Thermo Fisher Scientific ABI PRISM 310 Data Collection Software Owner's manual

Brand: Thermo Fisher Scientific

Model: ABI PRISM 310 Data Collection Software

Type: Owner's manual

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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Thermo Fisher Scientific ABI PRISM 310 Data Collection Software Owner's manual

Brand: Thermo Fisher Scientific

Model: ABI PRISM 310 Data Collection Software

Type: Owner's manual

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Thermo Fisher Scientific ABI PRISM 310 Data Collection Software Owner's manual

Thermo Fisher Scientific ABI PRISM 310 Data Collection Software Owner's manual

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