily Start Up routine also runs additional
fluidics routines if the instrument has been idle for some time.

Recommended routines — the software always recommends a routine if
it is required for the proper running of the instrument. There may be times
when a recommended routine requires additional steps; follow these steps.
Next Steps
After you have completed the Setup MAGPIX wizard, continue with Chapter 2, An
Overview of Bio-Plex Manager MP.
Getting Started Guide |
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1 |
Installing and Preparing Your System
8
Bio-Plex Manager MP Software
|
2 An Overview of
Bio-Plex Manager MP
Bio-Plex Manager™ MP Quick Guide
1
Run Daily Start Up at the start of each day.
1. Navigate to the Maintenance view.
2. Follow the instructions in the application window.
3. Click Start.
2
Create and run your protocols.
1. Navigate to the Create/Run Protocols view.
2. Click New in the toolbar.
3. Click Run in the toolbar to run the protocol
4. Save the protocol to reuse it later.
3
Export and analyze your results.
Export your results. Use Bio-Plex Manager 6.x to analyze your data.
4
Run Shut Down at the end of each day.
1. Navigate to the Maintenance view.
2. Select the Shut Down routine.
3. Follow the instructions in the application window.
4. Click Start.
Getting Started Guide
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2 |
An Overview of Bio-Plex Manager MP
Run the Daily Start Up Routine
To run the Daily Start Up routine
1.
Start Bio-Plex Manager MP software.
Bio-Plex Manager MP opens to the Maintenance view. From the Maintenance
view, you run the routines required to keep the MAGPIX instrument in good
working order. Bio-Plex Manager MP keeps track of the status of the
instrument so you do not have to remember which routines need to be run each
day.
2.
Start each day by running the routine in the Recommended Routine section. On
most days, this is the Daily Start Up routine.
Note: The software monitors the instrument and schedules the running of
the calibration and verification routines, as well as other
performance-related routines. These routines are included as part of the
Daily Start Up routine.
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Run the Daily Start Up Routine
In the Maintenance view, the Reagent Block section provides information on
filling the reservoirs and wells with the appropriate liquids and reagents. Click
the Description arrow to display or hide a brief explanation of the routine.
Recommended Routine
Reagent Block
Description of routine
Getting Started Guide
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2 |
An Overview of Bio-Plex Manager MP
After the routine has been successfully run, None is displayed indicating that
maintenance of the instrument is up to date.
Note: There may be times when you have to run more than one recommended
routine before maintenance is up to date. For example, Enhanced Maintenance
may be displayed as the recommended routine if calibration or verification fails.
After the Enhanced Maintenance routine is successfully completed, Daily Start
Up is displayed in the Recommended Routine section. Run the recommended
routines until None is displayed.
Tip: If calibration, verification, or both routines fail after successive attempts,
contact Bio-Rad Technical Support for assistance.
None is displayed when maintenance is up to date
The maintenance of the MAGPIX instrument is up to date and you can now create
and run your protocols.
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Create the Protocol
Create the Protocol
To create the protocol
1.
Click Create/Run Protocols in the navigation bar to open the Create/Run
Protocols view.
From this view, you create and run your protocols.
Create/Run Protocols
Getting Started Guide
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2 |
An Overview of Bio-Plex Manager MP
2.
Click New in the toolbar to open the protocol dialog box.
You create your protocols in the protocol dialog box. You click each of the
buttons in the navigation bar to select the analytes, format the plate, and define
the standards used.
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Create the Protocol
3.
Click Select Analytes in the protocol dialog box to choose your assay panel and
select your analytes.
You select the assay panel from the Assay Panel dropdown list. Once you make
your selection, the pane is populated with a list of the analytes in the panel.
Assay Panel
list
Select Analytes
Getting Started Guide
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2 |
An Overview of Bio-Plex Manager MP
Select the analytes you want displayed in your results. The assay you purchased
may include only a subset of the possible analytes. Refer to the product literature for
a list of the included analytes.
There may be times when your assay includes analytes from two or more assay
panels. You can combine analytes from multiple assay panels using the Manage
Assay Panels feature.
Manage Assay Panels
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Create the Protocol
4.
Click Format Plate to specify the types of wells in your plate.
Click the button in the toolbar to select the type of sample, then click the
squares in the template to format your wells with that sample type.
Blank
Control
Standard
Unknown
Autofill buttons
Format Plate
You can easily create replicate groups or format multiple wells at one time using
the Autofill buttons. For more information on these features, see the online help
for the software.
Getting Started Guide
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2 |
An Overview of Bio-Plex Manager MP
5.
Click Standards Info to choose the standard lot you are using with your
experiment.
You select the standard lot you are using with your panel from the Standard Lot
list and specify the dilution factor.
Note: You will not be able to specify the standards information until you select
your analytes and format your plate with standard wells. If the fields on the
pane are disabled, return to the Select Analytes pane and verify that you
selected one or more analytes, and return to the Format Plate pane and verify
that you have formatted at least one standard well.
Standard Lot
list
Standards Info
6.
If the predefined standard lots do not meet your needs, you can create new
standard lots or customize existing standard lots:

18
You can import a standard lot or make changes to existing standard lots
with the Manage Standard Lots button.
| Bio-Plex Manager MP Software
Create the Protocol

If the standards information is not available for your standard lot or you
want to use custom values, then you must create a new standard lot. You
do this with the New Standard Lot button.
New Standard Lot
Manage Standard Lots
You have completed your protocol definition and you are now ready to run the
protocol.
Getting Started Guide
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2 |
An Overview of Bio-Plex Manager MP
Run the Protocol
To run the protocol
1.
Click Create/Run Protocols to go to the Create/Run Protocols view.
2.
Click Start in the toolbar to open the Run Settings dialog box.
Start
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Run the Protocol
3.
Specify the settings for your run in the Run Settings dialog box.
Select the type of plate you are using in the Plate Type field. Refer to the table
below for the description of the supported plate types.
4.
Plate Type
Compatible Consumable
Flat bottom
plate
Bio-Plex Pro™ flat bottom plate (black plate comes
with Bio-Plex Pro assays, catalog #171-025001)
Filter plate
Millipore multiscreen plate (for example,
MSBVN1210)
PCR plate
Bio-Rad low-profile unskirted PCR plate (for
example, MLL-9601)
Auxiliary plate
Nunc PolySorp (for example, 475094), Nunc
MaxiSorp (for example, 445105)
(Optional) Specify a pre-run routine and a post-run routine.
Note: Bio-Rad recommends running the Wash Between Plates routine
between protocol runs. This is the default setting for Post-Run Routine.
5.
Click Create/Run Protocols.
Getting Started Guide
|
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An Overview of Bio-Plex Manager MP
Bio-Plex Manager MP populates the Create/Run Protocols view with the
results.
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Run the Protocol
If there are errors in your experiment, the wells with the error display a warning
symbol and the table displays a warning symbol for the analytes. Click the
Alerts icon to display information about the error. If a warning icon appears in
the status bar, then maintenance is out of date.
Wells with low
bead count
Instrument alerts
Analytes with
low bead count
Maintenance
out of date
Getting Started Guide
|
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2 |
An Overview of Bio-Plex Manager MP
Analyze Your Data in Bio-Plex Manager 6.x
You create and run your protocols in Bio-Plex Manager MP and you analyze your
data in Bio-Plex Manager 6.x. To analyze your data you first export the result to a
file.
Note: Analysis of Bio-Plex Manager MP results is supported only with
Bio-Plex Manager 6.0 or higher. Earlier versions of Bio-Plex Manager are not
supported.
To analyze your data
1.
After you run your protocol, click Export Results to analyze your results in
Bio-Plex Manager 6.x.
Export Results
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Analyze Your Data in Bio-Plex Manager 6.x
2.
Follow the prompts to save your results to a file.
After the file is saved, Bio-Plex Manager MP prompts you to open
Bio-Plex Manager 6.x to analyze your results. (You will see this prompt only if
Bio-Plex Manager 6.x is installed on your computer.)
For more information on analyzing your results, see Chapter 3, Analyzing Your
Data.
Getting Started Guide
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2 |
An Overview of Bio-Plex Manager MP
Run the Shut Down Routine
When you are done for the day, return to the Maintenance view and run the Shut
Down routine.
Shut Down routine
The Shut Down routine cleans the fluidics lines and prevents the buildup of
debris within the system. Bio-Rad recommends you run this routine each day
you use the MAGPIX system to maintain your instrument.
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3 Analyzing Your Data
You must first export your data to a file. Then this data file can be analyzed in
Bio-Plex Manager™ 6.x or other analysis software.
Exporting Your Data from the Analyze/Export View
You can analyze your data immediately after running your protocol using the Export
Results command as described in this chapter. Or you can return at a later time and
export your results from the Analyze/Export view into Bio-Plex Manager 6.x.
To export your result from the Analyze/Export view
1.
Click Analyze/Export to navigate to the Analyze/Export view.
The result from each run is stored in the run results table. You can return to this
view at any time and export your results to Bio-Plex Manager 6.x
Analyze/
Export view
Getting Started Guide
| 27
3 |
Analyzing Your Data
2.
Select the result you want to export and click Export Results.
3.
Follow the prompts to save your results to a file.
4.
Bio-Plex Manager MP prompts you to open Bio-Plex Manager 6.1 (or whatever
version of the software is installed on your machine) to analyze your results.
Click Yes.
Bio-Plex Manager 6.x displays the results.
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Optimizing the Standard Curve in Bio-Plex Manager 6.x
Optimizing the Standard Curve in Bio-Plex Manager 6.x
After you open your results in Bio-Plex Manager 6.x, follow these steps to optimize
your results.
To optimize the standard curve
1.
Click Standard Curve in the navigation bar.
Standard Curve
Getting Started Guide
|
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3 |
Analyzing Your Data
2.
Select “Apply across all analytes” and click Optimize.
Optimize
Apply across
all analytes
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| Bio-Plex Manager MP Software
Optimizing the Standard Curve in Bio-Plex Manager 6.x
3.
Review the optimization report and identify any analytes for which there are
comments or that have not been successfully optimized.
It will be difficult to generate meaningful results if many of your unknowns do
not fall within the usable range of the curve, that is, between the lower limit of
quantitation (LLOQ) and the upper limit of quantitation (ULOQ). Values between
the LLOQ and background fluorescence and values above the ULOQ can be
interpreted qualitatively.
Getting Started Guide
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3 |
Analyzing Your Data
Analyzing Your Data Using Other Software
You can export your data to other applications to group biological replicates for
further analysis.
To analyze your data
1.
Click Report Table in the navigation bar.
2.
Click “Export results to Bio-Plex Data Pro” to view your results in
Bio-Plex Data Pro™, or click Export Report Table to view your results in
Microsoft Excel.
Report Table
Export results to Bio-Plex Data Pro
Export Report Table
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4 Maintaining the MAGPIX
Instrument
This chapter describes the periodic maintenance that must be performed on the
MAGPIX instrument to keep it working according to the manufacturer’s
specifications.
Daily Maintenance
Each day you use the MAGPIX instrument, perform these maintenance tasks:

At the beginning of the day — at the beginning of each day you use the
instrument, run the recommended routine. Check the Recommended
Routine section in the Maintenance view. On most days this is the Daily
Start Up routine.

At the end of the day — at the end of each day you use the instrument,
run the Shut Down routine.
Weekly Maintenance
Clean the sample probe once a week to keep it free of any debris. Whenever you
remove the sample probe from the probe assembly, you must recalibrate the probe
before you read another plate. Therefore, cleaning the sample probe must always
be followed up with running the Adjust Probe Height maintenance routine.
Getting Started Guide
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4 |
Maintaining the MAGPIX Instrument
Cleaning the Sample Probe
To clean the sample probe
1.
Turn off the MAGPIX instrument and unplug the power cord.
2.
Remove the sample probe.
3.
Use either or both methods to clean the sample probe:

Bath sonicator — place the tip of the sample probe in the bath sonicator
for 2–5 min.

10 ml syringe — force distilled water through the tip of the sample probe to
its large end.
4.
Replace the sample probe. Screw the black fitting on top of the sample probe
until it clicks.
5.
From the Maintenance view, run the Adjust Probe Height procedure.
Adjust Probe Height
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MAGPIX Maintenance
MAGPIX Maintenance
Within the first year of use, Bio-Rad recommends that you perform the 6-month and
12-month maintenance. The maintenance kits are:

Bio-Plex® MAGPIX™ 6-Month Preventive Maintenance Kit — cleans the
air filters and replaces the syringe seals (catalog #171-012010).

Bio-Plex MAGPIX 12-Month Preventive Maintenance Kit — replaces the
sample probe tube and the drive fluid filter (catalog #171-012012).
Getting Started Guide |
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4 |
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Maintaining the MAGPIX Instrument
| Bio-Plex Manager MP Software
A License Activation
To have access to all of the features of Bio-Plex Manager™ MP software, you must
activate the product with a valid product license. You will need a separate license
for each computer on which you install Bio-Plex Manager MP.
Note: If you purchased a new MAGPIX instrument, the computer included with
the instrument comes with the software already activated. Therefore, you can
skip this step.
Activating the Bio-Plex Manager MP License
You can activate the product either online (if you have access to the Internet) or
through Technical Support (if you do not have Internet access).
Note: To activate your license, you will need the product activation code,
which can be found in the Bio-Plex Manager MP CD folder.
Activating the License Online
Follow the procedure below if the computer on which Bio-Plex Manager MP is
installed has an Internet connection. With this method, the software uses your
activation code to automatically activate your software.
To activate Bio-Plex Manager MP online
1.
Start the Bio-Plex Manager MP software.
Getting Started Guide
| 37
A |
License Activation
2.
If the product license has not been activated, the Product Activation Required
window appears.
3.
Select Activate Bio-Plex Manager MP Online and click Continue.
4.
Enter your activation code in the text box and click Activate.
Note: The activation code can be found in the CD folder.
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Activating the License through Technical Support
The Activation Successful window appears confirming that the software has
been activated.
5.
Click OK to exit the activation software and start Bio-Plex Manager MP.
Activating the License through Technical Support
If the computer on which Bio-Plex Manager MP is installed does not have an
Internet connection, you can request a product license from Bio-Rad Technical
Support to activate the software. This is a two-phase process:
1.
Generate a credentials file and email it to Technical Support.
Technical Support uses the credentials file to generate a license and emails the
file back to you.
2.
Use the license file to activate your software.
The procedures that follow describe this two-phase process.
Getting Started Guide
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39
A |
License Activation
Generating the Credentials File
To generate the credentials file
40
1.
Start the Bio-Plex Manager MP software.
2.
If the product license has not been activated, the Product Activation Required
window appears.
3.
Select Activate Bio-Plex Manager MP through Technical Support and click
Continue.
| Bio-Plex Manager MP Software
Activating the License through Technical Support
4.
Select Send credentials to Technical Support and click Continue.
5.
Enter your activation code in the text box and click Save.
Note: The activation code can be found in the CD folder.
6.
In the Save Licensing Credentials to a File dialog box, enter the name of the file
and click Save.
Getting Started Guide
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41
A |
License Activation
The File Successfully Saved window appears with instructions on how to send
the credentials file to Technical Support.
7.
Move the credentials file to a computer where you can send email, and email
the file to Bio-Rad Technical Support ([email protected]).
Activating the Software with a License File
Technical Support will generate a file with the license and email the file to you. When
you receive the email, transfer the file to the computer where Bio-Plex Manager MP
is installed. The file can be copied to a local hard drive, flash drive, or network drive.
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Activating the License through Technical Support
To activate Bio-Plex Manager MP with the license file
1.
Start the Bio-Plex Manager MP software.
2.
In the Product Activation Required window, select Activate Bio-Plex Manager
through Technical Support and click Continue.
3.
Select “Import license file and activate product” and click Continue.
Getting Started Guide
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A |
License Activation
4.
Click Activate.
5.
Navigate to where the license file is located, select the file, and click Open.
The Activation Successful window appears confirming that the software has
been activated.
6.
44
Click OK to exit the activation software and start Bio-Plex Manager MP.
| Bio-Plex Manager MP Software
Bio-Rad
Laboratories, Inc.
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Czech Republic 420 241 430 532 Denmark 44 52 10 00 Finland 09 804 22 00 France 01 47 95 69 65
Germany 089 31 884 0 Greece 30 210 9532 220 Hong Kong 852 2789 3300 Hungary 36 1 459 6100
India 91 124 4029300 Israel 03 963 6050 Italy 39 02 216091 Japan 03 6361 7000 Korea 82 2 3473 4460
Mexico 52 555 488 7670 The Netherlands 0318 540666 New Zealand 64 9 415 2280 Norway 23 38 41 30
Poland 48 22 331 99 99 Portugal 351 21 472 7700 Russia 7 495 721 14 04 Singapore 65 6415 3188
South Africa 27 861 246 723 Spain 34 91 590 5200 Sweden 08 555 12700 Switzerland 026 674 55 05
Taiwan 886 2 2578 7189 Thailand 800 88 22 88 United Kingdom 020 8328 2000
Life Science
Group
10032064 Rev A
US/EG
13-0781
0413
Sig 1212
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