User Bulletin
ABI PRISM®310 Genetic Analyzer
November 28, 2001
SUBJECT: ABI PRISM 310 Data Collection Software, v2.0 and v2.1:
Installation and Setup
Introduction
Overview The ABI PRISM®310 Data Collection software has been upgraded as
described in the table below.
Note The 310 Data Collection software v2.0 and v2.1 upgrades are for the
Macintosh® operating system only.
This user bulletin briefly describes these new features and provides
installation procedures for 310 Data Collection software v2.0 and v2.1.
For more information, please review the “About the 310 Data
Collection” file provided with the software at the time of installation.
Upgrade
Version New Feature Analysis Software
Affected
v2.0 and v2.1 Supports rapid sequencing
with POP-4™polymer ABI PRISM®DNA
Sequencing Analysis
software
v2.1 only Supports five-dye chemistry
for high-throughput
fragment analysis
ABI PRISM®GeneScan®
Analysis software
Page 2 of 28 ABI PRISM 310 Data Collection Software, v2.0 and v2.1: Installation and Setup
In This User
Bulletin The following topics are covered in this user bulletin:
Topic See Page
Installing 310 Data Collection Software v2.0 or v2.1 3
Installing the New Basecaller and Mobility Files 10
Setting Preferences in the 310 Data Collection Software 12
Troubleshooting the Installation 21
Using POP-4 Polymer for Rapid Sequencing (Sequencing
Analysis Software) 21
Using Five-Dye Chemistry (GeneScan Analysis Software) 24
ABI PRISM 310 Data Collection Software, v2.0 and v2.1: Installation and Setup Page 3 of 28
Installing 310 Data Collection Software v2.0 or v2.1
Overview To completely install the 310 Data Collection software v2.0 or v2.1, you
must:
♦Make a calibration file
♦Install the software
♦Set folder locations
♦Register the software
♦Reset the 310 instrument
♦Setthememorysize,ifnecessary
Making a
Calibration File Before running the 310 Data Collection software Installer, you will need
to make a file of your instrument calibration values.
Installing v2.0 or
v2.1
To make a calibration file:
Step Action
1Launch your existing version of the 310 Data Collection software.
2Go to the Window menu and select Manual Control.
3In the Function section of the window, select Calibration File Make
and click Execute.
4Quit your existing version of the 310 Data Collection software.
5 IMPORTANT If you have sample or customizedmodulesyou wish
to save, create a folder (outside the ABI PRISM 310 folder) and place
the modules there now. Installing the new software version
automatically overwrites any existing modules.
To install 310 Data Collection software v2.0 or v2.1:
Step Action
1Insert the ABI PRISM 310 Collection CD into the computer.
2Double-click the Installer icon to launch the software installer.
3Click Continue on the splash screen.
4Please read the license and warranty terms, then click Accept to
proceed.
5Please read the contents of the Notice window, then click Continue
to proceed.
Page 4 of 28 ABI PRISM 310 Data Collection Software, v2.0 and v2.1: Installation and Setup
Setting Folder
Locations After the 310 Data Collection software v2.0 or v2.1 has been installed,
you must set locations for the following folders:
♦Sample sheets
♦Modules
♦Runs
♦Firmware image
6In the 310 Collection Installer dialog box, click Install.
7After the installation is complete, click Quit.
To install 310 Data Collection software v2.0 or v2.1: (continued)
Step Action
To set the folder locations:
Step Action
1Double-click the ABI PRISM 310 Collection icon on the desktop to
launch the software.
The dialog box shown below appears.
ABI PRISM 310 Data Collection Software, v2.0 and v2.1: Installation and Setup Page 5 of 28
2To select the sample sheets folder, select Sample Sheets from the
list of folders, then click the Select “Sample Sheets” button at the
bottom of the screen.
3To select the modules folder, select Modules from the list of folders,
then click the Select “Modules” button at the bottom of the screen.
4To select the runs folder, select Runs from the list of folders, then
click the Select “Runs” button at the bottom of the screen.
To set the folder locations: (continued)
Step Action
Page 6 of 28 ABI PRISM 310 Data Collection Software, v2.0 and v2.1: Installation and Setup
Registering the
Software
5To select the firmware image folder, select Firmware Image from the
list of folders, then click the Select “Firmware Image” button at the
bottom of the screen.
6Continue with “Registering the Software” below.
To set the folder locations: (continued)
Step Action
To register the 310 Data Collection software:
Step Action
1After setting the folder locations, the Product Registration window
appears.
2Fill in the text fields:
a. Enter your name.
b. Enter your organization’s name.
c. Enter the product’s registration code. This is provided with your
copy of the software.
ABI PRISM 310 Data Collection Software, v2.0 and v2.1: Installation and Setup Page 7 of 28
Resetting the
310 Instrument After installing v2.0 or v2.1 of the 310 Data Collection software, but
before using the new version for the first time, you must reset the 310
Genetic Analyzer.
Note Leave the ABI PRISM 310 Collection CD in the computer until you are
instructed to remove it.
Setting the
Memory Size You will need to make sure the memory allocated for the 310 Data
Collection software is set to at least 5000 k.
3Click OK.
4 IMPORTANT To complete the registration process, fill out the
registration card included in the software kit and mail it to Applied
Biosystems.
To register the 310 Data Collection software: (continued)
Step Action
To reset the 310 Genetic Analyzer:
Step Action
1Turn off the 310 instrument.
2While holding down the Tray and Gel Pump buttons
simultaneously, turn the 310 instrument back on. Wait at least
10 seconds before releasing the Tray and Gel Pump buttons.
The new firmware is downloaded to the 310 instrument.
3When the download is complete, you will be prompted to quit and
relaunch the 310 Data Collection software.
Click Quit. The new firmware changes take effect after the software
is relaunched.
To set the memory size for the 310 Data Collection software:
Step Action
1Navigate to and open the ABI PRISM 310 folder on the your hard
drive. The path is:
Macintosh HD:ABI PRISM 310
2Click the ABI PRISM 310 Collection icon once to select it.
3On the desktop’s menu bar, go to the File menu.
Page 8 of 28 ABI PRISM 310 Data Collection Software, v2.0 and v2.1: Installation and Setup
4Select Get Info, then select Memory.
5In the ABI PRISM 310 Data Collection Info window, review the
Memory Requirements section. If necessary, change both the
Minimum Size and Preferred Size fields to at least 5000 K.
To set the memory size for the 310 Data Collection software: (continued)
Step Action
ABI PRISM 310 Data Collection Software, v2.0 and v2.1: Installation and Setup Page 9 of 28
Completing v2.0 or
v2.1 Installation To complete the installation:
Step Action
1 If you... Then...
use the Sequencing
Analysis software see “Installing the New Basecaller
and Mobility Files” on page 10.
do not use the
Sequencing Analysis
software
the installation is complete. Remove
the ABI PRISM 310 Collection CD from
the computer and store it in a secure
location.
Page 10 of 28 ABI PRISM 310 Data Collection Software, v2.0 and v2.1: Installation and Setup
Installing the New Basecaller and Mobility Files
Overview This procedure is only required if you would like to run sequencing
experiments using the new sequencing modules provided with 310
Data Collection software v2.0 or v2.1 and analyze this data using an
existing version of the Sequencing Analysis software.
Note The new sequencing modules are described on page 22.
Analyzing
377 Sample Files The new basecaller supplied with 310 Data Collection software v2.0 or
v2.1 only supports the analysis of sample files from the 310 Genetic
Analyzer.
To analyze sample files from the ABI PRISM®377 DNA Sequencer with
the Sequencing Analysis software, see “Changing Basecallers for
377 Sample Files” on page 23.
Saving the Old
Basecaller To save the old basecaller:
Step Action
1Navigate to and open the Sequencing Analysis folder on your hard
drive. The path is:
Macintosh HD:Applied Biosystems:Sequencing Analysis
2Create a new folder and name it Basecaller Archive.
3Drag the existing BasecallerPPC file from the Sequencing Analysis
folder into the Basecaller Archive folder you just created.
4Move the Basecaller Archive folder (which now contains the existing
BasecallerPPC file) from the Sequencing Analysis folder to another
location. A good place to store the Basecaller Archive folder is in the
ABI folder on your hard drive. The path is:
Macintosh HD:System Folder:ABI Folder
IMPORTANT In order for the Sequencing Analysis software to list
the new basecaller in the Sample Manager window, you MUST
REMOVE the Basecaller Archive folder from the Sequencing
Analysis folder.
5Keep the Sequencing Analysis and ABI folders open and continue
with “Installing the New Basecaller and Mobility Files” below.
ABI PRISM 310 Data Collection Software, v2.0 and v2.1: Installation and Setup Page 11 of 28
Installing the New
Basecaller and
Mobility Files
To install the new basecaller and mobility files:
Step Action
1If it is not there already, insert the ABI PRISM 310 Collection CD into
the computer.
2Navigate to and open the New Basecaller folderlocatedontheCD.
3Drag the new BasecallerPPC file from the New Basecaller folder on
the CD into the Sequencing Analysis folder on your hard drive.
4Drag the following files from the New Basecaller folder on the CD to
the ABI folder:
♦310POP4.bcp
♦ABI-CE1.bcp
♦ABI-CE2.bcp
♦DT310POP4{BD}v1.mob
♦DT310POP4{dRhod}v1.mob
♦DP310POP4{BD-21M13}v2.mob
♦DP310POP4{BD-M13Rev}v1.mob
5The new basecaller and mobility files are now installed. Close all
open folders.
Note For more information on the new basecaller and mobility
files, see page 22.
6Remove the ABI PRISM 310 Collection CD from the computer and
store it in a secure location.
Page 12 of 28 ABI PRISM 310 Data Collection Software, v2.0 and v2.1: Installation and Setup
Setting Preferences in the 310 Data Collection Software
Overview After you install 310 Data Collection software v2.0 or v2.1, you may
want to set the following preferences:
♦Folder location preferences for the GeneScan Analysis software:
– GeneScan Analysis Parameters Folder
– GeneScan Size Standard Folder
– Analysis Settings Folder
♦File names
♦Sample sheets
♦Injection lists
IMPORTANT After setting preferences, you must perform a CLEAR MEMORY
reset (instructions are on page 19).
Setting Folder
Location
Preferences for
GeneScan
To set folder location preferences for the GeneScan Analysis
software:
Step Action
1In the 310 Data Collection software, go to the Window menu.
2Select Preferences,thenFolder Locations.ThePreferences window
appears as shown below.
ABI PRISM 310 Data Collection Software, v2.0 and v2.1: Installation and Setup Page 13 of 28
3Set the location of the Analysis Parameters folder as follows:
a. Click the button to the right of GeneScan Analysis Parameters.
b. Set the folder location to the GS Parameters Folder inside the
GeneScan Analysis folder. The path is:
Macintosh HD:GeneScan Analysis:GS Parameters Folder
4Set the location of the Size Standards folder as follows:
a. Click the button to the right of GeneScan Size Standard Folder.
b. Set the folder location to the GS Standards Folder inside the
GeneScan Analysis folder. The path is:
Macintosh HD:GeneScan Analysis:GS Standards Folder
5Set the location of the Analysis Settings folder as follows:
a. Click the button to the right of Analysis Settings Folder.
b. Set the folder location to the Analysis Settings folder inside the
ABI Folder. The path is:
Macintosh HD:System Folder:ABI Folder
IMPORTANT If you are automatically analyzing your data (see
step 10 on page 17), the Analysis Settings Folder location is critical
in order to find the matrix files.
6Click OK to save your changes.
To set folder location preferences for the GeneScan Analysis
software: (continued)
Step Action
Page 14 of 28 ABI PRISM 310 Data Collection Software, v2.0 and v2.1: Installation and Setup
Setting File Names The 310 Data Collection software automatically creates and names
sample sheets, run folders, injection lists, and sample files. If you would
like to change the default naming conventions, follow this procedure.
To set the file names:
Step Action
1In the 310 Data Collection software, go to the Window menu.
2Select Preferences,thenDefault File Names.ThePreferences
window appears as shown below.
3Enter your file name preferences in each field, as desired.
Note Do not use dashes in the sample file names.
4Click OK to save your changes.
ABI PRISM 310 Data Collection Software, v2.0 and v2.1: Installation and Setup Page 15 of 28
Setting Sample
Sheet and
Injection List
Preferences
When you create sample sheets and injection lists, some of the
information is automatically filled in for you. If you would like to change
the default information, follow the procedures below for the GeneScan
or Sequencing Analysis software, as appropriate.
For GeneScan Analysis Software
To set GeneScan sample sheet and injection list preferences:
Step Action
1In the 310 Data Collection software, go to the Window menu.
2Select Preferences,thenGeneScan Sample Sheet Defaults.The
Preferences window appears as shown below.
3From the Size Standard Dye Color pull-down menu, select a size
standard color. We recommend the following:
If you are primarily
using a... Then select...
four-dye sample sheet R
five-dye sample sheet O
4Click OK.
Page 16 of 28 ABI PRISM 310 Data Collection Software, v2.0 and v2.1: Installation and Setup
5From the Page pull-down menu, select GeneScan Injection List
Defaults.ThePreferences window appears as shown below.
6Enteravalue(cm)intheLength to Detector field.
7Enter a name in the Operator field.
8Select a module.
If you are primarily
using a... Then select a module from...
four-dye sample sheet the 4Dye Module pull-down menu:
♦GS STR POP4 (1 mL) C
♦GS STR POP4 (1 mL) D
♦GS STR POP4 (1 mL) F
five-dye sample sheet the 5Dye Module pull-down menu:
♦GS STR POP4 (1 mL) E5
♦GS STR POP4 (1 mL) G5
Note If you have v2.1 of the Data Collection software installed,
you will only have a choice between four-dye and five-dye modules.
If you have v2.0, the pull-down menu is titled Module and only
four-dye modules are available.
9SelectamatrixfilefromtheMatrix file pull-down menu.
To set GeneScan sample sheet and injection list preferences: (continued)
Step Action
ABI PRISM 310 Data Collection Software, v2.0 and v2.1: Installation and Setup Page 17 of 28
For Sequencing Analysis Software
10 If you wish to have your data automatically analyzed, you must:
a. Check the Autoanalyze with box.
b. Navigate to and select the GeneScan Analysis software. The
path is:
Macintosh HD:GeneScan Analysis v3.1.2:310 GeneScan v3.1.2
c. From the Analysis Parameter file and Size Standard file pull-down
menus, select the files you would like to use for automatic
analysis. You may also choose these files when creating the
GeneScan injection List.
11 Click OK to save your changes.
To set Sequencing Analysis sample sheet and injection list
preferences:
Step Action
1In the 310 Data Collection software, go to the Window menu.
2Select Preferences,thenSequence Sample Sheet Defaults.The
Preferences window appears as shown below.
3Select a dye set/primer file from the DyeSet/Primer pull-down menu.
4SelectamatrixfilefromtheMatrix pull-down menu.
5Click OK.
To set GeneScan sample sheet and injection list preferences: (continued)
Step Action
Page 18 of 28 ABI PRISM 310 Data Collection Software, v2.0 and v2.1: Installation and Setup
6From the Page pull-down menu, select Sequence Injection List
Defaults.ThePreferences window appears as shown below.
Note The screen capture shown below was taken from v2.1 of
the Data Collection software. If you have v2.0, the screen will be
slightly different.
7Enteravalue(cm)intheLength to Detector field.
8Enter a name in the Operator field.
9Select a module.
If you installed... Then...
v2.1 select a module from the 4Dye
Module pull-down menu.
Note Leave the 5Dye Module set to
<none>. There are no five-dye
modules presently available for the
Sequencing Analysis software.
v2.0 select a module from the Module
pull-down menu.
Note You will only have a choice
between four-dye and five-dye
modules if you have v2.1 of the Data
Collection software installed.
To set Sequencing Analysis sample sheet and injection list
preferences: (continued)
Step Action
ABI PRISM 310 Data Collection Software, v2.0 and v2.1: Installation and Setup Page 19 of 28
Performing a
CLEAR
MEMORY Reset
IMPORTANT After setting your preferences in the 310 Data Collection
software, perform a CLEAR MEMORY reset. This will force a firmware
download and ensure all your changes go into effect.
Performing a CLEAR MEMORY reset will delete values in
Manual Control and your Autosampler calibrated values!
10 If you wish to have your data automatically analyzed, you must:
a. Check the Autoanalyze with box.
b. Navigate to and select the Sequencing Analysis software. The
path is:
Macintosh HD:Applied Biosystems:Sequencing Analysis
11 Click OK to save your changes.
To set Sequencing Analysis sample sheet and injection list
preferences: (continued)
Step Action
To perform a CLEAR MEMORY reset:
Step Action
1Before performing a CLEAR MEMORY reset (or performing a
“Calibration FIle Make”), go to the Manual Control window and
make a note of the following values:
♦CCD pixel position X
♦CCD pixel position Y
♦Syringepumpforce
♦Syringe Max. Travel
2Quit the 310 Data Collection software, then turn off the 310
instrument.
3While holding down the Tray and Gel Pump buttons
simultaneously, turn the 310 instrument back on. Wait at least
10 seconds before releasing the Tray and Gel Pump buttons.
On the front of the 310 instrument, all three status lights should be
on.
4Launch the 310 Data Collection software to send the firmware to
the 310 instrument.
CAUTION
!
Page 20 of 28 ABI PRISM 310 Data Collection Software, v2.0 and v2.1: Installation and Setup
5Using a pencil point or something similar, press the Reset button on
the back of the 310 instrument.
Note Do not reset the 310 instrument by cycling the power.
6In the Manual Control window, enter the values you wrote down in
step 1 above.
7Through Manual Control:
a. Home the Autosampler X, Y, and Z.
b. Home the syringe.
8Recalibrate the Autosampler.
9After performing a CLEAR MEMORY reset, you must wait
10 minutes before performing a run. After memory is cleared, it
takes 10 minutes to calibrate the temperature control circuitry.
To perform a CLEAR MEMORY reset: (continued)
Step Action
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