ABI PRISM® 3100 Genetic Analyzer and

ABI PRISM ® 3100-$YDQW Genetic Analyzer

User Reference Guide

ABI PRISM® 3100 Genetic Analyzer and
ABI PRISM ® 3100-$YDQW Genetic Analyzer

User Reference Guide

DRAFT
July 12, 2002 6:29 pm, AvantURTitle_Hitachi.fm
© Copyright 2002, Applied Biosystems. All rights reserved.
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.
SEE USER GUIDE FOR NOTICE TO PURCHASER: LIMITED LICENSE.
The ABI PRISM® 3100 and 3100-Avant Genetic Analyzer includes patented technology licensed from Hitachi, Ltd. as part of a strategic partnership between Applied
Biosystems and Hitachi, Ltd., as well as patented technology of Applied Biosystems.
ABI PRISM and its design, AmpFlSTR, Applied Biosystems, BigDye, COfiler, GeneScan, Identifiler, MicroAmp, Profiler Plus, SGM Plus, and SNaPshot are
registered trademarks of Applera Corporation or its subsidiaries in the U.S. and certain other countries.
AB (Design), Applera, Factura, Hi-Di, POP, POP-4, and POP-6 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.
Microsoft, Windows, and Windows NT are registered trademarks of the Microsoft Corporation in the United States and other countries.
Oracle is a registered trademark of the Oracle Corporation.
All other trademarks are the sole property of their respective owners.

Part Number 4335393 Rev. A

07/2002

Record information about your software below.

Software CD Serial Number Version Number Registration Code

3100 Software
Oracle® for NT
GeneScan® Application
Sequencing Analysis Application

DRAFT
July 12, 2002 6:29 pm, AvantURTitle_Hitachi.fm
Contents
1 Introduction and Safety
About the Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-2
Before You Begin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-2
Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-3
Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-4

2 System Overview
What the Instrument Does . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-2
How the Instrument Works . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-3
Front View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-5
Front View with Doors Open . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-7
Back View. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-8
Computer Workstation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-9
Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-10
Supported Dye Sets and Applications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-11
Polymers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-12
Injection Solution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-13
Capillary Array . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-14
Electrophoresis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-15
Electrophoresis Circuit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-16
Fluorescent Detection. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-17
Laser . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-17
Spectral Dispersion Device . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-18
CCD Camera . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-18

3 Software
Software CD-ROMs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-2
Software Suite . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-3
Applications in the Data Collection Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-5
Supporting Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-6
Types and Locations of Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-7
Edit Dye Display Information Dialog Box. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-8
Set Color Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-9
Manual Control Commands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-11
Run Modules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-13
Run Module Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-17

iii
 Transferring Run Modules Between Computers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-18
Sequencing Analysis Modules. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-21
Creating a Sequencing Analysis Module. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-24
Analysis Modules for Fragment Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-30
Setting Up Sequence Collector Project Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-37
Preparing a Plate for Uploading to Sequence Collector . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-39
After Extracting to the Sequence Collector Database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-44

4 Working with Plate Records

Creating Plate Records . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-2
Plate Record Fields . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-3
Tab-Delimited Text Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-7
Creating Tab-Delimited Text Files. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-8
Using Spreadsheets to Create Tab-Delimited Text Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-9
Spreadsheet or Tab-Delimited Text File Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-11
Running the Same Sample with Different Conditions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-15
Creating a Plate Record by Importing LIMS Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-16
Plate Import Table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-17
Creating a Plate File Using a Provided Template . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-19
Creating a Plate File from a New Spreadsheet . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-22
Creating a Plate File from a Custom Spreadsheet Template . . . . . . . . . . . . . . . . . . . . . . . . . . 4-23
Creating a Plate File from an Edited Plate Record . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-24
Importing Tab-Delimited Text Files and Linking Plate Records . . . . . . . . . . . . . . . . . . . . . . . 4-25
Deleting Plate Records and Run Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-27

5 System Management and Networking

Storing Run Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-2
Recovering Data: Extractor Utility . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-2
Deleting Processed Frame Data: Cleanup Database Utility . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-4
Importing: Method Import Utility . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-6
Removing Run Modules from the Instrument Database:
Remove Run Modules Utility . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-7
Reinitializing the Instrument Database: Initialize Database Utility . . . . . . . . . . . . . . . . . . . . . 5-8
Networking Options. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-9
Networking the Computer Workstation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-11
Requirements for a Networked Computer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-12

6 Troubleshooting
Instrument Startup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-2
Spatial Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-3
Spectral Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-4

iv
 Run Performance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-5
Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-11

A Technical Support
Services and Support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A-1

B Part Numbers
Applied Biosystems Part Numbers. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .B-1

Index

v
Introduction and Safety 1 1
In This Chapter The following topics are covered in this chapter:

Topic See Page

About the Instrument 1-2
Before You Begin 1-2
Documentation 1-3
Safety 1-4

Introduction and Safety 1-1

About the Instrument

System Components The ABI PRISM ® 3100 and 3100-Avant Genetic Analyzers are automated capillary
electrophoresis systems that can separate, detect, and analyze fluorescent-labeled
DNA fragments in one run.

The 3100 or 3100-Avant Genetic Analyzer system includes the following components:
♦ ABI PRISM ® 3100 or 3100-Avant Genetic Analyzer
♦ Computer workstation with Microsoft® Windows NT® operating system
♦ ABI PRISM ® 3100 or 3100-Avant Genetic Analyzer Data Collection software
♦ ABI PRISM ® DNA Sequencing Analysis or ABI PRISM ® GeneScan® Analysis
software
♦ Capillary array
♦ Reagent consumables

Before You Begin

Important Safety Before using the instrument, read the safety information starting on page 1-4 and in
Information the ABI PRISM® 3100 Genetic Analyzer Site Preparation and Safety Guide
(P/N 4315835).

Audience This manual is written for principle investigators and laboratory staff who are planning
to operate and maintain a 3100 or 3100-Avant Genetic Analyzer.

Before attempting the procedures in this manual, you should be familiar with the
following topics:
♦ Windows NT operating system
♦ General techniques for handling DNA samples and preparing them for
electrophoresis. Networking, which is needed if you want to integrate the 3100 or
3100-Avant Genetic Analyzer into your existing laboratory data flow system

1-2 Introduction and Safety

Documentation

List of User The following table lists the complete ABI PRISM ® 3100 and 3100-Avant Genetic
Documents Analyzer document set for users:
Title Contents P/N
Instrument
ABI PRISM 3100 Genetic Analyzer ♦ Laboratory requirements for 4315835
and 3100-Avant Genetic Analyzer installation
Site Preparation and Safety Guide
♦ Instrument and chemical safety
ABI PRISM 3100 Genetic Analyzer ♦ Theory of operations 4335393
and 3100-Avant Genetic Analyzer
♦ System management
User Reference Guide
♦ Troubleshooting
ABI PRISM 3100 Genetic Analyzer User procedures for using and 4334785
User Guide maintaining the instrument
ABI PRISM 3100-Avant Genetic User procedures for using and 4333549
Analyzer User Guide maintaining the instrument
Software
ABI PRISM DNA Sequencing Detailed procedures for analyzing 4308924
Analysis Software v. 3.7 NT User sequencing data
Guide
ABI PRISM GeneScan Analysis Detailed procedures for analyzing 4308923
Software v. 3.7 NT User Guide fragment analysis data
Chemistry
ABI PRISM 3100 Genetic Analyzer ♦ Detailed chemistry procedures 4315831
Sequencing Chemistry Guide specific for the 3100 Genetic Analyzer
♦ Chemistry troubleshooting for the
3100 Genetic Analyzer
ABI PRISM Automated DNA ♦ A description of DNA sequencing 4305080
Sequencing Chemistry Guide instruments, chemistries, and software
♦ Detailed procedures for preparing
DNA templates, performing cycle
sequencing, and preparing extension
products

User Bulletins User bulletins inform you of technical information, product improvements, and related
new products and laboratory techniques.

Applied Biosystems will mail user bulletins related to the use of this instrument to you.
We recommend storing the bulletins in this manual behind the tab labeled “User
Bulletins.”

Introduction and Safety 1-3

Safety

Documentation User Five user attention words appear in the text of all Applied Biosystems user
Attention Words documentation. Each word implies a particular level of observation or action as
described below.
Note Calls attention to useful information.

IMPORTANT Indicates information that is necessary for proper instrument operation, accurate
chemistry kit use, or safe use of a chemical.

Indicates a potentially hazardous situation which, if not avoided, may result in

minor or moderate injury. It may also be used to alert against unsafe practices.

Indicates a potentially hazardous situation which, if not avoided, could result in

death or serious injury.

Indicates an imminently hazardous situation which, if not avoided, will result in

death or serious injury. This signal word is to be limited to the most extreme situations.

Chemical Hazard CHEMICAL HAZARD. Some of the chemicals used with Applied Biosystems
Warning instruments and protocols are potentially hazardous and can cause injury, illness, or death.

♦ Read and understand the material safety data sheets (MSDSs) provided by the
chemical manufacturer before you store, handle, or work with any chemicals or
hazardous materials.
♦ Minimize contact with chemicals. Wear appropriate personal protective equipment
when handling chemicals (e.g., safety glasses, gloves, or protective clothing). For
additional safety guidelines, consult the MSDS.
♦ Minimize the inhalation of chemicals. Do not leave chemical containers open. Use
only with adequate ventilation (e.g., fume hood). For additional safety guidelines,
consult the MSDS.
♦ Check regularly for chemical leaks or spills. If a leak or spill occurs, follow the
manufacturer’s cleanup procedures as recommended on the MSDS.
♦ Comply with all local, state/provincial, or national laws and regulations related to
chemical storage, handling, and disposal.
\

1-4 Introduction and Safety

 Chemical Waste CHEMICAL WASTE HAZARD. Wastes produced by Applied Biosystems
Hazard Warning instruments are potentially hazardous and can cause injury, illness, or death.

♦ Read and understand the material safety data sheets (MSDSs) provided by the
manufacturers of the chemicals in the waste container before you store, handle, or
dispose of chemical waste.
♦ Handle chemical wastes in a fume hood.
♦ Minimize contact with chemicals. Wear appropriate personal protective equipment
when handling chemicals (e.g., safety glasses, gloves, or protective clothing). For
additional safety guidelines, consult the MSDS.
♦ Minimize the inhalation of chemicals. Do not leave chemical containers open. Use
only with adequate ventilation (e.g., fume hood). For additional safety guidelines,
consult the MSDS.
♦ After emptying the waste container, seal it with the cap provided.
♦ Dispose of the contents of the waste tray and waste bottle in accordance with
good laboratory practices and local, state/provincial, or national environmental
and health regulations.

Site Preparation and A site preparation and safety guide is a separate document sent to all customers who
Safety Guide have purchased an Applied Biosystems instrument. Refer to the guide written for your
instrument for information on site preparation, instrument safety, chemical safety, and
waste profiles.

About MSDSs Some of the chemicals used with this instrument may be listed as hazardous by their
manufacturer. When hazards exist, warnings are prominently displayed on the labels
of all chemicals.

Chemical manufacturers supply a current MSDS before or with shipments of

hazardous chemicals to new customers and with the first shipment of a hazardous
chemical after an MSDS update. MSDSs provide you with the safety information you
need to store, handle, transport and dispose of the chemicals safely.

We strongly recommend that you replace the appropriate MSDS in your files each
time you receive a new MSDS packaged with a hazardous chemical.
CHEMICAL HAZARD. Be sure to familiarize yourself with the MSDSs before
using reagents or solvents.

Introduction and Safety 1-5

 Ordering MSDSs You can order free additional copies of MSDSs for chemicals manufactured or
distributed by Applied Biosystems using the contact information below.
To order documents by automated telephone service:

1 From the U.S. or Canada, dial 1.800.487.6809.

2 Follow the voice instructions to order documents (for delivery by fax).

Note There is a limit of five documents per fax request.

To order documents by telephone:

In the U.S. Dial 1.800.345.5224, and press 1.
In Canada Dial 1.800.668.6913, and press 1 for English or 2 for French.

To obtain documents through the Applied Biosystems Web site:

Step Action

1 Go to http://docs.appliedbiosystems.com/msdssearch.html

2 In the SEARCH field, type in the chemical name, part number, or other information
that will appear in the MSDS and click SEARCH.

Note You may also select the language of your choice from the drop-down list.

3 When the Search Results page opens, find the document you want and click on it to
open a PDF of the document.

For chemicals not manufactured or distributed by Applied Biosystems, call the

chemical manufacturer.

Instrument Safety Safety labels are located on the instrument. Each safety label has three parts:
Labels ♦ A signal word panel, which implies a particular level of observation or action (e.g.,
CAUTION or WARNING). If a safety label encompasses multiple hazards, the
signal word corresponding to the greatest hazard is used.
♦ A message panel, which explains the hazard and any user action required.
♦ A safety alert symbol, which indicates a potential personal safety hazard. See the
ABI PRISM® 3100 Genetic Analyzer and 3100-Avant Genetic Analyzer Site
Preparation and Safety Guide for an explanation of all the safety alert symbols
provided in several languages.

1-6 Introduction and Safety

 About Waste As the generator of potentially hazardous waste, it is your responsibility to perform the
Disposal actions listed below.
♦ Characterize (by analysis if necessary) the waste generated by the particular
applications, reagents, and substrates used in your laboratory.
♦ Ensure the health and safety of all personnel in your laboratory.
♦ Ensure that the instrument waste is stored, transferred, transported, and disposed
of according to all local, state/provincial, or national regulations.
Note Radioactive or biohazardous materials may require special handling, and disposal
limitations may apply.

Before Operating the Ensure that everyone involved with the operation of the instrument has:
Instrument ♦ Received instruction in general safety practices for laboratories
♦ Received instruction in specific safety practices for the instrument
♦ Read and understood all related MSDSs
Avoid using this instrument in a manner not specified by Applied Biosystems.
Although the instrument has been designed to protect the user, this protection can be impaired
if the instrument is used improperly.

Computer Correct ergonomic configuration of your computer workstation can prevent

Workstation Safety stress-producing effects such as fatigue, pain, and strain. Minimize or eliminate these
effects on your body by designing your workstation to promote neutral or relaxed
working positions.
MUSCULOSKELETAL AND REPETITIVE MOTION HAZARD. These hazards
are caused by potential risk factors that include, but are not limited to, repetitive motion,
awkward posture, forceful exertion, holding static unhealthy positions, contact pressure, and
other workstation environmental factors.

♦ Use equipment that comfortably supports the user in neutral working positions
and maintains adequate accessibility to the keyboard, monitor, and mouse.
♦ Position keyboard, mouse, and monitor to promote relaxed body and head
postures.

Electric Shock ! WARNING ELECTRICAL SHOCK HAZARD. To reduce the chance of electrical shock, do
not remove covers that require tool access. No user serviceable parts are inside. Refer
servicing to Applied Biosystems qualified service personnel.

Lifting/Moving ! WARNING PHYSICAL INJURY HAZARD. Do not attempt to lift the instrument or any
other heavy objects unless you have received related training. Incorrect lifting can cause painful
and sometimes permanent back injury. Use proper lifting techniques when lifting or moving the
instrument. Two or three people are required to lift the instrument, depending upon instrument
weight.

Introduction and Safety 1-7

System Overview 2 2
In This Chapter The following topics are covered in this chapter:

Topic See Page

What the Instrument Does 2-2
How the Instrument Works 2-3
Front View 2-5
Front View with Doors Open 2-7
Back View 2-8
Computer Workstation 2-9
Software 2-10
Supported Dye Sets and Applications 2-11
Polymers 2-12
Injection Solution 2-13
Capillary Array 2-14
Electrophoresis 2-15
Electrophoresis Circuit 2-16
Fluorescent Detection 2-17
Laser 2-17
Spectral Dispersion Device 2-18
CCD Camera 2-18

System Overview 2-1

What the Instrument Does

Types of Analysis The ABI PRISM ® 3100 and 3100-Avant Genetic Analyzer perform two kinds of
analysis:

DNA Analysis Purpose

Sequencing analysis ♦ Separates a mixture of DNA fragments according to their
lengths
♦ Provides a profile of the separation
♦ Determines the order of the four deoxyribonucleotide bases
Fragment analysis ♦ Separates a mixture of DNA fragments according to their
lengths
♦ Provides a profile of the separation
♦ Determines the length of each fragment (in basepairs)
♦ Estimates the relative concentration of each fragment in the
sample

2-2 System Overview

How the Instrument Works

Typical Run The following table describes a typical run on the 3100 and 3100-Avant instrument:

Stage Description Diagram

1 Sample Preparation
During sample preparation, the DNA fragments in a sample are
chemically labeled with fluorescent dyes.
The dyes facilitate the detection and identification of the DNA.
Typically, each DNA molecule is labeled with one dye molecule,
but up to five dyes can be used to label the DNA sample.
Both the type of fluorescent labeling and the sample
composition vary with the sample preparation method used.
Samples are prepared in 96- or 384-well plates.

2 Software Setup
The operator creates a plate record and specifies the sample
type and run module in the 3100 or 3100-Avant Genetic
Analyzer Data Collection software.

3 Beginning the Run

The operator places the plates on the instrument and starts the
run.
The autosampler automatically moves the sample plate into
position to be sampled by the capillaries.

GR2142
4 Electrophoresis
Molecules from the samples are electrophoretically injected into
thin, fused-silica capillaries that have been filled with polymer.
Electrophoresis of all samples begins at the same time when a
voltage is applied across all capillaries.
The DNA fragments migrate towards the other end of the
capillaries, with the shorter fragments moving faster than the
longer fragments.
5 Excitation and Detection
As the fragments enter the detection cell, they move through the
path of a an excitation beam. The excitation beam causes the
dye on the fragments to fluoresce.
The fluorescence is captured by an optical detection device.
GR1940

System Overview 2-3

 Stage Description Diagram
6 Data Collection
The CCD camera converts the fluorescence information into
electronic information, which is then transferred to the computer
workstation for processing by the 3100 and 3100-Avant Data
Collection software.

7 Data Processing
After the data is processed, it is stored in the instrument
database and displayed as an electropherogram.
An electropherogram plots relative dye concentration (y-axis)
against time (x-axis) for each of the dyes used to label the DNA
fragments.
Each peak in the electropherogram represents a single
fragment size.
8 Automatic Data Extraction and Data Analysis
The processed data is automatically extracted and analyzed.
The positions and shapes of the electropherogram peaks are
used to determine either the base sequence or fragment profile,
depending on the type of run selected.
The analyzed data is stored as sample files on the hard drive of
the computer.
9 Viewing the Results
The analyzed data is viewed with either ABI PRISM ® DNA
Sequencing Analysis software (for sequencing) or ABI PRISM ®
GeneScan ® Analysis software (for fragment analysis).
If necessary, the data is reanalyzed using different analysis
parameters.

2-4 System Overview

Front View

Diagram and The following diagram shows the front of the instrument:
Description

Doors

Light switch
Tray button

Reset button
Status lights
On/Off button

Table of Front View Components

Part Function
Light switch Switches on and off the interior lights
On/Off button Switches on and off the instrument
Reset button Resets all of the electronics on the instrument including the
firmware and the calibration file

IMPORTANT Use this button only as a last resort when the

instrument is not responding. See the Maintenance section
of the ABI PRISM® 3100 Genetic Analyzer User Guide or the
ABI PRISM® 3100-Avant Genetic Analyzer User Guide for
procedure.
Tray button Brings the autosampler to the forward position

Note This button works only when the instrument and

oven doors are closed.

System Overview 2-5

 Table of Front View Components (continued)

Part Function
Status lights Indicates the status of the instrument as follows:

Light Appearance Instrument Status

All off Power off
Yellow solid Loading firmware
Yellow blinking ♦ Loading calibration file
♦ Initializing subsystems
Green solid Ready for use
Green blinking Running
Red blinking Error

2-6 System Overview

Front View with Doors Open

Diagram and The following diagram shows inside the instrument’s doors:
Description
Polymer-reserve syringe
Upper polymer
block Array-fill syringe
Oven

Detection cell

Capillary array
Buffer and water
reservoirs

Autosampler

Lower polymer block

Anode buffer reservoir

Table of Instrument Components

Part Function
Anode buffer reservoir Contains 9 mL of 1X running buffer.
Buffer and water Contains 16 mL of 1X running buffer or water.
reservoirs (four)
Autosampler Holds the sample plates and reservoirs and moves to align the
samples, water, or buffer with the capillaries.
Capillary array Enables the separation of the fluorescent-labeled DNA
fragments by electrophoresis. It is a replaceable unit composed
of 4 or 16 silica capillaries.
Detection cell Holds the capillaries in place for laser detection.
Lower polymer block Contains the anode electrode. The anode buffer reservoir
connects to this block.
Oven Maintains uniform capillary array temperature.
Polymer-reserve syringe Contains and dispenses the polymer that fills the polymer
blocks and the array-fill syringe. A 5-mL syringe.
Array-fill syringe Contains and dispenses the polymer under high pressure to fill
the capillaries. A 250-µL syringe.
Upper polymer block Connects the two syringes and the detection end of the
capillary array.

System Overview 2-7

Back View

Diagram and The following diagram shows the back of the instrument:
Description

Chassis fan

Laser fan
Air filter holder

Ethernet outlet

Power cord

Air inlet vents

Air inlet vents

Table of Back View Components

Part Function
Air filter holder Holds the filter that cleans the air entering the instrument
Air inlet vents Allows air into instrument

IMPORTANT To ensure adequate air flow, do not place

paper under the instrument.
Ethernet outlet Provides a network connection to the computer workstation
Chassis fan Pulls air out of the instrument
Laser fan Cools the laser
Power cord Supplies power to the instrument

2-8 System Overview

Computer Workstation

Overview The 3100 or 3100-Avant Genetic Analyzer is shipped with a computer workstation
running the Microsoft® Windows NT® operating system. An optional color printer is
available.

This manual is written with the assumption that you know how to use a computer
workstation running the Windows NT operating system. If you are not familiar with this
computer, refer to the Windows NT workstation documentation shipped with this
system for specific operating information.

Function The computer workstation collects and analyzes data from the 3100 and 3100-Avant
Genetic Analyzer.

System The following table lists the minimum requirements for the computer workstation:
Requirements
Item Minimum Requirements
Hard drive storage 2 drives, 9 GB each
Memory 256 MB RAM
Monitor 17-in. SVGA
Operating system Microsoft Windows NT v. 4.0 with Service Pack 5
Printer Optional
Processor Intel Pentium III 733 MHz

Hard Drive During installation, the hard drives of your computer workstation were partitioned to
Partitions create the following logical drives:
Physical Hard
Drive Drive Function
1 C System operating files
D Reserved for the 3100/3100-Avant software and the
analysis software
2 E Reserved for the instrument database

System Overview 2-9

Software

Overview The software installed on your computer workstation consists of:

♦ Data collection software that controls, monitors, and collects data from the
instrument
♦ An analysis application that either analyzes raw sequencing data or sizes and
quantifies DNA fragments
♦ Software that automatically extracts and analyzes the data
♦ A database
♦ Utilities that enable you to manage the files in the database
♦ A toolkit that enables you to develop customized applications

For a complete list of the software installed on your computer, see “Software
CD-ROMs” on page 3-2.
Note Other programs are available from Applied Biosystems to align sequences, identify
previously unsequenced regions, archive data, identify patterns of heredity, and perform other
kinds of data manipulation. See your Applied Biosystems representative.

Note To avoid software conflicts, we recommend that you do not install third-party software
onto the computer attached to the 3100 and 3100-Avant instrument.

2-10 System Overview

Supported Dye Sets and Applications

Overview DNA fragments are detected and identified by the fluorescent dyes with which they are
chemically labeled. Dyes are purchased and used as dye sets, which are optimized for
particular applications.

3100 Dye Sets and Use the table below to determine the correct dye set and matrix standard set for the
Applications application you are using.
Application or Kit Dye Set Matrix Standard Set
♦ ABI PRISM ® BigDye® v3.0 Terminator chemistry Z BigDye® v3.0 Matrix
Standards
♦ ABI PRISM ® BigDye® v3.0 Primer chemistry
BigDye® v3.0 Terminator
Sequencing Standard
♦ ABI PRISM ® BigDye® Terminator chemistry E DS-01
♦ ABI PRISM ® BigDye® Primer chemistry
♦ ABI PRISM ® dRhodamine Terminator chemistry
Custom oligos D DS-30
♦ ABI PRISM ® Mouse Mapping Set v1.0 D DS-31
(DS-30 + VIC™ Matrix
♦ Custom oligos
Standard)a
♦ AmpFlSTR® COfiler® Kit F DS-32
♦ AmpFlSTR® Profiler Plus™ Kit
♦ AmpFlSTR® SGM Plus® Kit
♦ Other 4-Dye AmpFlSTR® Kits
ABI PRISM ® SNaPshot™ Multiplex System E5 DS-02
♦ ABI PRISM ® Linkage Mapping Set (LMS) v2.5 G5 DS-33
♦ Custom Oligos
♦ AmpFlSTR® Identifiler™ Kit
♦ Other 5-Dye AmpFlSTR® Kits
a. Replace the HEX™ matrix standard in DS-30 kit with the VIC matrix standard.

System Overview 2-11

3100-Avant Dye Sets Use the table below to determine the correct dye set and matrix standard set for the
and Applications application you are using.
Application or Kit Dye Set Matrix Standard Set
ABI PRISM ® BigDye® Terminator v3.0 chemistry Z ABI PRISM ® BigDye®
v3.0 Matrix Standard
ABI PRISM ® BigDye®
v3.0 Terminator
Sequencing Standard
ABI PRISM ® BigDye® Terminator chemistry E DS-01
Custom oligos D DS-30
♦ ABI PRISM ® Mouse Mapping Set v1.0 D DS-31
(DS-30 + VIC™ Matrix
♦ Custom oligos
Standard)a
ABI PRISM ® SNaPshot™ Multiplex System E5 DS-02
♦ ABI PRISM ® Linkage Mapping Set (LMS) v2.5 G5 DS-33
♦ Custom Oligos
a. Replace the HEX™ matrix standard in DS-30 kit with the VIC matrix standard.

Polymers

Overview The ABI PRISM ® 3100 POP Polymer ™ is used as a replaceable sieving medium that
separates the DNA fragments by size during electrophoresis.

POP polymer is shipped ready to use.

Supported Polymers Two polymers used with the 3100 and 3100-Avant system are as follows:

Polymer Name Use for... Part Number

ABI PRISM ® 3100 POP-4™ polymer Fragment analysis 4316355
Long read sequencing
Ultra rapid sequencing
ABI PRISM ® 3100 POP-6™ polymer Standard sequencing 4316357
Rapid read sequencing

Chemical Hazard CHEMICAL HAZARD. POP polymer may cause eye, skin, and respiratory tract
irritation. Please read the MSDS, and follow the handling instructions. Wear appropriate
protective eyewear, clothing, and gloves. Use for research and development purposes only.

2-12 System Overview

 Storage and POP polymers are stable on the instrument for 7 days.
Expiration ® ™
Store any remaining ABI PRISM 3100 POP polymer at 2 to 8 °C until the expiration
date printed on the jar.
Note Excessively hot environments may shorten the working life of the polymer.

Proper Disposal As the generator of potentially hazardous waste, it is your responsibility to perform the
actions listed below:
♦ Characterize (by analysis if necessary) the waste generated by the particular
applications, reagents, and substrates used in your laboratory.
♦ Ensure the health and safety of all personnel in your laboratory.
♦ Ensure that the instrument waste is stored, transferred, transported, and disposed
of according to all local, state/provincial, or national regulations.
Note Radioactive or biohazardous materials may require special handling and disposal
limitations may apply.

Injection Solution

Overview The injection solution is a fluid that is used to:

♦ Denature (separate) the DNA strands.
♦ Resuspend DNA samples before starting a sample run.
♦ Resuspend calibration standards during the preparation of a calibration or sample
run.
♦ Maintain the electrical connection between the polymer in the capillaries and the
injection wells in the electrophoresis chamber by acting as an electrolyte
(necessary for electrophoresis).

Hi-Di Formamide The injection solution recommended for use with the 3100 and 3100-Avant is Hi-Di ™
Formamide (P/N 4311320) or formamide of equivalent quality.
! WARNING CHEMICAL HAZARD. Formamide is harmful if absorbed through the skin
and may cause irritation to the eyes, skin, and respiratory tract. It may cause damage to the
central nervous system and the male and female reproductive systems, and is a possible birth
defect hazard. Please read the MSDS, and follow the handling instructions. Wear appropriate
protective eyewear, clothing, and gloves.

System Overview 2-13

Capillary Array

Overview The capillary array is a replaceable unit composed of silica capillaries that, when filled
with polymer, enable the separation of the fluorescent-labeled DNA fragments by
electrophoresis.

Instrument Capillary Number in an Array

3100 16
3100-Avant 4

Diagram
Combs

Detection cell

Loading bar
GR1637

Capillary sleeve Capillary electrodes

Description Part Function

Capillary sleeve Provides a seal, along with the ferrule and array ferrule knob, with
the upper polymer block
Capillary electrodes Hold the capillary ends in position
Combs Separate the capillaries to maintain consistent positioning and heat
distribution in the oven
Detection cell Holds the capillaries in place for laser excitation
Loading bar Supports the capillaries and provides a high-voltage connection to
the capillary electrodes

2-14 System Overview

 Available Lengths Length (cm) Use for...
22 Rapid fragment analysisa
36 ♦ Fragment analysis
♦ Ultra rapid DNA sequencing
♦ Rapid DNA sequencing
50 Standard DNA sequencing
80 Long read sequencing
a. Not supported for forensic applications.

IMPORTANT Fragment Analysis: For optimal resolution, as in the case of fine mapping,
Applied Biosystems recommends using the 36-cm capillary array. However, the 22-cm capillary
array can be used to rapidly scan the genome when using markers less than 360 bp. Refer to
ABI PRISM ® 3100 22-cm Capillary Array for High Throughput Microsatellite and SNP
Genotyping User Bulletin for more information.

Part Numbers For capillary array part numbers, see page B-1.

Electrophoresis

Overview Samples separate electrophoretically as they travel through the polymer in the
capillary array.

Temperature Housing the capillary array in a sealed oven controls electrophoresis temperature.
The following table lists the normal electrophoresis temperature for each type of run:

Temperature
Type of Run (°C)
Standard DNA sequencing 50
Rapid DNA sequencing 55
Standard fragment analysis 60
Long read DNA sequencing 50
Ultra rapid DNA sequencing 55

System Overview 2-15

Electrophoresis Circuit

Overview A high-voltage electrical circuit facilitates the electrophoresis of DNA fragments. The
electrical charge is conducted through the circuit by:
♦ DNA and ions in the polymer
♦ Ions in the buffer
♦ Electrons in the electrical wires and electrodes

Diagram The electrophoresis circuit is shown below.

Capillaries containing polymer

Upper polymer block

Tubing

Loading bar (cathode) (-)

Electrode (anode) (+)

Description During electrophoresis, a high voltage is applied between the loading bar (cathode)
and the electrode located on the lower polymer block (anode). The voltage drives the
movement of negatively charged DNA fragments through the polymer in the
capillaries towards the anode. From the anode, the current flows back in electrical
wires through the power supply to the cathode to complete the circuit.
ELECTRICAL SHOCK HAZARD. To reduce the chance of electrical shock, do
not remove covers that require tool access. No user serviceable parts are inside. Refer
servicing to Applied Biosystems qualified service personnel.

2-16 System Overview

Fluorescent Detection

Detection Overview The dye-labeled DNA fragments are separated by electrophoresis within the capillary
array. Once the fragments enter the detection cell, they pass through a laser beam.
The laser light excites the attached dye labels causing them to fluoresce.

The detection components work together to collect the fluorescence and convert the
information into electronic form. The electronic information is then processed and
displayed by the 3100 and 3100-Avant Data Collection software.

Detection The main components of the detection system and their function are listed in the
Components following table.
Note The many lenses and mirrors integral to detection are not covered in this section.

Part Function
Laser Excites the attached dye labels as the DNA fragments pass
through the detection cell
Spectral dispersion device Disperses the light by wavelength and a second set of
lenses focuses the resulting light spectrum onto the CCD
camera
CCD camera Converts the incident fluorescence into digital information
that is processed by the 3100 and 3100-Avant Data
Collection software

Note More information on each of the components follows this section.

Laser

Overview When a dye-labeled DNA fragment moves into the path of the laser beam, some
electrons in the dye are excited to higher energy levels as the laser light is absorbed.
Shortly afterwards, the electrons return to their ground states and emit fluorescence
light energy. The light emitted from each dye has a different spectral profile (color).

Laser Type The laser used to excite the dyes is an argon-ion laser.

Emission The primary emission lines are at 488 nm and 514.5 nm.
Wavelengths
Interlock For your safety, an interlock switch shutters the laser and shuts off the electrophoresis
power supply if the doors of the instrument are opened.

For more information on laser safety, refer to the ABI PRISM® 3100 Genetic Analyzer
and 3100-Avant Genetic Analyzer Site Preparation and Safety Guide (P/N 4315835).
LASER HAZARD. Exposure to direct or reflected laser light at 40 mW for 0.1
seconds can burn the retina and leave permanent blind spots. Never look directly into the laser
beam or allow a reflection of the beam to enter your eyes.

System Overview 2-17

Spectral Dispersion Device

Overview The spectral dispersion device is a grooved disk that spectrally separates the
fluorescence emitted (light) from the dye-labeled DNA fragments. After the light is
spectrally separated, it is focused onto the charge-coupled device (CCD) camera.

CCD Camera

Overview The CCD camera includes a rectangular silicon chip that converts the incident
fluorescence light into digital information.

This digital information (data) will be processed by the 3100 and 3100-Avant Data
Collection software.

2-18 System Overview

Software 3 3
In This Chapter The following topics are covered in this chapter:

Topic See Page

Software CD-ROMs 3-2
Software Suite 3-3
Applications in the Data Collection Software 3-5
Supporting Software 3-6
Types and Locations of Files 3-7
Edit Dye Display Information Dialog Box 3-8
Set Color Dialog Box 3-9
Manual Control Commands 3-11
Run Modules 3-13
Run Module Parameters 3-17
Transferring Run Modules Between Computers 3-18
Sequencing Analysis Modules 3-21
Creating a Sequencing Analysis Module 3-24
Analysis Modules for Fragment Analysis 3-30
Setting Up Sequence Collector Project Information 3-37
Preparing a Plate for Uploading to Sequence Collector 3-39
After Extracting to the Sequence Collector Database 3-44

Software 3-1
Software CD-ROMs

Introduction The ABI PRISM ® 3100 and 3100-Avant Genetic Analyzer software was installed on
your computer by an Applied Biosystems service engineer.

Contents of the CDs This software is provided on a set of six CD-ROMs and their contents are listed below.

CD Title Contents
3100 or 3100-Avant Software ♦ ABI PRISM ® 3100 or 3100-Avant Firmware
♦ ABI PRISM ® 3100 or 3100-Avant Data Collection
software
♦ Auto Extractor
♦ Extractor utility
♦ Clean up database utility
♦ MethodImport utility
♦ Remove Run Modules utility
♦ Diskspace utility
♦ InitDB utility
♦ ABI Sample File Toolkit
♦ OrbixWeb™ v. 3.2 Professional Edition
♦ Orbix Desktop® v. 2.3 software
♦ Persistence Powertier ® v. 4.321
♦ Java Runtime Environment ® v.1.1.7b
♦ Adobe Acrobat Reader ® with Search v. 3.01
GeneScan Applications ABI PRISM® GeneScan® Analysis software, including
(optional) the GeneScan program and sizecaller
Sequencing Analysis Applications ABI PRISM® DNA Sequencing Analysis software,
(optional) including the Sequencing Analysis program,
basecaller, and Factura™ Software
Oracle® Software Oracle® v. 8.0.5 database standard edition
Diagnostic software This software consists of diagnostic utilities for use by
Applied Biosystems service engineers only.
PowerQuest Drive Image 5 This software makes an image of the hard drive.
software

Determining the To determine the 3100 and 3100-Avant firmware and the 3100 and 3100-Avant Data
Software Versions on Collection software versions installed on your system, click the About Data Collection
Your System button on the toolbar.
Note Both the software and the instrument have to be running.

3-2 Software
Software Suite

Firmware Firmware controls the most basic operations of the instrument, such as turning on the
laser. The firmware is largely controlled by the commands sent from the computer
workstation. It acts as the link between the software commands and hardware
operations.

The 3100 and 3100-Avant firmware resides on the computer workstation and is
downloaded when the instrument is started. Therefore, the instrument and the
computer workstation must be running to perform any functions.

Data Collection The 3100 and 3100-Avant Data Collection software performs the following functions:
Software ♦ Works in conjunction with the firmware to control the mechanical operation of the
instrument, such as moving the autosampler and switching on the oven
♦ Collects and stores plate record data in the instrument database
♦ Automatically schedules samples to particular runs
♦ Monitors and displays the status of the instrument, and saves it to the instrument
database as EPT data
♦ Collects and converts fluorescence emission data to digital data during runs
♦ Stores the processed data in tables in the database and in temporary files on the
hard drive
♦ Displays electropherograms for the current run or any previous run still stored in
the instrument database
♦ Provides wizards, that guide you through routine maintenance procedures
♦ Provides utilities, that when launched, automatically perform database
maintenance

Additional Additional information about the 3100 and 3100-Avant software can be found in the
Information readme files and release notes on the software CD-ROMs.

Software 3-3
 Data Collection
Software Menu Main Menus Submenus Submenus

Flowchart File Import Plate

Override Spatial Calibration

Override Spectral Calibration

Exit

View Plate View

Run View

Status View

Array View

Capillary View

Instrument Status Monitor

Preferences Data Collection

Sequence Collector Project Info Data Analysis

3100/3100-Avant Instrument Run

Data Collection
software window
with tabs: Skip to Next Run Set Color
• Plate View
• Run View Pause Display Run Data
• Status View
• Array View Stop Display EPT Data
• Capillary View
Manual Control Display Entire Run

Data Aquisition Extract Data into Sample Files

Tools Plate Editor

Module Editor

Change Polymer Wizard

Install Capillary Array Wizard

Autosampler Calibration Wizard

Update Capillary Array Info

Perform Spatial Calibration

Display Spatial Calibration

Display Spectral Calibration

Set Active Spectral Calibration

Service Verify Instrument

Send SCPI Command

Run Service Module

Help About Data Collection

3-4 Software
Applications in the Data Collection Software

Auto Extractor/AE Auto Extractor is used to automatically extract and analyze the data after each run.
Server The AE server is part of the Data Collection software and contains the Auto Extractor.

Diskspace Utility The Diskspace utility lists the amount of space that the database uses, the amount
that is free for use, and the percent filled.

Extractor Utility The extraction utility (Extractor) uses the run data in the instrument database to create
sample files. If an ABIF sample file becomes corrupt or if you accidently delete a file
that you want, you can use the Extractor utility to re-extract the data into the sample
file.

Directions for using the Extractor utility start on page 5-2.

Cleanup Database The Cleanup Database utility (CleanupDB) deletes some of the information stored in
Utility the instrument database to make room for new run data.
Directions for using the Cleanup Database utility start on page 5-4.

Method Import The Method Import utility (MethodImport) imports the data contained in method files
Utility into the instrument database. Use this utility to install new versions of methods sent
out by Applied Biosystems after your genetic analyzer is installed.

Directions for running the Method Import utility start on page 5-6.

Remove Run The Remove Run Modules utility (RemoveRunModules) removes all modules and
Modules Utility associated information from the instrument database. Use this utility to quickly delete
all old modules before importing new ones.

Directions for running the Remove Run Modules utility start on page 5-7.

Initialize Database The Initialize Database utility (InitDB) completely erases and reinitializes the
Utility instrument database. Use this utility only when instructed to do so by an Applied
Biosystems representative.

Directions for running the Initialize Database utility start on page 5-8.

ABI Sample File Use ABI Sample File Toolkit to read ABIF sample files and to develop customized
Toolkit applications for the 3100 and 3100-Avant Genetic Analyzer.

Software 3-5
Supporting Software

OrbixWeb OrbixWeb v. 3.2 Professional Edition provides database management services

between the 3100 or 3100-Avant Data Collection software, Extractor utility, and the
Oracle database. OrbixWeb v. 3.2 Professional Edition has no user interface; however,
it must always be running when the 3100 and 3100-Avant Data Collection software or
Extractor utility is running.

Orbix Desktop Orbix Desktop v. 2.3 software is middleware that is used by the 3100 and 3100-Avant
Data Collection software and the Extractor utility.

Persistence Persistence Powertier v. 4.321 is an application server that allows the 3100 and
Powertier 3100-Avant Data Collection software to interact with the instrument database.

Java Runtime Java Runtime Environment v. 1.1.8 is software that enables the 3100 and 3100-Avant
Environment Data Collection software to run.

Adobe Acrobat Adobe Acrobat Reader is a program that allows you to read electronic documents
Reader saved in the portable document format (PDF).

Oracle Database The Oracle® instrument database stores the following types of information:
♦ Processed, but unanalyzed, fluorescence data, which is collected from the CCD
♦ Plate records, which contain information about plates and their samples
♦ Run schedules, which are lists of runs automatically assigned by the software
♦ Run modules
♦ EPT data

This manual describes how the database is used by the 3100 or 3100-Avant software.
Consult an Oracle database administrator for more information about administering
the database.

GeneScan Analysis If you purchased the GeneScan option, GeneScan Analysis software will be installed
Software on the hard drive of your computer workstation. This software is used to:
♦ Review the fragment analysis profile and size data
♦ Reanalyze the data

DNA Sequencing If you purchased the sequencing option, DNA Sequencing Analysis software will be
Analysis Software installed on the hard drive of your computer workstation. This software is used to:
♦ Review basecalled sequences
♦ Reanalyze the data

3-6 Software
Types and Locations of Files

Introduction The 3100 and 3100-Avant software includes many different files and folders. Some of
these are created to store run data and calibration data. Others are required to run the
software.
IMPORTANT Never move or delete any file or folder unless specifically directed to do so by an
Applied Biosystems representative or by the 3100 and 3100-Avant documentation. Doing this
could render the software inoperable.

Filename Extensions You can recognize certain file types by the three-letter extensions in their file names.
The common file types and their extensions for the 3100 system are listed below.
Note The 3100-Avant system will show 3100-Avant instead of 3100 in the directory.

Extension File Type Directory (if Applicable)

.ab1 ABIF sample file for sequencing analysis D:\AppliedBio\3100\DataExtractor
.bat Batch file initiates a series of software —
events (e.g., 3100Collection.bat)
.bcp Basecaller parameter file D:\AppliedBio\Shared\Analysis\Basecaller\Params
.exe Executable program —
.fsa ABIF sample file for fragment analysis D:\AppliedBio\3100\DataExtractor
.fsf Factura settings file D:\AppliedBio\Shared\Analysis\Factura\Settings
.gsp Analysis module for GeneScan D:\AppliedBioi\Shared\Analysis\Sizecaller\Params
.ini Initialization file —
.log Log file in text file format —
.mcl Spectral calibration file D:\AppliedBio\3100\DataCollection\Spectral Cal
Logs\Spectral Cal
.mob Mobility file D:\AppliedBio\Shared\Analysis\Basecaller\Mobility
.modexp Exported run module file —
.mtd Method file D:\AppliedBio\Support Files\Data Collection Support
Files\Method Files
.par Spectral calibration parameter files D:\AppliedBio\Support Files\Data Collection Support
Files\Calibration Data\Spectral Calibration\Param Files
.pdf Portable document format file that can be —
read by Adobe Acrobat Reader
.plt Plate file (tab-delimited text file) for import D:\AppliedBio\Support Files\Data Collection Support
into the instrument database to create a Files\Plate Import Files
plate record
.saz Analysis module for sequencing analysis D:\AppliedBio\Shared\Analysis\Basecaller\Params
.scl Spatial calibration file D:\AppliedBio\3100\DataCollection\SpatialCalLogs
.scp Sizecaller parameter file D:\AppliedBioi\Shared\Analysis\Sizecaller\Params
.szs Size standard file D:\AppliedBio\Shared\Analysis\SizeCaller\SizeStandards
.tmp Temporary run or calibration data file written —
in code
.txt Text file that can be read by Notepad —

Software 3-7
Edit Dye Display Information Dialog Box

Introduction The formats for the dye colors shown in the electropherogram and capillary displays
are set in the Edit Dye Display Information dialog box.

You can use the Edit Dye Display Information dialog box to:
♦ View the current settings for the displayed dye colors (e.g., the blue plots may
represent the base cytosine)
♦ Hide the data for particular dyes so that it does not appear in the displays
♦ Change the names of the dye
♦ Change the color intensity
♦ Open the Set Color dialog box to change the colors shown. (See “Set Color Dialog
Box” on page 3-9.)

Opening the Dialog To open the Edit Dye Display Information dialog box:
Box
Step Action
1 Select Instrument > Data Acquisition.
2 Select Set Color.
This opens the Edit Dye Display Information dialog box as shown below.

Dialog Box The operations of the Edit Dye Display Information dialog box are summarized in the
Operations diagram below.

Slide to
Click in the Name text box increase/decrease
to change the name of the the color intensity
dye

Click to open the Set Color

dialog box
Clear to hide the
data for this dye in
the displays
Click to store any changes
you make in the Set Color
dialog box and close the
Click to undo test
Edit Dye Display
changes
Information dialog box

Click to test the effect of

any changes you make,
without storing the changes

3-8 Software
Set Color Dialog Box

Changing the It is a good idea to change the colors used in the electropherogram and capillary
Display Colors Using displays if you find it hard to distinguish the default colors.
the RGB System There are two ways to change the color used to represent the concentration of dye in
the 3100 or 3100-Avant Data Collection software user interface:
♦ Using the red green blue (RGB) color system
♦ Using the hue saturation value (HSV) color system

The RGB system uses the three primary colors (red, green, and blue) in various
proportions to create the other colors.

To change the displayed dye color using the RGB system:

Step Action
1 Select Instrument > Data Acquisition > Set Color.
2 a. Within the Edit Dye Display Information dialog box, click the Color box of the
color you want to change. See “Dialog Box Operations” on page 3-8.
b. Select the RGB tab.

RGB tab

3 Move the sliders to mix the three colors until you produce the display color that you
want.
4
To... Click...
Incorporate the change OK
Ignore the change Cancel
Revert to the default colors Reset

5 Close the Edit Dye Display Information dialog box.

Software 3-9
 Changing the The Hue Saturation Value (HSV) system describes colors in terms of three
Display Colors Using properties1:
the HSV System
Property Description
Hue The wavelength composition of the color, e.g., blue
Saturation (chroma) The purity of the color in a scale from gray to the most vivid version
of the color
Value (intensity) The relative lightness or darkness of a color in a range from black
to white; e.g., light red, dark green, etc.

To change the displayed dye color using the HSV system:

Step Action
1 Select Instrument > Data Acquisition > Set Color.
2 a. Within the Edit Dye Display Information dialog box, click the Color box of the
color you want to change. See “Dialog Box Operations” on page 3-8.
b. Select the HSV tab if it is not already selected.

HSV tab
Hue
Saturation
Value

3 Click in the circle and drag the cross-hair pointer around the circle to select the
desired hue.
4 Click in the inner square and drag horizontally to select the desired saturation.
5 Click in the inner square and drag vertically to select the desired value.
6
To... Click...
Incorporate the change OK
Ignore the change Cancel
Revert to the default colors Reset

7 Close the Edit Dye Display Information dialog box.

1. See the Essential Guide to User Interface Design, W. O. Galitz (1996), John Wiley & Sons.

3-10 Software
Manual Control Commands

Table of Commands The following table displays the manual control options as they are organized in the
Data Collection software.

Command Category Command Name Value

Electrophoresis Set Power Supply ♦ On
♦ Off
Set Voltage A number between 0 and 15 kV
Laser Set State ♦ Idle
♦ On
♦ Off
Set Power A number between 0 and 25 mW
Open/Close Shutter ♦ Open
♦ Closed
Oven Set State ♦ On
♦ Off
Set Temperature A number between 18 and 65 °C
Autosampler Move Forward N/A
Return N/A
Move Up/Down A number between –500 and 500 steps
Move to Site ♦ Site 1 (left, front for 1X running
buffer)
♦ Site 2 (left, rear for deionized water)
♦ Site 3 (right, front for deionized
water)
♦ Site 4 (right, rear for deionized
water)
Array-fill syringe Move Home N/A
Move Up A number between 1 and 1200 steps
Move Down A number between 1 and 1200 steps
Polymer-reserve Move Home N/A
syringe Move Up A number between 1 and 1200 steps
Move Down A number between 1 and 1200 steps
Pin-valve Set Position ♦ Open
♦ Closed
Capillary Fill ♦ 50 cm/POP6
♦ 36 cm/POP4
♦ 36 cm/POP6
♦ 22 cm/POP4
♦ 80 cm/POP4

Software 3-11
 Sending a Manual IMPORTANT The oven and instrument doors must be closed for manual control commands to
Control Command execute.
Note You cannot send a manual control command during a run.

To send a manual control command:

Step Action
1 Select Instrument > Manual Control.

2 Select a Command Category from the drop-down list.

3 Select a Command Name.
Note To check a command’s function, read the Comment box.
4 Enter or select a Value.
5 Click Send Command.

Note Some tasks require that you send more than one manual control command. For
example, to heat the oven to 50 °C, you first send a command to turn on the oven, and then you
send a command to set the temperature.

3-12 Software
Run Modules

Introduction The run module specifies the conditions for how the sample is run. Examples include:
♦ Duration of the run
♦ Run temperature
♦ Injection time

Viewing a Run To view a run module:

Module
Step Action
1 Select Tools > Module Editor or click the Module Editor button on the toolbar.

This opens the Module Editor dialog box.

2 a. In the Modules group box, select either the Sequencing or GeneScan tab, as
appropriate.

Note The Calibration tab lists the spatial and spectral calibration modules.

b. To view the parameters for a particular module, select the name of the module
from the list. All the parameters for the run module are displayed.

Software 3-13
 Creating a Run To create a new run module:
Module
Step Action
1 a. Click the Module Editor icon on the toolbar to open the Module Editor dialog box.

b. Click New.

2 a. Select the:
♦ Application
♦ Template module
♦ Name for the new module

b. Click OK.
3 Edit the parameter values that you want to change.

IMPORTANT Only whole numbers are accepted.

IMPORTANT Be sure that all values are red. Values in black are not saved.

3-14 Software
 To create a new run module: (continued)

Step Action
4 Click Save.
Option: Click Save As. Enter a unique descriptive name and click OK.

Note Save cannot be applied to default run modules. Save the module under a
different name.
5 When you are finished, click the Close button ( ) to exit the Module Editor.

Editing a Run To edit an existing run module or to create a new run module:
Module
Step Action
1 a. Click the Module Editor icon on the toolbar to open the Module Editor dialog box.

b. Select a module by double-clicking.

2 Edit the parameter values that you want to change.

IMPORTANT Enter whole numbers.

IMPORTANT Be sure that all values are red. Values in black are not saved.

Software 3-15
 To edit an existing run module or to create a new run module: (continued)

Step Action
3 Click Save As.
Enter a unique descriptive name and click OK.

Note Save cannot be applied to default run modules. Save the module under a
different name.
4 When you are finished, click the Close button ( ) to exit the Module Editor.

3-16 Software
Run Module Parameters
\

Introduction You can change the module parameters listed below when creating run modules. The
parameters are listed in the table below in the order in which they appear in the run
module editor.
Note Not all parameters are visible in the run module editor for all supplied sequencing,
GeneScan run method files, and calibration files.

Modifiable Run The following table lists the user-modifiable run module parameters:
Module Parameters
Parameter Comment
Run The temperature of the oven during the run. The speed of electrophoretic
Temperature migration decreases as the electrophoresis temperature decreases.
Cap The time set for the array-fill syringe to pump polymer into the capillaries.
FillVolume
IMPORTANT If this value is decreased from that in the supplied run
module, the polymer used during the previous run may not be completely
replaced. This could lead to an accumulation of residual, large DNA
fragments in the capillaries over time, causing an increase in background
signal.
Prerun Voltage The voltage applied across the capillaries during the prerun period of
electrophoresis. A prerun is performed to equilibrate the ionic strength
across the capillary array before electrokinetic injection.
Prerun Time The duration of the prerun period of electrophoresis.
Injection The voltage applied across each capillary during electrokinetic injection.
Voltage The injection voltage is directly proportional to the amount of DNA
injected. This works in conjunction with the Injection Time to control the
amount of DNA injected.
Injection Time The duration of electrokinetic injection. This works in conjunction with the
Injection Voltage to control the amount of DNA injected.
Run Voltage The editable voltage applied across each capillary during a run. You may
include a voltage ramp at the beginning of electrophoresis.
Data Delay The period of electrophoresis between the completion of electrokinetic
Time injection and the time at which the software starts to collect data.
Run Time The duration of electrophoresis, including the Data Delay Time. The
maximum run time for DNA sequencing and fragment analysis runs is
16,000 seconds.

Software 3-17
Transferring Run Modules Between Computers

Overview The process of transferring run modules between two instrument databases on
different computers is illustrated below.

Exporting a Module A run module cannot be transferred directly. The data in a run module must first be
copied into a file that is created and stored on a hard drive. This is known as exporting
the module because you are exporting it from the database.

The file created has the file name format: filename.modexp

The hard drive to which the run module file is saved could be the local drive of the
donor or acceptor computer, or it could be a server that is accessible to both
computers.

3-18 Software
 Exporting a Run To export a run module:
Module
Step Action
1 Click the Module Editor icon on the toolbar to open the Module Editor dialog box.

2 a. Select the appropriate application (GeneScan, Sequencing, or Calibration) tab.

b. Select the module in the Modules group box that you want to export.
c. In the Modules group box, click Export.
This opens the Export browse dialog box as shown for the 3100-Avant instrument
below.

3 Navigate to the folder in which you want to save the run module file.

Note Due to software limitations, you cannot select a folder on the desktop.
4 Double-click the destination folder so that its contents are displayed in the pane.
5 In the File name box, type a name for the file.

Note Keep the name to fewer than 32 characters. A file name longer than 32
characters will not import.
6 Click OK. This creates a run module in the specified folder.

This message confirms

a successful export.

Importing a Module The data in the exported file is copied to the donor database to recreate the original
run module. This is known as importing the module. The recreated run module has the
same name as the original except for a unique number added by the software. The
number is based on the date. This prevents conflicts with the original run module in
the donor database.
Note You cannot read a run module file because it is written in code.

Software 3-19
 Importing a Run Note A run module file name longer than 32 characters will not import. There is no error
Module File message.
To import a run module file:
Step Action
1 Go to the computer to which you want to transfer the run module.
2 Click the Module Editor icon on the toolbar to open the Module Editor dialog box.

3 In the Modules group box, click Import. This opens a browser dialog box as shown
for the 3100-Avant instrument below.

4 Navigate to the folder in which you saved the run module file and select the file.

Note Due to software limitations, you cannot select a folder on the desktop.
5 Click OK to import the file.

Your file shows up in the list. The Comments box confirms a successful import.

3-20 Software
Sequencing Analysis Modules

Introduction Sequencing analysis modules, created with DNA Sequencing Analysis software,
provide the Auto Extractor with the parameters needed to analyze sequencing data.

Some sequencing analysis modules are provided with the 3100 or 3100-Avant Data
Collection software. In the DNA Sequencing Analysis software, the sequencing
analysis module is called a sequencing analysis settings file.

Viewing and Editing To view or edit a sequencing analysis module (.saz file):
Analysis Modules for
Step Action
DNA Sequencing
1 Start the DNA Sequencing Analysis software.

Note You may have an icon for the program on the Start menu. If not, you can find
the DNA Sequencing Analysis software (SeqA.exe) in the following directory:

D:\AppliedBio\SeqAnal\Bin
2 Select File > Open > Seq. AZ Settings.

Software 3-21
 To view or edit a sequencing analysis module (.saz file): (continued)

Step Action
3 Select the analysis module that you want to view or edit.
The analysis modules are stored in the following directory:
D:\AppliedBio\Shared\Analysis\Basecaller\Params

3100 sequencing analysis

modules

3100-Avant sequencing
analysis modules

This opens the sequencing analysis setting file (.saz).

3-22 Software
To view or edit a sequencing analysis module (.saz file): (continued)

Step Action
4

You can edit the following settings:

♦ Basecaller Type can be Basecaller-3100 (for standard sequencing) or
Basecaller-3100RR (for rapid-run sequencing). The files (.bcp) are located in the
following directory:
D:\AppliedBio\Shared\Analysis\Basecaller\Params
♦ Basecaller Settings are specified in the Preferences dialog box (accessed from
the Edit menu).
♦ If the Write .Seq Files box is selected, text files of the basecalled sequence are
written in either ABI or FASTA formats.
♦ If a Factura Settings File is selected, Factura processing will be applied during
analysis.
– To view or edit a Factura settings file: Select File > Open > Factura Settings.
– The files are located in the following directory:
D:\AppliedBio\Shared\Analysis\Factura
5
If you have made changes to
the analysis module and
you... Then...
want to save the changes click Save As to create a new analysis
module. Enter a unique descriptive name and
click OK.
don’t want to save the changes click the Close button to close the window.

Software 3-23
Creating a Sequencing Analysis Module
\

Overview Creating a sequencing analysis module requires:

♦ Creating a basecaller settings file
♦ Creating a Factura settings file
♦ Creating a new sequencing analysis module
♦ Saving the sequencing analysis module

For detailed information about the topics covered in this section, see the ABI PRISM ®
DNA Sequencing Analysis Software v. 3.7 NT User Guide (P/N 4308924).

Creating a To create a basecaller settings file:

Basecaller Settings
Step Action
File
1 Quit the 3100 or 3100-Avant Data Collection software if it is running.
2 Start the DNA Sequencing Analysis software.
The Sample Manager window opens inside the Sequencing Analysis window.

3-24 Software
To create a basecaller settings file: (continued)

Step Action
3 To set a cutoff condition for the analysis, select Edit > Preferences > Basecaller
Settings.

Note The default setting has the cutoff conditions disabled.

4 In the Preferences dialog box, click Create a set.
5 Check one or more of the Set endpoint check boxes as appropriate.
6 If you checked the second, third, or fourth check box, type the number(s) that you
want to use into the text boxes.
The Create a set button becomes Save this set as.

Note “Ns” means bases that could not be assigned an identity.

7 Click Save this set as.

a. Type a name for the basecaller settings file into the text box.
b. Click Save.
8 In the Preferences dialog box, click OK.
This saves the basecaller settings.

Software 3-25
 Creating a New To create a new Factura settings file:
Factura Settings File
Step Action
1 Select File > New > Factura Settings.

2 Select the required options, then click the Close button.

A Sequencing Analysis alert box displays.
3 Click Save.
The Save this document as dialog box displays.
4 In the File name box, type the name you want to use for the Factura settings file.
Note Do not use any of the following characters in the file name: *< > ? | / \ : ”. Do
not use spaces.
5 Make sure that the file will be saved to the following directory:
D:\AppliedBio\Shared\Analysis\Factura\Settings

3-26 Software
 Creating a New To create a new sequencing analysis module:
Sequencing Analysis
Step Action
Module
1 Select File > New > Seq.AZ Settings.

2 From the Basecaller Type drop-down list, select a basecaller.

Either:
♦ Select the name of the basecaller settings file that you just created from the
Basecaller Settings drop-down list, or
♦ Use the default settings
3 Select Write .Seq Files if you want a .Seq file created (this saves the sequence as a
text file).
4 In the Sequence File Format group box, select either ABI or FASTA.
Note Select FASTA only if you intend to export the data to a program that accepts
FASTA files.
5
If you do... Then...
not want to use Factura leave Factura Settings File as Don’t Facturize.
software
want to use Factura software select a Factura settings file from the
drop-down list.

Software 3-27
 Saving the To save the newly created sequencing analysis module:
Sequencing Analysis
Step Action
Module
1 Click the Close button on the untitled dialog box.
2 Click Save.

3
3100-Avant
analysis modules

a. In the File name text box, type a name for the analysis module.

Note Do not use any of the following characters in the file name: * < > ? | / \ : “. Do
not uses spaces.

b. Make sure that the file will be saved to the following directory:
D:\AppliedBio\Shared\Analysis\Basecaller\Params
c. Click Save.
This creates an analysis module with the format file name.saz.

Note You can check that the analysis module was saved by examining a plate record in the
plate editor as described below.

3-28 Software
 Ensuring the To check that the analysis module was saved:
Analysis Module
Step Action
Was Saved
1 Open the 3100 or 3100-Avant Data Collection software.
2 In the Plate View page, double-click a plate record to open the plate editor.
If the plate record is already open, close it, and then re-open it.
3 Scroll horizontally to the Analysis Module 1 column.
4 Click in a cell that lists a sequencing analysis module. The list of sequencing
analysis modules drops down.

5 Make sure that the sequencing analysis module you just created is listed.

Note If it is not listed, you may have saved the sequencing analysis module in the
wrong folder.

Software 3-29
Analysis Modules for Fragment Analysis

Introduction Analysis modules for fragment analysis provide the Auto Extractor with the
parameters needed for analyzing data from fragment analysis.

Viewing and Editing To view or edit an analysis module for fragment analysis (.gsp file):
Analysis Modules
Step Action
1 Start the GeneScan Analysis software.

Note You may have a program icon for the GeneScan Analysis software on the
Start menu or a shortcut icon on your desktop. If not, you can find the application
(GeneScan.exe) in the following directory:

D:\AppliedBio\GeneScan\Bin
2 Select File > Open then select the Analysis Parameters icon.

3 Select the analysis module you want to view or edit. The analysis modules are
stored in the following directory:
D:\AppliedBio\Shared\Analysis\Sizecaller\Params

4 Click Open.

3-30 Software
To view or edit an analysis module for fragment analysis (.gsp file): (continued)

Step Action
5 If you want, you can make changes to the analysis module. For more information
about the parameters, see the ABI PRISM ® GeneScan® Analysis Software v. 3.7 NT
User Guide (P/N 4308923).

6
If you have made changes to
the analysis module and
you... Then...
want to save the changes ♦ Select File > Save As, assign a unique
name, and then click OK, or
♦ Select File > Save to save the changes to
the current analysis module.

IMPORTANT The analysis modules must be

stored in the following folder:
D:\AppliedBio\Shared\Analysis\
Sizecaller\Params
do not want to save the Click the Close button to close the window.
changes

Software 3-31
 Before Creating an Before creating an analysis module for fragment analysis, you may need to create a
Analysis Module custom size standard file.
You will need to create a custom file for performing:
♦ Denaturing runs but not using GeneScan™-350 Size Standard,
GeneScan™-400HD Size Standard, or GeneScan™-500 Size Standard
♦ Non-denaturing runs using applications such as SSCP
♦ Runs using one of the Applied Biosystems internal lane standards, but
significantly altering collection time or analysis range
♦ Runs where the size standard data differs significantly (i.e., extra or missing
peaks)

Creating a Size To create a size standard file:

Standard File
Step Action
1 Review the size standard data and optimize the analysis parameters.
2 Quit the 3100 or 3100-Avant Data Collection software if it is running.
3 Start GeneScan Analysis software.
You may have a program icon for the GeneScan Analysis software on the Start
menu or a shortcut icon on your desktop. If not, you can find the application
(GeneScan.exe) in the following directory:
D:\AppliedBio\GeneScan\Bin

4 Select File > New to open the Create New box.

5 a. Click the Size Standard icon to open a browser dialog box.

b. Navigate to the DataExtractor folder in the following directory:
D:\AppliedBio\3100\DataExtractor or
D:\AppliedBio\3100-Avant\DataExtractor

3-32 Software
To create a size standard file: (continued)

Step Action
6 Select the GeneScan sample file (with the extension .fsa) that you want to use as a
template.

7 a. Click Open.

b. From the Dye drop-down list, select the dye-color that was used to label the size
standard DNA fragments.
8 From the Analysis Parameters drop-down list, select <Analysis Parameters>.
This references the current analysis parameter settings rather than an analysis
parameter file.

Software 3-33
 To create a size standard file: (continued)

Step Action
9 Click OK.

10 In the Size column, enter the known sizes of the standard’s peaks.

11 Select File > Save.

12 Navigate to the SizeStandards folder located in the following directory:
D:\AppliedBio\Shared\Analysis\SizeCaller\SizeStandards
The folder contains a number of size standard (.szs) files.

13 a. In the File name text box, type a file name for the size standard file.
b. Click Save. The browser dialog box closes and the file is saved to the correct
directory location for Auto Extractor to read.
In the newly created Filename.szs dialog box, click the Close button.

3-34 Software
Creating an Analysis To create an analysis module for fragment analysis:
Module for
Step Action
Fragment Analysis
1 Select File > New.

2 Click the Analysis Parameters icon.

3 Fill out the untitled dialog box according to the directions given in the ABI PRISM®
GeneScan Analysis Software v. 3.7 NT User Guide.

In the AutoAnalysis Only group box, select the size standard file that you just
created from the Size Standard drop-down list.

Software 3-35
 To create an analysis module for fragment analysis: (continued)

Step Action
4 a. Select File > Save.
This opens a browser dialog box.
b. Navigate to the Params folder in the following directory:
D:\AppliedBio\Shared\Analysis\Sizecaller\Params

5 a. In the File name text box, type a file name for the analysis parameter file.
b. Click Save.
The browser dialog box closes and the file is saved to the correct directory location
for the Auto Extractor to read.
6 In the newly created Filename.szs dialog box, click the Close button.

3-36 Software
Setting Up Sequence Collector Project Information

Introduction In order to extract sample files into the Sequence Collector database, you must first
set up information for your Sequence Collector project(s) in the 3100 or 3100-Avant
Data Collection software. “Sequence Collector projects” are the Data Collection
software equivalent of “collections” in Sequence Collector.

When samples are extracted into the Sequence Collector database, they are added to
the specified Sequence Collector project.

Setting Up Sequence To set up the Sequence Collector project information:

Collector Project
Step Action
Information
1 Select View > Sequence Collector Project Info.

2
If you want to... Then...
add a new project a. Click Add Project and a blank row displays.
b. Continue with step 3.
delete an existing project a. Highlight the project you want to delete.
b. Click Delete Project.
c. Skip to step 4.

3 Enter the appropriate information in the text fields.

Text Field Description/Constraints

Project Name Type a descriptive name of your choice.

Note The Project Name will be the Collection Name in

the Sequence Collector database.
Project Owner Type in your name.

Note The Project Owner will be the Creator in the

Sequence Collector database.
Project Information Type in any comments, if desired.

Note The Project Information will be the Comment in

the Sequence Collector database.

Software 3-37
 To set up the Sequence Collector project information: (continued)

Step Action
4 Click OK to save your changes.
The new project(s) will be listed in the drop-down list under the Sequence Collector
Project column in the Plate Editor window.
5 Continue with “Preparing a Plate for Uploading to Sequence Collector” on
page 3-39.

3-38 Software
Preparing a Plate for Uploading to Sequence Collector

Introduction After you have set up the Sequence Collector project information, you must prepare a
plate record in the 3100 or 3100-Avant Data Collection software for extraction to the
Sequence Collector database. This requires:
♦ Specifying a Sequence Collector project in the plate’s sample sheet
♦ Setting Sequence Collector preferences for the plate

Specifying a To specify a Sequence Collector project in the plate’s sample sheet:

Sequence Collector
Step Action
Project
1 From the Tools menu, select Plate Editor.

2 Fill in the window items as follows:

Item Action
Plate Name Type the plate name.
Application Click on the appropriate application.
Plate Type Choose the appropriate type from the drop-down list.
Comments Type comments if desired.

Software 3-39
 To specify a Sequence Collector project in the plate’s sample sheet: (continued)

Step Action
3 Click Finish.
The Plate Editor spreadsheet opens with the plate name you assigned in step 2.

4 Fill in the spreadsheet, making sure to click on the Project Name column for each
well and select a Sequence Collector project from the drop-down list.

IMPORTANT All plates must have a Project Name.

5 Click OK.
Note You will receive a Please wait message before the software returns to the
Data Collection software window.
6 a. If it is not already selected, select the Plate View tab.
b. Make sure your plate is listed under Pending Plate Records.
7 Highlight your plate and continue with “Setting Sequence Collector Preferences” on
page 3-41.

3-40 Software
Setting Sequence To set Sequence Collector preferences for the plate:
Collector
Step Action
Preferences
1 Select View > Preferences.

2 In the Data Collection tab, set the following preferences:

a. In the Instrument Name field, enter a name for the instrument.
b. If you are importing plates from a database, then select the Enable plate import
from database check box and enter a polling interval.

Software 3-41
 To set Sequence Collector preferences for the plate: (continued)

Step Action
3 Select the Data Analysis & Extraction tab.

If you are… Then…

generating sample files complete step 4 and skip step 6.
uploading data to Sequence proceed to step 5.
Collector

Note When extracting to Sequence Collector the sample files are still created
under D:\AppliedBio\3100\Data Extractor or D:\AppliedBio\ 3100-Avant\Data
Extractor and they are uploaded to the Sequence Collector database.
4 a. In the Analysis and Extraction section, the Enable AutoAnalysis check box is
selected as default. Clear the box if you do not want your samples autoanalyzed.
b. In the Data Extraction Folder Root section, use the default or click Browse to
select a folder location for all generated data.
c. In Sample File Options, select how you want your sample files grouped. Select
the By run button to group by individual run or select the By plate button to group
by the entire plate.
d. In the Sample File Name Format section, use the drop-down lists to define the
sample file name format. A prefix and/or suffix can be added as needed.
e. In the Run Folder Name Format section, use the drop-down lists to define the
run folder name format. A prefix can be added as needed.
f. Click OK.

3-42 Software
To set Sequence Collector preferences for the plate: (continued)

Step Action
5 For database files, define the following:
a. In the Analysis and Extraction section, select Extract to Sequence Collector.
The Enable AutoAnalysis check box is selected as default. Clear the box if you
do not want your samples autoanalyzed.

b. In the Data Extraction Folder Root section, use the default or click Browse to
select a folder location for all generated data.
c. In the Sequence Collector Login section, define the server, DB name, login, and
password for the database you are using.

Note The server name is in the tnsnames.ora file and is the tnsalias name. This
name is on the left-hand side of the = sign in the tnsnames.ora file.

d. In the Sequence Collector Naming Format section, use the drop-down lists to
define the sample file name format. Add a prefix and/or suffix as needed.
6 Click OK.
The preferences will be applied to your highlighted plate.
7 Continue your setup and run your samples as usual.
When the run has completed, the sample files will be extracted to the Sequence
Collector database automatically.

Note View the xx_analysis.log or the xx_extraction .log file to see if the extraction
completed successfully.

Continue with “After Extracting to the Sequence Collector Database” on page 3-44.

Software 3-43
After Extracting to the Sequence Collector Database

Introduction After your samples have run, you must view the run log file to ensure the extraction to
the Sequence Collector database was successful.
IMPORTANT You will not receive any error messages if the extraction was not completed
successfully (e.g., if the database connection was not established, if the Sequence Collector
project information was entered incorrectly, etc.). The only way to check the status of the
extraction is to view the xx_analysis.log or the xx_extraction.log file.

Viewing a Run’s Log To view a run’s log file:

File
Step Action
1 Open the directory that contains the 3100 or 3100-Avant Data Collection software
and navigate to the ExtractedRuns folder. In most cases, the path will be either:
♦ D:\AppliedBio\3100\DataExtractor\ExtracedRuns
♦ D:\AppliedBio\3100-Avant\DataExtractor\ExtracedRuns
2 Open the ExtractedRuns folder.
A directory is created in this folder for each run you’ve performed on the instrument.
3 Find the run for which you want to check the status and open its directory.
All the data collected and extracted for this run is stored in this directory.
4 Open either the xx_analysis.log or the xx_extraction.log to check:

If the extraction was... Then...

completed successfully The following message appears after each sample
file listed “Successfully uploaded to Sequence
Collector.”
not completed A message appears after each sample file listed,
successfully explaining why the extraction was not successfully
completed. (For example “Failed to open connection
with database using specified credentials or database
was not alive.”)

You must manually upload the extracted data using

Sample2DB. See the Applied Biosystems Sequence
Collection Software Version 3.0 User's Guide,
(P/N 4319527) for instructions.

3-44 Software
Working with Plate
Records 4 4
In This Chapter The following topics are covered in this chapter:

Topic See Page

Creating Plate Records 4-2
Plate Record Fields 4-3
Tab-Delimited Text Files 4-7
Creating Tab-Delimited Text Files 4-8
Using Spreadsheets to Create Tab-Delimited Text Files 4-9
Spreadsheet or Tab-Delimited Text File Information 4-11
Running the Same Sample with Different Conditions 4-15
Creating a Plate Record by Importing LIMS Data 4-16
Plate Import Table 4-17
Creating a Plate File Using a Provided Template 4-19
Creating a Plate File from a New Spreadsheet 4-22
Creating a Plate File from a Custom Spreadsheet Template 4-23
Creating a Plate File from an Edited Plate Record 4-24
Importing Tab-Delimited Text Files and Linking Plate Records 4-25
Deleting Plate Records and Run Data 4-27

Working with Plate Records 4-1

Creating Plate Records

Introduction The instrument database stores information about the plates and the samples they
contain as data tables named plate records. Each plate placed on the instrument
requires a plate record.
Note A plate record is analogous to the Sample Sheet used with the ABI PRISM ® 377 DNA
Sequencer and an Injection List used with the ABI PRISM ® 310 Genetic Analyzer.

When to Create Create plate records in advance of placing the plates on the instrument or you can
Plate Records create a plate record while the instrument is running.
Data that will be imported for the creation of plate records can be prepared and stored
on any networked computer or transferred from a computer on a disk.

How to Create Plate There are numerous methods used to create plate records. The most convenient
Records method transfers data directly from a LIMS database. Once set up in the Preferences
dialog box of the ABI PRISM ® 3100 and 3100-Avant Data Collection software and the
LIMS program, the transfer of data and creation of plate records is completely
automatic, requiring no operator intervention.

Plate records can be created using the methods described in the following diagram:

Method 1 Method 2 Method 3 Method 4 Method 5 Method 6

Create a plate import In 3100/3100-Avant Open the provided, Make a new Open a spreadsheet In 3100/3100-Avant
record in a LIMS Data Collection tab-delimited text file spreadsheet in any template created Data Collection software
database. software, input the plate template program by you in any use the plate editor to
Import automatically and sample data directly (filename.plt) in compatible spread- modify an existing plate
into the plate editor Microsoft ® Excel sheet program record

Open the file as a Input the plate Modify the plate

spreadsheet and sample data and sample data

Modify the plate Save as a Save as a new

and sample data tab-delimited text file spreadsheet
(filename.plt)

Close the file, In 3100/3100-Avant Save it as a

saving changes Data Collection Change the plate tab-delimited text file
(as a tab delimited software import the name in Notepad using the
text file) filename.plt file Export command

Plate record

For instructions for each method, see the pages listed in the following table:

Method See Page... Method See Page...

1 4-16 4 4-22
2 ABI PRISM 3100 or 5 4-23
3100-Avant User
Guide
3 4-19 6 4-24

4-2 Working with Plate Records

Plate Record Fields

Introduction Plate record fields consist of the following:

♦ Dye sets
♦ Mobility files
♦ Size standards
♦ Run modules
♦ Analysis modules
♦ Sequence Collector

Dye Sets Provided Select a dye set from among the following options:

For... Select Dye Set

Fragment analysis D
Fragment analysis - SNP E5
Fragment analysis - Forensic applications F
Fragment analysis - high throughput LMS and HID applications G5
Fragment analysis - Molecular Diagnostic kits for the 3100 system only C
DNA sequencing analysis E
Z

Note See “Supported Dye Sets and Applications” on page 2-11 for more details on dyes.

IMPORTANT If you select the wrong dye set you will have to re-run your samples. You cannot
correct this after the run because multicomponenting is applied during the run.

Working with Plate Records 4-3

About Mobility Files Note Mobility files are identical to the dye set/primer files used on other ABI PRISM genetic
analyzers.

Mobility files are for DNA sequencing only. Mobility files are different for different dye
sets and instrument types.

A mobility file contains the data that is used to compensate for differences in the
electrophoretic mobilities of DNA fragments caused by labeling with different dye.

When a dye is bound to a DNA fragment, it changes the rate at which the fragment
migrates during electrophoresis. Electrophoresing DNA fragments that are labeled
with different dyes do not migrate with equal spacing because different dyes change
the migration rate to different extents. Without correction, this would lead to an uneven
separation of peaks in the electropherogram.

Mobility Files The following mobility files are provided with the 3100 and 3100-Avant software and
Provided stored in the following directory and are described in the mobility file table:
D:\AppliedBio\Shared\Analysis\Basecaller\Mobility

Dye primer mobility files for

3100 users only

dRhod v1.mob is an older

version mobility file. See note
below.

Note Select the newer version mobility file DT3100POP6{dRhod}v2.mob instead of the older
version DT3100POP6{dRhod}v1.mob file.

Note New versions of mobility files may become available from the Applied Biosystems Web
site. Mobility files for dye sets other than the ABI PRISM® BigDye® sets must be provided by the
manufacturer.

4-4 Working with Plate Records

 Run Modules A module is a collection of routines that perform a task. Run modules define the run
conditions for a sample. For a list of conditions you can set for running a sample, see
“Modifiable Run Module Parameters” on page 3-17.

Run Modules Provided

The following run modules are provided with the 3100 and 3100-Avant software.

Sequencing modules GeneScan modules Calibration modules

Analysis Modules A module is a collection of routines that perform a task. Analysis modules tell the
AutoAnalyzer which parameters to use for data analysis. You can use the analysis
modules provided and/or create your own to define different analysis parameters.

Analysis Modules Provided

The following analysis modules are provided with the 3100 and 3100-Avant software.
You can examine the settings for each of the files using the analysis software.

3100 Analysis Modules

Sequencing analysis modules Fragment analysis modules

Working with Plate Records 4-5

 3100-Avant Analysis Modules
Sequencing analysis modules Fragment analysis modules

Note Settings are described in the ABI PRISM® DNA Sequencing Analysis Software v. 3.7 NT
User Guide and the ABI PRISM® GeneScan® Analysis Software v. 3.7 NT User Guide.

Analysis Module Run Type

DNA Sequencing
BC-3100POP4UR_SeqOffFtOff.saz Ultra rapid DNA sequencing
BC-3100POP4_80cm_SeqOffFtOff.saz Long read DNA sequencing
BC-3100POP6RR_SeqOffFtOff.saz Rapid DNA sequencing
BC-3100POP6SR_SeqOffFtOff.saz Standard DNA sequencing
Fragment Analysis
GS120Analysis.gsp GeneScan using size standard GS120
GS350Analysis.gsp GeneScan using size standard GS350
GS400HDAnalysis.gsp GeneScan using size standard 400HD
GS500Analysis.gsp GeneScan using size standard GS500
GS400CubicAnalysis.gspa —
GS400Ord2Analysis.gspa
a. These modules are for advanced users with specific sizing needs. See the ABI PRISM ® GeneScan ®
Analysis Software v. 3.7 NT User Guide.

4-6 Working with Plate Records

Tab-Delimited Text Files

Introduction Tab-delimited text files are text-only files that contain groups of information, called
tokens, separated by tabs or end-of-line characters. Any text-only file (containing no
graphics or tables) created in a word-processing program is a text file. Using tab stops
to separate sections of text, and end-of-line characters to separate lines of text, makes
a file a tab-delimited text file.

Tab-delimited text files can be imported directly into the instrument database to create
plate records.

Examples A tab-delimited text file created in Microsoft® Word is shown below. The symbols do
not appear when the file is printed.

With the nonprinting symbols turned off, the file looks like this:

Word-Wrapped As in word-processed documents, tab-delimited text files with long lines wrap around
Example to the next line.

Word wrapping does not affect the performance of a file, but it does make the
information more difficult to comprehend.

Notepad The Microsoft® Windows NT® operating system includes a simple text-only word
processor called Notepad, located in the Accessories menu. Notepad will open any
text-only file, even if the file was created by a program using the Macintosh® operating
system. In this case, though, the end-of-line characters may need to be re-entered.

Working with Plate Records 4-7

Creating Tab-Delimited Text Files

Introduction Although it is possible to create tab-delimited text files by typing the required
information directly into a word-processing program, it is easier to first enter the data
into a spreadsheet, and then save the spreadsheet as a tab-delimited text file.
Spreadsheets are easier to work with because they organize data clearly in columns,
and because repetitive typing can be reduced by using their fill-down function.

You do not need to include all of the information required for a run before importing a
tab-delimited text file into the instrument database. Information can be added to the
plate record using the plate editor after the tab-delimited text file has been imported.
Note If you are importing data from a LIMS database, there cannot be any errors in the data
because there is no opportunity to review it and the import will fail (see page 4-16).

Overview of the The typical method for importing information to create a plate record is outlined below.
Method

4-8 Working with Plate Records

Using Spreadsheets to Create Tab-Delimited Text Files

Introduction You can enter plate record data into any spreadsheet program that can save files as
tab-delimited text files.

You can create spreadsheets in a program that uses the Macintosh operating system;
however, you must then convert the files into Microsoft Windows format files.
Examples are shown below.

Sequencing An example of a spreadsheet, prepared in Microsoft® Excel, for samples intended for
Spreadsheet DNA sequencing is shown below.
For an explanation of the labels, see page 4-11.

Version number

Plate header
Column header
Sample data

Sequencing When the above spreadsheet is converted to a tab-delimited text file and opened with
Tab-Delimited Text the Notepad program, it looks like the example below.
File

Fragment Analysis An example of a Microsoft Excel spreadsheet for samples intended for fragment
Spreadsheet analysis is shown below.

Version number
Plate header
Column header

Sample data

Working with Plate Records 4-9

 Fragment Analysis When the above spreadsheet is converted to a tab-delimited text file and opened with
Tab-Delimited Text the Notepad program, it looks like the example below.
File For an explanation of the labels, see page 4-11.

Empty Cells or Tab-delimited text files may be imported with empty tokens. Missing data can be
Tokens added using the plate editor.
IMPORTANT A space character (entered by pressing the space bar) must be entered
between tab stops in a tab-delimited text file, as a place marker for missing information. A space
character must be entered into each blank cell of a spreadsheet before converting it to a
tab-delimited text file.

IMPORTANT Do not leave whole empty rows (with the exception of the Well Location row) in a
spreadsheet or tab-delimited text file that is intended for import, as illustrated by the example
below.

Do this: Don’t do this:

Typing Accuracy It is extremely important to be accurate when typing information into a spreadsheet,
and Error Messages tab-delimited text file, or LIMS database that will eventually be imported into the 3100
or 3100-Avant Data Collection software.
When the 3100 or 3100-Avant Data Collection software is importing data from a text
file, it compares the relevant tokens with lists of run modules, analysis modules, etc.,
stored in the database or hard drive. The Data Collection software recognizes the data
only if it can make a match. If an “illegal” value is typed into a cell in certain columns,
the typed data will be deleted and the field will be blank in the imported plate record. If
the sample name contains restricted characters, the entire plate will not be imported.
IMPORTANT When naming the plate, you can use letters, numbers, and the following
punctuation only: -_(){}#.+. Do not use spaces.

When importing data from a LIMS database, an error will be logged and no plate
record will be created if the file contains a typing error.

4-10 Working with Plate Records

Spreadsheet or Tab-Delimited Text File Information

Introduction Four types of information are contained in a spreadsheet or tab-delimited text file
intended for import into the 3100 and 3100-Avant Data Collection software:
♦ Version number
♦ Plate header
♦ Column header
♦ Sample data

See the spreadsheet examples in “Using Spreadsheets to Create Tab-Delimited Text

Files” on page 4-9.

Version Number The version number is the only cell or token on the first row of a spreadsheet or
tab-delimited text file. It specifies the version of the formatting conventions used for
importing plate records.

Currently, the version that must be entered into all spreadsheets is 1.0. If there are
changes to the conventions, the version number will change, and you will be notified.

Plate Header The plate header is a sequence of five cells or tokens separated by tabs. These cells
or tokens must always be typed in the same order across the plate header.

Cell or Token Function

Plate Name Identifies a specific plate. The plate name you assign must not exceed
32 characters.

Note This is the same as the Plate ID listed in the plate record tables
of the Plate View page.
Application Identifies a plate as containing samples for either GeneScan analysis
(GS) or DNA sequencing (SQ).

IMPORTANT Do not mix samples for sequencing analysis and

fragment analysis in the same plate.
Plate Type Defines the type of plate. The codes used for the two plate types are
either:
♦ 96-Well
♦ 384-Well
Owner Identifies the name of the person who loaded the samples onto the plate
and/or created the spreadsheet
Comment Allows you to enter comments about the plate

Working with Plate Records 4-11

 Column Header for The column header for sequencing analysis contains up to eight cells or tokens that
Sequencing Analysis provide headings for the columns that will contain the sample data.
Column Headings
Column Head Function
Well Position Identifies the well in which the sample is located, e.g., A1, G6, O18, etc.
For 96-well plates, the well positions are A–H and 1–12. For 384-well
plates, the well positions are A–P and 1–24.

IMPORTANT This cell or token must always be first (from left to right).
Sample Name Identifies the sample. The sample name you assign must not exceed 63
characters.

IMPORTANT When naming the sample, you can use letters, numbers,
and the following punctuation only: -_(){}#.+. Do not use spaces.

IMPORTANT You must limit the sample name to 63 characters

(59-character filename and 4-character extension). If you exceed 63
characters, the name may be truncated when exported from the 3100 and
3100-Avant Data Collection software.

IMPORTANT This cell or token must always be second (from left to

right).
Dye Set Specifies the spectral information for the dyes used to label the DNA. This
name must match the names stored in the instrument database.

Note If you select the wrong dye set you will have to re-run your
samples. You cannot correct this problem after the run.
Mobility File Specifies the dye mobility file used for processing the fluorescence data.

Note This is identical to the dye set/primer file used with previous
ABI PRISM ® genetic analyzers.
Comment Allows you to enter comments about the sample.
Project Name Designates the Sequence Collector™ Genetic Information Management
System Collection name into which this sample will be added.

Note Do not leave this cell blank.

Run Module Specifies the run module used for the sample.

IMPORTANT This cell or token must always be next to last (from left to
right).

IMPORTANT The name of the run module must be typed correctly. If the
name is typed incorrectly, the plate will be imported but the run module will
not be entered in the plate record.
Analysis Specifies the analysis module used to run the sample. Sequencing
Module analysis modules have the file format: filename.saz

IMPORTANT This cell or token must always be last (from left to right).
You must always select an analysis module if you want the data to be
extracted and analyzed.
The name of the analysis module must be typed correctly. If the name is
typed incorrectly, the plate will be imported but the analysis module will not
be entered in the plate record.

4-12 Working with Plate Records

Column Header for The column header for fragment analysis contains up to 10 cells or tokens that provide
Fragment Analysis headings for the columns that will contain the sample data.
Column Headings
Cell or Token Function
Well Position Identifies the well in which the sample is located e.g., A1, G6, O18, etc.
For 96-well plates, the well positions are: A–H and 1–12. For 384-well
plates, the well positions are A–P and 1–24.

IMPORTANT This cell or token must always be first (from left to right).
Sample Name Identifies the sample. The sample name you assign must not exceed 63
characters.

IMPORTANT When naming the sample, you can use letters, numbers,
and the following punctuation only: -_(){}#.+. Do not use spaces.
You must limit the sample name to 63 characters (59-character filename
and 4-character extension). If you exceed 63 characters, the name may
be truncated when exported from the 3100 and 3100-Avant Data
Collection software.

IMPORTANT This cell or token must always be second (from left to

right).
Color Number Corresponds to a specific color button of the plate record Dye field.

Color Number Color Button

1 B
2 G
3 Y
4 R
5 O

Standard Dye Represents the size-standard color. This should be the number 4 for all
4-dye applications, which corresponds to the red dye. Selecting the
number 4 in this field is equivalent to selecting the diamond in the “R”
color box of the GeneScan Analysis software.
Use the number 5 for all 5-dye applications.
Dye Set Specifies the spectral information for the dyes used to label the samples.
It must match the names stored in the instrument database.
Color Info Enables you to identify the sample in GeneScan analysis software when
you are examining samples by color if you enter the sample name in this
optional field.
Color Comment (Optional) Enables you to customize the output for downstream analysis.
Project Name Designates the Sequence Collector™ Genetic Information Management
System Collection name into which this sample will be added.

Note Do not leave this cell blank.

Working with Plate Records 4-13

 Column Headings (continued)

Cell or Token Function

Run Module Specifies the run module used for the sample.

IMPORTANT This cell or token must always be next to last (from left to
right).

IMPORTANT The name of the run module must be typed correctly. If

the name is typed incorrectly, the plate will be imported but the run
module will not be entered in the plate record.
Analysis Module Specifies the analysis module used to run the sample. Fragment
analysis modules have the file format: file name.gsp

IMPORTANT This cell or token must always be last (from left to right).

IMPORTANT You must always select an analysis module if you want

the data to be extracted and analyzed.
The name of the analysis module must be typed correctly. If the name is
typed incorrectly, the plate will be imported but the analysis module will
not be entered in the plate record.

Sample Data The sample data begins on row 4 of a spreadsheet. A 96-well plate for sequencing
analysis contains up to 96 rows of sample data (one row for each sample, and
therefore each well). A 96-well plate for fragment analysis contains a multiple of 96
rows, since one well can contain several dye channels, each labeled with a differently
colored dye.

4-14 Working with Plate Records

Running the Same Sample with Different Conditions

Sample Run Options You can run the same sample up to five times using different combinations of analysis
modules and run modules as follows:
♦ Same run module, but different analysis module
♦ Same analysis module, but different run module
♦ Different run module and analysis module
♦ Same run module and analysis module (replicate run)
Note Make sure that you have enough sample for the number of runs you specify.

Setting Up Multiple Multiple runs of the same sample are set up in the plate record or tab-delimited text
Runs files imported to create a plate record. To perform more than one run with the same
sample, add additional pairs of run modules and analysis modules to the tab-delimited
text file as shown in the examples below.

Example One: A Sample Running with More Than One Run Module
Below is part of a spreadsheet showing data for a sample that will be run with three
different run modules with the same analysis module:

♦ The Run Module and Analysis Module column headings are used only once.
♦ Run modules and analysis modules are grouped in pairs with the run module
always placed to the left of its paired analysis module.

Example Two: A Sample Running with More Than One Analysis Module
Below is part of a spreadsheet showing data for a sample that will be run with three
different analysis modules, but with the same run module:

♦ The Run Module and Analysis Module column headings are used only once.
♦ Run modules and analysis modules are grouped in pairs, with the run module
always placed to the left of its paired analysis module.

Working with Plate Records 4-15

Creating a Plate Record by Importing LIMS Data

Introduction This section provides an overview of transferring data from a laboratory information
management system (LIMS) to the plate import table and a description of the format in
which the LIMS data must be written.

This section does not describe the detailed procedure, which is beyond the scope of
this manual.
Note To import LIMS data, you must know how to import binary data BLOBS into an Oracle®
database.

Advantages of Data transferred from a LIMS database creates plate records that are identical to plate
Importing Data from records created from tab-delimited text files.
a LIMS Database The advantages of using a LIMS database over tab-delimited text files are:

♦ The sample data is already entered into a LIMS database. Therefore, the data can
be assembled quickly into the format required for import.
♦ Transferring data from a LIMS database is completely automatic.

Automatic Data The data transfer process is automatic, it does not need to be initiated by a manual
Transfer import command in the Data Collection software.
When the software is configured to import LIMS data, it:
♦ Periodically polls the plate import table (described below) for new data transferred
into it by the LIMS database
♦ Automatically:
– Creates plate records from the transferred data
– Enters an event describing the import in the Events log
– Registers the plate record in the Pending Plate Record table of the Plate View
page

Configuring the To use the automatic LIMS data-transfer feature, the 3100 and 3100-Avant Data
Data Collection Collection software must be configured to automatically poll the instrument database
Software for LIMS for plate import table entries.
Import Sequence Collector is a type of LIMS database. For information about Sequence
Collector, see page 3-37.

4-16 Working with Plate Records

Plate Import Table

Introduction The instrument database contains a plate import table. It is the only part of the
database that can be safely accessed by outside programs, as there are no links to
other tables in the database.

Plate Import Table The number of sets of plate data that can be accommodated in the plate import table
Capacity is dependent on the amount of available space in the instrument database. Once the
data in the table has been successfully imported into the main database, the data is
stored as a plate record. As a result, there is little need to keep the imported data in
the plate import table once the success of the import has been verified.
Applied Biosystems recommends that you periodically delete data from the plate
import table. It is best to do this when the 3100 and 3100-Avant Data Collection
software is not running. To delete data from the plate import table, consult your Oracle
database administrator.

Errors If an error occurs while importing data from the plate import table, the error is
registered in the following locations:
♦ Errors pane on the Status View page
♦ Run log table on the Run Log page
♦ Plate import table (status will be set to “Bad”)

Required Fields A LIMS entry into the plate import table must contain the following five fields:

Field Format
Plate ID Up to 32 characters
Name Up to 32 characters
Status Up to 32 characters
Plate BLOB BLOB
Plate BLOB version Integer

Plate ID The plate ID is a unique identifier or primary key for the plate. This ID should not be
the same as the plate name. The instrument database will not allow entry of a plate ID
if that value is already used by another row in the plate import table.

Name The name is the name of the plate. This name should not be the same as the plate ID.
The name is not a unique identifier for the plate in the plate import table and can be
used more than once within the plate import table. However, once the data is used to
create a plate record, the name becomes the database plate ID and must be unique
among all existing plates.

Having the name field in addition to the plate ID field allows you to delete a plate
record from the plate import table and then re-import it with the same name (but a
different Plate ID).

Working with Plate Records 4-17

 The name must also be the same as the plate name given to the header in the BLOB
equivalent of the tab-delimited text file. It can be up to 32 characters and must not
contain any restricted characters.
IMPORTANT Use only the following characters, which are a subset of the characters allowed
by the Windows NT operating system: letters, numbers, and -_(){}#.+

Status There are three status options:

Status Assigned when... Set by...

New the data is ready for transfer LIMS
Old a plate table has been successfully imported 3100 or 3100-Avant Data
Collection software
Bad the transfer was unsuccessful 3100 or 3100-Avant Data
Collection software

The status of any data set stored in the plate import table can be checked at any time
through the LIMS software.

Plate BLOB The plate BLOB is an array of binary data that is equivalent (except in language) to a
Definition tab-delimited text file used for data import. The plate BLOB is written from a table in
the LIMS database that contains data and formatting equivalent to a tab-delimited text
file or spreadsheet used for data import.

The plate ID in the header of the binary BLOB must exactly match the plate name in
the plate import table.

Converting the data into a plate BLOB format requires a knowledge of SQL and is a
topic beyond the scope of this manual.

Plate BLOB Version The plate BLOB takes its version number from the header of the table used to create
Number the plate BLOB.
This number is 1.0 for the current release of the software, which is identical to the
version in the tab-delimited text files prepared for import into the instrument database.

4-18 Working with Plate Records

Creating a Plate File Using a Provided Template

Locating the This method uses a tab-delimited text file template and Microsoft Excel to create a
Templates plate file. Templates are provided with the 3100 and 3100-Avant software and are
listed below (See “Template File Names”). In Microsoft Excel, you are able to view a
tab-delimited text file template in a spreadsheet format without saving it as a
spreadsheet.

A plate file is a tab-delimited text file saved with the file name extension .plt.

The templates provided with the 3100 and 3100-Avant Data Collection software are
located in the following directory:

D:\AppliedBio\Support Files\Data Collection Support Files\Plate Import Files

Template File Names The templates provided with the 3100 and 3100-Avant Data Collection software are
listed in the table.

Template File Name Type of Template

FullPlate_GSWell_384.plt 384-well for fragment analysis
FullPlate_GSWell_96.plt 96-well for fragment analysis
FullPlate_SeqWell_384.plt 384-well for sequencing analysis
FullPlate_SeqWell_96.plt 96-well for sequencing analysis

Creating a Plate To create a plate record using a template:

Record Using a
Step Action
Template
1 Launch Microsoft Excel.

Working with Plate Records 4-19

 To create a plate record using a template: (continued)

Step Action
2 Select File > Open.

3 Navigate to the Plate Import Files folder in the following directory:

D:\AppliedBio\Support Files\Data Collection Support Files\Plate Import Files
Notice that no files are displayed. This is because there are no Microsoft Excel files
in this folder.
4 In the Files of type list box, select All Files.

5 Select the plate file (.plt file) template you want to use and click Open.
The Text Import Wizard dialog box opens.

6 Click Finish.
The file is displayed as a spreadsheet.

4-20 Working with Plate Records

To create a plate record using a template: (continued)

Step Action
7 Modify any data in the cells by clicking the cell and retyping.
To save time, use the Fill Down command:
♦ Select the cell containing the information that you want to copy.
♦ From the Edit menu, select Copy.
♦ Drag the fill-down handle in the bottom-right corner of the cell to copy the
information into adjacent cells.

8 Click the Close button.

Either a standard Windows NT message box or an equivalent Office Assistant
message box is displayed.

9 Click Yes.
This opens the Save As dialog box.
10 a. In the File name drop-down list, delete the name of the file that you selected and
type a new name for the edited file. Make sure that you add the .plt extension.
b. Click Save. This saves the edited file as a new file.
11 Follow the directions starting on page 4-25 for importing a tab-delimited text file to
create a plate record.

Working with Plate Records 4-21

Creating a Plate File from a New Spreadsheet

Creating a Plate File To create a plate file (.plt file) from a new spreadsheet:
from a New
Step Action
Spreadsheet
1 On a computer using a Windows NT operating system, open a new spreadsheet file
in a program that allows you to save a spreadsheet as a tab-delimited file.
2 Using the spreadsheet examples and the information about each token starting on
page 4-11, type your information into the file.
3 Select File > Save As.
In most spreadsheet programs, the Save As dialog box will open.
4 Type in a name for the tab-delimited file that you are about to create.

IMPORTANT Use only the following characters, which are a subset of the
characters allowed by the Windows NT operating system: letters, numbers, and
-_(){}#.+. Do not use spaces.
5 a. Save the file with the following file name format:
filename.plt.
b. In the File Type text box (or equivalent), select the text file (tab delimited) file
type or equivalent.

Note If you close Microsoft Excel before performing this step, the Office Assistant
opens. Click Yes, and then Save.
6 Follow the directions starting on page 4-25 for importing a tab-delimited text file to
create a plate record.

4-22 Working with Plate Records

Creating a Plate File from a Custom Spreadsheet Template

Introduction This method can be used to create a read-only spreadsheet template, that you can
save as a different name and then modify to suit your needs.

If you are using similar samples and run conditions, this method allows you to type
less each time you want to create a new plate record.

There are two parts to the procedure:

♦ Creating the template
♦ Modifying the template

Creating the To create a custom spreadsheet template:

Template
Step Action
1 Use the directions starting on page 4-19 to create a plate file (.plt file) that contains
the basic information that you need for a plate record.
2 Open the .plt file in a spreadsheet program.
3 Save the spreadsheet as a read-only file to ensure that it does not get overridden.

Modifying the To modify or create a plate record from a custom spreadsheet template:
Template
Step Action
1 Open the spreadsheet that you just created to use as a template.
2 Save the spreadsheet under a different name, making sure that it is not read-only
as above.
3 Edit the plate and sample data in the spreadsheet according to the specific plate
and samples you are using.
4 Save the spreadsheet as a tab-delimited text file, giving it the .plt extension.
5 If needed, repeat steps 1 to 4 to create other tab-delimited text files.
6 Follow the directions starting on page 4-25 for importing a tab-delimited text file to
create a plate record.

Working with Plate Records 4-23

Creating a Plate File from an Edited Plate Record

Introduction To save time when preparing plate records, you can save the data entered into the
plate editor table as a tab-delimited text file. After changing the plate name, the file can
be re-imported. Alternatively, it can be saved as a read-only file and used as a
template.

Creating a Plate File To create a plate file from an edited plate record:
from an Edited Plate
Step Action
Record
1 Open the Plate View page of the 3100 or 3100-Avant Data Collection software.
2 a. In one of the plate record tables, double-click the plate record that you want to
edit.
b. Edit the plate record as required.
3 From the File menu, select Export.
This opens a browser dialog box.
4 Navigate to the folder in which you want to save the file. You may want to use the
plate import files folder in the following directory:
D:\AppliedBio\Support Files\Data Collection Support Files\Plate Import Files

Note You cannot see Network Neighborhood directories from this browser dialog
box.
5 a. In the File name dialog box, type a name for the file and add the extension .plt.
b. Click Save.
This saves the file as a tab-delimited text file to the specified directory.
6 If you want to use this file as a template, give the file a read-only status:
a. Right-click the Start icon on the Windows NT taskbar, and from the pop-up menu
select Explore. This opens Windows NT Explorer.
b. Navigate to the file that you just created.
c. Right-click the file and from the pop-up menu select Properties.
d. From the Attributes group box, select Read-only.
e. Click OK.
7 Follow the directions starting on page 4-25 for importing a tab-delimited text file to
create a plate record.

4-24 Working with Plate Records

Importing Tab-Delimited Text Files and Linking Plate Records

Introduction To create and link a plate record by importing a plate file into the instrument database
you must:
♦ Import the data
♦ Place the plates
♦ Link the plates

In general, the steps for importing, placing, and linking are summarized in the diagram
below.

Create .plt files

Sequentially import and link

Place plates
(now or later)

Import one .plt file to Simultaneously import

create one plate record multiple .plt files to
create multiple plate
records

Repeat

Place plates
(if not done yet)

Link one plate/

plate record

Repeat

Working with Plate Records 4-25

 Sequentially You can sequentially import a tab-delimited text file to create a plate record and then
Importing and link it to its plate. It takes longer to perform these steps separately for a single plate
Linking a Plate record; however, you can import many tab-delimited text files at once.
Record
To import one or more tab-delimited text files to create plate records:
Step Action
1 In the Plate View page of the 3100 and 3100-Avant Data Collection software, click
Import.

This opens an untitled browser dialog box.

2 Navigate to the directory location of the plate file(s) (.plt) that you want to import
and link.

If you want to create... Then...

a single plate record Select the .plt file.
more than one plate record a. Click the Up One Level button.

b. Select a folder of .plt files.

All .plt files are imported and appear in the
pending plate records table ready to be linked.

3 Click OK.
This imports the .plt file(s) and creates one or more plate records.

Note If there is missing information in the file, you may be warned by an

information box. This may happen, for example, if you make a typing error or list a
module that no longer exists. Depending on the problem, the warning may
accompany rejection of the entire plate record. However, in some circumstances,
the data will be imported despite a warning. When this happens, the purpose of the
warning is to prompt you to examine and correct the data in the plate editor.
4 Review the plate records in the plate editor.
5 Link the plate record to the plate.

4-26 Working with Plate Records

Deleting Plate Records and Run Data

Introduction Delete the plate records and run data when the used space on drive E is more than
8 GB.

There are two ways to delete the processed frame data that is associated with plate
records. You can:
♦ Use the Cleanup Database utility (CleanUpDB.bat)
♦ Delete individual plate records

Recommended The Cleanup Database utility is the recommended way to delete plate records
Procedure because:
♦ It is much faster to delete the processed frame data than to delete individual plate
records.
♦ It prevents problems that result from incomplete deletion of data.

Reference to the ! CAUTION The Cleanup Database utility deletes all run data and plate records from the
Cleanup Database database. Before running the utility, be sure that all runs have been extracted from the
Utility database.
To delete plate records and run data from the instrument database using the Cleanup
Database utility, see “Deleting Processed Frame Data: Cleanup Database Utility” on
page 5-4.

When to Delete Use this method if you want to delete only:

Individual Plate ♦ Plate records that have no associated run data
Records
♦ Certain plate records

When a plate record is deleted, the run data associated with samples in the plate is
also deleted from the instrument database.
Note A new run cannot be started while a plate record is being deleted.

IMPORTANT You cannot delete a linked plate record, but plate records for unlinked, partially
processed plates can be deleted. If the processed runs from unlinked partially processed plates
have not yet been extracted, the run information will be deleted from the database. The pending
plate record table is where unlinked partially processed plates are listed.
Make sure that processed runs have been extracted by looking in the
D:Appliedbio\3100\DataExtractor or D:Appliedbio\3100-Avant\DataExtractor and verifying all
sample files for all runs performed are there.

Working with Plate Records 4-27

 Deleting Individual To delete individual plate records:
Plate Records
Step Action
1 Click the Plate View tab in the 3100 and 3100-Avant Data Collection software.
This opens the Plate Setup page.
2 In either the Pending or Processed Plate Record table, select the row that names
the plate record you want to delete.

Note You can select more than one row at a time by pressing CTRL while selecting
additional rows.
3 Click Delete.
Note If you have created, linked or edited plates after runs have been deleted, the
deleted runs will be rescheduled.

4-28 Working with Plate Records

System Management and
Networking 5 5
In This Chapter The following topics are covered in this chapter:

Topic See Page

Storing Run Data 5-2
Recovering Data: Extractor Utility 5-2
Deleting Processed Frame Data: Cleanup Database Utility 5-4
Importing: Method Import Utility 5-6
Removing Run Modules from the Instrument Database: Remove Run Modules 5-7
Utility
Reinitializing the Instrument Database: Initialize Database Utility 5-8
Networking Options 5-9
Networking the Computer Workstation 5-11
Requirements for a Networked Computer 5-12

System Management and Networking 5-1

Storing Run Data

Types of Run Data Run data is stored in different forms, depending on the configurations selected in the
Storage Preferences and Auto Extractor dialog boxes:

Approximate Data Storage

Data Storage Type Where Stored Space
Processed frame data In the instrument database E drive of the local computer 100 MB for a 2.5-h run
workstation
ABIF sample file On the local or networked hard drive D drive, at a ♦ 250 KB per sample file for a
directory location specified in the Extraction Directory ABI PRISM ® 3100 POP-4™
dialog box of Auto Extractor polymer sequencing analysis
run
The default setting is to store ABIF sample files in the
following directory: ♦ 210 KB per sample file for a
D:\AppliedBio\3100\Data Extractor or ABI PRISM ® 3100 POP-6™
D:\AppliedBio\3100-Avant\Data Extractor polymer fragment analysis
run
♦ 300 KB per sample file for a
ABI PRISM ® 3100 POP-4™
polymer fragment analysis
run
Sequence Collector Sequence Collector database on another networked –
data computer

Recovering Data: Extractor Utility

Function The auto extractor should automatically extract data from stopped runs. If
autoextraction fails, use the Extractor utility as described below.

Extractor Utility’s re-extracted data will go to either:

♦ D:\Appliedbio\3100\Data Extractor\Extracted Runs
♦ D:\Appliedbio\3100-Avant\Data Extractor\Extracted Runs
Note Re-extracted data can also be stored to Sequence Collector if set up.

Note View the xx_analysis.log or the xx_extraction.log file to see if the extraction completed
successfully.

Selecting and You can queue runs for extraction. This is especially useful for extracting failed runs or
Queuing Runs for batches of runs.
Extraction To select and queue runs for extraction:

Step Action
1 Verify that the OrbixWeb™ Daemon and AEServer are running.
2 Quit the Data Collection software.

Note The Extractor utility and Data Collection cannot run simultaneously.

5-2 System Management and Networking

 To select and queue runs for extraction: (continued)

Step Action
3 a. Click the Start menu.
b. Point to Applied Biosystems > 3100 Utilities > Extractor Utility or
Applied Biosystems > 3100-Avant Utilities > Extractor Utility

4 Select a run or runs to extract.

Note Do not select runs with Not extractable status.

5 Click Extract.
The data will be extracted to the location defined in your preferences or the default
location.
For the 3100 system:
D:\AppliedBio\3100\Data Extractor\Extracted Runs
For the 3100-Avant system:
D:\AppliedBio\3100-Avant\Data Extractor\Extracted Runs

Preferences You may set the same preferences as in the data collection software by going to
Extract > Preferences in the Extractor Utility.

System Management and Networking 5-3

Deleting Processed Frame Data: Cleanup Database Utility

Function The Cleanup Database utility deletes the processed frame data and all associated run
information stored in the 3100 or 3100-Avant Data Collection software database. This
utility is used to make room for new run data.

The Cleanup Database utility deletes all of the:

♦ Processed frame data
♦ Plate records and run data

This utility does not delete the:

♦ Electrophoresis modules automatically imported from the supplied method files
♦ Run modules that you have created
♦ Spatial and spectral calibration data obtained from the last calibration runs
performed
♦ Instrument-specific information such as the instrument name, serial number, user
names, dye set information, etc.
Note The utility defragments the E partition.

File Name and The Cleanup Database utility is named CleanUpDB.bat and is located in either
Directory following directory:
♦ D:\AppliedBio\3100\Bin
♦ D:\AppliedBio\3100-Avant\Bin

When to Perform You will be prompted by the software to run the Cleanup Database utility when the
database is approximately 75% full.
IMPORTANT Never run the Cleanup Database utility more than once a day because
previously extracted sample files may be overwritten. This can happen due to the format used
for a run name.

Deleting Processed ! CAUTION The Cleanup Database utility deletes all run data and plate records in the
Frame Data database. Before running the utility, be sure that all runs have been extracted from the
database.

To delete processed frame data using the Cleanup Database utility:

Step Action
1 Ensure that OrbixWeb Daemon and AE server are running.
2 Quit the 3100 or 3100-Avant Data Collection software.
3 Using Windows NT Explorer, navigate to the following directory:
D:\AppliedBio\3100\Bin or D:\AppliedBio\3100-Avant\Bin

5-4 System Management and Networking

To delete processed frame data using the Cleanup Database utility: (continued)

Step Action
4 Locate and double-click CleanUpDB.bat.
This runs the Cleanup Database utility, which takes a few seconds to complete.
5 Shut down and then relaunch OrbixWeb Daemon.
! CAUTION If you do not perform this step, any new run data will not be saved
to the database.

Note There is no need to re-import the spatial, spectral, and run calibration methods or the
calibration data obtained from the last calibration runs.

Deleting the plate record for a plate of samples is another way to delete processed
frame data stored in the instrument database.

Directions for deleting individual plate records start on page 4-28.

System Management and Networking 5-5

Importing: Method Import Utility

Function Method files contain the parameters that define the run conditions (along with the
SCPI commands that direct the operation of the instrument).

New methods provided by Applied Biosystems must be imported into the instrument
database before they can be used. The Method Import Utility imports these methods.

Importing a Method An application replaces editing and running the MethodImportUtility.bat batch file.
To import a method:
Step Action
1 Ensure OrbixWeb Daemon is running.
2 Quit the data collection software.

Note The method import utility and data collection software cannot run
simultaneously.
3 Navigate to the following location:
D:\AppliedBio\3100\Bin or D:\AppliedBio\3100-Avant\Bin
4 Open the MethodImportUtility.bat file.

5 Click Browse and locate the method file you want to import into the database.

Note All method files have an .mtd extension.

6 Click Import.
7 View the results in the Status section.

5-6 System Management and Networking

Removing Run Modules from the Instrument Database:
Remove Run Modules Utility

Function The Remove Run Modules utility removes all modules and associated information
from the instrument database. This utility is used to quickly delete all old modules
before you import new ones.

File Name and The Remove Run Modules utility is named RemoveRunModules.bat and is located in
Directory the following directory:
D:\AppliedBio\3100\Bin or D:\AppliedBio\3100-Avant\Bin

Removing Run To remove run modules using the utility:

Modules
Step Action
1 Ensure OrbixWeb Daemon and AE are running.
2 Quit the 3100 or 3100-Avant Data Collection software.
3 Using Windows NT Explorer, navigate to the following directory:
D:\AppliedBio\3100\Bin or D:\AppliedBio\3100-Avant\Bin
4 Locate and double-click RemoveRunModules.bat.

System Management and Networking 5-7

Reinitializing the Instrument Database: Initialize Database Utility

Function The Initialize Database utility completely erases and reinitializes the instrument
database.

File Name and The Initialize Database utility is named InitDB.bat and is located in the following
Directory directory:
D:\AppliedBio\3100\Bin or D:\AppliedBio\3100-Avant\Bin

Erasing and IMPORTANT Do not run this utility unless instructed to do so by a Applied Biosystems
Reinitializing the representative.
Instrument ! CAUTION The Initialize Database utility completely erases the instrument database. All
Database raw data, plate records, customized run modules, spatial and spectral calibrations, and
instrument-specific information such as polymer and capillary array information will be deleted.

To remove, erase, and reinitialize the instrument database using the utility:
Step Action
1 Ensure OrbixWeb Daemon and AE are running.
2 Quit the 3100 or 3100-Avant Data Collection software.
3 Using Windows NT Explorer, navigate to the following directory:
D:\AppliedBio\3100\Bin or D:\AppliedBio\3100-Avant\Bin
4 Locate and double-click InitDB.bat.
5 Locate and double-click CreateIndex.bat.
6 Restart the computer.

5-8 System Management and Networking

Networking Options

Introduction You have the option of using the ABI PRISM ® 3100 or 3100-Avant Genetic Analyzer as
a stand-alone system. However, you will achieve optimal performance by integrating
the 3100 or 3100-Avant Genetic Analyzer into your existing laboratory data flow
system. The 3100 and 3100-Avant systems have flexible import and export
capabilities that can be tailored to meet your needs. Other computers can, for
example, be used for preparing plate records, providing more comprehensive
analysis, and storing data.
The networking options are configured in the 3100 and 3100-Avant Data Collection
software.

Overview Diagram The diagram below summarizes the relationships among the different elements of the
software and the options for networking with external computers.

External Computers

3100 or 3100-Avant
LIMS database Detector
Instrument

Import 3100 or 3100-Avant 3100 or 3100-Avant

External computer with sample NT Workstation
data Data Collection
records in a spreadsheet to create software
plate
records

Sequence Export
analyzed or Instrument
Collector
unanalyzed database
database
data

ABIF sample files

External computer with: Export unanalyzed

• GeneScan Analysis software or analyzed data
• DNA Sequencing Analysis software

External computer with customized

GeneScan Analysis DNA Sequencing Analysis
software prepared with ABIF
software software
Sample File Toolkit

System Management and Networking 5-9

 Using an Additional Using an additional networked computer makes more efficient use of the 3100 and
Networked 3100-Avant Genetic Analyzer. While the instrument is performing a run, you cannot
Computer create plate records, review data from past runs, or reanalyze data. By using another
computer to perform these functions, you can perform more runs in a day.

The networked computer can run with a Microsoft® Windows NT® or Macintosh®
operating system; however, if Macintosh versions of analysis applications are used,
you can only view and edit the data. To reanalyze the data, you must use the Windows
NT versions of analysis applications.

LIMS Database An external LIMS database can be used to assemble all of the data needed to create
Option plate records. Once a LIMS database has been set up correctly and the data has
been entered into the LIMS database, the creation of plate records in the LIMS
database becomes automatic. Those plate records can then be exported from LIMS
and imported into the 3100 or 3100-Avant Data Collection software.

Sequence Collector With the Sequence Collector database system, data is collected on the computer
Option workstation and written to a Sequence Collector database on a networked server
using Auto Extractor. The data can later be viewed and reanalyzed using DNA
Sequencing Analysis software or GeneScan Analysis software. These programs can
either be on the computer workstation, which is used to collect the data, or on a
different computer that has access to the Sequence Collector database. The data can
also be viewed and edited (but not analyzed) using DNA Sequencing Analysis
software or GeneScan Analysis software on a Macintosh computer with access to the
Sequence Collector database.

Stand-Alone Option With the stand-alone option, all operations, including the creation of plate records,
collection of data, and review of data with GeneScan Analysis software or DNA
Sequencing Analysis software, are carried out on the computer workstation.

5-10 System Management and Networking

Networking the Computer Workstation

Introduction The 3100 and 3100-Avant Genetic Analyzer fully support connections to local area
networks (LANS). Your network system must be planned and set up by a systems
administrator who is familiar with the Windows NT operating system.

If you plan to add the computer workstation to a LAN, you should be aware of the
following:
♦ The person logged in as 3100User or 3100-AvantUser must have system
administration rights on the computer workstation.
♦ The computer workstation has two network interface cards.

Administrator For installation and upgrades to the software, the person logged in as 3100User or
Privileges 3100-AvantUser must be a member of the Administrators group.

Network Interface The computer workstation has two network interface cards. These cards are:
Cards ♦ On the motherboard, which is connected to the instrument
♦ Installed in an expansion slot in the system unit, which can be used to connect to
the network. (This card requires that drivers be installed.)
IMPORTANT Use only the network interface card in the expansion slot to connect to the LAN.
The network interface card on the motherboard is reserved for the Ethernet connection to the
instrument.

IP Address Your network system administrator must provide you with an IP address for networking
to the LAN. This is not the same as the Internet Protocol (IP) address already being
used to connect the computer workstation to the instrument.
IMPORTANT Do not modify the given IP address.

Windows NT User IMPORTANT Do not change the default Windows NT logon user name from “3100User” or
Name “3100-AvantUser.” This will break the connection with the 3100 or 3100-Avant Data Collection
software and make the software inoperable.

To view the Windows NT logon user name:

Step Action
1 Press Ctrl+Alt+Delete.
This opens the Windows NT Security dialog box. The user name is displayed in the
Logon Information group box in the following message:
Name is logged on as name-instrument serial number

System Management and Networking 5-11

 Viewing the The computer name is set during installation using the 3100 or 3100-Avant instrument
Computer Name serial number.
To see the computer name and network domain:
Step Action
1 Select Start > Settings > Control Panel.
2 In the Control Panel window, double-click Network.
This opens the Network property sheet. The Identification tabbed page displays the
computer name and domain.

Requirements for a Networked Computer

Minimum The minimum requirements for running either DNA Sequencing Analysis or
Requirements GeneScan Analysis software are:
♦ Intel Pentium processor, 400 MHz or faster
♦ Microsoft® Windows NT® 4.0 operating system with Service Pack 5
♦ 256-color display adapter card
♦ CD-ROM drive

For... RAM (MB) Hard Disk Space (MB)

Extraction only 64 80
Extraction and analysis 256 120

Hard Disk Space Ensure that the networked computer has sufficient hard disk space to hold as many
sample files as desired. One analyzed sample file is about 250 KB.

5-12 System Management and Networking

Troubleshooting 6 6
In This Chapter The following troubleshooting topics are covered in this chapter:

Topic See Page

Instrument Startup 6-2
Spatial Calibration 6-3
Spectral Calibration 6-4
Run Performance 6-5
Software 6-11

Troubleshooting 6-1
Instrument Startup

Troubleshooting Instrument Startup

Observation Possible Cause Recommended Action
No communication between the Incorrect Ethernet configuration. Check the configuration of the IP
instrument and the computer. The address.
event viewer is blank. a. Select Start > Programs >
Command Prompt.
b. At the C:\ prompt, type
IPconfig /all.
c. Press Enter. The command prompt
window displays information on
the network.
d. Ensure the IP address for Ethernet
adapter 1 is set for the machine
(i.e., the motherboard Ethernet
connection). The correct IP
address is: 192.168.0.1

Note The local IT group should use

Adapter 2 for networking.
Red light is blinking. Incorrect start up procedure. Start up in the following sequence:
a. Log out of the computer.
b. Turn off the instrument.
c. Boot up the computer.
d. After the computer has booted
completely, turn the instrument on.
Wait for the green status light to
come on.
e. Launch the Data Collection
software.
Data Collection software will not Did not launch OrbixWeb™ Daemon Relaunch application following
launch. first. OrbixWeb Daemon.
Computer screen is frozen. Communication error. This may be There will be no loss of data.
due to leaving the user interface in However, if the instrument is in the
the Capillary View or Array View middle of a run, wait for the run to
window. stop. Then, exit the Data Collection
software and restart as described
above.
Autosampler does not move to the Possible communication error. Restart the system, and then press
forward position. the Tray button.
Oven or instrument door is not a. Close and lock the oven door.
closed. b. Close the instrument doors.
c. Press the Tray button.
Instrument does not respond to Autosampler reinitializes its location. Wait for the autosampler to home
commands immediately after closing before continuing.
the doors.

6-2 Troubleshooting
Troubleshooting Instrument Startup (continued)

Observation Possible Cause Recommended Action

Auto analysis did not occur. The AE server was not launched first. Launch AE server.
Auto analysis was not set in Select Auto analysis.
Preferences.

Spatial Calibration

Troubleshooting Spatial Calibrations

Observation Possible Cause Recommended Action
Unusual peaks or a flat line for the The instrument may need more time Check or repeat spatial calibration.
spatial calibration. to reach stability. An unstable
instrument can cause a flat line with
no peaks in the spatial view.
Improper installation of the detection Reinstall the detection window and
window. make sure it fits in the proper position.
Broken capillary resulting in a bad Check for a broken capillary,
polymer fill. particularly in the detection window
area. If necessary, replace the
capillary array using the Install Array
Wizard.
Dirty detection window. Place a drop of methanol onto the
detection window, and dry with
compressed air. Use only light air
force.
CHEMICAL HAZARD.
Methanol is a flammable liquid and
vapor. Exposure may cause eye, skin,
and respiratory tract irritation, and
central nervous system depression
and blindness. Read the MSDS, and
follow the handling instructions. Wear
appropriate protective eyewear,
clothing, and gloves.
Persistently bad spatial calibration Bad capillary array. Replace the capillary array, and then
results. repeat the calibration. Call Technical
Support if the results do not improve.

Troubleshooting 6-3
Spectral Calibration

Troubleshooting Spectral Calibrations

Observation Possible Cause Recommended Action
No signal. Incorrect preparation of sample. Replace samples with fresh samples
prepared with fresh Hi-Di™
formamide.
CHEMICAL HAZARD.
Formamide causes eye, skin, and
respiratory tract irritation. It is a
possible reproductive and birth defect
hazard. Read the MSDS, and follow
the handling instructions. Wear
appropriate protective eyewear,
clothing, and gloves.
Air bubbles in sample tray. Centrifuge samples to remove air
bubbles.
Autosampler not correctly aligned. Check the autosampler calibration. If
The capillary tips may be hitting the necessary, recalibrate the
bottom of the wells, or they may not autosampler using the Autosampler
be touching the samples. Calibration Wizard.
If the spectral calibration fails, or if a Clogged capillary. Refill the capillaries using manual
message displays “No candidate control. Look for clogged capillaries
spectral files found.” during capillary fill on the cathode
side.
Incorrect parameter files and/or run Correct the files and rerun the
modules selected. calibration.
Insufficient filling of array. Check for broken capillaries and refill
the capillary array.
Expired matrix standards. Check the expiration date and storage
conditions of the matrix standards. If
necessary, replace with a fresh lot.
Data Error - One or more peaks fall One or more peaks fall below the Rerun the spectral standards, and if
below the minimum required minimum required amplitude of 750. necessary, increase the amount of
amplitude of 750. spectral standard added.
Spikes in the data. Expired polymer. Replace the polymer with a fresh lot
using the Change Polymer Wizard.
! WARNING CHEMICAL HAZARD.
POP-4 polymer and POP-6 cause eye,
skin, and respiratory tract irritation.
Read the MSDS, and follow the
handling instructions. Wear
appropriate protective eyewear,
clothing, and gloves.
Air bubbles, especially in the polymer Refill the capillaries using manual
block tubing assembly. control.
Possible contaminant or crystal Properly bring the polymer to room
deposits in the polymer. temperature; do not heat to thaw
rapidly. Swirl to dissolve any solids.
Replace the polymer if it has expired.

6-4 Troubleshooting
Run Performance

Troubleshooting Run Performance

Observation Possible Cause Recommended Action
No data in all capillaries. ♦ Bubbles in the system. Visually inspect the polymer block and the
syringes for bubbles.
♦ No sample injection
Remove any bubbles using the Change Polymer
Wizard.
If bubbles still persist, perform the following:
a. Remove the capillary array.
b. Clean out the polymer block and syringes.
c. Replace polymer with fresh polymer. Make
sure to draw the polymer into the syringe very
slowly.
! WARNING CHEMICAL HAZARD. POP-4
polymer and POP-6 causes eye, skin, and
respiratory tract irritation. Read the MSDS,
and follow the handling instructions. Wear
appropriate protective eyewear, clothing, and
gloves.
Possible contaminant in the polymer Wash the polymer block with hot water. Pay
path. attention to the upper polymer block, the ferrule,
the ferrule screw, and the peek tubing. Dry the
parts with compressed air before replacing them
onto the instrument.

IMPORTANT Do not wash syringes in hot water

because the Teflon plungers will get damaged.
Possible contaminant or crystal Bring the polymer to room temperature, swirl to
deposits in the polymer. dissolve any deposits.
Replace the polymer if it has expired.
! WARNING CHEMICAL HAZARD. POP-4
polymer and POP-6 cause eye, skin, and
respiratory tract irritation. Read the MSDS, and
follow the handling instructions. Wear appropriate
protective eyewear, clothing, and gloves.

Troubleshooting 6-5
Troubleshooting Run Performance (continued)

Observation Possible Cause Recommended Action

No signal. Autosampler calibration is not Check the injection with 20-µL samples. If the
optimal. injection is OK, recalibrate the autosampler using
the Autosampler Calibration Wizard. Pay
particular attention to the Z-axis.
If the injection is not OK, perform the procedures
below.
Dead space at bottom of sample Centrifuge the sample tubes.
tube.
Bent capillary array. Replace the capillary array and recalibrate the
autosampler using the Calibrate Autosampler
Wizard.
Failed reaction. Repeat reaction.
Cracked or broken capillary Visually inspect the capillary array, including the
detector window area for signs of breakage.
Signal too high. Sample concentration is too high. Dilute the sample.
Decrease the injection time.
Too much DNA added to the reaction, Optimize chemistry.
resulting in uneven signal distribution.
Low signal strength. Poor quality formamide. Use a fresh lot of Hi-Di formamide.
CHEMICAL HAZARD.
Formamide causes eye, skin, and respiratory
tract irritation. It is a possible reproductive and
birth defect hazard. Read the MSDS, and follow
the handling instructions. Wear appropriate
protective eyewear, clothing, and gloves.
Pipetting error; not enough sample. Increase the amount of DNA added.
Recalibrate the pipets.
Sample has high salt concentration. Dilute in high-quality water.
Desalt using a column purification method.
Insufficient mixing. Vortex the sample thoroughly, and then
centrifuge the tube to condense the sample to
the bottom of the tube.
Autosampler out of calibration. Check the injection with 20-µL samples. If the
injection is OK, recalibrate the autosampler using
the Autosampler Calibration Wizard. Pay
particular attention to the Z-axis.
Weak amplification of DNA. Reamplify the DNA.
Check DNA quality.

6-6 Troubleshooting
Troubleshooting Run Performance (continued)

Observation Possible Cause Recommended Action

Elevated baseline. Possible contaminant in the polymer Wash the polymer block with hot water. Pay
path. attention to the upper polymer block, the ferrule,
the ferrule screw, and the peek tubing. Dry the
parts with compressed air before replacing them
onto the instrument.

IMPORTANT Do not wash syringes in hot water

because the Teflon plungers will get damaged.
Possible contaminant or crystal Bring the polymer to room temperature, swirl to
deposits in the polymer. dissolve any deposits.
Replace the polymer if it has expired.
! WARNING CHEMICAL HAZARD. POP-4
polymer and POP-6 cause eye, skin, and
respiratory tract irritation. Read the MSDS, and
follow the handling instructions. Wear appropriate
protective eyewear, clothing, and gloves.
Poor spectral calibration. Perform new spectral calibration.
Detection cell is dirty. Place a drop of methanol onto the detection
window and dry with compressed air. Use only
light air force.
Loss of resolution. Too much sample injected. Dilute the sample and re-inject.
Poor quality water. Use high-quality, ultra-pure water.
Poor quality or dilute running buffer. Prepare fresh running buffer from 10X 3100
buffer with EDTA.
CHEMICAL HAZARD. 10X Genetic
Analyzer Buffer with EDTA may cause eye, skin,
and respiratory tract irritation. Read the MSDS,
and follow the handling instructions. Wear
appropriate protective eyewear, clothing, and
gloves.
Poor quality or breakdown of polymer. Use a fresh lot of polymer.
Capillary array used for more than Replace with new capillary array.
100 injections.
Degraded formamide. Prepare fresh Hi-Di formamide and re-prepare
samples.
CHEMICAL HAZARD.
Formamide causes eye, skin, and respiratory
tract irritation. It is a possible reproductive and
birth defect hazard. Read the MSDS, and follow
the handling instructions. Wear appropriate
protective eyewear, clothing, and gloves.
High salt concentration in samples. Use a recommended protocol for salt removal.
Dilute salts with water.
Poor resolution in some Insufficient filling of capillary array. Refill the capillary array and look for cracked or
capillaries. broken capillaries. If problem persists contact
Technical Support.
Re-inject the same samples.
Poor quality samples. Check the sample preparation.

Troubleshooting 6-7
Troubleshooting Run Performance (continued)

Observation Possible Cause Recommended Action

No current. Poor quality water. Use only high-quality ultra-pure water.
Water placed in buffer reservoir Replace with fresh 3100 1X running buffer.
position 1.
Not enough buffer in anode reservoir. Add buffer up to the fill line.
Buffer too dilute. Prepare 1X running buffer.
Add 3 mL 10X Genetic Analyzer Buffer with
EDTA to 27 mL deionized water.
CHEMICAL HAZARD. 10X Genetic
Analyzer Buffer with EDTA may cause eye, skin,
and respiratory tract irritation. Read the MSDS,
and follow the handling instructions. Wear
appropriate protective eyewear, clothing, and
gloves.
Bubble(s) present in the polymer Pause run and inspect for the instrument for
block and/or the capillary and/or bubbles. They may be hidden in the PEEK
PEEK tubing. tubing.
Remove any bubbles according to the remove
bubble procedure in the Replace Polymer
Wizard.
Elevated current. Decomposed polymer. Open fresh lot of polymer and store at 4 °C.
Incorrect buffer dilution. Prepare 1X running buffer.
Add 3 mL 10X Genetic Analyzer Buffer with
EDTA to 27 mL deionized water.
CHEMICAL HAZARD. 10X Genetic
Analyzer Buffer with EDTA may cause eye, skin,
and respiratory tract irritation. Read the MSDS,
and follow the handling instructions. Wear
appropriate protective eyewear, clothing, and
gloves.
Arcing in the gel block. Check for moisture in and around the septa, the
reservoirs, the oven, and the autosampler.

6-8 Troubleshooting
Troubleshooting Run Performance (continued)

Observation Possible Cause Recommended Action

Fluctuating current. Bubble in polymer block. Pause the run, check the polymer path for
bubbles, and remove them if present.
A slow leak may be present in the Check polymer blocks and syringes for leaks.
system. Tighten all fittings.
Incorrect buffer concentration. Prepare 1X running buffer.
Add 3 mL 10X Genetic Analyzer Buffer with
EDTA to 27 mL deionized water.
CHEMICAL HAZARD. 10X Genetic
Analyzer Buffer with EDTA may cause eye, skin,
and respiratory tract irritation. Read the MSDS,
and follow the handling instructions. Wear
appropriate protective eyewear, clothing, and
gloves.
Not enough buffer in anode reservoir. Add buffer up to the fill line.
Clogged capillary. Refill capillary array and check for clog.
Arcing Check for moisture in and around the septa, the
reservoirs, the oven, and the autosampler.
Poor performance of Poor quality samples, possible Desalt samples using a recommended
capillary array used for cleanup problems. purification protocol.
fewer than 100 runs. Poor quality formamide. Prepare fresh Hi-Di formamide and re-prepare
samples.
CHEMICAL HAZARD.
Formamide causes eye, skin, and respiratory
tract irritation. It is a possible reproductive and
birth defect hazard. Read the MSDS, and follow
the handling instructions. Wear appropriate
protective eyewear, clothing, and gloves.
Incorrect buffer. Use 10X Genetic Analyzer Buffer with EDTA to
prepare 1X running buffer.
CHEMICAL HAZARD. 10X Genetic
Analyzer Buffer with EDTA may cause eye, skin,
and respiratory tract irritation. Read the MSDS,
and follow the handling instructions. Wear
appropriate protective eyewear, clothing, and
gloves.
Migration time becomes Leak in system. Tighten all ferrules, screws, and check valves.
progressively slower. Replace any faulty parts.
Improper filling of polymer block. Check polymer pump force. If the force needs to
be adjusted, call a service representative.
Expired polymer. Check expiration of polymer. If necessary,
change the lot.
Migration time becomes Water in syringe resulting in diluted Clean the syringe and dry it with compressed air.
progressively faster. polymer.

Troubleshooting 6-9
Troubleshooting Run Performance (continued)

Observation Possible Cause Recommended Action

Extra peaks in the Data off scale. Dilute the sample and re-inject the sample.
electropherogram. Possible contaminant in sample. Re-amplify the DNA.
Sample renaturation. Heat-denature the sample in good-quality
formamide and immediately place on ice.
CHEMICAL HAZARD.
Formamide causes eye, skin, and respiratory
tract irritation. It is a possible reproductive and
birth defect hazard. Read the MSDS, and follow
the handling instructions. Wear appropriate
protective eyewear, clothing, and gloves.
Peaks exhibit a shoulder Sample renaturation. Heat-denature the sample in good-quality
effect in GeneScan formamide and immediately place on ice.
applications.
CHEMICAL HAZARD.
Formamide causes eye, skin, and respiratory
tract irritation. It is a possible reproductive and
birth defect hazard. Read the MSDS, and follow
the handling instructions. Wear appropriate
protective eyewear, clothing, and gloves.
Purging of polymer from Arcing in the anode gel block. Replace the lower polymer block.
the polymer reserve Bubbles in syringes. Remove bubbles.
syringe.
Leaking polymer at the top Insufficient seal around the Teflon tip Make sure to wet the Teflon before filling the
of either syringe. of the plunger. syringe with polymer. If the leaking persists,
replace the syringe.

Note Do not mix and match barrels and

plungers
Leaking polymer at the Improper tightening of the array Ensure the array ferrule knob is tightened.
bottom of the ferrule knob to the syringe or/and to
polymer-reserve syringe. the polymer block.
Error message, “Leak Air bubbles in the polymer path. Check for bubbles and remove if present. Then,
detected” appears. The look for leaks.
run aborts.
Buffer jar fills very quickly Air bubbles in the polymer path. Check for bubbles and remove if present.
with polymer. Bubbles can cause polymer to fill the jar.
Detection window pops Tightening of the array ferrule knob at Loosen the array ferrule knob to allow the secure
out while replacing the the gel block causes high tension. placement of the window. Retighten and close
capillary array. Replacing the detection door.
the window in the correct
orientation is difficult.
Detection window stuck. It To loosen the detection window:
is difficult to remove when a. Undo the array ferrule knob and pull the
changing the capillary polymer block towards you to first notch.
array.
b. Remove the capillary comb from the holder in
oven.
c. Hold both sides of the capillary array around
the detection window area, and apply gentle
pressure equally on both sides.
d. Release.

6-10 Troubleshooting
Software

Troubleshooting Software
Observation Possible Cause Recommended Action
An imported run module file does not The file name is longer than 32 Rename the run module file using
import. characters. less than 32 characters.
There is no error message.

Troubleshooting 6-11
Technical Support A A
Services and Support

Applied Biosystems A services and support page is available on the Applied Biosystems Web site. To
Web Site access this, go to:
http://www.appliedbiosystems.com

and click the link for services and support.

At the services and 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 services and support page provides worldwide telephone and fax
numbers to contact Applied Biosystems Technical Support and Sales facilities.

Technical Support A-1

Part Numbers B B
Applied Biosystems Part Numbers

Introduction Part numbers for many consumables are given in this appendix. Refer to these part
numbers when ordering from Applied Biosystems.

More information about Applied Biosystems kits and consumables is available from
your sales representative or on the web at http://www.appliedbiosystems.com

Instrument Description Part Number

Hardware
ABI PRISM ® 3100 Genetic Analyzer with computer workstation 3100-01
ABI PRISM ® 3100-Avant Genetic Analyzer with computer workstation 3100-AVANT
Printers (sold only with ABI PRISM instruments)
HP Deskjet 990CXI 4328881

Plate Assembly Kits Description Part Number

96-well plate kit 4316471
384-well plate kit 4316472

Software Kits Description Part Number

®
ABI PRISM ® 3100 GeneScan Analysis Software Module Kit 4317379
ABI PRISM ® 3100 DNA Sequencing Analysis Software Module Kit 4317380

Instrument Description Part Number

Consumables
96-well plate septa 4315933
®
MicroAmp Optical 96-well Reaction Plates N801-0560
384-well plate septa 4315934
®
MicroAmp 384-well Reaction Plates 4305505
Reservoir septa 4315932

Part Numbers B-1

 DNA Sequencing Description Part Number
Reagents and
ABI PRISM ® 3100 POP-6™ polymer 4316357
Consumables
ABI PRISM ® 3100 POP-4™ polymer 4316355
ABI PRISM ® 3100 capillary array, 50-cm 4315930
ABI PRISM ® 3100 capillary array, 36-cm 4315931
ABI PRISM ® 3100 capillary array, 80-cm 4319899
ABI PRISM ® 3100-Avant capillary array, 50-cm 4333466
ABI PRISM ® 3100-Avant capillary array, 36-cm 4333464
ABI PRISM ® 3100-Avant capillary array, 80-cm 4333465
Genetic Analyzer Buffer with EDTA (10X) 402824
Matrix Standard Set DS-01 (dROX, dTAMRA, dR6G, dR110) 4315974
ABI PRISM ® BigDye® Terminator Sequencing Standards Kit 4304154
Hi-Di™ Formamide, 25-mL bottle 4311320

GeneScan Reagents Description Part Number

and Consumables
ABI PRISM ® 3100 POP-4™ polymer 4316355
ABI PRISM ® 3100 capillary array, 36-cm 4315931
ABI PRISM ® 3100 capillary array, 22-cm 4319898
ABI PRISM ® 3100-Avant capillary array, 36-cm 4333464
ABI PRISM ® 3100-Avant capillary array, 22-cm 4333463
Genetic Analyzer Buffer with EDTA (10X) 402824
Matrix Standard Set DS-02 (dR110, dR6G, dTAMRA™, dROX™, LIZ™) 4323014
Matrix Standard Set DS-30 (6FAM™, HEX, NED, ROX™) 4316100
Matrix Standard Set DS-32 (5-FAM, JOE, NED, ROX) 4323018
Matrix Standard Set DS-33 (6FAM, VIC, NED, PET™, LIZ™) 4323016
ABI PRISM ® 3100 GeneScan™ Installation Standard DS-30 4316144
Hi-Di™ Formamide, 25-mL bottle 4311320

Instrument Spare Description Part Number

Parts
96-well plate retainer 4317241
96-well plate base (AB) 4317237
384-well plate retainer 4317240
384-well plate base 4317236
Reservoirs (for buffer, water, and waste) 628-0163
Glass syringe, 5.0-mL polymer-reserve 628-3731
Glass syringe, 250-µL array-fill 4304470
Syringe O-rings 221102
Syringe ferrule 005401
Anode buffer reservoir jar 005402
Upper polymer block drip tray 628-3720

B-2 Part Numbers

 Description Part Number
Lower polymer block drip tray 628-3088
Autosampler drip tray 628-3059
Polymer block tubing assembly 628-3732
Array calibration ruler 628-3214
Array comb holders 628-3403
Array ferrule sleeves 628-0165
Array ferrule knob 628-3730

Reference Materials Description Part Number

ABI PRISM ® 3100 Genetic Analyzer and ABI PRISM ® 3100-Avant Genetic 4335393
Analyzer User Reference Guide
ABI PRISM® 3100 Genetic Analyzer Sequencing Chemistry Guide v. 3.7 4315831
ABI PRISM® GeneScan® Analysis v. 3.7 NT User Guide 4308923
ABI PRISM® 3100 Genetic Analyzer User Guide 4334785
ABI PRISM® Sequencing Analysis Software v. 3.7 NT User Guide 4308924
ABI PRISM® 3100-Avant Genetic Analyzer User Guide 4333549
ABI Prism® 3100 Genetic Analyzer Operator Training CD 432559

Part Numbers B-3

Index
Numerics current, troubleshooting 6-8
3100 and 3100-Avant software CDs 3-2 customer support. See technical support A-1

A D
.ab1 files. See ABIF sample files data
ABI Sample File Toolkit 3-5 hiding for specific dyes 3-8
ABIF sample files none in capillaries 6-5
access through developer’s toolkit 3-5 recovering 5-2
discussed 5-2 storage 5-2
Adobe Acrobat Reader 3-6 Data Collection software 3-3
AE server 3-5 will not launch 6-2
analysis module Data Delay Time run module parameter 3-17
provided modules 4-5 data flow, overview 5-9
analysis parameter files. See sequencing database
analysis.log file 5-2 LIMS. See LIMS database
array. See capillary array reinitializing 5-8
auto extractor 3-5 removing run modules using utility 5-7
autosampler Sequence Collector. See Sequence Collector database
controlling. See manual control commands debug.log 3-44
will not move forward 6-2 deleting
from plate import table 4-17
plate record 4-27
B processed frame data from database 5-4
basecaller settings file, creating 3-24 developer’s toolkit 3-5
BLOB 4-18 directories, list 3-7
display colors, changing using HSV 3-9, 3-10
C displayed dye colors 3-8 to 3-10
camera, CCD. See CCD camera documents, list 1-3, B-3
capillary array 2-14 dye colors
filling. See manual control commands changing 3-8
poor performance 6-9 changing the name or color intensity 3-8
CCD camera 2-18 See also displayed dye colors
CD list, software 3-2 dye sets 4-3
chemical hazard warning 1-4 composition 2-11
chemistry
dye sets 2-11 E
overview 2-13 Edit Dye Display Information dialog box 3-8
types supported 2-11 electrophoresis, discussed 2-15 to 2-16
Cleanup Database utility 4-27, 5-4 elevated baseline 6-7
colors, displayed dye. See displayed dye colors event viewer, blank 6-2
commands, manual control 3-11 Excel. See Microsoft Excel
Computer 1-7 exporting run modules to file 3-19
computer extensions, filename 3-7
checking logon user name 5-11 extracting data.See auto extractor
frozen 6-2 extracting to Sequence Collector 3-39
hard drive partitions 2-9 extraction.log file 5-2
name, finding 5-12 Extractor Utility 5-2
network domain, finding 5-12
networked computer requirements 5-12
networking 5-9 to 5-12 F
requirements 2-9 FASTA format for .Seq files 3-27
system administration privileges 5-11 file types 3-7
computer, safety 1-7 ABIF sample 5-2
Control Panel window 5-12 analysis modules for fragment analysis (.gsp) 3-35

Index-1
 basecaller settings (.bcp) 3-24 "Leak detected" 6-10
portable document format (.pdf) 3-6 LIMS database
run data 5-2 importing plate records from 4-16 to 4-18
run module (.modexp) 3-18 option 5-10
sequencing analysis module (.saz) 3-27 log file, analysis or extraction 5-2
size-standard (.szs) 3-32 log file, viewing for a run 3-44
tab-delimited text files, plate records 4-7 to 4-15 logging on, checking user name 5-11
filename extensions 3-7 loss of resolution 6-7
firmware 3-3 low signal strength 6-6
fluorescence detection, discussed 2-17
fragment analysis M
analysis modules, creating 3-35 to 3-36
Macintosh computer
analysis modules, viewing 3-30
using to view data 5-10
chemistry, types supported 2-11
manual control commands 3-11
polymer 2-12
manual set B-3
Method Import Utility 5-6
G Method Import utility
GeneScan Analysis Software 3-6 overview 3-5
.gsp files. See fragment analysis modules Microsoft Excel
creating plate records 4-9, 4-19 to 4-21
H middleware. See Orbix Desktop
migration time, too fast or too slow 6-9
hard drive 2-9
mobility files
hardware overview 2-5 to 2-8
provided 4-4
hazardous 1-4
.modexp (run module) files 3-18
Hi-Di formamide 2-13
MSDSs, ordering 1-6
HSV color system 3-10

I N
networking 5-9 to 5-12
importing
"No candidate spectral files found" 6-4
linking a plate record 4-26
plate records from a LIMS 4-16 to 4-18
run modules from file 3-20 O
Initialize Database utility 5-8 Oracle database
Injection Time run module parameter 3-17 See also Sequence Collector database
Injection Voltage run module parameter 3-17 See instrument database
instrument Orbix Desktop 3-6
hardware 2-5 to 2-8 OrbixWeb software 3-6
operation overview 2-3 to 2-4 oven, controlling. See manual control commands
status lights 2-6
instrument database 3-6 P
deleting from 5-4
partitions, computer hard drive 2-9
plate import table 4-17
parts list B-1 to B-3
See also processed frame data
.pdf (portable document format) files 3-6
IP address
peaks, troubleshooting 6-10
for networking to LAN 5-11
Persistence Object Layer 3-6
plate file
J creating 4-19 to 4-24
Java Runtime Environment 3-6 plate import table 4-17
plate record 3-39
L deleting 4-27
deleting individual plate records 4-28
labels, instrument safety 1-6
sequentially importing and linking 4-26
LAN. See networking 5-9
.plt (plate record) files 4-19 to 4-26
laser
plate records
controlling. See manual control commands
creating, overview of procedures 4-2
discussed 2-17
polymer
hazard warning 2-17
discussed 2-12

Index-2
POP. See polymer Sequencing Analysis software 3-6
Pre Run Time run module parameter 3-17 directory path for SeqA.exe 3-21
Pre Run Voltage run module parameter 3-17 sequencing chemistry
processed frame data types supported 2-11
deleting 5-4 Set Color command 3-8 to 3-10
size of 5-2 signal too high 6-6
processed frame data, storing 5-2 size-standard (.szs) files
creating 3-32 to 3-34
R software
list of applications 3-2
red status light 6-2
overview of suite 3-3
reinitializing the database 5-8
spatial calibration
RemoveRunModules.bat file 5-7
persistently bad results 6-3
reset button, location 2-5
unusual peaks 6-3
resolution, loss 6-7
spectral calibration
RGB color system 3-9
no signal 6-4
run
spectral dispersion device, discussed 2-18
elevated baseline 6-7
spectrograph 2-18
elevated current 6-8
spreadsheet programs
fast migration time 6-9
creating plate records 4-9, 4-23
fluctuating current 6-9
status lights 2-6
high signal 6-6
syringes
loss of resolution 6-7
controlling. See manual control commands
low signal 6-6
leaking 6-10
no current 6-8
system administration privileges
no signal 6-6
computer 5-11
options 4-15
system management options 5-9 to 5-10
setup for multiple runs 4-15
.szs (size-standard) files
slow migration time 6-9
creating 3-32 to 3-34
run modules 3-13 to 3-20
creating 3-14
editing 3-15 T
editing or creating 3-14 technical support A-1
exporting to file 3-19 temperature, electrophoresis 2-15
importing and exporting 3-18 templates, location 4-19
importing from file 3-20 text files
parameters, described 3-17 See also .seq (sequence text) files
provided 4-5
removing from the database 5-7 U
transferring between computers 3-18
user name 5-11
viewing 3-13
utilities
Run Time run module parameter 3-17
Cleanup Database 5-4
Run Voltage run module parameter 3-17
Initialize Database 5-8
Method Import 5-6
S Remove Run Modules 5-7
safety 1-4
.seq (sequence text) files W
option to write 3-27
warning 1-4
Sequence Collector database
warning, laser 2-17
option discussed 5-10
waste, disposal 1-7
working with 3-37 to 3-44
Windows NT Security dialog box 5-11
sequencing
write .seq files option 3-27
analysis modules, creating 3-24 to 3-29
analysis modules, discussed 3-21 to 3-29
polymer 2-12
.saz (sequencing analysis module) file
creating 3-27
saving 3-28
viewing 3-21

Index-3
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Printed in U.S.A., 07/2002

Part Number 4335393 Rev. A