Thermo Fisher Scientific DataBankSTR™ Software Utility Owner's manual

DataBankSTR

™

Software Utility

User’s Manual

For Research Use Only. Not for use in diagnostic procedures.

The CODIS export format of this program has been designed and tested for compatibility with the current release (Import

version 1.6 or earlier) of the CODIS database software. Applied Biosystems does not warrant the performance of this

program with future releases of the CODIS database, or with any other database. This software program in not endorsed by

the FBI, by the developers of the CODIS database, or any related organization.

ABI P

RISM

, AmpF

l

STR, GeneScan, Genotyper, and Applied Biosystems are registered trademarks of Applera Corporation

or its subsidiaries in the U.S. and certain other countries.

ABI, AmpF

l

STR Profiler, AmpF

l

STR Profiler Plus, DataBankSTR, are trademarks of Applera Corporation or its

subsidiaries in the U.S. and certain other countries.

Macintosh is a registered trademark of Apple Computer Inc.

All other trademarks are the sole property of their respective owners.

Contents

iii

About DataBankSTR Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1

What Is the DataBankSTR Software?. . . . . . . . . . . . . . . . . . . . . . . . . . .1

Integrated Systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1

Process Flow Diagram . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .2

Using the DataBankSTR Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . .3

Compatable Platforms. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .3

Using the Macintosh Computer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .4

Macintosh Computer Vocabulary and Operations . . . . . . . . . . . . . . . . .4

Guidelines for Optimal Performance . . . . . . . . . . . . . . . . . . . . . . . . . . .4

Macintosh Computer Terms Used in This Manual . . . . . . . . . . . . . . . . .5

Installing the DataBankSTR Software. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .8

System Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .8

Installing the Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .8

Determining How Much RAM to Specify . . . . . . . . . . . . . . . . . . . . . . .9

Creating a Genotyper Software Table File. . . . . . . . . . . . . . . . . . . . . . . . . . . . .9

Create a Genotyper Software Table File . . . . . . . . . . . . . . . . . . . . . . . . .9

Setting DataBankSTR Software Preferences. . . . . . . . . . . . . . . . . . . . . . . . . .10

Introduction. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10

CODIS Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10

Color Preferences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .11

Global Default Record . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .12

Importing Files into the DataBankSTR Software . . . . . . . . . . . . . . . . . . . . . .14

DataBankSTR Table Window Diagram . . . . . . . . . . . . . . . . . . . . . . . .14

Creating a Default Record for a Speciﬁc DataBankSTR Software File14

Importing Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .16

Inserting Additional Genotyper Software Table Files. . . . . . . . . . . . . .17

Formatting the DataBankSTR Software Results . . . . . . . . . . . . . . . . . . . . . . .18

iv

Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

Modifying Specimen Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

Adding and Removing Specimens. . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

Adding and Removing Markers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

Sorting Specimens . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

Changing Date . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24

Changing Time. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24

Adding User Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

Adding General Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26

Exporting the DataBankSTR Software Data . . . . . . . . . . . . . . . . . . . . . . . . . 27

About the Exported File. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27

Export File Example . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27

Procedure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28

Printing the DataBankSTR Table Window . . . . . . . . . . . . . . . . . . . . . . . . . . . 29

Procedure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29

Troubleshooting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30

Troubleshooting Table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30

Technical Support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31

Contacting Technical Support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31

To Contact Technical Support by E-Mail. . . . . . . . . . . . . . . . . . . . . . . 31

Hours for Telephone Technical Support. . . . . . . . . . . . . . . . . . . . . . . . 31

To Contact Technical Support by Telephone or Fax . . . . . . . . . . . . . . 32

To Reach Technical Support Through the Internet . . . . . . . . . . . . . . . 35

To Obtain Documents on Demand . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36

CODIS Help. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37

Software License. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38

License . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38

Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41

1

About DataBankSTR Software

What Is the

DataBankSTR

Software?

The DataBankSTR

™

software (P/N 4304665) is a utility program that

allows users to convert data generated using the ABI P

RISM

Genotyper

®

software into a format acceptable for uploading into the

Combined DNA Index System (CODIS) database.

Used in conjunction with the ABI P

RISM

GeneScan

®

Analysis Software

and the Genotyper software, the DataBankSTR software completes the

Applied Biosystems library of software that enables laboratories to

contribute specimen information to the CODIS database.

Integrated Systems

Applied Biosystems provides an integrated system of reagents,

instruments, and software to process DNA samples and facilitate the

transfer of data into a database.

Step Action

1

DNA specimens are ampliﬁed on GeneAmp

®

PCR Instrument

Systems using the AmpF

l

STR

®

PCR Ampliﬁcation Kits. The

resulting ﬂuorescently labeled products are run on either the

ABI P

RISM

377 DNA Sequencer or the ABI P

RISM

310 Genetic

Analyzer.

2

Data is analyzed using the GeneScan Analysis Software, which

automatically provides fragment size, peak height, and peak area

information.

3

In order to standardize the exchange of data between instrument

platforms and laboratories, the sizing information is converted into

genotypes.

The GeneScan Analysis Software sample ﬁles are analyzed using

Genotyper v. 2.X software, in conjunction with the appropriate

AmpF

l

STR Template File, to provide allele designations for

ampliﬁed fragments.

The alleles are automatically assigned by the Genotyper software

by comparison with the known alleles in the AmpF

l

STR Allelic

Ladders.

4

For subsequent entry of the data into CODIS, the genotypes are

saved as a Genotyper Software Table File using the “Make CODIS

Table” macro.

5

The DataBankSTR software imports the Genotyper Software Table

File and allows the user to add sample (specimen) information.

2

Process Flow

Diagram

GeneScan Analysis Software, Genotyper software, and DataBankSTR

software are designed to work in conjunction with each other to transfer

data as an easy to use, integrated system. Figure 1 shows the process

ﬂow and related ﬁles, for analyzing, genotyping, and uploading data into

the CODIS database.

Figure 1

Files created in the processing of STR data

6

The completed DataBankSTR Table is exported as a Common

Message Format (CMF) ﬁle. The export step converts the tabular

data into a format compatible with the CODIS software. The CMF

ﬁle contains one piece of information per line (versus tabular).

7

The CMF ﬁle is saved onto a PC-formatted diskette and transferred

to the CODIS workstation computer. Alternatively, the CMF ﬁle may

be transferred over a network.

Step Action

Step 1 Step 2

Step 3 Step 4

GeneScan

Sample File

CODIS

File

Ste

p

5

Import

Export

Genotyper

Project File

Genotyper

Table File DataBankSTR

Software File

Import

Export

3

Using the

DataBankSTR

Software

The DataBankSTR software is initially installed onto the computer and

the steps below are followed:

Compatable

Platforms

The DataBankSTR software is currently designed for use on the Power

Macintosh

®

computer. The exported ASCII ﬁles are compatible with the

Microsoft Windows NT

®

environment.

Step Action Comment

1

Create the Genotyper Software

Table File for the data set using

the “Make CODIS Table” macro.

Use the Genotyper software in

conjunction with the AmpF

l

STR

Template Files.

2

Open the DataBankSTR

software.

3

Set general preferences. Preferences need to be set the

ﬁrst time the program is used.

4

Verify that the Global Default

Settings are correct for the ﬁle

to be imported.

Default settings can be modiﬁed

for a speciﬁc ﬁle.

5

Import Genotyper Software

Table Files.

More than one Genotyper

Software Table File can be

imported into a single

DataBankSTR software ﬁle.

Default settings can be

customized for each Genotyper

Software Table File.

6

Modify specimen records as

necessary.

Additional information can be

added to each specimen.

7

Fill in User Information dialog

box.

Dialog box must be completed

to export the table.

8

Export the completed

DataBankSTR software ﬁle.

Data is saved as an ASCII ﬁle.

9

Transfer to a CODIS computer. Transfer can be done using a

diskette or over the network.

10

Print the DataBankSTR

software ﬁle, if desired.

4

Using the Macintosh Computer

Macintosh

Computer

Vocabulary and

Operations

To use the DataBankSTR software, you should be familiar with the

following basic Macintosh computer vocabulary and operations:

If you do not understand some or all of these, refer to the

Macintosh

®

System Software User’s Guide or the Owner’s Guide

for more

information.

Guidelines for

Optimal

Performance

Computers require regular attention and maintenance to operate

efﬁciently and consistently. The DataBankSTR software works with

large ﬁles and accesses the hard disk often, so it is especially important

to follow the maintenance procedures to minimize the occurrence of

errors during operation.

Follow these general guidelines for optimal performance:

♦

Install only one Macintosh system per hard disk.

♦

Back up all programs and ﬁles regularly.

♦

Remove nonessential ﬁles from the hard disk.

♦

Use a hard disk maintenance program regularly, such as

DiskExpress

®

Pro Optimizer.

♦

Use discretion when adding software programs, especially Control

Panel (CDEV) and Extension (INIT) ﬁles.

Refer to the

ABI P

RISM

Instrument User’s Manual

for more details.

Vocabulary and Operations Description

Using the mouse Clicking and double-clicking,

selecting and dragging.

Choosing commands Using pull-down and pop-up menus,

dialog boxes, radio buttons and

checkboxes.

Working with windows Opening and closing, resizing and

repositioning, scrolling,

understanding the active window.

Using the Macintosh program

hierarchical ﬁle system

Finding ﬁles and creating folders.

5

Macintosh

Computer Terms

Used in This

Manual

The following Macintosh computer terms are used frequently in this

manual to describe how to use the DataBankSTR software.

Macintosh computer terms used in this manual.

Item Description

Dialog Boxes Appear when you must make a

decision or enter information.

All other actions on the monitor

screen are suspended until you

close the dialog box by clicking a

button, such as Cancel, OK, or

Done.

Menus Provide access to various functions

you can perform with the software.

A heavy arrow ( ) after a menu item

indicates that a submenu appears

when you click that choice and hold

down the mouse button.

When you choose a menu command

followed by an ellipsis (…) a dialog

box appears.

Dialog

box

Submenu

6

Pop-up menus Display a heavy arrow ( ) and are

found in dialog boxes.

When you click a pop-up menu and

hold down the mouse button, a

submenu appears.

These menus allow you to choose

dialog box entries from speciﬁc lists

of items.

Windows Display information, and, in some

cases, allow you to edit or enter

additional information.

The top border of an active window

always has six horizontal lines and

usually has a Close box in the

upper-left corner.

If many windows are open, click one

window to make it active.

When a window is active, you can

click the top border, hold down the

mouse button, and drag the window

to another location on the screen.

When you are ﬁnished working with

a window, click the Close box to

remove the window from the screen,

or click another window.

Macintosh computer terms used in this manual.

(continued)

Item Description

7

Entry ﬁelds Rectangular areas in which you can

enter information.

Click in an entry ﬁeld to display a

cursor, and use the keyboard to

enter the information.

Buttons Rectangles that allow you to accept

or cancel the contents of a dialog

box or perform functions, such as

printing, within the dialog box.

A button with a heavy outline is the

default button that applies if you

press the Return key.

Macintosh computer terms used in this manual.

(continued)

Item Description

Window

Close box

Zoom box

Buttons

8

Installing the DataBankSTR Software

System

Requirements

The following are the system requirements:

♦

Macintosh computer with a PowerPC

®

processor.

♦

5 MB of RAM allocated to the DataBankSTR software.

♦

Operating System 7.0 or later.

Installing the

Software

To install the DataBankSTR software:

Step Action

1

Choose New Folder from the File menu and enter the name

DataBankSTR software for the folder name.

2

Insert the DataBankSTR software Installer Disk into the Macintosh

disk drive.

3

Double-click the DataBankSTR software folder and double-click the

DataBankSTR software icon on the installer disk.

4

In the window that appears:

♦

Choose the hard drive.

♦

Select the destination folder for the DataBankSTR software

and the Help folder (DataBankSTR software folder created in

step 1).

♦

Click Open.

5

Click Extract.

Follow the prompts on the screen and insert the remaining 3 disks

as you are prompted to do so.

The DataBankSTR software decompresses and is loaded on your

hard drive.

6

Remove the DataBankSTR software disks from the hard drive and

store them in a safe place.

7

Open the DataBankSTR software folder and locate the

DataBankSTR software icon.

The installation is complete.

Note

When the DataBankSTR software is launched for the ﬁrst

time, you must accept the software licensing agreement outlined on

page 38 by clicking the Accept button.

9

Determining How

Much RAM to

Specify

To determine how much RAM to specify:

Creating a Genotyper Software Table File

Create a

Genotyper

Software Table

File

To utilize the DataBankSTR software, a Genotyper Software Table File

must be ﬁrst created for the genotyped data. Using the Genotyper v. 2.x

software in conjunction with the appropriate AmpFlSTR template ﬁle,

save the data with the “Make CODIS Table” macro.

For information on how to create a Genotyper Software Table File, refer

to Chapter 10, “Automated Genotyping,” in the AmpF

l

STR Proﬁler™

User’s Manual (P/N 402945) or the AmpF

l

STR Proﬁler Plus™ User’s

Manual (P/N 4303501).

Step Action

1Click the DataBankSTR software icon.

2Choose Get Info from the File menu. The DataBankSTR software

Info dialog box appears.

3Ensure that the Preferred size memory box is set to at least

5000 kb. If the Minimum size memory box is not set to at least 5000

kb, then enter that amount.

10

Setting DataBankSTR Software Preferences

Introduction This section describes how to customize the following:

For information on setting the default record, see “Importing Files into

the DataBankSTR Software” on page 14.

\

CODIS

Parameters

To set CODIS parameters:

Topic See page

CODIS Parameters 10

Color Preferences 11

Global Default Record 12

Step Action

1Choose DataBankSTR software Preferences from the Edit menu.

The Preferences dialog box appears.

If CODIS Parameters is not listed in the pop-up menu, then choose

it from the pop-up menu.

Pop-up menu

11

Color Preferences To change the color preferences:

2Enter the following information and click OK.

Step Action

Field For example

Imaging System ABI PRISM 377 DNA Sequencer or

ABI PRISM 310 Genetic Analyzer.

Laboratory This must be the ORI for the laboratory

importing the data.

Note ORI is a unique identifying

number assigned to law enforcement

agencies by the National Crime

Information Center (NCIC).

This value is checked by the import

program to ensure that only data for that

laboratory is being imported.

Company The name of your laboratory.

Imaging Used Genotyper software.

Step Action

1Choose DataBankSTR software Preferences from the Edit menu.

The Preferences dialog box appears.

2Select Color Preferences from the pop-up menu.The color

preferences appear.

Pop-up menu

12

Global Default

Record

Before using the DataBankSTR software, create a global default record

so that you do not have to manually label each ﬁeld in the

DataBankSTR table window each time that you import data from the

Genotyper software.

3You can take the following action:

4Click OK.

Step Action

Use the...

To select a color from the

palette for the...

Specimen Color pop-up menu specimen color.

Marker Color pop-up menu marker color.

Field Color pop-up menu edit ﬁeld color.

Background Color pop-up

menu

background color.

To create a global default record:

Step Action

1Choose DataBankSTR software Preferences from the Edit menu.

The Preferences dialog box appears.

2Choose Default Record from the pop-up menu (See below).

The Settings dialog box appears.

Pop-up menu

13

3Use the pop-up menus for each ﬁeld to create a default record.

These settings will automatically be applied to every Genotyper

Software Table File that is imported unless changed for a speciﬁc

ﬁle by the user.

For more information, see “Formatting the DataBankSTR Software

Results” on page 18.

For example, if you are creating a large Caucasian database using

stains from blood specimens, you might want to create a default

record with each of the ﬁelds pre-labeled as shown in the ﬁgure

below.

4Click OK.

To create a global default record: (continued)

Step Action

Blood Stain Caucasian

Click on column

labels in this row

14

Importing Files into the DataBankSTR Software

DataBankSTR

Table Window

Diagram

The following is an example of the DataBankSTR table window.

Creating a Default

Record for a

Speciﬁc

DataBankSTR

Software File

Why Create a Default Record?

Use the Default Record pop-up menu in the Settings dialog box to

create a default record to use before importing a speciﬁc Genotyper

Software Table File. The settings in this record override the global

default record.

Procedure

Marker row

Specimen

file

Fi

e

ld

s

Specimen

row

To create a default record for a speciﬁc DataBankSTR software ﬁle:

Step Action

1Launch the DataBankSTR software by double-clicking the

DataBankSTR software icon.

2Choose Save As from the File menu to name the ﬁle.

3Choose “ﬁlename” Settings from the Table menu (-T), where

“ﬁlename” is the name of the saved DataBankSTR software ﬁle.

15

4The Settings dialog box appears.

Choose Default Record from the pop-up menu.

5Use the pop-up menus for each ﬁeld to create a default record.

For more information, see “About the Pop-Up Menus” on page 19.

6Click OK.

These settings will now be applied to the Genotyper Software Table

Files inserted into this DataBankSTR table window. For all

subsequent DataBankSTR software ﬁles, the original global default

record will be used.

To create a default record for a speciﬁc DataBankSTR software

Step Action

Pop-up menu

16

Importing Files There are two ways to import Genotyper Software Table Files into the

DataBankSTR software.

Step Action

1Open the DataBankSTR software by double-clicking the

DataBankSTR software icon.

2Take the following action.

Note Before importing a Genotyper Software Table File, you can

create a default record that applies to this Genotyper Software

Table File and subsequent Genotyper Software Table Files that are

imported into this DataBankSTR table window. This can be

accomplished by using the “Untitled” Settings command from the

Table menu. See “Creating a Default Record for a Speciﬁc

DataBankSTR Software File” on page 14.

If you want to... Then...

automatically import a

ﬁle

Drag the Genotyper Software Table

File icon into the DataBankSTR table

window.

import a ﬁle a. Choose Insert from the Table

menu.

A directory dialog box appears

that shows the ﬁles saved from

the Genotyper software.

You may have to navigate the

hard disk to ﬁnd the ﬁles.

b. Select the desired ﬁle and click

OK.

The results should appear in the

DataBankSTR table window.

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Thermo Fisher Scientific DataBankSTR™ Software Utility Owner's manual

Thermo Fisher Scientific DataBankSTR™ Software Utility Owner's manual

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