Thermo Fisher Scientific Applied Biosystems SDS Plate Utility User guide

Brand: Thermo Fisher Scientific

Model: Applied Biosystems SDS Plate Utility

Type: User guide

Applied Biosystems

SDS Plate Utility v2.2

For the ABI PRISM® 7900HT

Sequence Detection System

User Guide

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

Information in this document is subject to change without notice. Applied Biosystems assumes no responsibility for any errors that

may appear in this document. This document is believed to be complete and accurate at the time of publication. In no event shall

Applied Biosystems be liable for incidental, special, multiple, or consequential damages in connection with or arising from the use

of this document.

NOTICE TO PURCHASER:

APPLERA CORPORATION MAKES NO WARRANTY OF ANY KIND WITH REGARD TO THIS MATERIAL,

INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A

PARTICULAR PURPOSE. Applera Corporation shall not be liable for errors contained herein or for incidental or consequential

damages in connection with the furnishing, performance, or use of this material.

DISCLAIMER OF LICENSE

Purchase of this software product alone does not imply any license under any process, instrument or other apparatus, system,

composition, reagent or kit rights under patent claims owned or otherwise controlled by Applera Corporation, either expressly or by

estoppel.

TRADEMARKS:

ABI PRISM and Applied Biosystems are registered trademarks of Applera Corporation or its subsidiaries in the U.S. and/or certain

other countries.

AB (Design), Applera, and Assays-on-Demand are trademarks of Applera Corporation or its subsidiaries in the U.S. and/or certain

other countries.

TaqMan is a registered trademarkare of Roche Molecular Systems, Inc.

Microsoft and Windows NT are registered trademarks of Microsoft Corporation.

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

Part Number 4343738 Rev. B

04/2004

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Contents

SDS Plate Utility v2.2 User Guide iii

Preface

How to Use This Guide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v

How to Obtain More Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii

How to Obtain Support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . viii

Chapter 1 Introduction

Creating SDS Plate Documents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-2

Generating Detector and Marker List Files . . . . . . . . . . . . . . . . . . . . . . 1-3

Log Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-4

Chapter 2 Installation

Configurations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-1

Installing the Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-1

Hardware . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-2

Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-3

Chapter 3 Creating SDS Plate Documents

Database Setup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-4

SDS Template Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-4

Creating an SDS Template Document . . . . . . . . . . . . . . . . . . . . . . . . . 3-5

Creating Container Setup Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-5

Container Setup Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-6

Container Setup File Specification . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-6

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iv SDS Plate Utility v2.2 User Guide

Chapter 4 Detector and Marker List Files for SDS Software

Creating Detector and Marker List Files . . . . . . . . . . . . . . . . . . . . . . . . 4-1

Assay Information Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-2

Electronic Data Sheet Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-4

Chapter 5 Using the Command Line

Glossary

Index

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SDS Plate Utility v2.2 User Guide v

Preface

How to Use This Guide

Purpose of this

Guide

The SDS Plate Utility v2.2 software is designed for users who

perform high-throughput analyses and need to generate SDS plate

documents automatically. It is designed for use with the

ABI PRISM®7900HT Sequence Detection System and

Assays-on-DemandTM SNP Genotyping Products and Gene

Expression Products.

Audience This guide is intended for novice and experienced users:

•Laboratory Manager – Sets up the application for use by end-

users and manages the testing and data analysis. The setup has

two stages: 1) planning the setup and 2) entering the system and

template information.

•Lead Scientist – Works with Lab Manager.

•Scientist – Analyzes and reviews data.

•Technician – Prepares and runs samples according to protocol,

and loads data and performs experiments under the direction of

a scientist.

Assumptions This guide assumes that your instrument has been installed by an

Applied Biosystems technical representative.

Text Conventions This guide uses the following conventions:

•Bold indicates user action. For example:

Type 0, then press Enter for each of the remaining fields.

•Italic text indicates new or important words and is also used for

emphasis. For example:

Before analyzing, always prepare fresh matrix.

• A right arrow bracket (>) separates successive commands you

select from a drop-down or shortcut menu. For example:

Select File > Open > Spot Set.

Right-click the row, then select View Filter > View All Runs.

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Preface

vi SDS Plate Utility v2.2 User Guide

User Attention

Words

Two user attention words appear in Applied Biosystems user

documentation. Each word implies a particular level of observation

or action as described below:

Note: Provides information that may be of interest or help but is not

critical to the use of the product.

IMPORTANT! Provides information that is necessary for proper

instrument operation, accurate chemistry kit use, or safe use of a

chemical.

Examples of the user attention words appear below:

Note: The size of the column affects the run time.

Note: The Calibrate function is also available in the Control

Console.

IMPORTANT! To verify your client connection to the database, you

need a valid Oracle user ID and password.

IMPORTANT! You must create a separate Sample Entry Spreadsheet

for each 96-well plate.

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How to Obtain More Information

SDS Plate Utility v2.2 User Guide vii

How to Obtain More Information

Documentation

The following references contain useful information about the

Applied Biosystems software and instrument:

• ABI PRISM® 7900HT Sequence Detection System and SDS

Enterprise Database User Guide (P/N 4317596)

• Assays-on-Demand™ SNP Genotyping Products Protocol

(P/N 4332856)

• Assays-on-Demand™ SNP Gene Expression Products Protocol

(P/N 4333458)

• Automation Controller Software online Help

• Container Setup File Format Specification (PDF file on

installation directory)

• SDS Software v2.2 online Help

• SDS Plate Utility v2.2 online Help

• SDS Enterprise Database Administrator Guide (P/N 4346513)

Portable document format (PDF) versions of this guide are available

on the software installation CD.

Note: For additional documentation, see “How to Obtain Support”

on page viii.

Instructions about the instrument and robots are in the associated

instrument user guides.

Send Us Your

Comments

Applied Biosystems welcomes your comments and suggestions for

improving its user documents. You can e-mail your comments to:

[email protected]

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Preface

viii SDS Plate Utility v2.2 User Guide

How to Obtain Support

For the latest services and support information for all locations, go to

http://www.appliedbiosystems.com, then click the link for

Support.

At the Support page, you can:

• Search through frequently asked questions (FAQs)

• Submit a question directly to Technical Support

• Order Applied Biosystems user documents, MSDSs, certificates

of analysis, and other related documents

• Download PDF documents

• Obtain information about customer training

• Download software updates and patches

In addition, the Support page provides access to worldwide telephone

and fax numbers to contact Applied Biosystems Technical Support

and Sales facilities.

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SDS Plate Utility v2.2 User Guide 1-1

Introduction 1

The SDS Plate Utility v2.2 software is designed for users who

perform high-throughput analyses and need to generate SDS plate

documents automatically. It is designed for use with the

ABI PRISM®7900HT Sequence Detection System and

Assays-on-DemandTM SNP Genotyping Products and Gene

Expression Products.

The SDS plate utility performs two related functions:

• Creates SDS plate documents for gene expression and

genotyping reaction containers.

• Generates a detector information text file and a marker

information text file using the Detector and Marker List Builder

software, based on Assay Information Files from the

Assays-on-Demand™ products CD.

You can set up the SDS plate utility to run manually or automatically.

Note: The SDS plate documents generated by the SDS plate utility

are compatible with SDS Software v2.2 applications, not with SDS

Software v2.0.x applications.

In Enterprise mode, the SDS Plate Utility v2.2 software provides

21CFR11 support in the following ways:

• Security: User authentication and security are enforced in the

same way as SDS Software v2.2 in Enterprise mode.

• Auditing: Creation of plates by the SDS plate utility is audited

based on settings in SDS Software v2.2 in Enterprise mode.

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Chapter 1 Introduction

1-2 SDS Plate Utility v2.2 User Guide

Creating SDS Plate Documents

The SDS plate utility creates SDS plate documents for gene

expression and genotyping using the following files:

• Container setup files (which contain plate information)

• SDS template documents (which contain thermal-cycling

information)

• (optional) Assay Information Files (which contain detector

and marker information)

Note: Applied Biosystems recommends that you generate user-

provided container setup files with an automated LIMS or other

software mechanism. To generate the tab-delimited text file in

container setup file format, you can also use a spreadsheet program

such as Microsoft® Excel. Applied Biosystems also recommends that

you create single SDS plate documents using the graphical user

interface in the SDS software.

Enterprise Mode If the application is running in Enterprise mode, a temporary SDS

plate document is written to the hard disk. The temporary SDS plate

document is then added to the SDS Enterprise Database and the

temporary file is deleted from the hard disk.

If the SDS plate utility and the Automation Controller Software are

connected to the same SDS Enterprise Database, 7900HT

instruments running Automation Controller Software in SDS

Enterprise mode will query the SDS Enterprise Database for SDS

plate documents when a reaction container is presented to the

7900HT instrument. Assuming the SDS plate utility has previously

saved an SDS plate document for the reaction container, the

Automation Controller Software will extract the appropriate SDS

plate document from the SDS Enterprise Database.

Non-Enterprise

Mode

If the application is running in Non-Enterprise mode, the output SDS

plate documents are added to a designated folder on the hard disk.

If the SDS Plate Utility v2.2 and the SDS Software v2.2 applications

have been installed with the Non-Enterprise option and with

Automation Accessories options, the software moves the SDS plate

document to the Automation Controller Software queue.

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Generating Detector and Marker List Files

SDS Plate Utility v2.2 User Guide 1-3

Generating Detector and Marker List Files

The SDS plate utility generates the Detector List File, which is a list

of all SDS detector information contained in Assay Information Files

(AIF). AIF are supplied by Applied Biosystems on the

Assays-on-Demand™ products CD and copied to the hard disk by

the user. The SDS plate utility also generates the Marker List File,

which is a list of all SDS marker information contained in

Assay Information Files (AIF).

A new Detector List File and a new Marker List File are generated

each time the SDS plate utility is launched. Alternatively, they can be

generated by launching the application from the Detector and Marker

List Builder Windows shortcut.

After you build the Detector List File, you can import it into the

Detector Manager of the SDS software for use with the Sequence

Detection System. You can import the Marker List File into the

Marker Manager of the SDS software for use with the 7900HT SDS.

Note: The SDS plate utility does not provide a GUI to define

reaction containers. For customers that do not generate plate-specific

container setup files with an automated software mechanism (for

example, a LIMS system), it is recommended to use the Detector and

Marker List Builder to extract SDS detector and marker information

from all your AIF and EDS files and import the Detector List and

Marker List into the SDS software Detector Manager and Marker

Manager. You can then select the list of available

“Assays-on-Demand” detectors and markers in the SDS software and

use the SDS software GUI to design SDS plate documents.

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Chapter 1 Introduction

1-4 SDS Plate Utility v2.2 User Guide

Log Files

An ASCII text file is generated every time the application is

launched.

The log file names have the format:

[email protected]

For example:

[email protected]

The log files are in the application installation directory in the

“SDS Plate Utility Log Files” folder.

The application displays a Run Log window. You can close this

window without affecting output to the Run Log file.

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SDS Plate Utility v2.2 User Guide 2-1

Installation 2

The SDS Plate Utility v2.2 can be installed in one of two

configurations, Enterprise and Non-Enterprise. In both

configurations, the Detector and Marker List Builder software is

installed.

Configurations

Non-Enterprise If you install on the same machine as the Automation Controller

Software, the SDS plate utility automatically adds created SDS plate

documents to the Automation Controller Software queue. However,

you can prevent adding SDS plate documents to the Automation

Controller Software queue by running the SDS plate utility in DOS

Command Line mode and using the '-noqueue' option.

Enterprise The SDS plate utility automatically adds created SDS plate

documents to the SDS Enterprise Database defined during the

installation.

Installing the Software

IMPORTANT! Before installing in Non-Enterprise mode with the

Automation Accessories option, install SDS Software v2.2 with the

Automation Accessories options.

IMPORTANT! Before installing in Enterprise mode, install and start

the SDS Enterprise Database (on the server).

To install the software:

1. Close any open applications.

2. Insert the SDS Plate Utility v2.2 CD into the CD drive and close

the drive door.

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Chapter 2 Installation

2-2 SDS Plate Utility v2.2 User Guide

3. In Windows Explorer, open the CD directory

(SDS Plate Utility 2.2) and double-click

SDSPlateUtilitySetup.exe.

4. In the Introduction screen of the SDS Plate Utility dialog box,

click Next.

5. Select Enterprise Mode or Non-Enterprise Mode. If you

select Enterprise Mode, set up the database connection.

Note: If SDS Software v2.2 was installed in Non-Enterprise

mode, the SDS plate utility is installed in Non-Enterprise mode.

Note: The SDS plate utility installs in the folder where

SDS Software v2.2 is installed.

6. In the Pre-Installation Summary dialog box, click Next.

7. In the Install Complete dialog box, click Finish.

8. Eject the SDS Plate Utility v2.2 CD from the drive.

Upon installation, the SDS plate utility creates a default AIF-EDS

watch folder entitled “Applied Biosystems\Put AIF and EDS files

here.” If the software is unable to create the folder or if it is

subsequently deleted, the software prompts you to specify the

AIF-EDS watch folder upon launch of the SDS plate utility.

Hardware

The computer needs the following minimum hardware:

•Intel

® Pentium® III processor (or equivalent)

• 256 MB RAM

• CD Drive

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Software

SDS Plate Utility v2.2 User Guide 2-3

Software

The computer needs to have the following software:

• Microsoft Windows® 2000 (Service Pack 3)

The SDS plate utility requires the following for installation or

operation:

• SDS Software v2.2 (does not work with SDS Software v2.0.x)

The SDS plate utility works with the following software, but does not

require it for installation or operation:

• Automation Controller Software

Note: Applied Biosystems recommends installing the SDS plate

utility onto the computer attached to an

ABI PRISM®7900HT Sequence Detection System. In this

configuration, the software can work with the 7900HT SDS,

Automation Controller Software, and Detector and Marker List

Builder software for the instrument.

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Chapter 2 Installation

2-4 SDS Plate Utility v2.2 User Guide

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SDS Plate Utility v2.2 User Guide 3-1

Creating SDS Plate Documents 3

The SDS Plate Utility v2.2 creates SDS plate documents for the

ABI PRISM®7900HT Sequence Detection System using container

setup files (reaction container information), SDS template documents

(thermocycle information), and optional Assay Information Files

(Assays-on-Demand™ SNP Genotyping Products and Gene

Expression Products information).

In Non-Enterprise mode, the SDS plate utility writes the new SDS

plate documents to the local hard disk (default output folder is

“Applied Biosystems\SDS Documents”). The software also adds the

SDS plate documents to the Automation Controller Software queue if

the SDS Automation Accessories software is available.

In Enterprise mode, new SDS plate documents are added to the SDS

Enterprise Database.

Note: You must have a user access level of Scientist or above to run

the SDS plate utility in Enterprise mode. Just as in the SDS software,

users must have Scientist or higher privileges to save SDS plate

documents to the SDS Enterprise Database.

You must designate at least one container setup file watch folder.

A container setup file watch folder is a folder on the local hard disk

that, as the name implies, is watched by the SDS plate utility for

container setup files. When container setup files are added to the

watch folder, the SDS plate utility attempts to build an SDS plate

document from each container setup file.

Each watch folder must contain only one SDS template document.

Thermocycle information from the SDS template document is

combined with the container setup files added to that watch folder to

produce SDS plate documents. For example, a customer who has

three different thermocycle protocols would need three SDS template

documents and three container setup file watch folders. Each watch

folder would contain one of the SDS template documents.

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Chapter 3 Creating SDS Plate Documents

3-2 SDS Plate Utility v2.2 User Guide

Before creating SDS plate documents:

1. If you are using Genomic Assays Assays-on-Demand™

products, copy the Assay Information Files (AIF) and Electronic

Data Sheets from the Assays-on-Demand™ products CD to the

“Put AIF and EDS files here” folder. (The files contain the

detector and marker information required for the SDS plate

documents to be made.)

Note: Do not edit AIF or EDS files. Never remove AIF or EDS

files from the “Put AIF and EDS files here” folder.

2. Place a single SDS template document (with extension .sdt and

containing the assay method, thermal cycling parameters, and

data collection options) into the container setup file watch folder

you intend to use. (Each SDS template document has its own

watch folder.)

To create SDS plate documents:

1. Open the SDS plate utility by double-clicking the SDS Plate

Utility icon or selecting Start > Programs > Applied

Biosystems > SDS Plate Utility to display the SDS Plate Utility

dialog box listing the container setup file watch folders.

If you are running in Enterprise mode, you must first log in at

the Login dialog with your User Name and Password.

Note: If you are running in Enterprise mode, you can also click

Database Setup to open the Options dialog where you enter the

Host Name, Port Number, and Service Name.

IMPORTANT! If the “Select an AIF-EDS Folder” dialog box appears,

select a folder from the Applied Biosystems or other directory, for

example, “Applied Biosystems\Put AIF and EDS files here,” then

click Select Folder to use that folder.

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SDS Plate Utility v2.2 User Guide 3-3

2. To designate a watch folder:

a. In the SDS Plate Utility dialog box, click Add a New

Watch Folder.

b. In the Select a New Watch Folder dialog box, select a

folder from the Applied Biosystems or other directory, for

example, “Applied Biosystems\Put Container Setup Files

here”.

c. Click Select Folder to use that folder.

Note: The SDS Plate Utility dialog box closes after the

configured period of inactivity. You can set the time-out period

using the SDS Software v2.2 User Account Manager.

3. Add the container setup files (containing the barcodes, Sample

IDs, and Assay IDs) to the selected watch folder.

The system then creates the SDS plate documents, and:

• In Enterprise mode – Places the SDS plate documents in

the SDS Enterprise Database.

• In Non-Enterprise mode – Places the SDS plate documents

in the “Applied Biosystems\SDS Documents” folder.

In Non-Enterprise mode, if the Automation Controller Software

is present on the computer, the system also places the reaction

containers on the Automation Controller Software queue for the

7900HT instrument.

The system places processed container setup files in the

“Processed Files” folder, for example, “Applied Biosystems\Put

Container Setup Files here\Processed Files”.

Note: If the SDS plate utility is run from the DOS Command

Line and the -input command line argument refers to a single

file, the container setup file is left in its original location.

If the SDS plate utility cannot make an SDS plate document, it

moves the container setup file to the “Problem Files” folder, for

example, “Applied Biosystems\Put Container Setup Files here\

Problem Files,” and notes the action failed in the Command

Prompt window.

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Chapter 3 Creating SDS Plate Documents

3-4 SDS Plate Utility v2.2 User Guide

Database Setup

To change databases:

1. In the SDS Plate Utility Log In dialog box, click Database

Setup. The Options dialog box displays the current connection

parameters:

•Host Name

•Port Number

•Service Name

2. Enter the new Host Name, Port Number, and Service Name.

3. Click Verify to verify the new connection.

Note: In the Options dialog box, you can change the connection to a

different SDS Enterprise Database.

SDS Template Files

The SDS template document (extension *.sdt) contains information

used to run the plate on the 7900HT instrument:

• Thermal cycling conditions

• Data collection parameters

To combine an SDS template document to be combined with a

container setup file, the plate size of the two files must be identical.

For example, an SDS template document that defines a 384-well

reaction container cannot be combined with a container setup file that

defines a 96-well reaction container.

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Thermo Fisher Scientific Applied Biosystems SDS Plate Utility User guide

Brand: Thermo Fisher Scientific

Model: Applied Biosystems SDS Plate Utility

Type: User guide

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Thermo Fisher Scientific Applied Biosystems SDS Plate Utility User guide

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