Thermo Fisher Scientific Expedite™ 8900 Workstation Software User guide

Expedite™ 8900

Workstation Software

User’s Guide

Printed in the United States of America. This book or parts thereof may not be reproduced in any form without the written

permission of the publishers.

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

NOTICE

Applied Biosystems supplies or recommends certain configurations of computer hardware, software, and peripherals for use

with its instrumentation. Applied Biosystems reserves the right to decline support for or impose extra charges for supporting

nonstandard computer configurations or components that have not been supplied or recommended by Applied Biosystems.

Applied Biosystems also reserves the right to require that computer hardware and software be restored to the standard

configuration prior to providing service or technical support.

Information in this document is subject to change without notice and does not represent a commitment by Applied

Biosystems. Applied Biosystems assumes no responsibility for any errors that may appear in this document. This manual is

believed to be complete and accurate at the time of publication. In no event shall Applied Biosystems be liable for incidental

or consequential damages in connection with or arising from the use of this manual.

Nucleic acid synthesis reagents sold by Applied Biosystems are covered by U.S. patent RE34,069 and patents in Austria,

Belgium, Canada, France, Germany, Japan, Luxembourg, Netherlands, Sweden, Switzerland, and U.K.

Applied Biosystems is a registered trademark, and Expedite is a trademark, of Applera Corporation or its subsidiaries in the

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Microsoft, MS, Windows, and MS-DOS are registered trademarks of Microsoft Corporation.

Table of Contents

Expedite 8900 Workstation Software User’s Guide iii

Table of Contents

How to Use This Guide ............................................................................. ix

Chapter 1 Expedite Workstation Software

1.1 Expedite Workstation Software Features ....................................... 1-2

1.2 Hardware Requirements............................................................ 1-3

1.3 Software Overview ................................................................... 1-5

1.3.1 Expedite Windows Overview .................................................. 1-5

1.3.2 Menu Overview ...................................................................... 1-9

1.4 Installin

g

the Software ............................................................. 1-13

Chapter 2 Preparing the System

2.1 Overview ............................................................................... 2-2

2.2 Startin

g

the Instrument.............................................................. 2-3

2.3 Startin

g

the Software ................................................................ 2-6

2.3.1 Startin

g

the Workstation Software .......................................... 2-6

2.3.2 Confi

g

urin

g

Instruments ......................................................... 2-8

2.3.3 Communication Between Workstation and Instrument ...........2-10

2.4 Specifyin

g

the Operatin

g

Environment ......................................... 2-13

2.4.1 Settin

g

the Control Mode ......................................................2-13

2.4.2 Specifyin

g

the Operator Name and Folder ............................2-16

2.4.3 Settin

g

Alarms ......................................................................2-17

2.5 Checkin

g

Instrument Setup ....................................................... 2-20

Chapter 3 Performing a Synthesis

3.1 Overview of a Synthesis ............................................................ 3-2

3.2 Creatin

g

or Editin

g

the Sequence ................................................ 3-3

3.3 Preparin

g

and Loadin

g

the Rea

g

ents............................................ 3-5

3.3.1 Installin

g

the Rea

g

ents .......................................................... 3-6

3.3.2 Primin

g

the System ................................................................ 3-8

Table of Contents

iv Applied Biosystems

3.4 Startin

g

the Synthesis .............................................................. 3-12

3.4.1 Specifyin

g

the Synthesis Parameters ....................................3-12

3.4.2 Transferrin

g

Sequence Sets ..................................................3-18

3.4.3 Checkin

g

Rea

g

ent Resources ...............................................3-20

3.4.4 Installin

g

the Columns ...........................................................3-21

3.4.5 Startin

g

the Instrument ..........................................................3-22

3.5 Monitorin

g

the Synthesis .......................................................... 3-23

3.5.1 Instrument Window ...............................................................3-23

3.5.2 Trityl Viewer ..........................................................................3-28

3.5.3 Status Window ......................................................................3-30

3.6 Addin

g

Operator Notes to the Run Lo

g

........................................ 3-32

3.7 Stoppin

g

a Synthesis ............................................................... 3-36

3.7.1 Holdin

g

a Synthesis ..............................................................3-36

3.7.2 Stoppin

g

a Synthesis ............................................................3-39

3.7.3 Abortin

g

a Synthesis .............................................................3-40

Chapter 4 Using the Expedite Database

4.1 Overview of the Database.......................................................... 4-2

4.2 Importin

g

and Exportin

g

............................................................ 4-3

4.2.1 Importin

g

............................................................................... 4-3

4.2.2 Exportin

g

............................................................................... 4-7

4.3 Mana

g

in

g

Data in the Database ................................................. 4-12

4.4 Mana

g

in

g

Folders ................................................................... 4-14

4.5 Deletin

g

and Movin

g

Files......................................................... 4-17

4.6 Filterin

g

and Sortin

g

the Data Displayed....................................... 4-19

4.7 Creatin

g

a List-by Filter ............................................................ 4-20

4.7.1 Specifyin

g

Filter Criteria ........................................................4-25

4.7.2 Specifyin

g

Sort Criteria .........................................................4-26

Table of Contents

Expedite 8900 Workstation Software User’s Guide v

Chapter 5 Viewing and Printing Reports

5.1 Overview of Reports................................................................. 5-2

5.2 Displayin

g

Reports................................................................... 5-3

5.3 Usin

g

the Report Window .......................................................... 5-6

5.4 Displayin

g

Trityl Data................................................................ 5-7

5.5 Printin

g

a Report .................................................................... 5-10

5.5.1 Settin

g

Up the Report ...........................................................5-10

5.5.2 Printin

g

a Report ...................................................................5-12

5.5.3 Printin

g

Multiple Reports .......................................................5-12

5.6 Renamin

g

a Run .................................................................... 5-14

5.7 Savin

g

a Run Report as Text ..................................................... 5-15

5.8 Report Viewer Menus .............................................................. 5-16

Chapter 6 Using the Sequence Editor

6.1 Overview of the Sequence Editor................................................. 6-2

6.2 Creatin

g

and Editin

g

Sequences ................................................. 6-3

6.2.1 Openin

g

a Sequence ............................................................. 6-3

6.2.2 Usin

g

the Sequence Editor Windows ..................................... 6-6

6.2.3 Creatin

g

or Editin

g

a Sequence ............................................6-10

6.2.4 Printin

g

a Sequence ..............................................................6-13

6.2.5 Savin

g

and Closin

g

a Sequence ...........................................6-14

6.2.6 IUB Mix Codes, Numeric Codes, Extended Cycle, Lowercase

Codes ...................................................................................6-17

6.3 Usin

g

Forei

g

n Sequences ......................................................... 6-21

6.4 Viewin

g

Sequence Information ................................................... 6-25

6.4.1 Displayin

g

the Complement of a Sequence ...........................6-25

6.4.2 Displayin

g

Sequence Statistics .............................................6-26

6.4.3 Displayin

g

Summary Information ...........................................6-29

6.4.4 Chan

g

in

g

Base Groupin

g

......................................................6-31

Table of Contents

vi Applied Biosystems

6.5 Customizin

g

the Sequence Editor ............................................... 6-33

6.5.1 Settin

g

Sequence Editor Preferences ...................................6-33

6.5.2 Settin

g

Molecular Wei

g

hts ....................................................6-35

6.6 Searchin

g

for Specific Base Combinations .................................... 6-37

6.7 Proofreadin

g

Sequences .......................................................... 6-38

6.8 Sequence Editor Menus ........................................................... 6-39

Chapter 7 Using the Protocol Editor

7.1 Overview of the Protocol Editor ................................................... 7-2

7.2 Understandin

g

Protocols ........................................................... 7-3

7.2.1 Cycles in Protocols ................................................................ 7-4

7.2.2 Subcycles (Operations) in Cycles .......................................... 7-6

7.2.3 Steps in Subcycles ...............................................................7-10

7.2.4 Delivery Modes in Steps .......................................................7-12

7.2.5 Functions in Steps ................................................................7-14

7.2.5.1 Fluidic Functions ..................................................7-15

7.2.5.2 Special Functions .................................................7-18

7.2.6 Description of the Adenosine (A) Cycle .................................7-19

7.3 Determinin

g

the Rea

g

ent Delivery Volumes for Protocols ................. 7-23

7.4 Creatin

g

and Editin

g

Protocols................................................... 7-26

7.4.1 Openin

g

a Protocol ...............................................................7-26

7.4.2 Usin

g

the Protocol Editor Windows .......................................7-30

7.4.3 Creatin

g

a New Protocol .......................................................7-32

7.4.4 Settin

g

Scale and Chemistry for a Protocol ...........................7-33

7.4.5 Editin

g

a Protocol ..................................................................7-34

7.4.5.1 Insertin

g

or Editin

g

a Step ....................................7-34

7.4.5.2 Editin

g

a Cycle .....................................................7-36

7.4.5.3 Findin

g

and Replacin

g

Text ..................................7-38

7.4.6 Printin

g

a Protocol ................................................................7-41

Table of Contents

Expedite 8900 Workstation Software User’s Guide vii

7.4.7 Displayin

g

Summary Information ...........................................7-43

7.4.8 Savin

g

and Closin

g

a Protocol ..............................................7-44

7.4.9 Validatin

g

a Protocol .............................................................7-47

7.5 Protocol Editin

g

Examples ........................................................ 7-49

7.5.1 Editin

g

Standard Protocols to Enhance Trityl Intensity ..........7-49

7.5.2 Creatin

g

an RNA Protocol from a THIO Protocol ...................7-51

7.5.3 Editin

g

Standard Protocols for Trityl Quantitation ..................7-54

7.5.4 Editin

g

Standard Protocols to Add a Specialized Monomer ...7-57

7.6 Protocol Editor Menus.............................................................. 7-60

Appendix A Installing the Serial Board ....................................... A-1

Appendix B Warranty/Service Information................................ B-1

Appendix C Technical Support and Training........................... C-1

Index

Expedite 8900 Workstation Software User’s Guide ix

1

How to Use This Guide

Purpose of this

guide

The Applied Biosystems

Expedite



8900 Workstation

Software User‘s Guide

describes the features and use of the

Expedite workstation software.

Audience

This

g

uide is intended for novice and experienced Expedite

workstation users who are synthesizin

g

nucleic acids.

Structure of this

guide

Applied Biosystems

Expedite 8900 Workstation Software

User’s Guide

is divided into chapters. Each chapter pa

g

e is

marked with a tab and a header to help you locate information

within the chapter.

The followin

g

table describes the material covered in each

chapter.

Chapter 1,

Expedite Workstation

Software

Describes the features of the software and

how to install the software.

Chapter 2,

Preparin

g

the System

Describes how to start up the Expedite Nucleic

Acid Synthesis instrument and the Expedite

8900 Workstation Software. It also tells you how

to set the operatin

g

environment.

Chapter 3,

Performin

g

a

Synthesis

Describes how to create, run, and monitor a

synthesis.

Chapter 4,

Usin

g

the Expedite

Database

Describes how to import and export, store,

mana

g

e, and view information in the Expedite

workstation database.

Chapter 5,

Viewin

g

and Printin

g

Reports

Describes how to

g

enerate, view, and print

reports.

How to Use This Guide

x Applied Biosystems

1

Microsoft

Windows

versions

The Expedite Workstation software runs on either Microsoft®

Windows® version 3.1 software or Microsoft Windows 95

software. All screen examples shown in this book are from the

Windows 3.1 software. Windows 95 software screens have

the same functionality.

Conventions

This

g

uide uses the followin

g

conventions to make text easier

to understand.

General

conventions

•Bold indicates user action:

“Type 0 and press Enter for the remainin

g

fields.”

•

Italic

text denotes new or important words, and is also

used for emphasis:

“Before analyzin

g

,

always

prepare fresh

matrix.”

Chapter 6,

Usin

g

the Sequence

Editor

Includes procedures for usin

g

the Sequence

Editor.

Chapter 7,

Usin

g

the Protocol

Editor

Describes cycles and protocols, and includes

procedures for usin

g

the Protocol Editor.

Appendix A,

Installin

g

the Serial

Board

Contains procedures for confi

g

urin

g

and

installin

g

the board, and connectin

g

the

workstation to the instrument.

Appendix B,

Warranty/Service

Information

Contains warranty, service, return, and spare

parts information.

Appendix C

,

Technical Support

and Trainin

g

Describes how to contact Technical Support,

obtain technical documents, and obtain

cutomer trainin

g

information.

Expedite 8900 Workstation Software User’s Guide xi

1

Notes, Cautions,

and Warnings

A note callin

g

out important information to the operator

appears as:

NOTE: Record your result before proceeding with the next

step.

A caution callin

g

out information to avoid dama

g

e to the

system or equipment appears as:

CAUTION

Changing reagent bottles during a synthesis is not

recommended. Check the reagent resources prior to

initiating a synthesis to make sure that there is a sufficient

supply.

A warnin

g

callin

g

out information essential to the safety of the

operator appears as:

WARNING

The Expedite cabinet weighs 102 pounds (46 kg). Two

people are required to safely lift the instrument cabinet.

Expedite 8900 Workstation Software User’s Guide 1-1

1Expedite Workstation

Software

This chapter contains the following sections:

1.1 Expedite Workstation Software Features ... 1-2

1.2 Hardware Requirements............................ 1-3

1.3 Software Overview .................................... 1-5

1.4 Installin

g

the Software ............................. 1-13

1

Chapter 1 Expedite Workstation Software

1-2 Applied Biosystems

1

1.1 Expedite Workstation Software

Features

Expedite

workstation

The Expedite Workstation Software provides monitorin

g

and

control of the Expedite Nucleic Acid Synthesis System. The

Expedite Workstation software runs on either Microsoft®

Windows® version 3.1 software or Microsoft Windows 95

software.

The Expedite Workstation software allows you to:

•Control up to six Expedite instruments

NOTE: If any Expedite instrument includes a Multiple

Oligo Synthesis System (MOSS) unit, you can control

only four instruments from the Expedite Workstation.

•Create and edit sequences and protocols

•Check rea

g

ent resources and reset rea

g

ent volumes

•Start and stop syntheses

•View and print reports

•Store sequence, protocol, and report information in the

Expedite Workstation database

•Search, view, filter, and sort information in the database

Tasks you

perform on the

Expedite

instrument

The Expedite Workstation software allows you to perform

most synthesis preparation and control tasks. However, you

must perform these tasks on the Expedite instrument:

•Set the Instrument Address (Tools:Confi

g

:Host)

•Specify the User Profile (Tools:Confi

g

:Profile)

•Select the Chemistry (Tools:Confi

g

:Profile)

•Run dia

g

nostics tests (Tools:Dia

g

)

•Prime the rea

g

ent passa

g

es (Prime)

This manual tells you when you need to perform a task on the

Expedite instrument and refers you to the

Expedite Nucleic

Acid Synthesis System User’s Guide

for detailed information.

Hardware Requirements

Expedite 8900 Workstation Software User’s Guide 1-3

1

1.2 Hardware Requirements

Expedite

hardware

The Expedite Workstation hardware consists of:

•RS-422 serial board

•RS-422 communications cable (14 ft)

Computer

hardware

The Expedite Workstation software requires a minimum

confi

g

uration of:

•PC-compatible 386SX 16MHz computer with a

dedicated COM port

NOTE: The Expedite Workstation requires a

dedicated COM port. The COM port cannot be

connected to or configured for any other device.

•4 MB RAM minimum, 8 MB RAM recommended

•60 MB hard disk, 5 MB free

•3.5-inch disk drive

•VGA color

g

raphics monitor

•MS-DOS® 5.0 or hi

g

her

•Microsoft Windows version 3.1, confi

g

ured in

386 enhanced mode, or Microsoft Windows 95 software

•Serial mouse

Chapter 1 Expedite Workstation Software

1-4 Applied Biosystems

1

NOTE: Parallel mouse devices interfere with proper

operation of the Expedite Workstation.

•16-bit soundblaster-compatible sound board for

sequence readin

g

, supplied by the user

See Appendix A, Installin

g

the Serial Board, for

information on installin

g

the Expedite serial board in a

computer, and for connectin

g

instruments to the

Expedite Workstation.

Software Overview

Expedite 8900 Workstation Software User’s Guide 1-5

1

1.3 Software Overview

This section describes:

•Expedite windows overview

•Expedite menu overview

1.3.1 Expedite Windows Overview

This Expedite Workstation software includes:

•Instrument window

•Sequence Editor window

•Reports window

•Protocol Editor window

Instrument

window

The Instrument window (Fi

g

ure 1-1) is displayed when you

start the Expedite Workstation software or start a synthesis.

The Instrument window monitors the Expedite Nucleic Acid

Synthesis instruments and provides access to other Expedite

windows.

Figure 1-1 Expedite Instrument Window

Chapter 1 Expedite Workstation Software

1-6 Applied Biosystems

1

The Instrument window allows you to:

•Set up and control syntheses on up to six Expedite

Nucleic Acid Synthesis instruments

NOTE: If any instrument includes a MOSS unit, you

can control only four instruments from the Expedite

Workstation.

•Monitor syntheses

•Add comments to the run lo

g

•View trityl data

•Automatically transfer information from individual

instruments to the Workstation for lon

g

term stora

g

e

•Access the Sequence Editor, Report Viewer, and

Protocol Editor

Sequence Editor

window

The Sequence Editor window (Fi

g

ure 1-2) allows you to create

new sequences, edit existin

g

sequences, and mana

g

e

database stora

g

e and display of sequences.

Figure 1-2 Sequence Editor Window

Software Overview

Expedite 8900 Workstation Software User’s Guide 1-7

1

To access the Sequence Editor, do one of the followin

g

:

•Select Run Sequence Editor from the Edit menu in the

Instrument window.

•Click Edit Sequence in the Run Synthesis dialo

g

box.

•If the Expedite Workstation software is not runnin

g

, you

can run the Sequence Editor in stand-alone mode by

double-clickin

g

the Sequence Editor icon in the

Expedite window in the Pro

g

ram Mana

g

er.

Reports window

The Reports window (Fi

g

ure 1-3) allows you to view and print

run statistics, runtime lo

g

, and trityl data for completed runs.

Figure 1-3 Reports Window

To access Reports, do one of the followin

g

:

•Select Run Report Viewer from the File menu in the

Instrument window.

•If the Expedite Workstation software is not runnin

g

, you

can run the Report Viewer in stand-alone mode by

double-clickin

g

the Reports icon in the Expedite

window in the Pro

g

ram Mana

g

er.

Chapter 1 Expedite Workstation Software

1-8 Applied Biosystems

1Protocol Editor

window

The Protocol Editor window (Fi

g

ure 1-4) allows you to modify

existin

g

protocols or create new protocols.

.

Figure 1-4 Protocol Editor Window

To access the Protocol Editor, do one of the followin

g

:

•Select Run Protocol Editor from the Edit menu in

Instrument window.

•If the Expedite Workstation software is not runnin

g

, you

can run the Protocol Editor in stand-alone mode by

double-clickin

g

the Protocol Editor icon in the

Expedite window in the Pro

g

ram Mana

g

er.

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