Octet Data Analysis 

Software 7.0 User Guide

ForteBio, Inc.
1360 Willow Road, Suite 201
Menlo Park, CA 94025
888.OCTET-QK
650.322.1360
www.fortebio.com

Copyright 2011© ForteBio, Inc. All rights reserved

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Table of Contents
Chapter 1:  Ending a User Session. . . . . . . . . . . . . . . .33
Welcome. . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
About the Octet System. . . . . . . . . . . . . . . . . . .6 Chapter 4: 
What’s New in the Octet System Data Analysis Quantitative Analysis . . . . . . . . . . . . . . .35
Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .7 Working with Experiments . . . . . . . . . . . . . .36
Conventions Used in This Guide. . . . . . . . . . .9 Loading an Experiment for Analysis . .36
ForteBio Technical Support . . . . . . . . . . . . . . .9 Editing Experiments . . . . . . . . . . . . . . . . .38
Viewing Binding Curves . . . . . . . . . . . . . .41
Chapter 2:  Closing Experiments . . . . . . . . . . . . . . . . .46
Getting Started. . . . . . . . . . . . . . . . . . . . . 11
Analyzing Data . . . . . . . . . . . . . . . . . . . . . . . . .46
Launching the Octet System Data Analysis 7.0
Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 Analyzing Binding Data. . . . . . . . . . . . . .46
Main Menu . . . . . . . . . . . . . . . . . . . . . . . . . 13 Specifying Analysis Settings. . . . . . . . . .47
Defining Replicate Groups . . . . . . . . . . .51
Chapter 3: 
Calculating Accelerated Binding Rate55
21 CFR Part 11 Compliance. . . . . . . . . . 17
Octet System 7.0 21 CFR Part 11 Software Working with Analyzed Data . . . . . . . .55
Overview. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18 Saving Standards Data. . . . . . . . . . . . . . . . . .57
ForteBio GxP Server Module . . . . . . . . . . . . 19 Saving Analysis Settings. . . . . . . . . . . . . . . . .57
Selecting a Server Location . . . . . . . . . . . . . 20 Processing Batch Quantitation Analysis .57
Starting a User Session . . . . . . . . . . . . . . . . . 24 Creating a Settings_DataAnalysis.ini File
Compliance Features . . . . . . . . . . . . . . . . . . . 26 57

Experiment and Method File Compliance Selecting Experiments and Running the
27 Batch Analysis . . . . . . . . . . . . . . . . . . . . . . .60

Verifying Digital Signatures . . . . . . . . . 27 Applying Alerts . . . . . . . . . . . . . . . . . . . . . .61

Viewing the Audit Trail . . . . . . . . . . . . . . 29 Exporting Data. . . . . . . . . . . . . . . . . . . . . . . . . .64

Changing Projects During a User Session Saving Raw Data . . . . . . . . . . . . . . . . . . . .64

31 Saving a Quantitation Results Report 64
Changing the User Password. . . . . . . . 32
Locking the Application . . . . . . . . . . . . . 32

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Chapter 5:  Kinetics Analysis Results . . . . . . . . . . . . . . . 115

Basic Kinetics Analysis . . . . . . . . . . . . . . 67
Fitting View and Residual View. . . . . 115
Working with Experiments. . . . . . . . . . . . . . 68
Grouping Results for Viewing . . . . . . 118
Starting a Basic Kinetics Experiment. 68
Display Graphs in Custom Groupings119
Loading an Experiment for Analysis . 68
Selecting Data for Viewing . . . . . . . . . 121
Analyzing Binding Data. . . . . . . . . . . . . 72
Analysis Results Table. . . . . . . . . . . . . . 123
Editing Experiments. . . . . . . . . . . . . . . . . 73
Working with the Analysis Results Table
Viewing Binding Curves . . . . . . . . . . . . . 76 125
Closing Experiments . . . . . . . . . . . . . . . . 79 Searching Analysis Results . . . . . . . . . 126
Working with Raw Data . . . . . . . . . . . . . . . . 80 Color-Coding Data . . . . . . . . . . . . . . . . 128
Viewing Raw Data . . . . . . . . . . . . . . . . . . 80 Sorting Analysis Results . . . . . . . . . . . . 131
Exporting Raw Data . . . . . . . . . . . . . . . . 83 Working with Graphs. . . . . . . . . . . . . . . . . . 132
Quantitating Raw Data . . . . . . . . . . . . . 83 X-Y Graphs . . . . . . . . . . . . . . . . . . . . . . . . 132
Processing Kinetic Data. . . . . . . . . . . . . . . . . 88 Iso-Affinity Graphs . . . . . . . . . . . . . . . . . 133
Step 1: Sensor Selection . . . . . . . . . . . . . 88 Steady State Analysis Graphs . . . . . . 134
Step 2: Reference Subtraction . . . . . . . 91 Data Export Options . . . . . . . . . . . . . . . . . . 134
Step 3: Align Y Axis . . . . . . . . . . . . . . . . . . 96 Generating a Report. . . . . . . . . . . . . . . . . . . 135
Step 4: Interstep Correction . . . . . . . . . 97 Experiment Summary Options . . . . . 136
Step 5: Process . . . . . . . . . . . . . . . . . . . . . . 98 Processing Options . . . . . . . . . . . . . . . . 137
Step 6: Viewing Results . . . . . . . . . . . . . . 99 Analysis Options. . . . . . . . . . . . . . . . . . . 140
Step 7: Saving Results and/or Processing
Parameters . . . . . . . . . . . . . . . . . . . . . . . . 104 Appendix A: 
Kinetics Analysis. . . . . . . . . . . . . . . . . . . . . . . 105 Using Octet384 Systems with an
Automation Interface . . . . . . . . . . . . . 143
Curve Fitting Analysis . . . . . . . . . . . . . . 106
Automation Interface Overview . . . . . . . 144
Steady State Analysis . . . . . . . . . . . . . . 110
Design of the Automation Interface . . . 144
Processing Batch Kinetics Analysis . . . . . 111
Automation Interface Control Setup145
Creating a Kinetic
Settings_DataAnalysis.ini File . . . . . . 111 Analysis Automation API. . . . . . . . . . . 145

Creating a Kinetic Settings_WellInfo.xml

File (Optional) . . . . . . . . . . . . . . . . . . . . . 112 Appendix B: 
21 CFR Part 11 Software Administrator
Creating a Kinetic Settings_TableInfo.xml
Options . . . . . . . . . . . . . . . . . . . . . . . . . . 149
File (Optional) . . . . . . . . . . . . . . . . . . . . . 112
Installing the Data Acquisition 7.0 21 CFR Part
Selecting Experiments and Running the
11 Software . . . . . . . . . . . . . . . . . . . . . . . . . . . 150
Batch Analysis . . . . . . . . . . . . . . . . . . . . . 113

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Installing the Data Analysis 7.0 21 CFR Part 11 Software153

Installing the ForteBio GxP Server Module156
Administrator Account Setup . . . . . . . . . . 159
Starting an Administrator User Session 163
Accessing Administrator Options . . . . . . 166
Administrator Tabs . . . . . . . . . . . . . . . . 167
User Account Administration. . . . . . . 168
Group Administration. . . . . . . . . . . . . . 172
Project Administration . . . . . . . . . . . . . 175
Administrator Constants . . . . . . . . . . . 176
Event Log . . . . . . . . . . . . . . . . . . . . . . . . . . 178
Accessing the ForteBio GxP Server Module Directly180
Restarting the ForteBio GxP Server Module183

Octet System Data Analysis Software User Guide

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Octet System Data Analysis Software User Guide

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
CHAPTER 1:

Welcome
About the Octet System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

What’s New in the Octet System Data Analysis Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

Conventions Used in This Guide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

ForteBio Technical Support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

page 6 Chapter 1: Welcome

Welcome to the Octet System Data Analysis software for the ForteBio Octet system. This
guide explains how to:
• Start a data analysis session and load a quantitation or kinetics experiment (.frd)
• View and analyze the experiment data
• View the analysis results in tabular and graphical formats
• Export analysis results and generate reports

ABOUT THE OCTET SYSTEM

The Octet system enables real-time quantitation or kinetic characterization of biomolecular
interactions. A system includes the Octet instrument and two applications:
• Data Acquisition
• Data Analysis
For more details on the Data Acquisition software, please see the Octet System Data Acquisi-
tion User Guide. The Octet system includes the Octet instrument and two applications; see
Table 1-1:
• Data Acquisition
• Data Analysis
For information on preparing samples for quantitation or kinetics experiments, please see
the appropriate ForteBio Octet Biosensor product instructions.

Table 1-1: Octet System Functions

Octet Software Functions

Data Acquisition • Define a quantitation or kinetic experiment and save the
experiment for future use.
• Define custom assays.
• Run the experiment and acquire binding data.
• View and save binding data to a user-specified location.
Data Analysis • Analyze binding data and view analysis results.
• Export or copy analysis results.
• Generate a report of quantitation or kinetic results in table
and graph formats.

Octet System Data Analysis Software User Guide

What’s New in the Octet System Data Analysis Software page 7

WHAT’S NEW IN THE OCTET SYSTEM DATA ANALYSIS SOFTWARE

Table 1-2 lists and describes the new features in the Octet System Data Analysis software.

Table 1-2: Octet System Data Analysis Software—New Features

New Software for 21 The Data Acquisition and Data Analysis software for 18
CFR Part 11 Octet systems is available in an optional 21 CFR Part 11
version that enables users in GMP and GLP laboratories
to comply with 21 CFR Part 11 regulations. This version
of the software includes features such as user account
management, audit trails and electronic signatures.
New Software for During user sessions, the GxP Server module manages 19
the ForteBio GxP and stores this recorded information.
Server Module
Updated Procedure Includes new screen captures of latest system desktop 12
for Launching the icons and procedural text.
Data Analysis 7.0
Software
Updated Security This menu now provides the following functions: 15
Menu • Verify document—Utility that tests if a method
(.fmf ) or data (.frd) file was created using a CFR
version of the ForteBio software.
• View Audit Trail—Displays the recorded events
for CFR documentation. Events may be viewed by
project or machine.
• Change Project—Switches active projects or run
experiment without a project title (“none”).
• Change Password—Edits password for an active
user.
• Server administration—Modifies settings for
users, groups, projects, and constants.
• Lock Application—Disables acquisition software
with screen lock.
• Logoff—Exits program as user.
Accelerated Bind- The calculation of the binding rate has been increased 55
ing Rate Calculation 15–20 fold by implementing a new algorithm.

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Table 1-2: Octet System Data Analysis Software—New Features (Continued)

Replicate Groups Replicate groups can be assigned as the sample plate is 51

defined during experiment setup. For quantitation
experiments, average binding rate, average concentra-
tion and corresponding standard deviation and CV%
statistics are calculated for all samples in each replicate
group automatically. For kinetics experiments, samples
in each replicate group are identified by the same color.
Sample Alerts The “Sample Alert” highlights data that fit user specified 63
criteria.
Flip Data Allows acquisition data to be inverted. This function 77
is useful when the observed wavelength shift is neg-
ative due to use of large particles, such as liposomes
and phage, during the assay.
Grouped View Displays graphs in custom groupings. This feature 118
allows you to display graphs organized into groups
according to sample attribute or results category. This is
a highly useful feature when working with large data
sets.
X-Y Graph An X-Y plotting tool that graphs several important 132
parameters such as binding rate, R2, calculated concen-
tration, and residual.
1:2 Bivalent Analyte The model is intended to fit data derived from systems 106
Model where two molecules of analyte (solution-based mole-
cule) bind to one molecule of the immobilized ligand.
The model is available in the Analysis tab (Kinetics
mode) > Model menu.

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Conventions Used in This Guide page 9

CONVENTIONS USED IN THIS GUIDE

NOTE: A note presents pertinent details on a topic.For example, general infor-

mation about tips or alternate options.

IMPORTANT: An important message for instances where the assay or p roce-

dure will not work if not properly followed.

WARNING: A warning informs the user that specific actions could cause irre-
versible consequences or damage.

Table 1-3: Octet Instrument Labels

Symbol Definition
Electrical hazard

Heat/hot

Fuse

FORTEBIO TECHNICAL SUPPORT

You can contact ForteBio technical support at:

Table 1-4: ForteBio Technical Support

Main Office European Office Asia Office

ForteBio, Inc. ForteBio, UK, Ltd. ForteBio 
1360 Willow Road,  83 Victoria Street,  (Aria Biotechnology Co. Ltd.)
Suite 201 Suite 407 917 Halley Road, Bldg. 4
Menlo Park, CA 94025 London, SW1H 0HW Zhangjiang High Tech Park
USA UK Shanghai, China 201203
Tel: +1-650-322-1360 Tel: +44-(0)20-31784425 Tel: +86-21-51320387
Fax: +1-650-322-1370 Fax: +44-(0)20-31787070 E-mail: info@fortebio.com
E-mail: info@fortebio.com E-mail: info@fortebio.co.uk

Octet System Data Analysis Software User Guide

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Octet System Data Analysis Software User Guide

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
CHAPTER 2:

Getting Started
Launching the Octet System Data Analysis 7.0 Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
page 12 Chapter 2: Getting Started

LAUNCHING THE OCTET SYSTEM DATA ANALYSIS 7.0 SOFTWARE

NOTE: The installation shall be performed by ForteBio, Inc. personnel only. 

WARNING: If the Octet system is not used as specified, injury to the user and/or
damage to the instrument may result.

NOTE: Do not position the Octet instrument such that it is difficult to discon-
nect the power.

NOTE: For information about how to connect the Octet instrument to the
computer, refer to the insert sheet that is provided with the Octet instrument.

To launch the system and Octet Data Acquisition or Data Analysis software:
1. Turn the Octet instrument on using the power switch located on the external electrical
box.

NOTE: The instrument requires a minimum of one-hour warm-up time. It is

recommended that you leave the instrument on for a minimum of eight hours
prior to use.

2. Launch the Data Acquisition or Data Analysis software by double-clicking the respec-
tive desktop icon (Figure 2-1).

Figure 2-1: Data Acquisition and Data Analysis Desktop Icons

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Launching the Octet System Data Analysis 7.0 Software page 13

NOTE: When using the CFR 11 version of the Octet System Data Analysis soft-
ware, you are required to log in and start a user session before the software
launches. For more information, refer to “Starting a User Session” on page 24.

Launching the Octet System Data Analysis software application displays the main
screen (Figure 2-2).

Main Menu

Figure 2-2: Main Screen for Data Analysis

Main Menu
The main menu is located in the upper left corner of the main screen (Figure 2-2). Menu
options are described in this section.
Figure 2-2 displays the non-21 CFR Part 11 main menu; Figure 2-3 displays the main menu
for the 21 CFR Part 11.

Figure 2-3: Main Menu—21 CFR Part 11 Version of the Data Analysis Software

Octet System Data Analysis Software User Guide

page 14 Chapter 2: Getting Started

File Menu
The File menu (Figure 2-4) allows users to open and save re-analyze, work with experiments
in different modes, save reports, and set port options.

Figure 2-4: File Menu

Table 2-1: File Menu Commands

Menu Command Function

Load a Folder Loads an experiment method file (.frd).
Quantitation Batch Opens the Quantitation Batch Mode dialog
Mode box.
Kinetics Batch Mode Opens the Kinetics Batch Mode dialog box.
Save Report Saves all open report files.
Options Allows you to determine the port automa-
tion options:
• TCP-IP with a localhost option
• Serial (RS-232)
Exit Closes the application after prompting to
save any changes.

NOTE: When using the 21 CFR Part 11 version of the Octet System Data Acqui-
sition software, only 21 CFR Part 11-compliant experiments and re-analyze
generated using the 21 CFR Part 11 version of the software can be opened.
Files generated using the non-compliant version of the software or with a
non-compliant system cannot be opened, and a message indicating this will
be presented.

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Launching the Octet System Data Analysis 7.0 Software page 15

Security Menu
The Security menu is only available in the 21 CFR Part 11 version of the Octet System Data
Analysis software.

NOTE: The Security menu is only available in the CFR 11 version of the Octet
System Data Analysis software. For complete details on menu options, refer to
“Compliance Features” on page 26.

Figure 2-5: Security Menu

Table 2-2: Security Menu Commands

Menu Command Function

Verify Document Utility that tests if a method (.fmf ) or data
(.frd) file was created using a CFR version of
the ForteBio software.
View Audit Trail Displays the recorded events for CFR docu-
mentation. Events may be viewed by project
or machine.
Change Project Switches active projects or run experiment
without a project title (“none”).
Change Password Edits password for active user
Server Administration Modifies settings for users, groups, projects
and constants.
Lock Application Disabled the Octet System Data Analysis
software with a screen lock. A password is
required to unlock the program.
Logoff Exits the program. A password is required to
log in again.

Octet System Data Analysis Software User Guide

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Help Menu
The Help menu provides access to software and instrument support information.

Figure 2-6: Help Menu

Table 2-3: Help Menu Commands

Menu Command Function

Data Analysis User Opens the online Octet System Data Analysis Software User
Guide Guide.
ForteBio Web Site Opens a web browser and displays the ForteBio web page
(www.fortebio.com).
About ForteBio Data Displays software, user, and instrument information.
Analysis

NOTE: Clicking the ForteBio logo (in the upper right corner of the main screen)
also displays the About window.

Octet System Data Analysis Software User Guide

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
CHAPTER 3:

21 CFR Part 11 Compliance

Octet System 7.0 21 CFR Part 11 Software Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

ForteBio GxP Server Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

Selecting a Server Location . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

Starting a User Session . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24

Compliance Features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
page 18 Chapter 3: 21 CFR Part 11 Compliance

OCTET SYSTEM 7.0 21 CFR PART 11 SOFTWARE OVERVIEW

The Data Acquisition and Data Analysis software for Octet systems is available in an
optional 21 CFR Part 11 version that enables users in GMP and GLP laboratories to comply
with 21 CFR Part 11 regulations. This version of the software includes features such as user
account management, audit trails and electronic signatures. In addition, the 21 CFR Part 11
version utilizes the ForteBio GxP Server module to manage the information recorded dur-
ing user sessions. This chapter explains how to use the ForteBio GxP Server module, compli-
ance features and administrative functions specific to the 21 CFR Part 11 versions of the
Data Acquisition and Data Analysis software.

NOTE: The 7.0 21 CFR Part 11 Data Analysis software only opens data files
generated in CFR data acquisition. 7.0 21 CFR Part 11 files from software ver-
sion 6.X are fully compatible with the 7.X 21 CFR Part 11 software.

NOTE: For details on how to install the Octet System Data Acquisition or Data
Analysis software, see Appendix B, 21 CFR Part 11 Software Administrator
Options on page 149.

Octet System Data Acquisition Software User Guide

ForteBio GxP Server Module page 19

FORTEBIO GXP SERVER MODULE

When the Data Acquisition or Data Analysis 7.0 21 CFR Part 11 software is launched, users
are prompted to logon to the ForteBio GxP Server module. This initiates a user session
where all system, software and user events are recorded. During user sessions, the GxP
Server module manages and stores this recorded information.User sessions are closed
when the user logs out or a set period of inactivity is reached. A new user session is initiated
each time a user accesses the software.

NOTE: For details on how to install the ForteBio GxP Server module, see
Appendix B, 21 CFR Part 11 Software Administrator Options on page 149.

NOTE: The ForteBio GxP Server is required for 21 CFR Part 11.

NOTE: The GxP Server can be installed in multiple locations with user selection
of the employed copy at the launch of the Acquisition or Analysis software,
although a single copy per network is recommended by ForteBio to ensure
that all records are saved to one location.

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SELECTING A SERVER LOCATION

NOTES: 
Please contact your administrator to determine best location to use for the
GxP Server module.

Once the GxP Server module host location is selected, this location should be
used as the default selection for the user account. It does not need to be rese-
lected each time a new user session is initiated.

Users must select the host location of the GxP Server module during the login process. The
GxP server can be run on the local host computer where the Data Acquisition or Data Anal-
ysis software is installed or from a network location.
To select a server location:

NOTE: You must select the host location of the GxP Server module during the
login process. You can use the GxP Server on the local host computer where
the Data Acquisition or Data Analysis software is installed, or from a network
location.

1. Launch the Data Acquisition or Data Analysis software by double-clicking the respec-
tive desktop icon (Figure 3-1).

Figure 3-1: Data Acquisition and Data Analysis Desktop Icons

The Login dialog box displays (Figure 3-2).

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Selecting a Server Location page 21

Figure 3-2: Login Dialog Box

2. Click ... (browse) to select a Server location.

The Authentication Server dialog box displays (Figure 3-3).

Figure 3-3: Authentication Server Dialog Box

3. Click Default to recall the default server settings of localhost and Port 2002.
• Local host—If the local computer is to be used as the GxP Server module host,
click the Localhost check box. Change the Port number if necessary.
• Remote host on same subnet—If the GxP Server module is hosted on the same
subnet, deselect the Localhost check box and click Find. A list of potential GxP
Server module addresses will be listed. Choose the desired location from the list
and click OK.

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Figure 3-4: Choose Server Address

• Remote host on another subnet—If the GxP Server module is hosted on a differ-
ent subnet, deselect the Localhost check box. Enter the IP address of the com-
puter hosting the GxP Server module.

Figure 3-5: Authentication Server Dialog Box

4. When the GxP Server module host location has been selected or entered, click OK to
save changes and exit the Authentication Server dialog box.
The GxP Server module location is listed as the Server in the Login dialog box
(Figure 3-6).

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Selecting a Server Location page 23

Figure 3-6: Login Dialog Box—GxP Server Information

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page 24 Chapter 3: 21 CFR Part 11 Compliance

STARTING A USER SESSION

NOTE: Before starting your first user session, contact your administrator to
determine the GxP Server module host location to use.

To start a user session:

1. Launch the Data Acquisition or Data Analysis software by double-clicking the respec-
tive desktop icon (Figure 3-1: on page 20).
The Login dialog box displays (Figure 3-2: on page 21).
2. Confirm that the Server location is correct. If not, see “Selecting a Server Location” on
page 20.
•If the local machine is to be used as the GxP server, ensure that Localhost is
selected.
• If a remote machine is to be used and it is located on the same subnet, de-select
Localhost and click Find to display a list of potential GxP server addresses.
Choose the desired GxP server from this list and click OK. Click OK in the Authen-
tication Server dialog to finish. The new GxP server should be listed in the Login
dialog box (next to Server).
• If a remote machine is to be used and it is located on a different subnet, de-
select Localhost and enter the IP address of the machine running the GxP
server. Click OK to close the authentication server.
3. Select your login name from the User drop-down list (Figure 3-7). (For the first time log-
ging in, select Administrator.)

NOTE: To start an administrator session, select Administrator in the User

drop-down list.

Figure 3-7: Selecting Login Username

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Starting a User Session page 25

4. Enter your password in the Password field. Click ? for a password reminder if needed
(Figure 3-8). (For the first time logging in, leave the Password field blank.)

Figure 3-8: Password Reminder Option

5. Optional. Select a project from the Project drop-down list (Figure 3-9). (For the first
time logging in, leave as (none).)

Figure 3-9: Project Selection

6. Click OK.
The Data Acquisition or Data Analysis software launches and starts the user session.
During the session, the user account and project selected at login are displayed in the
Data Acquisition software status bar.

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page 26 Chapter 3: 21 CFR Part 11 Compliance

NOTES: 
Software operation may be restricted based on your user privileges. For more
information on user privileges, please contact your administrator. 

User sessions are automatically locked after a period of inactivity which is set
by the administrator. The Login box will display and a message indicating the
session has been locked will be shown. You can choose to log back into the
session or log off at this time. User sessions will not be locked during experi-
mental data acquisition.NOTE: To create and edit new users, groups, and proj-
ects, see “User Account Administration” on page 168, “Group Administration”
on page 172, and “Project Administration” on page 175.

COMPLIANCE FEATURES
You can access the 21 CFR Part 11 compliant features provided in the 21 CFR Part 11 ver-
sions of the Data Acquisition and Data Analysis software by selecting the Security menu
from the main menu (Figure 3-10).

Figure 3-10: Security Menu—Octet System Data Analysis Software

NOTES: 
The Server Administration option in the Security menu can be accessed
only if you have administrator or review privileges. 

Security menu options in the Data Acquisition and Data Analysis software
applications are identical.

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Experiment and Method File Compliance

When using the 21 CFR Part 11 version of the Octet System Data Acquisition software, only
21 CFR Part 11 compliant experiments and method files generated using the 21 CFR Part 11
version of the software can be opened. Files generated using the non-compliant version of
the software cannot be opened, and a message indicating this will be presented.

Verifying Digital Signatures

The electronic signature of method (.fmf ) and data (.frd) files can be verified to ensure they
were generated using 21 CFR Part 11 compliant software.
To verify digital signatures:
1. Click Security > Verify Document.
The Verify Digital Signature dialog box displays (Figure 3-11).

Figure 3-11: Verify Digital Signature

2. Click ... to browse for the desired .fmf or .frd file.

NOTE: When verifying digital signatures, both method (.fmf) and data (.frd)
files can be selected in the Data Acquisition and Data Analysis software.

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File Type

Figure 3-12: Selecting Method or Data Files

To change the file type available for selection, click the file type box and select a differ-
ent format (Figure 3-13).

Figure 3-13: Changing File Type

3. Select the desired file and click OK.

A message displays in the Verify Digital Signature dialog box, indicating file compli-
ance status (Compliant or Non-Compliant) (Figure 3-14).

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Figure 3-14: File Compliant (top), File Not Compliant (bottom)

Viewing the Audit Trail

The Audit Trail displays a historical log of user, system and software events recorded during
user sessions. To view and display the Audit Trail, click Security > View Audit Trail
(Figure 3-15).

Figure 3-15: Audit Trail

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NOTE: Events displayed in the Audit Trail are those associated with the user
account that is currently logged in and active only.

Sorting Events in the Audit Trail

Events in the Audit Trail can be sorted by clicking any of the column headers (Figure 3-16).

Figure 3-16: Events Listed in the Audit Trail

Viewing Events for a Specific Project or Computer

By default, the events initially displayed in the Audit Trail are those associated with the proj-
ect selected at login and the machine (computer) currently being used. To view events for a
specific project or computer, click the Project or Machine drop-down list and select an
entry (Figure 3-17).

Figure 3-17: Viewing a Specific Project in the Audit Trail

NOTE: Selections can be made in either one or both of the Project or Machine
drop down lists.

The list only displays events for the selected entries (Figure 3-18).

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Figure 3-18: Project-Based Audit Trail Events

In addition to the specific project and machine selections, the following list options are also
available:
• (any)—Displays all project and/or machine events for the user account.
• (none)—Displays all project or machine events not associated with a specific project
(Project list only).

Changing Projects During a User Session

During an active session, you can switch to another project in the Data Acquisition or Data
Analysis software without having to log out.
To change projects during a user session:
1. Click Security > Change Projects.
A list of projects assigned to your user account displays with the active project high-
lighted (Figure 3-19).

Figure 3-19: Changing Projects

2. Select the desired project from the list.

The selected project becomes the active project for the user session.

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Changing the User Password

To change the user password:
1. Initiate a new user session with your existing password.
2. When the software launches, click Security > Change Password.
The Change Password dialog box displays (Figure 3-20).

Figure 3-20: Change Password

3. Enter the Current password for your user account. Click ? for a password reminder.
4. Enter the New Password, confirm the new password, and optionally enter a Password
reminder.
5. Click OK to save the changes and exit.

Locking the Application

The Data Acquisition or Data Analysis software can be locked during a user session to pre-
vent another user from interrupting a session or experiment. When the application is
locked, any experiments started will continue to run.
To lock the Octet System Data Acquisition software application, click Security > Lock
Application.
The Octet System Data Acquisition software is placed in locked mode immediately and the
Application Locked window displays (Figure 3-21).

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Figure 3-21: Application Locked Mode

The application will remain locked until it is unlocked or the active user logs off.
• Unlock—To resume the user session, enter your password and click Unlock.
• Log off—To discontinue the user session, click Logoff.

Ending a User Session

To end a user session:
1. Click Security > Log Off.
2. Click OK in the dialog box displayed.

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
CHAPTER 4:

Quantitative Analysis
Working with Experiments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36

Analyzing Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46

Saving Standards Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57

Saving Analysis Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57

Processing Batch Quantitation Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57

Exporting Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64

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WORKING WITH EXPERIMENTS

A quantitation experiment enables you to determine sample concentration using a refer-
ence set of standards. After an experiment is run, start a data analysis session (double-click
the icon on the desktop); see “Analyzing Binding Data” on page 46.

Loading an Experiment for Analysis

A data analysis session can be used to:
• Load and analyze an experiment.
• Re-analyze an experiment.

NOTE: More than one experiment can be opened during a session. If multiple
quantitation experiments are open, the analysis includes the data from all of
the biosensors that are check marked in the Results tab.

NOTE: When using the 21 CFR Part 11 version of the Octet System Data Acqui-
sition software, only 21 CFR Part 11-compliant experiments and re-analyze
generated using the 21 CFR Part 11 version of the software can be opened.
Files generated using the non-compliant version of the software or with a
non-compliant system cannot be opened, and a message indicating this will
be presented.

To load an experiment:
1. On the desktop, click the icon, or click the Windows Start button and select All Pro-
grams > ForteBio > Data Analysis 7.0.
The Data Selection tab displays (Figure 4-1).

Figure 4-1: Data Selection Tab

2. Load an experiment: right-click the experiment folder in the workstation directory tree
and select Load Folder, or on the menu bar, click File > Load a Folder.
3. In the Loading Files dialog box, enter the folder name or click the Browse button ,
select the desired folder, and click Load.
The experiment is added to the Loaded Data directory tree (see Figure 4-2 example).

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Loaded Data Directory Tree

Figure 4-2: Data Selection Window—Loading an Experiment

4. In the Loaded Data directory, click the experiment name to open.

The binding curves, sample plate, and sample plate table appear (Figure 4-3).

Figure 4-3: Data Selection Window—Opening an Experiment

5. Repeat steps 2–3 to load and open another experiment.

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NOTE: When multiple experiments are loaded, select an experiment by click-

ing its tab above the binding chart (in the Data Selection window), or click the
experiment name in the Loaded Data directory tree.

Editing Experiments
The Octet System Data Analysis software enables you to change sample designations, stan-
dard concentrations, or exclude samples from analysis. For example, you can exclude a
standard that does not meet the sample r2 or residual threshold, then re-analyze the data.
You can also modify some processing parameters.

Changing Sample Designations

To change sample designations:
1. Click the Data Selection tab, then perform one of the following tasks:
• In the sample plate map, select the well(s), right-click, and select one of the fol-
lowing options (see left image in Figure 4-4):
• Change to Standard
• Change to Unknown
• Change to Control
• Change to Reference
• Edit Sample Information
• In the results table, in the Well Type column, right-click a table cell and make a
selection from the drop-down menu (see right image in Figure 4-4).

Selecting wells in the sample plate map

Selecting a cell in the Well Type column of the results table

Figure 4-4: Changing Sample Designations

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Excluding/Including Samples from Analysis

To toggle sample analysis in the Results window, perform one of the following tasks:
• In the sample plate map, select the well(s), right-click and select Exclude Wells. If the
selection is already excluded from analysis, select Include Wells to return (include)
the samples to the analysis.
• In the results table, to exclude wells, de-select the check box in the first column, or
right-click the selected rows and select Exclude Selected Wells. If the selection is
already excluded from analysis, click the check box for the desired rows, or right-click
the desired rows, and select Include Selected Wells.

Selecting wells in the sample plate map

Selecting rows in the results table

Figure 4-5: Excluding Samples from Analysis

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Editing Standard Concentration or Well Information

To edit standard concentration or well information:
1. Click the Data Selection tab.
2. In the results table, click a Conc. or Well Info cell, and enter the desired information. (To
access a shortcut menu of editing commands, right-click the cell.)

Figure 4-6: Data Selection Window—Editing Sample Information

Editing Processing Parameters

To edit processing parameters:
1. Modify the following parameters as appropriate:
• Read time—The amount of data that is analyzed.
• Zero concentration threshold—Binding rates that are less than the zero con-
centration threshold are considered zero.
• Low concentration threshold—Clicking Calculate binding rate! causes the
initial rate to be calculated using both a linear and exponential equation. The
low concentration threshold determines which value is reported in the results
table. Changing this threshold can improve the precision of low concentration
samples.
• If the result from a linear fit is below the low concentration threshold, then the
value from the linear fit is reported in the analysis table.
• If the result from a linear fit is greater than the low concentration threshold,
then the value from the exponential fit is reported in the analysis table.

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2. In the Results window, select the cell to edit and enter a new value. Or, right-click the
cell to access a shortcut menu of edit commands.
The modified parameters are saved in the Settings_DataAnalysis.ini file when you
click Calculate Binding Data!.

Figure 4-7: Editing Processing Parameters in the Results Window

Viewing Binding Curves

To view binding curves, in the sample plate, select a well(s), or in the sample plate table,
select a row(s).
To select non-adjacent rows or wells, press and hold the Ctrl key while clicking the wells or
rows.

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Figure 4-8: Selecting Sample Wells or Rows to Display in the Binding Curve Graph

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Viewing Options
Table 4-1: Viewing Options in the Data Selection Window

Option Description
Align X Select this option if there is an artifact at the beginning of the
binding step to remove. Enter a time (seconds) at which to start
the alignment.
Reference Subtrac- If the experiment includes reference biosensors, select the Ref-
tion Average of erence Subtraction option and select one of the following:
• All—Computes the average binding curve from the ref-
erence wells and subtracts this average from each sam-
ple curve.
• Row—If a row includes both samples and references, the
Octet System Data Analysis software computes the aver-
age reference curve for the row and subtracts this curve
from the samples in the same row.
• Column—If a column includes both samples and refer-
ences, the Octet System Data Analysis software com-
putes the average reference curve for the column and
subtracts this curve from the samples in the same col-
umn.
Ignore errors in files If this option is selected, the Octet System Data Analysis soft-
when loading ware ignores errors in data files. All data files, regardless of
errors or runtime issues, will be loaded for analysis.
Show All Traces Displays all binding curves.
Flip Data The Flip Data function inverts signals from positive to negative
or from negative to positive. This is used most often when the
observed nm shift is negative due to the presence of large ana-
lytes, such as phage, cells, and lipoparticles on the biosensor
surface. For examples of flipping data, see Figure 4-9 and
Figure 4-10.
Grouped View Displays graphs in custom groupings. Choose this option to dis-
play graphs organized into groups according to sample attri-
bute or results category. This is a highly useful feature when
working with large data sets.
• Options—Click to show the Grouped View Options dia-
log box.
• Refresh—Updates the graph display.

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Table 4-1: Viewing Options in the Data Selection Window (Continued)

Option Description
Edit Legends Select the sample information displayed in the legend. Options
include Sensor, Sample, Sample ID, Group, and Concentra-
tion.

Figure 4-9: Flip Data—Example of Flipping Data to Example in Figure 4-10

Figure 4-10: New Flip Data from Figure 4-9

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Opening Binding Curve in Separate Window

To open the binding curve chart in a separate window, double-click the graph.
Customizing Appearance of Graph or Binding Curve
To customize the appearance of the graph or a binding curve; see Figure 4-11. Right-click
the graph or a curve for a shortcut menu of display options.
• Hover over a binding curve to display a tooltip of the X-Y coordinates.
• Right-click the graph to view a shortcut menu of display options.
• Right-click a curve to view a shortcut menu of display options.
• Right-click the graph and select Toolbar. Toolbar buttons enable you to save, copy,
or print the graph.

Figure 4-11: Viewing Binding Curves

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Closing Experiments
To close an experiment, in the Loaded Data directory tree, right-click the experiment name
and select Remove Run (see left side of Figure 4-12).
To close all experiments in the Kinetics or Quantitation folder, right-click the folder and
select Remove All (see right side of Figure 4-12).

Figure 4-12: Closing a Selected Experiment (left) or All Experiments (right) in the Quantitation or Kinetics
Folder

ANALYZING DATA
More than one experiment can be opened during a session. If multiple quantitation experi-
ments are open, the analysis includes the data from all of the biosensors that are selected in
the Results tab.

NOTE: When analyzing a large number of experiments, batch mode may be

more convenient. For more details on batch analysis, see “Processing Batch
Quantitation Analysis” on page 57.

Analyzing Binding Data

To analyze the binding data:
1. Start an analysis session and select the experiment(s) to use.
2. Select a standard curve equation.
3. If the sample plate does not include standards, load a standards file (.fsc).
4. Confirm or set new values for the processing parameters.
5. Calculate the binding rate.

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NOTE: For information on preparing biosensors, see the product insert packed
with the biosensors. For information on data acquisition, see the Octet System
Data Acquisition User Guide.

Specifying Analysis Settings

To specify analysis settings:
1. If the experiment includes reference biosensors, click the Reference Subtraction Aver-
age of check box (Figure 4-13) and select to average the data by one of the following:
• All—Computes the average binding curve from the reference wells and sub-
tracts this average from each sample curve.
• Row—If a row includes both samples and references, the Octet System Data
Analysis software computes the average reference curve for the row and sub-
tracts this curve from the samples in the same row.
• Column—If a column includes both samples and references, the Octet System
Data Analysis software computes the average reference curve for the column
and subtracts this curve from the samples in the same column.

Figure 4-13: Reference Subtraction Average of Methods

2. Confirm the sample designations (for details, see “Changing Sample Designations” on
page 38).

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3. Confirm the standard concentrations (for details on changing standard concentration,

see “Editing Standard Concentration or Well Information” on page 40).
4. Click the Results tab and select samples to include in the analysis (for details, see
“Excluding/Including Samples from Analysis” on page 39).

Figure 4-14: Results Window

5. Select a standard curve equation from the drop-down list:

• Linear Point to Point—The Octet System Data Analysis software connects the
points of the standard curve with straight line segments.
• Dose Response–4PL (Default; Unweighted)—A symmetrical dose response
curve. No points are weighted during the curve fitting.
• Dose Response–4PL (Weighted Y2)—Anon-symmetrical dose response curve
with weighting applied as 1/Y2.
• Dose Response–4PL (Weighted Y)—A non-symmetrical dose response curve
with weighting applied as 1/Y (as Y increases, weighting decreases).
• Dose Response–5PL (Default; Weighted Y2)—A non-symmetrical dose
response curve with weighting applied as 1/Y2.
• Dose Response–5PL (Unweighted)—A symmetrical dose response curve. No
points are weighted during the curve fitting.
• Dose Response–5PL (Weighted Y)—A non-symmetrical dose response curve
with weighting applied as 1/Y.

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NOTE: The Octet System Data Analysis software uses the data from the stan-
dards in all of the open experiment(s) to generate one standard curve. Stan-
dards with the same concentration are treated as replicates. Remove any standards or
samples that you do not want to include in the analysis. (For more details on excluding
samples, see “Excluding/Including Samples from Analysis” on page 39. Alternatively, an
experiment can be analyzed using only the standards from the same experiment plate
or from a user-selected experiment).

6. Optional. If multiple experiments are open and you want to analyze an experiment
using the standards from the same experiment plate, click the Calibrate within plate
check box.

NOTE: When two quantitation datasets are opened, you have the option to
merge data across plates. This happens, by default, if the Calibrate within
plate check box is not checked. Further to this, replicate groups of standards will be
merged and the statistics will be calculated across the entire new replicate group, BUT
replicate groups of unknowns will not be merged.

NOTE: You can navigate between multiple experiments using the tabs above
the sample plate map.

7. Optional. Analyze the data using standards from another experiment:

a. Click Load Standards.
b. In the displayed dialog box, select a standard curve (.fsc) and click Open.
c. Click the Use standards from loaded file check box.
8. Confirm or edit the processing parameter settings (for details, see “Editing Processing
Parameters” on page 40)
• Binding Rate Equation—The curve-fitting equation that models the binding
data.
• Initial Slope—Calculates the initial slope of the acquired quantitation data
(nm/second). Choose this equation for a basic quantitation or basic quantita-
tion with regeneration experiment.
• R equilibrium—This equation is recommended for an advanced quantitation
experiment that includes amplification. This equation uses the calculated
equilibrium, not the initial slope, to model the data.
• Read Time—The length of acquired data analyzed (seconds).
• Zero Conc. Threshold—Calculated binding rates less than the zero concentra-
tion threshold are reported as zero in the results table.

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• Low Conc. Threshold—Clicking Calculate Binding rate! causes the initial rate
to be calculated using both a linear and exponential equation. The low concen-
tration threshold determines which value is reported in the results table. If the
result from a linear fit is below the low concentration threshold, then the value
from the linear fit is reported in the analysis table. If the result from a linear fit is
greater than the low concentration threshold, then the value from the exponen-
tial fit is reported in the analysis table. Changing this threshold can improve the
precision of low concentration samples.
9. Click Calculate Binding Rate!
The standard curve and results table display (Figure 4-15).

Standard Curve

Figure 4-15: Results Window for a Quantitation Experiment

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Defining Replicate Groups

The Replicate Group feature enables data to be organized into custom groups during anal-
ysis (see Figure 4-16). Replicates can be defined during acquisition (or analysis) as a group.
For each group, the average binding rate, average concentration, and corresponding stan-
dard deviation, CV% are calculated.
To define replicate groups:
1. Enter replicate grouping information in the Results table: right-click and select Edit
Sample Information (Figure 4-16).

Figure 4-16: Edit Sample Information

NOTE: Replicate Group information can also be entered in the Octet System
Data Acquisition software.

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Assigning Replicate Groups in the Sample Plate Map

To assign Replicate Groups in the Sample Plate Map:
1. Select the samples to group, right-click and select Set Well Data.
2. In the Set Well Data dialog box (see Figure 4-17), enter a name in the Replicate Group
box and click OK.

Figure 4-17: Set Well Data Dialog Box—Add Replicate Group from the Sample Plate Map

3. Repeat the previous steps to assign new samples to the existing Replicate Group, or to
designate another set of samples to a new Replicate Group. Multiple groups can be
used in an experiment.

IMPORTANT: The Octet System Data Analysis software will only recognize and
group samples that use the same Replicate Group names, spacing and capi-
talization must be identical. For example, samples assigned to Group 2 and
group2 are treated as two groups.

4. Wells in the Sample Plate Map will show color-coded outlines as a visual indication of
which wells are in the same group (see Figure 4-18).

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Figure 4-18: Replicate Groups Displayed in Sample Plate Map

The Sample Plate Table updates with the Replicate Group names entered (see
Figure 4-19).

Figure 4-19: Replicate Groups Displayed in Sample Plate Table

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Assigning Replicate Groups in the Sample Plate Table

To assign Replicate Groups in the Sample Plate Table:
1. Double-click the desired cell in the Replicate Group table column.
2. Enter a group name (see Figure 4-20).

Figure 4-20: Add Replicate Group from the Sample Plate Table

Edit commands (Cut, Copy, Paste, Delete) and shortcut keys (Cut [Ctrl+x], Copy
[Ctrl+c], Paste [Ctrl+v], Undo [Ctrl+z]) are available in the Sample Plate Table. To view
edit commands, double-click the cell. This highlights the value and allows it to be
edited. Next, right-click to view the edit menu.

NOTE: The right-click menu is context-dependant. Right-clicking on a cell

where the value is not highlighted and in edit mode opens the Sample Plate
Map menu used to designate sample types.

3. Repeat the previous steps to assign new samples to the existing Replicate Group, or to
designate another set of samples to a new Replicate Group. Multiple groups can be
used in an experiment.

IMPORTANT: The Octet System Data Analysis software only recognizes and
groups samples that use the same Replicate Group names where spacing and
capitalization must be identical. For example, samples assigned to Group 2
and group2 are treated as two groups.

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Calculating Accelerated Binding Rate

The calculation of the binding rate has been increased 15–20 fold by implementing a new
algorithm (see Table 4-2 for example data).

Table 4-2: Example Data

Data Size Time Required Time Required Speed

to Calculate to Calculate Enhancement
Binding Rate in Binding Rate in
Software 6.X Software 7.X
384-well plate Q data folder 122 7 17X
96-well plate Q data folder 62 3 21X

Working with Analyzed Data

On the Results window, the following parameters (see columns) define the analyzed data:
• Check boxes toggle the corresponding well’s data between inclusion and exclusion
from the data analysis:
• To exclude a sample from subsequent analyses, de-select the corresponding bio-
sensor number in the results table and click Calculate Binding Rate! to re-ana-
lyze. Or, select one or more wells in the results table, right-click and select
Exclude Wells.
• To include a sample in subsequent analyses, checkmark the corresponding bio-
sensor number in the results table and click Calculate Binding Rate! to re-ana-
lyze. Or, select one or more wells in the results table, right-click and select
Include Wells.
• Plate—A unique number assigned to individual sample plates.
• Sensor—The biosensor number.
• Index—A unique number assigned to each data point during data analysis.
• Dilution factor—The dilution factor used to prepare the assay sample. The dilution
factor is multiplied by the well concentration to determine the calculated concentra-
tion.
• Well concentration—The concentration of the analyte determined from the standard
curve. The well concentration is multiplied by the dilution factor to determine the
calculated concentration.
• Flip—Inverts the magnitude of all data. Used during analysis of large particles where
negative signals can be observed.
• Information—Annotations about the sample.
• Replicate Group—A set of replicate values organized as a set to facilitate calculation
of statistics.
• BR AVG—The average binding rate of the replicate group
• BR SD—The standard deviation of the binding rate of the replicate group

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• BR CV—The coefficient of variance of the binding rate of the replicate group

• Concentration avg—The average concentration of the replicate group
• Concentration SD—The standard deviation of the concentration of the replicate
group
• Concentration CV—The coefficient of variance of the concentration of the repli-
cate group
• Sensor Type—The biosensor chemistry utilized in the assay.
• Lot Number—The lot number of the biosensor tray used in the assaySample—The
well location in the sample plate.
• Sample ID—The name of the sample entered in the Octet System Data Analysis soft-
ware.
• Group Type—The well designation (Standard, Unknown, Reference, or Control).
• Binding Rate—The rate of sample binding to the biosensor computed by the Octet
System Data Analysis software using the binding rate equation specified.
• Known Conc.—The user-specified standard concentration that was entered during
sample plate definition.
• Calc. Conc.—The sample concentration computed from the standard curve.
• Residual (%)–Residual = (Expected standard concentration—Calculated standard
concentration)/Expected standard concentration
• r2 (COD)—The r2 of the curve fit used to determine the binding rate.
• Well Information—User-specified notes about the wells.

Sample Plate Map

The sample plate map displays well data, and can be used to select which type of results to
display. Select the type of results to display in the sample plate map (Show Table Column
drop-down list). For example, select Calc. Conc. to display the computed sample concen-
trations on the map.

Results Table
The results table displays detailed results for each well in the plate map.
Sorting Results Table Entries
The information in the results table can be sorted in ascending or descending order based
on the values in any of the columns:
• To sort the entries in ascending, alphanumeric order, click a column header.
• To sort the entries in descending order, click the column header again.

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SAVING STANDARDS DATA

After analysis, the standards data can be saved for use with other quantitation experiments;
to do so:
1. In the Results tab (see Figure 4-15: on page 50), click Save Standards.
2. In the displayed dialog box, select the file folder and enter a filename (.fsc).
3. Click Save.

SAVING ANALYSIS SETTINGS

To save the analysis settings in the Results and Data Selection windows, click Save Analysis
Settings.
A Settings_DataAnalysis file (.ini) is saved in the experiment folder. These settings are dis-
played the next time the experiment is loaded.

NOTE: The Settings_DataAnalysis.ini file is also automatically saved when

you click Calculate Binding Rate! The Settings_DataAnalysis.ini file may
also be used during batch processing.

PROCESSING BATCH QUANTITATION ANALYSIS

In batch mode, multiple quantitation data sets may be processed without attended opera-
tion. The Octet System Data Analysis software analyzes experiment data using the data pro-
cessing parameters in a designated Settings_DataAnalysis.ini file. The experiments in a
batch can be analyzed using the same or different .ini files. The processed data can be saved
to either the original data folder or an alternative folder.

Creating a Settings_DataAnalysis.ini File

NOTE: The Settings_DataAnalysis.ini file is also automatically saved when

you click Calculate Binding Rate!

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To create a Settings_DataAnalysis.ini file:

1. Load and open an experiment that will be included in the batch.
The Data Selection window displays (Figure 4-21).

Figure 4-21: Data Selection Window

2. Set the data viewing options (refer to Table 4-1 on page 43).
The Results window displays (Figure 4-22).

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Figure 4-22: Results Window

3. Set the analysis options (standard curve equation, processing parameters, standards
sample alerts). For more details, see “Analyzing Data” on page 46.
4. Click Save Analysis Settings.
The .ini file is saved in the experiment folder.
5. Optional. To analyze each experiment using a different .ini file, repeat steps1–4 to cre-
ate a .ini file for each experiment in the batch.

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Selecting Experiments and Running the Batch Analysis

To select experiments and run the batch analysis:
1. On the menu bar, click File > Quantitation Batch Mode.
The Quantitation Batch Model dialog box displays (Figure 4-23).

Figure 4-23: Quantitation Batch Mode Dialog Box

2. Set the batch mode options as follows:

• Ini File
• Use the one in each folder—Analyzes each experiment using the .ini file
found in the same experiment folder.
• Use one for all folders—Analyzes all experiments using a user-selected .ini
file.
• Well Information—Specifies a path within the experiment folder to the
Settings_WellInfo.xml file. Select only a Well Information file if you modified
the original well information by editing (for more information, see “Editing
Experiments” on page 38). The Settings_WellInfo.xml file can be found in
the experiment folder of an experiment that has been edited in the Octet Sys-
tem Data Analysis software. Select a well information file if the Use one for all
folders option is selected.
• Output Folder
• Use the original data folder—Analysis results are saved in the experiment
folder.
• Use this folder—Saves the analysis results to a user-selected folder.
3. Click Add Folders to select the experiments for batch analysis.

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4. In the displayed dialog box, select an experiment folder and click Add. Repeat to select
each experiment in the batch.
5. Optional. To remove experiments from the batch, select the corresponding folders and
click Remove Selected.

Figure 4-24: Selecting Experiments for Batch Analysis

6. Click Analyze Data.

Applying Alerts
Applying Standard Alerts
In the Results window, you can select threshold(s) that are applied to the standards. You
can also edit the alert threshold value:
• Min Sample r2—The threshold r2 value for a standard or unknown binding curve. If
the r2 value of a standard or unknown binding curve is less than the threshold value,
the standard or unknown sample is highlighted in the results.
• Max Residual—Specifies a threshold residual value for standards. If a calculated
standard concentration deviates +10% or greater from the expected concentration,
the standard is highlighted in the results.
• Sample Alert—Specifies highlights data that fit user specified criteria. Thresholds
can be set for r2, max residual, or both.
• Both Min r2 and Max Residual—Applies both the Min Sample r2 and Max Residual
thresholds to the data.
• Do not use alerts—Select if you do not want to apply any thresholds to the
unknown or standard sample data.

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To apply a standards alert:

1. In the sample plate map, select the type of data to display data from the drop-down
list.
2. Select a type of alert.
Samples that do not meet the threshold are highlighted in the sample plate map and
results table.
3. Edit an alert threshold value:
a. Select the cell and enter a new value.
a. Right-click the cell to display a shortcut menu of editing commands.

Figure 4-25: Results Window—Displaying Standards Sample Alerts

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Applying Sample Alerts

The Sample Alert highlights data that fit user specified criteria.
To apply sample alerts:
1. Set the thresholds for r2, max residual, or both (Figure 4-26).

Figure 4-26: Sample Alerts

2. Alternatively, set either a positive or negative threshold on the standard deviation of

either the binding rate or the calculated well concentration (Figure 4-27).

Figure 4-27: Sample Alert Dialog Box

Rows that match criteria specified in the “Sample Alert” are highlighted in the results
table of the quantiation experiment (Figure 4-28).

Figure 4-28: Sample Alert Results

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The highlighted rows are marked in the Alert column in the analysis table (Figure 4-29).

Figure 4-29: Alert Column

EXPORTING DATA
Raw data or quantitation result reports can be exported.

Saving Raw Data

To save raw data:
1. In the Results window (Figure 4-25), click Save Raw Data.
2. In the displayed dialog box, select a destination directory.
3. Enter a filename and click Save.
The raw data are saved as a .csv file that can be opened in a spreadsheet application
such as Microsoft® Excel® software.

Saving a Quantitation Results Report

All information in the results window can be saved to a report. The Octet System Data Anal-
ysis software generates an Excel spreadsheet (.xls file) that includes the current contents of
the results window:
• Calibration curve(s)
• Sample plate map that shows the user-selected type of data
• Results table

NOTE: If multiple experiments are open, the report will include a separate
worksheet for each experiment.

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To save a quantitation results report:

1. On the menu bar, click File > Save Report, or click the Save Report button.
The Report Selection dialog box displays; see Figure 4-30.

Figure 4-30: Report Selection Dialog Box

2. Select the components from the analysis to be exported, enter a file name and click
Save.
The report is saved to the data folder.

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
CHAPTER 5:

Basic Kinetics Analysis

Working with Experiments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68

Working with Raw Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80

Processing Kinetic Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88

Kinetics Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105

Processing Batch Kinetics Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111

Kinetics Analysis Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115

Working with Graphs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 132

Data Export Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 134

Generating a Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135

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WORKING WITH EXPERIMENTS

Starting a Basic Kinetics Experiment
A basic kinetics experiment enables you to determine the association and dissociation rate
of a molecular interaction. After an experiment is run, start a data analysis session (double-
click the icon on the desktop).
There are several ways to start a basic kinetics experiment:
• Use the Experiment wizard.
• Open a method file (fmf ). An experiment method file (.fmf ) is automatically saved
after you define and run an experiment.
• On the menu bar, click Experiment > Templates > Kinetics.

NOTE: When using the 21 CFR Part 11 version of the Octet System Data Acqui-
sition software, only 21 CFR Part 11-compliant experiments and re-analyze
generated using the 21 CFR Part 11 version of the software can be opened.
Files generated using the non-compliant version of the software or with a
non-compliant system cannot be opened, and a message indicating this will
be presented.

Loading an Experiment for Analysis

A data analysis session can be used to:
• Load and analyze an experiment.
• Re-analyze an experiment.

To load an experiment for analysis:

1. On the desktop, click the icon. Or, click the Windows Start button and select All Pro-
grams > ForteBio > ForteBio Data Analysis 7.0.
The Data Selection window displays.
2. Load an experiment:
a. Right-click the experiment folder in the workstation directory tree and select Load
Folder; or, on the menu bar, click File > Load a Folder.
b. In the Load Folder dialog box, enter the folder name or click the Browse button
and select the desired folder, and then click Load.
The experiment is added to the Loaded Data directory tree (Figure 5-1).

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Figure 5-1: Data Selection Window—Loading an Experiment

3. In the Loaded Data directory, click an experiment name to open it.

The experiment summary appears (Figure 5-2).

NOTE: Multiple kinetics can be loaded, but only one kinetic can be open at a
time. The icon in the Loaded Data directory tree indicates the open experi-
ment.

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Experiment information and data files (.frd)

List of all available steps for the assay Steps performed in the assay

Figure 5-2: Data Selection Window—Displaying Experiment Summary Information

4. Optional. If any step types have been incorrectly assigned in the Octet System Data
Analysis software, change them before beginning analysis. To do so, right-click the step
and select the correct step type from the shortcut menu (Figure 5-3).

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Figure 5-3: Changing a Step Type

5. In the Sensor Tray tab, confirm the biosensors to be analyzed.

The first group of biosensors is automatically selected for analysis.
Biosensors that are assigned to the same type of assay step and have the same assay
(step) times are displayed in the same color, providing convenient identification of mul-
tiple types of assays executed in one experiment and using one biosensor tray (red
in Figure 5-4). Only biosensors of the same color processed simultaneously. This pro-
vides a convenient way to identify multiple experiments on a biosensor tray.
6. Select particular biosensors for the analysis:
a. Click a biosensor. To select non-adjacent biosensors, press and hold the Ctrl key
while you click the biosensors.
b. Select a column(s) or row(s). To select non-adjacent columns or rows, press and hold
the Ctrl key while you click the columns or rows.
c. Draw a box around the biosensors using the mouse.
The number of biosensors selected for analysis in the current tray will be displayed
in the upper-right corner of the Sensor Tray tab.
7. Choose the Ignore error in files option when loading to load data files regardless of
whether a runtime error was identified. This enables data visualization even if a sensor
error occurred during runtime.

NOTE: Only the selected biosensors will be available in the Processing window.

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Number of biosensors selected for analysis

Figure 5-4: Selecting Biosensors for Analysis

Analyzing Binding Data

To analyze the binding data:
1. Start an analysis session and select the experiment(s) to use.
a. Confirm or change the biosensor and sample type selected for the analysis.
b. Process the data (compile binding curves with or without reference subtraction).
2. Analyze the binding data:
•Curve fitting analysis—Determines the kinetic constants ka, kd and the affinity
constant KD from fusing a specified binding model.
• Steady state analysis—Determines the affinity constant KD from the calculated
or measured equilibrium response.
3. View the results in graphical and tabular formats.
4. Export the results and generate a report.

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Editing Experiments
The Octet System Data Analysis software enables you to change sample designations, stan-
dard concentrations, or exclude samples from analysis. For example, you can exclude a
standard that does not meet the sample r2 or residual threshold, then re-analyze the data.
You can also modify some processing parameters.

Changing Sample Designations

To change sample designations:
1. Click the Data Selection tab, then do either of the following:
• In the sample plate map, select the well(s), right-click and select an option from
the shortcut menu.
• In the results table, right-click a table cell in the Well Type column, then make a
selection from the drop-down menu.

Selecting wells in the sample plate map Selecting a cell in the Well Type column of the results table

Figure 5-5: Changing Sample Designations

Excluding/Including Samples from Analysis

To toggle sample analysis in the Results window, perform one of the following tasks:
• In the sample plate map, select the well(s), right-click and select Exclude Wells to
remove the samples from the analysis. If the selection is already excluded from anal-
ysis, select Include Wells to return the samples to the analysis.
• In the results table, to exclude wells, de-select the check box in the first column or
right-click selected rows and select Exclude Wells. If the selection is already
excluded from analysis, click the check box for the desired rows or right-click desired
rows and select Include Wells.

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Selecting wells in the sample plate map Selecting rows in the results table

Figure 5-6: Excluding Samples from Analysis

Editing Standard Concentration or Well Information

To edit standard concentration or well information:
1. Click the Data Selection tab.
2. In the sample plate, right-click and select Edit Sample Information to display the Edit
Sample Information dialog box (Figure 5-7).

Figure 5-7: Edit Sample Information Dialog Box

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Figure 5-8: Data Selection Window—Editing Sample Information

Editing Processing Parameters

To edit processing parameters:
1. Modify the following parameters as appropriate:
• Read time—The amount of data that is analyzed.
• Zero concentration threshold—Binding rates that are less than the zero con-
centration threshold are considered zero.
• Low concentration threshold—When you click Calculate Binding Rate!, the
raw data are fit using both a linear and an exponential equation. Both sets of fit-
ting data are not reported. The user-specified low concentration threshold deter-
mines which binding rates are taken from the linear fit and which binding rates
are taken from the exponential fit.
• If the result of the linear fit is below the user-specified low concentration
threshold, then this value is reported as the binding rate in the results table.
• If the result of the linear fit is above the user-specified low concentration
threshold, then the binding rate value obtained from the exponential fit is
reported in the binding rate column of the results table.
2. In the Results window, select the cell that you want to edit and enter a new value. Or,
right-click the cell to access a shortcut menu of edit commands.
The modified parameters are saved in the Settings_DataAnalysis.ini file and are auto-
matically loaded when the data is analyzed again. If a new data set is loaded, the
default parameters are restored.

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Figure 5-9: Editing processing parameters in the Results window.

Viewing Binding Curves

To view binding curves, in the sample plate, select a well(s), or in the sample plate table,
select a row(s).
To select non-adjacent rows or wells, press and hold the Ctrl key while clicking the wells or
rows.

Figure 5-10: Selecting Sample wells or Rows to Display in the Binding Curve Graph

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Viewing Options
Table 5-1: Viewing Options in the Data Selection Window

Option Description
Align X Choose this option if there is an artifact at the beginning of the
binding step that you want to remove. Enter a time (seconds) at
which to start the alignment.
Reference Subtrac- If the experiment includes reference biosensors, choose the
tion Average of Reference Subtraction option and select one of the following:
• All—Computes the average binding curve from the ref-
erence wells and subtracts this average from each sam-
ple curve.
• Row—If a row includes both samples and references, the
Octet System Data Analysis software computes the aver-
age reference curve for the row and subtracts this curve
from the samples in the same row.
• Column—If a column includes both samples and refer-
ences, the Octet System Data Analysis software com-
putes the average reference curve for the column and
subtracts this curve from the samples in the same col-
umn.
Flip Data The Flip Data function inverts signals from positive to negative
or from negative to positive. This is used most often when the
observed nm shift is negative due to the presence of large ana-
lytes, such as phage, cells, and lipoparticles on the biosensor
surface.
Grouped View Displays graphs in custom groupings. Choose this option to dis-
play graphs organized into groups according to sample attri-
bute or results category. This is a highly useful feature when
working with large data sets.
• Options—Click to show the Grouped View Options dia-
log box.
• Refresh—Updates the graph display.
Ignore errors in files If this option is chosen, the Octet System Data Analysis software
when loading ignores errors in data files. All data files, regardless of errors or
runtime issues, will be loaded for analysis.
Show All Traces Displays all binding curves.
Edit Legends Select the sample information displayed in the legend. Options
include Sensor, Sample, Sample ID, Group, and Concentra-
tion.

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Opening Binding Curve in Separate Window

To open the binding curve chart in a separate window, double-click the graph.
Customizing Appearance of Graph or Binding Curve
To customize the appearance of the graph or a binding curve; see Figure 5-11. Right-click
the graph or a curve for a shortcut menu of display options.
• Hover over a binding curve to display a tooltip of the XY coordinates.
• Right-click the graph to view a shortcut menu of display options.
• Right-click a curve to view a shortcut menu of display options.
• Right-click the graph and select Toolbar. Toolbar buttons enable you to save, copy,
or print the graph.

Figure 5-11: Viewing Binding Curves

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Closing Experiments
To close an experiment, in the Loaded Data directory tree, right-click the experiment name
and select Remove Run (see left side of Figure 5-12).
To close all experiments in the Kinetics or Quantitation folder, right-click the folder and
select Remove All (see right side of Figure 5-12).

Figure 5-12: Closing a Kinetics Experiment

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Figure 5-13: Removing All Kinetics Experiments from Processing

WORKING WITH RAW DATA

Viewing Raw Data
In the Processing window, the Raw Data view enables you to conveniently examine the
binding data.
To view raw data:
1. Inthe Processing window, the Processing tab and confirm that the Raw Data View
option is selected.

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Selected step

Raw data from all steps (displays all biosensors Raw data from selected step (displays all bio-
by default) sensor data for the selected step by default)

Figure 5-14: Processing Window—Raw Data View Selected

2. View the step data and align the binding curves (click a step bounded by lines in
the Raw Data chart).

NOTE: The lines represent individual assay steps. Populate the step charts
(below) with detailed views of an individual step by clicking inside the step
boundaries.

The “All Steps Aligned by step xx” chart displays all of the assay data aligned by the step
selected in the Raw Data chart (Figure 5-15).

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Selected biosensor Selected step

All step data for biosensor C1 Selected step data for biosensor C1

Figure 5-15: Processing Window (Raw Data View)—Displaying Data from a Single-Selected Biosensor
(C1)

3. Select which biosensor data to display:

• To view the data from a selected biosensor, click the biosensor in the table.
The step charts will display all of the binding data for the selected biosensor and the
data from the selected step aligned starting at y = 0.
• To display data from multiple biosensors in the step charts, select the biosensors
in the Sensor location list.
• To select a contiguous block of biosensors from the list, hold down the Shift key
and click the first and last biosensors in the group.
• To select non-contiguous biosensors, hold down the Ctrl key and click the
desired biosensors.
• To include all biosensor data in the step charts, click Show All Sensors.

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Figure 5-16: Selecting contiguous (left) and discontiguous (right) biosensors in the Sensor location list.

4. Align the data (select an alignment option):

• Show All Steps Aligned—Aligns all steps. Aligns baseline steps and association
steps to the start of the step. Aligns all dissociation steps to the end of the step.
• All Aligned to One Step—Enables the following options:
• Align by Begin Point—Aligns the displayed curves to the start of the cur-
rently-selected step.
• Align by End Point—Aligns the displayed curves to the end of the currently-
selected step.
• Align All Baselines—Aligns all steps according to the baseline step data.

Exporting Raw Data

To export raw data:
1. Click Export Aligned Step (.csv files).
2. In the displayed dialog box, navigate to a destination directory, enter a filename, and
click Save.

Quantitating Raw Data

To quantitate raw data from a selected step:
1. In the Raw Data view, select the step to quantitate and click Quantitate Selected Step
(Figure 5-17).

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Figure 5-17: Processing Window—Raw Data View—Quantitating a Selected Step

2. In the system prompt that displays, click Yes to proceed with the quantitation.
The selected step data is displayed in a quantitation window (Figure 5-18). By default,
samples are designated as unknowns.
For more details on viewing the quantitation data, see “Viewing Binding Curves” on
page 76.

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Figure 5-18: Quantitation Window—Displaying Selected Step Data from a Kinetic Assay

NOTE: When step data from a kinetic assay is open, additional quantitation
experiments cannot be opened.

3. Optional. Change the sample type:

a. Select wells in the sample plate map or sample rows in the table.
b. Right-click the selection in the plate map or table and select a sample type.

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Figure 5-19: Changing the Sample Type in the Sample Plate Map or Sample Table

4. Set a standard concentration value: in the sample table, double-click the Conc. cell and
enter a value (Figure 5-20). (To access a shortcut menu of editing commands, right-click
the cell.)

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Figure 5-20: Setting Concentration Values

5. In the Results window, select a standard curve equation, set the processing parameters,
and then click Calculate Binding Rate!
The binding rates will be calculated and displayed; see Figure 5-21.
For more details on analyzing quantitation data, see “Loading an Experiment for Analy-
sis” on page 68

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Figure 5-21: Results Window with Calculated Binding Rates

NOTE: To return to kinetics analysis mode, reload the kinetics experiment data
(in the Loaded Data directory tree, click the experiment).

PROCESSING KINETIC DATA

The Processing window provides tools for correcting binding curves using different refer-
ence subtraction and alignment options.The data processing steps specify how to refer-
ence the data and produce the final binding curves (processed data).

Step 1: Sensor Selection

When a kinetics experiment is opened for the first time, the sensor tray map depicts all
active biosensors as ligand biosensors (biosensors with immobilized ligand). If the experi-
ment included reference biosensors (biosensors without immobilized ligand), you must
specify their location in the sensor tray map. If the experiment included reference buffer
wells (to correct for system drift), you must specify their location in the sample plate map.

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Working with the Sample Tray Map and Sensor Tray Map
To use the sample tray map and the sensor trap map (Figure 5-22):
1. Hover the cursor over a biosensor or sample to display a tooltip with information about
the item.
2. Click a biosensor or sample to highlight the associated row in the corresponding table
at the bottom of the window.
3. Optional. Copy the sensor tray map or sample plate map to the system clipboard, right-
click the map and select Copy to Clipboard.
The clipboard contents can be saved as a graphic file for drawing applications.

Selecting Sensors
To select sensors:
1. In the Step 1: Data Selection pane, select the Sensor Selection option (Figure 5-22).

Data Selection:
Raw Data View or Sensor Selection

Figure 5-22: Selecting Biosensors in the Processing Window

2. Specify reference biosensors:

a. In the sensor trap map, select the appropriate biosensors.
b. Right-click and select Change Sensor Type > Reference Sensor (Figure 5-23).

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Figure 5-23: Changing the Biosensor Type

NOTE: The biosensor designations can also be edited in the sensor tray table
(Figure 5-22: on page 89).

3. Specify reference wells:

a. In the sample plate map, select the appropriate wells.
b. Right-click and select Change Well Type > Reference Well (Figure 5-24).

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Figure 5-24: Specifying Reference Wells

4. Exclude wells from analysis:

a. In the sample plate map, select the wells.
b. Right-click and select Exclude Wells for Analysis (Figure 5-24).

Step 2: Reference Subtraction

Reference subtraction is optional and is not required for all applications. There are two
types of references used in Octet experiments: reference biosensors and reference wells.
• Reference biosensors—Used as a references throughout the entire assay; for exam-
ple, biosensors without active capture molecules.
• Reference wells—Contain only assay buffer, and are used to measure system drift.

To apply reference subtraction during data processing:

1. In the Step 2: Subtraction pane, select the Subtraction method.
The subtractions that will be executed (based on the subtraction method, biosensor
designation and sample plate well designation) are listed in the Sensors to be Analyzed
box.
If the subtraction method is not compatible with the sensor tray map and the sample
plate map, a question mark is displayed in the Sensors to be Analyzed box.
2. Confirm the biosensor subtraction in the Sensors to be Analyzed box.

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Reference well H1 will

be subtracted from
sample wells

Selected subtraction
method

Reference well = H1

Figure 5-25: Confirming the Reference Well is Subtracted from the Sample Wells

If an experiment includes reference biosensors and reference wells, the Octet System Data
Analysis software offers multiple reference subtraction methods for data processing:
• Reference Wells—Corrects binding data for system drift. For example, drift is mea-
sured by the interaction of the immobilized biosensors with the assay buffer. This
method requires at least one row of reference wells in the sample plate. If more than
one row of reference wells is selected (checked), the signals are averaged and the
average signal is subtracted from the samples.

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Figure 5-26: Reference Wells—Subtraction Method where Biosensor H1 is the Reference

• Parallel Reference Sensors—Corrects data for system artifacts or non-specific bind-

ing of the sample to the biosensor surface. This method requires one reference bio-
sensor for each ligand biosensor.

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Figure 5-27: Parallel Reference Sensor—Reference Subtraction Method

• Double Reference—Corrects the binding data for signal due to system artifacts,
non-specific binding, and system drift. This method requires one reference biosensor
per ligand biosensor and one or more rows of reference buffer in the sample plate.

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Figure 5-28: Double Reference Subtraction Method

NOTE: In Figure 5-28, A1–A3=Target biosensor A1 corrected by reference bio-

sensor A3, both probing reference wells B1–B3=Target biosensor B1 corrected
by reference biosensor B3 for biosensor and microplate well artifacts, both probing pos-
itive sample. (B1–B3)–(A1–A3)=Double reference subtraction fully corrects for biosen-
sor and microplate well artifacts and the effect of sample media.

• Average Reference Sensors—Corrects the binding data using either a single refer-
ence biosensor or the average signal of multiple biosensors.

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Figure 5-29: Average Reference Sensors Subtraction Method

NOTE: In Figure 5-29, AB1–(A1+A2+A3+A4)/4 = Target biosensor B1 corrected for

sample medium interference by the average of all reference biosensors.

Step 3: Align Y Axis

In order to fit curves correctly, they must be aligned to a common reference point upon
both the X and Y axes:
• Alignment along the X axis is achieved during assay due to the parallel movement of
all biosensors.
• Alignment along the Y axis is achieved using Align Y Axis by specifying both a step
and time with which to execute the alignment.
The time range from the specified step will be used to calculated an average and that aver-
age will then be set to y=0. For example, for alignment to the baseline, select baseline and
specify the time within the baseine step to set to an average y = 0.
To align to association:
1. Select the Align Y Axis option and make a selection from the Step drop-down list.
2. Confirm the time range defaults or enter new start and finish times. If you choose to
align to the association step, set the shortest time range possible at the beginning of
the association step to align Y=0.

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The time range over which the

data are averaged to align Y=0.

Figure 5-30: Aligning the Y Axis

NOTE: The time window should be minimized to the beginning of the associa-
tion. The data within this window is set to an average of zero and cannot be
included in the final curve fit.

Step 4: Interstep Correction

The interstep correction feature corrects misalignment between two steps due to system
artifacts. The association step can be aligned to the dissociation step or to the baseline.

IMPORTANT: For the most effective interstep correction, the baseline and dis-
sociation steps of an assay cycle must be performed in the same microplate
well.

• Align to Dissociation—Moves the association step on the Y axis to align the end of
the association step with the beginning of the adjacent dissociation step.
• Align to Baseline—Moves the association step on the Y axis to align the beginning
of the association step with the end of the adjacent baseline step.

NOTE: Interstep correction is not recommended for very fast kinetics because
some kinetic information may be lost.

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Step 5: Process
Savitzky-Golay filtering removes high-frequency noise from the data. Its use is optional, but
is recommended unless the data being analyzed has less than 20 data points in a step.
To process the data (select and confirm the biosensors to analyze):
1. Apply Savitzky-Golay filtering by clicking the Savitzky-Golay Filtering check box; see
Figure 5-31.

Figure 5-31: Selecting and Confirming the Biosensors to Analyze

2. Click Process Data!.

The processed binding curves are displayed with "Raw", "Align-Y" and "Align-" windows.
The processing parameters are automatically saved to the Settings_DataAnalysis.ini
file in the data folder.
The processing parameters may also be saved by clicking Save Proc. Parameters.
These processing settings are displayed the next time the experiment is loaded.
The processed results (Figure 5-32) include:
• Raw Data—Binding curves with no reference subtraction.
• Subtracted Data—Binding curves after the user-specified reference subtraction
method is applied.
• Align Y—Binding curves after user-specified Y alignment.
• Align X—Binding curve association steps aligned at the same time point.

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Figure 5-32: Processed Results View

3. Click Save Proc. Parameters to save the process settings.

A Settings_DataAnalysis.ini file (.ini) is saved in the experiment folder. These process-
ing settings are displayed the next time the experiment is loaded.

Step 6: Viewing Results

The Octet System Data Analysis software provides multiple display options (Figure 5-33) for
processed data:
• “Processed Results” on page 100
• Sensor Summary
• Report Points

Figure 5-33: Options for Viewing Results

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Processed Results
• Double-click a graph to display it in a separate window (Figure 5-34).
• Hover the cursor over a curve to highlight the curve and display a tooltip of the
time(X axis) and nmshift (Y axis) at that point (Figure 5-34).
• Customize the graph by right-clicking the graph for a shortcut menu of display
options (Figure 5-35).
• Customize the curve display, right-click the curve for a shortcut menu of display
options (Figure 5-35).

NOTE: The same display options are also available for binding charts in the
Fitting and Residual views in the Analysis tab.

Figure 5-34: Double-click a Binding Chart to View it in a Separate Window

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Right-click chart for chart display options Right-click curve for curve display options

Figure 5-35: Binding Chart—including Toolbar and Data Grid

Sensor Summary
The Sensor Summary view displays the binding charts generated during data processing
(Figure 5-36).
The Sensor Summary view controls enable you to select the sensor data to display:
• Hover over a binding curve displays a tooltip with sample data.
• Click a sensor tab or one of the arrow buttons in the Sensorgrams controls
at the bottom of the window to view data for a specific biosensor.
• Set the number of sensorgrams per row and the number of rows to display.
• Use the Top View check boxes to show or hide the raw data and subtraction graphs
in the top row.

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Figure 5-36: Processed Data in the Sensor Summary View

NOTE: In Figure 5-36, the data were processed using the Reference Well sub-
traction method.

Report Points
The Report Points view displays the raw binding data in tabular format (Figure 5-37). Report
point analysis can also be performed in the Analysis window; the data will be added to the
Report Point Analysis table.

NOTE: Click a sensor tab at the bottom of the binding chart to view data for a
particular biosensor.

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Figure 5-37: Report Points View of Processed Results

Report Point Analysis Features

• Input times after beginning of Association Step—The Octet System Data Analysis
software measures the sample binding (nm shift) at Time 1 (within the association
step) and Time 2 (within the dissociation step). Both time points refer to time in sec-
onds after the beginning of the association step. You can edit Time 1 or Time 2.
• Use 20 point average—Each reported nm shift in the table represents an average of
20 data points centered around the time point specified.
• Apply—If you modify Time 1 or Time 2, click Apply to re-analyze the sample binding
of the active ligand biosensor at the new time points. Report points can also be
determined in the Analysis window.
• Apply All—If you modify Time 1 or Time 2, click Apply All to re-analyze the sample
binding of all ligand biosensors at the new time points.
• Export File (.txt)—Opens a Save As dialog box so that you can save the Report Point
Analysis table.

Results Information
• Sensor Location—Ligand biosensor location.
• Sample Location—The well location of the sample in the sample plate.
• Sample ID—User-specified ligand biosensor information.

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• Concentration (mM)—Sample concentration.

• Time 1 (sec)—Time at which the first binding measurement is acquired.
• Binding 1 (nm shift)—The binding signal at Time 1.
• Time 2 (sec)—Time at which the second binding measurement is acquired.
• Binding 2 (nm shift)—The binding signal at Time 2.

Step 7: Saving Results and/or Processing Parameters

In this step, you can save the following parameters:
• Raw data
• X,Y data for the curves in the final Processed Results graph to a file format that can be
imported to third party applications like Scrubber2 from BioLogic Software.
• Processing parameter settings. The processing parameters are set to the saved val-
ues the next time the experiment is loaded.
• Binding chart

To save the processed data:

1. Click Save Processed Data (Figure 5-38).
2. In the displayed dialog box, select a destination folder and click OK.
The Octet System Data Analysis software generates a separate file (.xls) for each biosen-
sor that includes the time, nm shift and sample concentration for each processed curve.
This file is suitable for import into third party applications.
To save the raw data:
1. Click Save Raw Data (Figure 5-38).
2. In the displayed dialog box, select a destination folder and click OK.
The Octet System Data Analysis software generates one file (.xls) that includes time and
nm shift data for all of the biosensors.
To save the processing parameters:
1. Click Save Proc. Parameters (Figure 5-38).
The processing parameter values are saved as an .ini file in the experiment folder.

Figure 5-38: Save Results Options

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To print or copy a binding chart:

1. Right-click the chart and select Toolbar (Figure 5-39) to access the printing and copy-
ing buttons (the buttons will appear at the upper left of the binding chart).

Figure 5-39: Binding Chart Shortcut Menu

2. Select the desired command:

• Opens a dialog box that enables you to save the chart in several different for-
mats ((cfx, txt [data only], xml [properties only], bitmap, or metafile).
• Opens a dialog box that enables you to copy the chart in several different for-
mats (data only, bitmap, or metafile) to the system clipboard.
• Opens a dialog box that enables you to print the chart.

KINETICS ANALYSIS
In the Analysis window, two types of kinetics analysis are available:
• Curve fitting—Determines the kinetic constants ka, kd and the affinity constant KD
by fitting the data to a specified binding model.
• Steady state analysis—Determines the affinity constant KD from the calculated or
measured equilibrium response.

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Curve Fitting Analysis

To analyze the processed kinetic data, specify the curve fitting options:
• Steps to analyze
• Curve fitting model
• Type of fitting (local or global) to apply to the data
• Step time to analyze

Curve Fitting Kinetics Analysis Options

• Steps to Analyze—Select the step(s) to include in the analysis: association, dissocia-
tion, or both.
• Association only—Generates kobs.
• Dissociation only—Generates kdis.
• Association & dissociation—Generates kobs, kon, kdis, and KD.
• Model—The mathematical model that is used to generated the fitted view.
• 1:1 Model—Fits one analyte in solution binding to one binding site on the sur-
face
• 2:1 (HL) Model—Fits the binding of one analyte in solution to two different
binding sites on the surface. Kinetic parameters are calculated for two interac-
tions (kon1, kon2, kdis1, kdis2, KD1, KD2).
• 1:2 Bivalent Analyte Model—Fits the binding of one bivalent analyte to a
monomeric immobilized ligand. Kinetic parameters are calculated for two inter-
actions (kon1, kon2, kdis1, kdis2, KD1, KD2). The model is available in the Analysis
tab—Model menu—in Kinetics mode.
• Mass Transport—A Heterogeneous Ligand model that fits the binding of the
analyte taking into account two steps: 1) transport of the analyte from the bulk
solution to the surface, and 2) molecular interaction of the analyte with the
ligand.
• Fitting-Local— If this option is selected, the Octet System Data Analysis software
computes kinetic constants for each curve. The constants that are calculated depend
on the steps that are analyzed (association only, dissociation only, or association and
dissociation).
• Full—If this option is selected, the Octet System Data Analysis software assumes
that the off rate eventually reaches the pre-association baseline and forces the
curve fit to that point.
• Partial—If this option is selected, the Octet System Data Analysis software does
not assume the dissociation will reach the pre-association baseline.
• Fitting-Global (Full)—If this option is chosen, an analysis includes all of the binding
curve data in the group and the Octet System Data Analysis software generates
kinetic constants for the entire group. The kinetic constants that are calculated
depend on the model selected.

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• By Sensor—Groups all data from one biosensor (for example, Biosensor A1)
together and applies a global fit to the group.
• By Color—Groups all data that is the same color and applies a global fit to that
group. For more details on defining colors by sample attributes, see “Working
with the Analysis Results Table” on page 125.
• Rmax Unlinked option for Global Fitting—When fitting data, the theoretical
response maximum (Rmax) can be calculated assuming equivalent surface capacity
between biosensors (Rmax linked) or non-equivalent surface capacity between bio-
sensors (Rmax unlinked).
• Window of Interest (From Start of Step)
• Association—The time range of the association step data to analyze.
• Dissociation—The time range of the dissociation step data to analyze.
• Use Entire Step Times—Analyzes the entire time duration of the selected
step(s).

Figure 5-40: Analysis Window

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Excluding Data from Analysis

To exclude data from the analysis:
1. In the table:
a. Select the biosensor data (rows) to exclude:
• To select adjacent rows, hold down the Shift key while you click the first and
last row in the selection.
• To select non-adjacent rows, hold down the Ctrl key while you click the rows.
b. Right-click the selected row(s), and select Exclude Wells (Figure 5-41) or press the
space bar. Press the space bar again to toggle the include/exclude status of the
curve.
Biosensors that will be included in the analysis have an “X” in the Include column;
excluded biosensors do not (Figure 5-41).

Figure 5-41: Excluding Wells from the Biosensor Table

2. Click Fit Curves!

The analysis results are displayed; data from wells marked for exclusion will not be
included (Figure 5-42).

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Figure 5-42: Analysis Results Table

3. Save the settings in the Analysis window: click Save Data Analysis Parameters
(Figure 5-43).
A Settings_DataAnalysis.ini file is saved in the experiment folder. These settings are
displayed the next time the experiment is loaded.

NOTE: The Settings_DataAnalysis.ini file is also automatically saved when

you click Fit Curves!

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Figure 5-43: Save Data Analysis Parameters Button—Analysis Window

Steady State Analysis

To analyze the processed kinetic data:
1. Set the analysis options (for more details, see Table 5-1 on page 77).
2. Click Calculate Response! to display the analysis results. For more information on
viewing results, see “Kinetics Analysis Results” on page 115.

Excluding Data from the Analysis

To exclude specific data from the analysis, remove the check mark next to the row in the
analysis results table. Or, right-click the selected row(s) and select Exclude Wells.

Steady State Kinetics Analysis Options

• R equilibrium—Fits the binding curve to a 1:1 model and uses the calculated Req to
determine the steady state affinity. If this option is selected, you first must perform a
curve fitting kinetic analysis.
• Response—Takes the average response from the user-specified time window and
uses it to calculated the steady state affinity.

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• Average from—The of amount of equilibrium state data to analyze, from the

time equilibrium was reached to the time at which the response should be calcu-
lated.

PROCESSING BATCH KINETICS ANALYSIS

In batch mode, multiple kinetic data sets may be processed without attended operation.
The Octet System Data Analysis software analyzes experiment data using the data process-
ing parameters in the Settings_DataAnalysis.ini file. Batch mode processing may be per-
formed using either a single or multiple .ini files.
During batch processing, sample well and sensor information may be substituted with new
text, a useful feature if the naming convention requires editing after data acquisition.
• Sample Well information, which includes Well Type, Sample ID, Description and
Molar concentration, can be replaced during batch processing by specifying a
Settings_WellInfo.xml file during batch processing.
• Sensor information as well as some sample information, which includes Sensor Type,
Sensor Info, Sample ID and Molar Concentration can be replaced by specifying a
Settings_TableInfo.xml file during batch processing.
• If both Settings_WellInfo.xml and Settings_TableInfo.xml are specified, then the
Sample ID and Molar Concentration values from Settings_TableInfo.xml are used
during batch processing while the corresponding information from
Settings_TableInfo.xml is ignored.

Creating a Kinetic Settings_DataAnalysis.ini File

To create a kinetic Settings_DataAnalysis.ini file:
1. Load and open a kinetic experiment that will be included in the batch process.
2. Click the Processing tab.
3. Enter processing parameters. (For more details see “Processing Kinetic Data” on
page 88).
4. Click Process Data!.
5. Click the Analysis tab.
This creates a Settings_DataAnalysis.xml file in the experiment folder.

NOTE: To batch process data sets with individual .ini files, create an .ini file for
each experiment in the batch.

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Creating a Kinetic Settings_WellInfo.xml File (Optional)

To create a kinetic Settings_WellInfo.xml file:
1. Load and open a kinetic experiment that will be included in the batch process.
2. Click the Processing tab and select Sensor Selection.
3. In the sample plate map, right-click a welland select Edit Sample Properties.
4. Enter the new information for Well Type, Sample ID, Description and Molar Concen-
tration, and then close the dialog box.
5. Click Process Data! or Save Proc. Parameters.
The Settings_WellInfo.xml file is saved to the experiment folder.

Creating a Kinetic Settings_TableInfo.xml File (Optional)

To create a kinetic Settings_TableInfo.xml file:
1. Load and open a kinetic experiment that will be included in the batch process.
2. Click the Processing tab.
3. Enter processing parameters.
4. Click Process Data!
5. Click the Analysis tab.
The Settings_TableInfo.xml file is saved to the experiment folder.

NOTE: If there is an existing Settings_TableInfo.xml file in the experiment

folder, it will be overwritten. The original Settings_TableInfo.xml file that
contained information entered during data acquisition is deleted.

6. Right-click the analysis table and select Edit Sample/Sensor Information.

7. Enter the new information for Sensor Type, Sensor Info, Sample Info and Molar Con-
centration, and then close the dialog box.
The Settings_TableInfo.xml file is saved to the experiment folder.

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Selecting Experiments and Running the Batch Analysis

To select experiments and run the batch analysis:
1. Select File > Kinetic Batch Mode.
The Quantitation Batch Mode dialog box displays (Figure 5-44).

Figure 5-44: Kinetics Batch Mode—Quantitation Batch Mode Dialog Box

2. Set the batch mode options:

• Use the one in each folder—Analyzes each experiment using the .ini file found
in the same experiment folder.
• Use one for all folders—Analyzes all experiments using a single .ini file that is
selected by the user.
• Well Information—Specifies a Settings_WellInfo.xml file in the experiment
folder that contains four types of sample information:
• Well Type
• Sample ID
• Description
• Molar Concentration
This feature can be used to edit sample information after data acquisition. It is use-
ful, for example, if naming conventions (within a project) change over time and the
sample information used during data acquisition requires updating.

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• Select a Well Information file only if you edited an experiment in data analysis.
For more information about editing an experiment, see “Editing Experiments”
on page 38. A Settings_WellInfo.xml file will be put in the experiment folder
of any experiment that has been edited in the Octet System Data Analysis
software.
• Selet a well information file if the Use one for all folders option is selected.
If no .xml file is specified, the well information from the original data acquisition file
will be utilized.
• Table Information—Specifies a Settings_TableInfo.xml file in the experiment
folder that contains four types of sensor/sample information:
• Sensor Type
• Sensor Info
• Sample ID
• Molar Concentration
This feature can be used to edit sensor/sample information after data acquisition. It
is useful, for example, if naming conventions (within a project) change over time
and the sample information used during data acquisition requires updating or if the
original plate assignment was incorrect. A Settings_TableInfo.xml file will be
found in the experiment folder of any experiment after the data has been processed
(in the Processing tab of the Octet System Data Analysis software) and the Analysis
tab has been activated. The Settings_TableInfo.xml file is updated after closing
the Edit Sensor/Sample Information dialog box (of the Analysis tab). If no .xml file is
specified, the well information from the original data acquisition file is used.
3. Select the experiments for batch analysis:
a. Click Add Folders.
b. In the displayed dialog box, select an experiment folder and click Add. Repeat to
select each experiment in the batch.
c. Optional. To remove an experiment(s) from the batch, select the folder(s) and click
Remove Selected.
4. Click Analyze Data.

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KINETICS ANALYSIS RESULTS

Kinetics analysis results (Figure 5-45) are presented in graphical and tabular formats. Some
viewing options in the Analysis window do not require data fitting (analysis) and are avail-
able for processed data.

Figure 5-45: Analysis Window with Sample Curve Fitting Results

Fitting View and Residual View

When the analysis is completed, the fitting view displays the processed binding data and
the fitted binding curve (red) for all analyzed biosensors (Figure 5-46). The residual view dis-
plays the difference between the raw binding data and the fitted curve for all analyzed bio-
sensors. For more details on graph options, see “Working with Graphs” on page 132.

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Figure 5-46: Fitting View and Residual View—Stacked Option

NOTE: In Figure 5-46, a local, full fitting analysis was applied to the data. (For
detailed information on graph display options, see “Step 6: Viewing Results”
on page 99.)

Fitting view options:

• Stacked—Displays the binding curves of all ligand biosensors in one graph
(Figure 5-46).
• Individual—Displays the binding curve from each biosensor in a separate graph
(Figure 5-47).
• Grouped—Displays graphs organized into groups according to sample attribute or
results category. This is a highly useful feature when working with large data sets.
• Options—Click to display the Grouped View Options dialog box.
• Refresh—Updates the graph display.
• Y Axis Scaling
• Auto Scale—Scales the y axis to the data in each graph.
• Full Scale—Scales the y axis to in all graphs to the range needed to accommo-
date all of the data.
• Report Points
• Time (sec)—A user-specified time point in the experiment. The Octet System
Data Analysis software computes the response at that time point.

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• Use __ Point Average—Each data point represents an average of the number of

data points specified centered around the time point chosen.
• Add to Table—Adds the response computed for the user-specified time point to
the analysis results table. Up to 10 response points can be added to the table.
• Remove All—Removes all of the response data for user-specified time points
from the analysis results table.

Processed binding data and fitted curves Residual curves

Figure 5-47: Fitting View and Residual View—Individual Option

NOTE: The data for all biosensors and samples is displayed.

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Grouping Results for Viewing

To group results for viewing:
1. Select the Grouped option and click Options to display the Grouped View Options dia-
log box (Figure 5-48)

Figure 5-48: Grouped View Options Dialog Box

2. From the drop-down lists, select up to three categories for grouping.

The following Grouped view options are available:
• Group Graphs By—Select up to three categories for grouping the data across
three independent parameters.
• Legend by—Select up to two categories to include in the graph legends
(Figure 5-49).
• Additional Graphs—Select other graphs to display with the analyzed (fitted)
data.
• Data Options—Click the Use ”Included” Traces Only check box to graph only
the biosensors that are included in the analysis (marked with an “X” in the analy-
sis results table.
• Graph Size in Pixels—Options for graph size and the number of graphs to dis-
play per row.
• Graph Options—Options for graph labels and other graph display features.

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Graph leg-
end speci-
fied in the
“Legend
by” op-
tions set in
the
Grouped
View Op-
tions dialog
box

Click a graph to
highlight the
data in the
analysis results

Figure 5-49: Fitting View—Grouped Option

Display Graphs in Custom Groupings

To display graphics in custom groupings:
1. Open a kinetics data file.
2. In the Data Selection tab, click Grouped View (Figure 5-50).

Figure 5-50: Grouped View Option

3. Select the desired method of grouping.

In Figure 5-51’s example, the raw data is grouped by known concentration.

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Figure 5-51: Grouped View Options

NOTE: For Grouped View options, see Figure 5-48: on page 118. 

4. Click OK to close the dialog box.

The raw sensograms are grouped by the known concentration (Figure 5-52: on
page 120).

Figure 5-52: Raw Sensograms Grouped by Known Concentration Example

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NOTE: The Grouped View for quantitation analysis is also available in the
Results tab. In the Results tab, process the data by clicking Calculate Bind-
ing Rate and the Grouped View radio button.

5. Edit the Grouped View options as necessary.

In this example, the sensograms are sorted by known concentration (Figure 5-53).

Figure 5-53: Grouped View—Sensograms Sorted by Known Concentration

If multiple data sets are loaded and the Calibrate within plate check box is enabled to
calculate binding rates, Individual Standards and Overlay Standards are presented
within the Options dialog box of the Group View (Figure 5-54).

Figure 5-54: Individual and Overlay Standards

Selecting Data for Viewing

The following options are available for selecting data for viewing:

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• To view specific biosensor data, select the rows in the analysis results table.
• To select adjacent rows, hold down the Shift key while you click the first and last row
in the selection.
• To select non-adjacent rows, hold down the Ctrl key while you click the rows of inter-
est. The Fitting view, Residual view, and graphs (X-Y, iso-affinity, and steady state) are
updated after each data selection.
After a kinetics analysis is completed, the default Fitting and Residual views display the data
for all biosensors and samples.

Figure 5-55: Selecting Analysis Results for Viewing in the Fitting View and Residual View

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Analysis Results Table

Each row in the Analysis Results table displays the results for one set of association/dissoci-
ation data. By default, the Fitting and Residual views include all of the results in the table.
Kinetic analysis results:
• Index—Numbered order of the curves processed. The index is useful to sort back to
the original order. It is also useful in the graphing applications in the lower right win-
dow pane.
• Include—“X” indicates data included in the analysis. If this field is blank, the data is
not included in the analysis.
• Color—The color of the biosensor binding curve in the Fitting and Residual view.
• Sensor Location—Location of the biosensor in the sensor tray map.
• Sensor Type—The type of biosensor chemistry.
• Sensor Info—Information about the biosensor that was entered in the Octet System
Data Analysis software.
• Baseline Loc.—Well location in the sample plate or reagent plate (Octet 384 instru-
ments only) in which the baseline was performed.
• Assoc. (Sample) Loc.—Sample well location in the sample plate.
• Sample ID—The sample ID entered during assay setup.
• Dissoc. Loc.— Well location in the sample plate or reagent plate (Octet 384 instru-
ments only) where the dissociation was performed.
• Conc (nM)—The molar concentration of the sample used in the association step. The
molar concentration is entered by the user or computed by the molarity calculator
during experiment setup.
• Response—Response calculated from the time window entered in the Steady State
Analysis section.
• KD (M)—Affinity constant. For the 2:1 and 1:2 models, the Octet System Data Analy-
sis software computes two KD values.
• kon (1/Ms)—Rate of association. For the 2:1 and 1:2 models, the Octet System Data
Analysis software computes two kon values.
• kon Error—Standard error of the rate of association.
• kdis (1/s)—Rate of dissociation. For the 2:1 and 1:2 models, the Octet System Data
Analysis software computes two kdis values.
• kdis Error—Standard error of the rate of dissociation.
• Rmax—The maximum response determined from the fit of the binding data.
• Rmax Error—The standard error of Rmax. For the 2:1 and 1:2 models, the Octet Sys-
tem Data Analysis software computes two Rmax values.

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• kobs (1/s)—Observed binding rate. For the 2:1 and 1:2 models, the Octet System
Data Analysis software computes two kobs values.
• km—The mass transport rate constant.
• km error—The standard error of the mass transport rate constant.
• Req—The calculated response at equilibrium that is determined from a fit of the
binding data.
• Req/Rmax(%)—Ratio of Req to Rmax.
• Full X2—A measure of the goodness of curve fitting (not directly related to a param-
eter estimate). It is the sum of squared deviations, where deviation is the difference
between the actual data point and the fitted curve. There is one value for each curve-
fit. Values close to zero indicate a good curve fit.
• Full R2—R2 is the coefficient of determination (COD). It is an estimate of the good-
ness of the curve fit and is not directly related to the estimate of a specific parameter.
Values close to 1.0 indicate a good curve fit.
• Report point #1–10—Up to 10 report points can be added to the analysis results
table using the Report Points feature in the Analysis window. The column heading of
each report point is time value used to generate that report point. For example, if a
report point is generated at 100 seconds, the column heading is "X=100".
• SSG KD—The steady state group KD value. Use this feature to quickly view the steady
state derived KD values of groups defined within grouped view (not replicate
groups). The column is populated by opening Grouped view, selecting up to three
grouping parameter and activating Steady-State under additional graphs. The SSG
KD value is reported for the set of data within each pane of the Grouped view. Repli-
cate grouping and global analysis are not used to determine this value.
• SSG Rmax—The steady state group Rmax value. Use this feature to quickly view the
Rmax value of steady state data for a group defined within Grouped view (not repli-
cate groups). The column is populated by opening Grouped view, selecting up to
three grouping parameter and activating Steady-State under additional graphs. The
SSG Rmax value is reported for the set of data within each pane of the Grouped view.
Replicate grouping and global analysis are not used to determine this value.
• SSG R^2—The steady state group R^2 value. Use this feature to quickly view the R^2
value of steady state data for a group defined within Grouped view (not replicate
groups). The column is populated by opening Grouped view, selecting up to three
grouping parameter and activating Steady-State under additional graphs. The SSG
R^2 value is reported for the set of data within each pane of the Grouped view. Rep-
licate grouping and global analysis are not used to determine this value.
• Loading Well Location—Location of the sample well used during the load step of
the experiment.
• Cycle—Number of biosensor regeneration cycles.
• Sample ID—User-defined annotation that describes the sample.

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Working with the Analysis Results Table

To view a shortcut menu of display options (Figure 5-56), right-click the Analysis Results
table.

Figure 5-56: Analysis Results Table Shortcut Menu

Analysis results table display options:

• Advanced Search—Searches the contents of the results table of the Analysis tab.
Multiple levels and operators are available. Searches may be combined (using AND/
OR operator) and saved (see Figure 5-57).
• Set Color—Opens the color palette that enables you to choose a color for the
selected results (see Figure 5-58).
• Set Color By Group—Color-codes the results according to the groups set in the
Grouped View Options dialog box (see Figure 5-48).
• Set Color By—Enables you to color-code results according to a user-selected cate-
gory from the analysis results table (see Figure 5-59).
• Include Wells—Removes the “X” in the Include column for the selected biosensors.
Re-run the analysis to include these biosensors in the analysis.
• Exclude Wells—Adds an “X” in the Include column for the selected biosensors. Re-
run the analysis to exclude these biosensors from the analysis.
• Size Columns by Title—Automatically sets the column width to fit the column title.

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• Size Columns by Data—Automatically sets the column width to fit the data.
• Select All Rows—Selects all biosensors in the table and displays the data in the Fit-
ting view and graphs.
• Invert Selection—Changes the wells status so that included wells become excluded
wells and excluded wells become included wells. You must re-run the analysis to
apply the inverted settings.
• Order Columns—Opens a dialog box that enables you to change the order of the
table columns.

Searching Analysis Results

The complete contents of the Analysis tab—results table is searchable using the
Advanced Search tool. The search result is a highlighted set of table rows that meet the
specified search criteria. The set of rows selected before activation of the Advanced Search
dialog box may be combined with the results of the search using ALL, AND, and OR opera-
tors specified within the Advanced Search dialog box.

Figure 5-57: Advanced Search Dialog Box

Advanced Search options:

• Column—The column of the results table searched.
• Operator—The method of matching the search term with the searchable text.
Options include Starts with, Ends with, Contains, Does not contain, and Is empty.
• Value—The search term for a single level.
• Add Level—Adds one additional search level to the search. The AND operator
applies to all levels

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• Remove Level—Removes the selected search level.

• Case Sensitive—Requires that the case of all characters (uppercase and lowercase)
of the search results match the search term.
• Include Excluded Traces—Includes all data acquisition traces within the search
regardless of exclusion during analysis.
• Treat Empty Cells as Match—Returns empty cells of the column as positive
matches, useful for searches in which cells were inadvertently left empty during
plate assignment or sample annotation.
• Search Options
• Search All—Specifies all text within the Analysis table as searchable regardless
of the set of rows selected before activation of the Advanced Search dialog. The
search return is a highlighted set of rows in the table that match the search the
search criteria.
• Search all but keep current selection (implies OR)—Specifies all text in the
Analysis table as searchable regardless of the set of rows selected before open-
ing the Advanced Search dialog box.
• Search only current selection (implies AND)—Specifies the text as the set of
rows selected beforeopening the Advanced Search dialog box.

Searching Contents of Results Table

To search the contents of the Results table:
1. On the Analysis tab, right-click a cell in the Results table, and select Advanced
Search > Edit Search.
2. Using the Column Name pull-down menu, select a column to search.
3. Using the Operator pull-down menu, assign an operator.
4. Enter the search term under Value.
5. If the search is case sensitive, select the Case Sensitive option.
6. Optional. Select the Include Excluded Traces option to include traces excluded from
analysis in the search.
7. Optional. Select the Treat Empty Cells as a Match option to include empty cells in the
search.
8. Optional. Click Add Level and repeat steps 2–4 to add additional levels to the search.
The set of rows selected in the table (when the Advanced Search dialog box was
opened) can be applied to the search using ALL, OR, and AND operators.
a. Select Search All to search the entire table (ALL operator).
b. Select Search All but keep current selection to search the entire table with reten-
tion of the selection present when the Advanced Search dialog box was opened
(OR operator).

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c. Select Search only current selection to search only the rows selected when the
Advanced Search dialog box was opened (AND operator).
The search can be saved by specifying a name under Search Name and clicking Save.
The name of the saved search will appear in the Saved Searches list.
9. Click OK to execute the search.
Rows that contain cells meeting the search criteria will be highlighted.

Editing a Search
To edit a search:
1. On the Analysis tab, right-click any cell in the Results table, and select Advanced
Search > Edit Search.
2. Select a saved search from the Saved Searches list.
3. Click Load Search.
The parameters for the specified search are restored.
4. Edit the search (see steps 2–9 in “Searching Contents of Results Table” on page 127).
The search can be saved by specifying a new name under Search Name and clicking
Save. The name of the saved search will appear in the Saved Searches list.
5. Click OK to execute the search.
Rows that contain cells meeting the search criteria will be highlighted.

Color-Coding Data
You can assign different colors to the binding curves as a follows:
• A particular color to user-selected results. This is useful when grouping for a global
fit.
• Color according to a results category.

Color-Coding User-Selected Results

To color-code user-selected results:
1. Select one or more rows in the analysis table (click the row header).
2. Right-click and select Set Color.

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Figure 5-58: Changing the Color of User-Selected Results

3. In the color palette that appears, select a basic color or create a custom color. To define
a custom color, click Define Custom Colors.
4. Click OK in the color palette.
The selected color is applied to the binding curve and appears in the table.
Results can be color-coded by category to group them for a global fit (for example, colored
by compound), then fit using global fit by color. For the final display, the wells can be re-col-
ored without affecting the results.

Color-Coding Analysis Results by Category

To color-code analysis results by category:
1. Right-click the analysis results table and select Set Color By.
2. Make a selection from the shortcut menu (Figure 5-59).
In Figure 5-59’s example, category = sample concentration.

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Figure 5-59: Setting Data Color by Category

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Sorting Analysis Results

To sort results by any category (column header):
1. Click a column header.
The results are displayed in descending order. In Figure 5-60, the results were color-
coded by sample concentration, and then sorted.

Figure 5-60: Color-Coded Analysis Results—Sorted by Color

2. Click the column header again to sort the results in ascending order.

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WORKING WITH GRAPHS

The active analysis results are automatically presented in three graphical formats:
• X-Y
• Iso-Affinity
• Steady State Analysis

X-Y Graphs
The X-Y graph is a scatter plot from user-selected analysis results (x and y-variables). Both
axes may be presented on either a logarithmic or linear scale.

Logarithmic scale option

Select the analysis result to plot

from the drop-down lists

Figure 5-61: X-Y Graph

An X-Y plotting tool has been added to the Results tab of quantitation analysis. Previously
available only in kinetics analysis, the X-Y plotting tool graphs several important parame-
ters, such as binding rate, R2, calculated concentration, and residual. The axes may be inde-
pendently selected to by logarithmic. In the example shown, the calculated concentration
is plotted versus the R2 (Figure 5-62).

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Figure 5-62: X-Y Plotting Tool

Iso-Affinity Graphs
The Iso-Affinity graph enables viewing of the continuum of kdis and kon values that gener-
ate a single value of KD, providing a convenient way to view both kinetic and affinity data.
The value of the affinity constant, KD, is the ratio of the association rate kon and dissociation
rate kdis. A single value of KD can, therefore, be obtained from varying values of kon and kdis;
for example, a KD value of 1 uM can be the result of kdis=1x10–3 1/S and kon=1x10+3 1/Ms
or kdis=1x10-2 1/S and kon=1x10+4 1/Ms.
Each Iso-Affinity plot has two red lines that correspond to a single KD value. The position of
the KD lines is determined by taking the average of all KD values and plotting one redline 10
fold lower than the average and one red line 10 fold higher than the average.

Figure 5-63: Iso-Affinity graph—X axis = ka, Y -axis = kd

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Steady State Analysis Graphs

The Steady State Analysis graph (Figure 5-64) displays the results from the steady state
analysis (see “Steady State Analysis Graphs” on page 134). The graph plots the response or
Req vs. concentration and the curve fit.

Calculated affinity constant KD

and calculated RMax

Figure 5-64: Steady State Analysis Graph

DATA EXPORT OPTIONS

The analysis results can be exported (.txt or .csv) or copied to the system clipboard. Infor-
mation from the Data Selection, Processing, or Analysis windows can be selected to gener-
ate custom reports (.xls).

Figure 5-65: Data Export Options in the Analysis Window

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The data export options include:

• Export Fitting Results—Saves the binding data and analysis results for each biosen-
sor to a separate text file (.txt).
• Export Table to .csv File—Saves the results table to a .csv file that can be opened in
a spreadsheet application.
• Copy Table to Clipboard—Saves the binding data and analysis results for the
selected biosensors to the system clipboard.

GENERATING A REPORT

NOTE: Generating reports for large data sets may take a few minutes. For
faster report generation, minimize the number of items selected for the report.
In particular, the sensor summary for a large data set can be time-consuming.

To generate a report:
1. On the menu bar, click File > Save Report.
2. In the displayed dialog box, select the information to include in the report.
3. Confirm the default location to which the file will be saved or specify a different loca-
tion.
4. Click Export.

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Figure 5-66: Report Selection Form

Experiment Summary Options

To use the available experiment summary options, select the following from the Data Selec-
tion window ( tab):
• Steps data table
• Assay steps data table

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Steps data table Assay steps data table

Figure 5-67: Report Data Types—Experiment Summary Options

Processing Options
To use the available processing options, select the following from the Processing window
( tab):
• Raw and aligned data
• Sensor tray image
• Sample plate image
• Processed results
• Sensor summary
• Sensor tray data table
• Sample plate data table
• Report points

NOTE: When working with large data sets, including the sensor summary in a
report significantly increases the time required to generate the report.

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Figure 5-68: Report Data Types—Processing Options—Raw Data and Aligned Data

Sensor tray images Sample plate data images

Sensor tray data table Sample plate data table

Figure 5-69: Report Data Types—Processing Options—Sensor Tray and Sample Tray Information

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Figure 5-70: Report Data Types—Processing Options—Processed Data

Figure 5-71: Types of Report Data Included by the Processing Options—Sensor Summaries

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Figure 5-72: Report Data Types—Processing Options—Report Point Analysis

Analysis Options
To use the available analysis options, select the following from the Analysis window (
tab):
• Kinetics analysis
• Iso-Affinity analysis
• Steady State analysis

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Figure 5-73: Report Data Types—Analysis Options—Kinetics Analysis Results

Figure 5-74: Report Data Types—Processing Options—Iso-Affinity and Steady State Analysis Graphs

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
APPENDIX A:

Using Octet384 Systems with

an Automation Interface
Automation Interface Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144

Design of the Automation Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144

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AUTOMATION INTERFACE OVERVIEW

The Octet System Data Analysis software provides support for an automation interface
using a COM port (RS-232) or a Transmission Control Protocol/Internet Protocol (TCP/IP)
socket/port (Figure A-1).

Figure A-1: Options for Automation

An example application for testing the automation interface (AutomationClient.exe) is

included in the applications and Dynamic Link Libraries (DLLs) installed with the Octet Sys-
tem Data Analysis software. The file is located in the C:\Program Files\ForteBio\DataAnal-
ysis directory.

NOTES: 
The automation interface can be used with Octet384 systems only. The exam-
ples that follow are illustrated using a TCP/IP connection, but the serial port
connection behaves identically.

DESIGN OF THE AUTOMATION INTERFACE

The automation interface is designed to be as universal as possible, making no assump-
tions about the communication medium or the language of the client application connect-
ing to the Octet System Data Analysis software.
The following guidelines apply:
• All commands and responses are ASCII strings, one per line.
• All lines are terminated with both carriage-return and line-feed characters ("\r\n").
• Each command starts with the name of the command and may then be followed by
required and optional parameters.
• Each parameter starts with a switch definition (a la dos/unix command line) followed
by the parameter itself, which allows parameters to be sent in any order.
• The command or response is terminated with a new line (CR/LF) sequence.
• Parameters containing embedded spaces need to be enclosed in double quotes.

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Automation Interface Control Setup

Before the Octet System Data Analysis software can be controlled using an automation
interface, the correct automation options must be set. To do this, go to File > Options and
select the appropriate port in the Automation box (Figure A-1).

NOTE: The Octet System Data Analysis software can be controlled via the
Automation interface through a serial port (RS-232) or a TCP/IP socket.

NOTE: The Localhost option can be useful in developing the automation cli-
ent on the same computer that runs the Octet System Data Analysis software.

NOTE: ForteBio recommends that the Data File repositories be set using
shared folders addressed by "UNC" folder names so that the internal path used
by the Data Analysis application corresponds to the external path used to
access/retrieve the data files recorded during the experiment. Alternatively,
the path returned by the GetRunInfo command to access the data files from
another computer on the LAN.

Analysis Automation API

//
**********************************************************************
***
//
// Copyright (c) 2011 ForteBio.
// All rights reserved.
//
//
**********************************************************************
***
// HEADER: AutomationAPI.h
// PURPOSE: Defines the commands supported by the automation API.
// AUTHOR: BHI Nov 2008
//
#ifndef INC_ANALYSIS_AUTOMATIONAPI_H
#define INC_ANALYSIS_AUTOMATIONAPI_H

// NOTES:
// * The automation interface is string based. Commands and responses
are

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// strings, one per line.

// * Each command starts with the name of the command and may then be
// followed by required and
// optional parameters.
// * Each parameter starts with a switch definition (a la dos/unix com-
mand
// line) followed by the
// parameter itself. This allows parameters to be sent in any order.
// * The command or response is terminated with a new line (CR/LF)
sequence.
// * Parameters containing embedded spaces must be enclosed in double
// quotes.
// * Response items containing embedded spaces will be enclosed in dou-
ble
// quotes.

// Version of thew API described in this header file.

const char AUT_API_VERSION[] = "1.0";

// Status return values

const char AUT_OK[] = "OK";
const char AUT_RUNNING[] = "Running";
const char AUT_ERROR[] = "ERROR";
const char AUT_BUSY[] = "Busy";
const char AUT_STOPPED[] = "Stopped"; // Stopped by user.
const char AUT_EOL[] = "\r\n";

// Parameter switches for the LOAD command

const char AUT_SWITCH_DATASET = 'd';

// Parameter switches for the ANALYZE command

const char AUT_SWITCH_PARAMS = 'p';
const char AUT_SWITCH_XMLINFO = 'x';

// COMMAND API
// ===========

const char AUT_CMD_VERSION[] = "Version";

// Returns the version of the app being automated, and the API version.
// Args: (none)
// Response: App product version (e.g. "6.3.1.12 1.0\r\n")

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const char AUT_CMD_LOAD[] = "Load";

// Loads an experiment
// Args:
// -d <path> Path to experiment data files
// Response:
// "OK\r\n"
// "Error: <reason>\r\n"

const char AUT_CMD_ANALYZE[] = "Analyze";

// Runs an analysis
// Args:
// -p <path> Path to parameters (INI file)
// -x <path> Path to XML information file (optional, can be mul-
tiple XML info files)
// Response:
// "OK\r\n"
// "Error: <reason>\r\n"

const char AUT_CMD_STATUS[] = "Status";

// Returns status: OK=ready, Busy=running, Error=Action was terminated
by an error.
// Busy is followed by descriptive information on the progress of the
experiment (% complete)
// Args: (none)
// Response:
// "OK\r\n"
// "Busy\r\n"
// "Running (nn%)\r\n"
// "Error: <reason>\r\n"

#endif // INC_ANALYSIS_AUTOMATIONAPI_H

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
APPENDIX B:

21 CFR Part 11 Software

Administrator Options
Installing the Data Acquisition 7.0 21 CFR Part 11 Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . 150

Installing the Data Analysis 7.0 21 CFR Part 11 Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153

Installing the ForteBio GxP Server Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 156

Administrator Account Setup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 159

Starting an Administrator User Session . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163

Accessing Administrator Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 166

Accessing the ForteBio GxP Server Module Directly . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 180

Restarting the ForteBio GxP Server Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 183

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INSTALLING THE DATA ACQUISITION 7.0 21 CFR PART 11 SOFTWARE

To install the Data Acquisition 7.0 21 CFR Part 11 software:
1. Insert the software V7.0 CFR CD (7.00.35/7.0.0.9) into your CD drive.
• If the Autoplay dialog box displays, choose to open the CD to view files.
• If the Autoplay dialog box does not display, navigate to the CD using Windows
Explorer.
Optical drives are typically found under the D:\ or E:\ drive.
2. Double-click DataAcquisition-CFR-7_0_0_x.exe to launch the installation wizard (see
Figure B-1).

Figure B-1: Data Acquisition 7.0 (for 21 CFR Part 11) Software Setup Wizard

3. Click Next to display the Choose Install Location dialog box (Figure B-2).

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Figure B-2: Choose Install Location Dialog Box

The default location for the software on the local machine is C:\Program Files\Forte-
Bio\DataAcquisition7.
4. Click Next to accept this path location.
The Choose Start Menu Folder dialog box displays (Figure B-3).

Figure B-3: Choose Start Menu Folder Dialog Box

The default Start Menu folder is ForteBio.

5. Click Install.
The installation wizard takes a few seconds to install.
When the installation is complete, the installation wizard displays the Completing the
Data Acquisition 7.0 Setup Wizard dialog box (Figure B-4).

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Figure B-4: Completing the Data Analysis 7.0 Setup

6. Click Finish to complete the installation.

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INSTALLING THE DATA ANALYSIS 7.0 21 CFR PART 11 SOFTWARE

To install the Data Analysis 7.0 21 CFR Part 11 software:
1. Insert the software CD into your CD drive.
2. Navigate to the window listing the files located on the installation CD.
3. Double-click DataAnalysis-CFR-7_0_0_x.exe to launch the installation wizard (see
Figure B-5).

Figure B-5: Data Analysis 7.0 (for 21 CFR Part 11) Software Setup Wizard

4. Click Next to display the Choose Install Location dialog box (Figure B-6).

Figure B-6: Choose Install Location Dialog Box

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The default location for the software on the local machine is C:\Program Files\Forte-
Bio\DataAnalysis7.
5. Click Next to accept this path location.
The Choose Start Menu Folder dialog box displays (Figure B-7).

Figure B-7: Choose Start Menu Folder Dialog Box

The default Start Menu folder is ForteBio.

6. Click Install.
The installation wizard takes a few seconds to install (Figure B-8).

Figure B-8: Installation Progress

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The installation wizard displays the Completing the Data Analysis 7.0 Setup Wizard dia-
log box (Figure B-9).

Figure B-9: Completing the Data Analysis 7.0 Setup

7. Click Finish to complete the installation.

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INSTALLING THE FORTEBIO GXP SERVER MODULE

The ForteBio GxP Server module can be installed and run from the following locations:
• A local host computer where the ForteBio Data Acquisition or Data Analysis 7.0 21
CFR Part 11 software is installed
• A remote host computer networked to a machine where the ForteBio Data Acquisi-
tion or Data Analysis 7.0 21 CFR Part 11 software is installed
Upon launching the Octet System Data Acquisition or Data Analysis 7.0 CFR 11 software,
you are required to select the GxP Server module host location. If the GxP Server module is
installed in multiple locations, you can select any host server. The user session event record
will be saved only to the host location selected, making it possible to have records for the
same user in multiple locations.

NOTE: For administrators only. To ensure that all records are saved to one
location, ForteBio recommends that administrators install a single copy of the
ForteBio GxP Server module on the network that can then be accessed by all
users.

To install the ForteBio GxP Server software:

1. Navigate to the window listing the files located on the installation CD.
2. Double-click ForteBio GxP Server 7.0.exe to launch the installer.
3. If prompted with the Do you want the following program from an unknown publisher to
make changes to this computer? message, reply Yes.
The installation wizard should display (Figure B-10).

Figure B-10: ForteBio GxP Server 7.0 Software Setup Wizard

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4. Click Next to display the Choose Install Location dialog box (Figure B-11).

Figure B-11: Choose Install Location

The default location for the software on the local machine is C:\Program Files\Forte-
Bio\DataAnalysis7.
5. Click Next to accept this path location.
The Choose Start Menu Folder dialog box displays (Figure B-12).

Figure B-12: Choose Start Menu Folder Dialog Box

The default Start Menu folder is ForteBio.

6. Click Install.
The installation wizard takes a few seconds to install (Figure B-13).

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Figure B-13: Installation Progress

The installation wizard displays the Completing the ForteBio GxP Server 7.0 Setup Wiz-
ard dialog box (Figure B-14).

Figure B-14: Completing the ForteBio GxP Server Software 7.0 Setup

7. Click Finish to complete the installation.

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ADMINISTRATOR ACCOUNT SETUP

To set up the administrator account:
1. Launch the Octet System Data Acquisition or Data Analysis software by double-clicking
the respective desktop icon; see Figure B-15.

Figure B-15: Data Acquisition or Data Analysis Software Desktop Icons

The Login dialog box displays (Figure B-16).

Figure B-16: Login Dialog Box

2. Select a Server location by clicking ... (browse).

The Authentication Server dialog box displays (Figure B-17).

Figure B-17: Authentication Server

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3. Click Default to recall the default server settings of localhost and Port 2002.
• Local host—If the local computer is to be used as the GxP Server module host,
click the Localhost check box. Change the Port number if needed.
• Remote host on same subnet—If the GxP Server module is hosted on the same
subnet, deselect the Localhost check box and click Find. A list of potential GxP
Server module addresses will be listed. Choose the desired location from the list
and click OK.

Figure B-18: Choose Server Address

• Remote host on another subnet— If the GxP Server module is hosted on a dif-
ferent subnet, deselect the Localhost check box. Enter the IP address of the
computer hosting the GxP Server module.

Figure B-19: Authentication Server

When the GxP Server module host location has been selected or entered, click OK to
save changes and exit the Authentication Server dialog box. The GxP Server module
location will now be listed as the Server in the Login dialog box.

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NOTE: Once the GxP Server module host location is selected, this location will
be used as the default selection for the administrator account. It does not need
to be reselected each time a new session is initiated.

Figure B-20: Login Dialog Box with Server Parameter Configured

4. Select Administrator from the User drop-down list (Figure B-20).

5. Leave the Password blank, set the Project to (none) and click OK (Figure B-21).

Figure B-21: Login Dialog Box with Server, User, and Project Settings Configured

The Change Password dialog box displays; see Figure B-22.

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Figure B-22: Change Password Dialog Box

6. Enter a New password and Password reminder (optional) and click OK.
The Octet System Data Acquisition or Data Analysis software launches and initiates an
administrator user session that will allow access to administration options.

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STARTING AN ADMINISTRATOR USER SESSION

Administrators initiate new user sessions the same way non-administrative users do.
1. Launch the Octet System Data Acquisition or Data Analysis software by double-clicking
the respective desktop icon; see Figure B-23.

Figure B-23: Data Acquisition or Data Analysis Software Desktop Icons

The Login dialog box displays; see Figure B-24.

Figure B-24: Login Dialog Box

2. Confirm that the Server location is correct. If not, see “Administrator Account Setup” on
page 159.
3. Select Administrator from the User drop-down list (Figure B-25).

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Figure B-25: Login Dialog Box with Server, User, and Project Settings Configured

4. Enter your Password. Click ? for a password reminder (Figure B-26) if necessary.

Figure B-26: Password Reminder

5. If required, select a project from the Project drop-down list (Figure B-27).

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Figure B-27: Login Dialog Box with Project Selections

6. Click OK.
The Octet System Data Acquisition or Data Analysis software launches and initiates the
administrator session. During the session, the administrator account and project
selected at login are displayed in the Data Acquisition software status bar.

NOTE: Administrator and user sessions are automatically closed after a period
of inactivity set using the UserIdleMin constant. Please see “Administrator
Constants” on page 176 for more information.

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ACCESSING ADMINISTRATOR OPTIONS

The 21 CFR Part 11 software Server Administration options allow administrators to mange
users, groups, projects and constants and view associated events.
These options can be accessed in the Octet System Data Acquisition and Data Analysis soft-
ware or by launching the ForteBio GxP Server module directly.
• Data Acquisition and Data Analysis software—Click Security > Server Adminis-
tration (Figure B-28).

Data Acquisition Software Data Analysis Software

Figure B-28: Security > Server Administration Menu

• ForteBio GxP Server module on network location—Double-click the 

FBServerConfig.exe file in the FBServer7 folder from the installed location
(Figure B-29).

Figure B-29: Installation Location

• ForteBio GxP Server module on a local host computer—Double-click the ForteBio

GxP Server desktop icon (Figure B-30).

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Figure B-30: ForteBio GxP Server Desktop Icon

NOTE: When accessing the ForteBio GxP Server module directly, additional
tools are also provided to test server functionality. Please see “Accessing the
ForteBio GxP Server Module Directly” on page 180 for more information.

The ForteBio GxP Server Configuration window displays.

Administrator Tabs
Five tabs are available in the ForteBio GxP Server Configuration window:
• Users—Allows user and password management and individual privileges selection.
• Groups—Allows user group management and group privileges selection.
• Projects—Allows project management and setup.
• Constants—Allows setup of password requirements, cached server credentials and
screen lock due to inactivity.
• Events—Displays event logs for individual user accounts, projects, or machines.
Click any of the tabs to view the respective information contained within the tab.

Tab View
Each tab displays a list of administrator entries and associated setting information that can
be sorted by clicking any of the column headers (Figure B-31).

Figure B-31: Tab View Example

Tab Menu
Right-clicking an entry or a blank area in the tab displays the tab menu. Tab menu options
vary depending on the tab selected.

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User Account Administration

The Users tab allows administrators to add and delete user accounts, as well as set and
change individual user account privileges and passwords.

Creating a New User Account

To create a new user account:
1. Right-click anywhere in the Users tab and select New User, or double-click in a blank
area; see Figure B-32.

Figure B-32: New User Menu

The New User dialog box displays (Figure B-33).

Figure B-33: New User Dialog Box

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2. Assign Account Details. Enter the user’s Login name, Full name, Information
(optional), Password, and Password reminder (optional).
3. Assign a User Group. Select a user group from the Group drop-down list. The following
default group selections are available:
• Administrator—Add, delete, and change user accounts and groups.
• Supervisor—Review data and events.
• Developer—Create, run, save, and export data.
• Lab User—Only run experiments.
• Guest—No explicit privileges; these must be assigned by the administrator.
If other user groups have been created by an administrator, they will also be available for
selection in the Group drop down box. For more information, please see “Creating a New
User Group” on page 173.
4. Assign Privileges. Each user account can be assigned specific privileges. The privileges
displayed initially will be those defined in the user group selected in the previous step.
Table B-1 outlines the privileges for the default user groups. If needed, change user
account privileges by selecting or deselecting the check boxes next to each privileges.
• Administration—Can administer the user database.
• Review—Can review changes and events.
• Change—Can change methods and configuration values.
• Plate—Can change sample plate properties.
• Run—Can run experiments and analyses.

Table B-1: Default user group privileges.

Privilege Administrator Supervisor Developer Lab User Guest

Administration
Review
Change
Plate
Run

5. Options—Click the Password does not expire check box if desired. By default, this
check box is not selected. Clicking this option will let user account passwords expire at
the set PasswordTTL constant. For more information on setting constants, see “Admin-
istrator Constants” on page 176.
6. Click OK to save changes and exit.

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Viewing and Changing User Account Settings

To view and change user account settings:
1. On the Users tab, right-click the user account and select Edit User, or double-click the
user account.
The Edit User window displays (Figure B-34).

Figure B-34: Edit User Dialog Box

2. If needed, modify the user account settings. For more details on individual settings, see
“Creating a New User Account” on page 168.
3. Click OK to save changes and exit.

Deleting User Accounts

To delete a user account:
1. On the Users tab, right-click the user account and select Delete User.
2. Click OK in the dialog box displayed.

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Changing User Account Passwords

To change a user account password:
1. On the Users tab, right-click the user account and select Set Password.
The Change Password dialog box displays (Figure B-35).

Figure B-35: Change Password Dialog Box

2. Enter the New Password, confirm the new password, and provide a Password
reminder (optional).
3. Click OK to save changes and exit.

Changing the Administrator Password

To change the administrator password:
1. Initiate a new administrator user session.
2. When the software launches, on the main menu, click Security > Change Password.
The Change Password window displays (Figure B-36).

Figure B-36: Change Password Dialog Box (Administrator)

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NOTE: You can also access the Change Password dialog box by right-clicking
on the administrator account in the Users tab and selecting Set Password
from the tab menu.

3. Enter the Current password for your user account. Click ? for a password reminder.
4. Enter the New Password and Password reminder (optional).
5. Click OK to save changes and exit.

Group Administration
The Groups tab (Figure B-37) allows administrators to add and delete user groups as well as
set and change group privileges.

Figure B-37: ForteBio GxP Server Administration

When a user account is assigned to a user group, the privileges defined in the group are
also applied to the individual user account. The following default user groups are available
and the privileges assigned to each are shown Table B-2:
• Administrators—Can add, delete and change user accounts and groups
• Supervisors—Can review data and events
• Developers—Can create, run, save and export data
• Lab Users—Can only run experiments
• Guests—Have no explicit privileges, these must be assigned by the administra-
tor

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Table B-2: Default User Group Privileges

Privilege Administrator Supervisor Developer Lab User Guest

Administration
Review
Change
Plate
Run

Creating a New User Group

To create a new user group:
1. Right-click anywhere in the Groups tab and select New Group or double-click in a
blank area.
The New Group window displays (Figure B-38).

Figure B-38: New Group Dialog Box

2. Enter the Group name and Information (optional).

3. Privileges—Each group can be assigned specific privileges. Add group privileges by
selecting or de-selecting the check boxes next to each privilege:
• Administration—Can administer the user database
• Review—Can review changes and events
• Change—Can change methods and configuration values
• Plate—Can change sample plate properties
• Run—Can run experiments and analyses
4. Click OK to save changes and exit.

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Viewing and Changing Group Settings

To view and change group settings:
1. Right-click on the group and select Edit Group, or double click the group.
The Edit Group window displays (Figure B-39).

Figure B-39: Edit Group Dialog Box

2. If needed, modify the group settings. For more details on individual settings, see “Cre-
ating a New User Group” on page 173.
3. Click OK to save changes and exit.

Deleting a User Group

To delete a user group:
1. Right-click the group and select Delete Group.
2. Click OK in the dialog box displayed.

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Project Administration
The Projects tab (Figure B-40) allows administrators to add and delete user projects. Proj-
ects are selected when a new user session is initiated in the Octet System Data Acquisition
or Data Analysis software, allowing all user, system and software events for a particular proj-
ect to be monitored.

Figure B-40: Projects

Creating a New Project

To create a new project:
1. Right-click anywhere in the Projects tab and select New Project, or double-click in a
blank area.
The New Project window displays (Figure B-41).

Figure B-41: New Project

2. Enter the Project name and Information (optional).

3. Click OK to save changes and exit.

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Viewing and Changing Project Settings

To view and change project settings:
1. Right-click on the project and select Edit Project, or double-click on the project.
The Edit Project window displays (Figure B-42).

Figure B-42: Edit Project

2. If needed, modify the project settings.

3. Click OK to save changes and exit.

Deleting a Project
To delete a project;
1. Right-click the project and select Delete Project.
2. Click OK in the dialog box displayed.

Administrator Constants
The Constants tab allows administrators to set GxP Server module constant settings.

Figure B-43: Constants Tab

Available administrator constants and their associated value ranges are shown in Table B-3.

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Table B-3: Administrator Constants

Constant Description Default Value

Value Range
CredentialsTTL The number of days that the 5
server settings are stored in the
cache. This allows the software to
operate in case the server is tem-
porarily down.
PasswordMin- Minimum number of characters 0
Length that a password must contain.
PasswordSecure ? 0
PasswordTTL Amount of time that a password 180
is allowed to remain unchanged.
UserIdleMin Idle time allowed during a user 15
session after which the session is
automatically closed.

Creating a New Constant

To create a new constant:
1. Right-click anywhere in the Constants tab and select New Constant, or double-click in
a blank area.
The New Constant window displays (Figure B-44).

Figure B-44: New Constant

2. Enter the Constant name and Value. Refer to Table B-3 for a list of available constants
and value ranges.
3. Click OK to save changes and exit.

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Viewing and Changing Constants

To view and change constants:
1. Right-click the constant and select Edit Constant, or double-click the constant.
The Edit Constant dialog box displays (Figure B-45).

Figure B-45: Edit Constant Dialog Box

2. If needed, modify the constant settings. For more information on available constants
and their values, see Table B-3 on page 177.
3. Click OK to save changes and exit.

Deleting a Constant
To delete a constant:
1. Right-click the constant and select Delete Constant.
2. Click OK in the dialog box displayed.

Event Log
The Events tab allows administrators to view all the user, system, and software event infor-
mation recorded by the ForteBio GxP Server module.

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Figure B-46: Event Log

Events are tracked for individual user accounts, projects and machines. By default, a histori-
cal log of all events recorded on the active ForteBio GxP Server module displays.

Viewing Events
To view events for a specific user account, project, or computer, click the User (Figure B-47),
Project, or Machine drop-down list, and select an entry:

Figure B-47: Viewing Events from the User Drop-Down List

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NOTE: Selections can be made in either one or all of the User, Project, or
Machine drop-down lists.

The list then only displays events for the entries selected (Figure B-48).

Figure B-48: Selected Entries

In addition to the specific user, project, and machine selections, the following list options
are also available:
• (any)—Displays all user, project, or machine events.
• (none)—Displays all user and machine events not associated with a specific project
(Project list only).

ACCESSING THE FORTEBIO GXP SERVER MODULE DIRECTLY

Administrators can directly access the ForteBio GxP Server module without initiating an
administrator user session. Direct access provides server testing options, as well as access to
all administrative functions discussed earlier in this section.
To access the ForteBio GxP Server module directly:
• If the ForteBio GxP Server module is installed on a network location—Double-click
the FBServerConfig.exe file in the FBServer7 folder from the installed location
(Figure B-49).

Figure B-49: ForteBio GxP Server Module Installed on a Network Location

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• If the GxP Server module is installed on a local host computer—Double-click the

ForteBio GxP Server desktop icon (Figure B-50).

Figure B-50: ForteBio GxP Server Desktop Icon

The ForteBio GxP Server Configuration window displays (Figure B-51).

Figure B-51: ForteBio GxP Server Configuration Window

Use of the User, Groups, Projects, Constants, and Events tabs are described in “Accessing
Administrator Options” on page 166.

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ForteBio GxP Server Module Testing

The ForteBio GxP Server module can be tested to ensure it is accessible and functioning
properly? Wasn’t sure about this functionality.
To test the ForteBio GxP Server module:
1. Optional. In the Connections to Clients box (Figure B-52), make changes to the server
settings if necessary.

Figure B-52: Connection to Clients

2. Click Apply & Test.

If the ForteBio GxP Server module is found and functioning properly, the following
message displays (Figure B-53):

Figure B-53: Message Confirmation of Found Server

To return to the originally configured ForteBio GxP Server module settings, click
Default at any time.

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RESTARTING THE FORTEBIO GXP SERVER MODULE

If the host location of the GxP Server module cannot be found during user login, or if you
are unable to log in with valid credentials, the ForteBio GxP Server module may be offline
and must be restarted.

NOTE: ForteBio recommends contacting your IT department to confirm

whether or not network or firewall settings may have been changed. This may
also be preventing access to the ForteBio GxP Server module.

To restart the ForteBio GxP Server module, choose one of the following two options:
• If the ForteBio GxP Server module is installed on a network location—Double-click
the FBServer.exe file in the FBServer7 folder from the installed location
(Figure B-54).

Figure B-54: ForteBio GxP Server Module Installed on a Network Location

• If the GxP Server module is installed on a local computer—Double-click the Restart

Server desktop icon (Figure B-55).

Figure B-55: Restart Server Desktop Icon

The Restart Server console display momentarily as the ForteBio GxP Server module
restarts (Figure B-56).

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Figure B-56: Restart Server Console

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 page 185

Symbols Search all but keep current selection (implies OR)

127
.fmf files (method files) 68 Search only current selection (implies AND) 127
Treat Empty Cells as Match 127
Value 126
Numerics
Advanced Search tool 126
1 to 2 Bivalent Analyte Model 106
Advanced Search, display option 125
2 to 1 (HL) Model 106
Affinity constant 123
affinity constant KD 72

A alert threshold value, editing 62

Align All Baselines alignment option 83
About ForteBio Data Analysis (menu) 16
Align by Begin Point alignment option 83
Accelerated Binding Rate Calculation (new feature) 7
Align by End Point alignment option 83
accessing
Align to Baseline, interstep correction feature 97
GxP Server module 180
Align to Dissociation, interstep correction feature 97
Add Folders menu 60, 114
Align X viewing option
Add Level, Advanced Search option 126
basic kinetics analysis 77
Add to Table, Fitting view option 117
quantitative analysis 43
adding
aligning
Replicate Group from the Sample Plate Table
(figure) 54 the Y axis (figure) 97
Additional Graphs, view option 118 to association 96
administrator constants 176 alignment options
administrator password, changing 171 Align All Baselines 83
Advanced Search dialog box (figure 126 Align by Begin Point 83
Advanced Search options Align by End Point 83
Add Level 126 All Aligned to One Step 83
Case Sensitive 127 Show All Steps Aligned 83
Column 126 All Aligned to One Step alignment option 83
Include Excluded Traces 127 analysis
listed 126 excluding samples 39
Operator 126 including samples 39
Remove Level 127 options, listed 140
Search All 127 Analysis results table (figure) 109

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Analysis results table display options

Advanced Search 125
Exclude Wells 125
Include Wells 125
Invert Selection 126
listed 125
Order Columns 126
Select All Rows 126
Set Color 125
Set Color By 125
Set Color By Group 125
Size Columns by Data 126
Size Columns by Title 125
Analysis Results table shortcut menu (figure) 125
analysis results, sorting by any category 131
analysis settings
saving 57
specifying 47
Analysis window (figure) 107
Analysis window with sample curve fitting results (figure) 115
Analyze Data button 61
analyzed data
Binding Rate 56
BR AVG 55
BR CV 56
BR SD 55
Calc. Conc. 56
Concentration avg 56
Concentration CV 56
Concentration SD 56
dilution factor 55
flip 55
Group Type 56

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index 55
information 55
Lot Number 56
plate 55
r2 (COD) 56
replicate group 55
Residual 56
Sample ID 56
sensor 55
Sensor Type 56
well concentration 55
Well Information 56
analyzing
binding data 72
binding data (kinetics) 72
binding data (quantitative) 46
entire time duration of selected step 107
equilibrium state data 111
experiments 36
processed kinetic data
curve fititng analysis 106
steady state analysis 110
applications, closing 14
Apply All, Report Point Analysis feature 103
Apply, Report Point Analysis feature 103
applying
reference subtraction during data processing 91
sample alerts 63
standards alert 62
assigning
Replicate Groups in the Sample Plate Map 52
Replicate Groups in the Sample Plate Table 54
assigning different colors to binding curves 128

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Assoc. (Sample) Loc., kinetic analysis result 123

Association & dissociation, analysis option 106
Association only, analysis option 106
Association, analysis option 107
Audit Trail
described 29
listing events 30
sorting events 30
viewing 29
Auto Scale, Fitting view option 116
Autoplay dialog box 150
Average from, steady state kinetics analysis option 111
Average Reference Sensors
reference subtraction method (figure) 96
reference subtraction method, described 95

B
Baseline Loc., kinetic analysis result 123
basic kinetics experiment 68
batch analysis, running 113
batch mode
kinetics analysis 111
quantitation analysis 57
batch mode options
kinetics 113
quantitative 60
Table Information, kinetics 114
Use one for all folders
kinetics 113
quantitation 60
Use the one in each folder
kinetics 113
quantitative 60

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Use the original data folder 60

Use this folder 60
Well Information
kinetics 113
quantitation 60
batch process data sets with individual .ini files 111
Binding 1 (nm shift) 104
Binding 2 (nm shift) 104
binding chart
copying 105
including toolbar and data grid 101
printing 105
shortcut menu (figure) 105
viewing in separate window (figure) 100
binding curve chart, opening in a separate window 45, 78
binding curves
after user-specified reference subtraction method is used 98
after user-specified Y alignment 98
assigning different colors 128
association steps aligned at the same time point 98
customizing appearance 45, 78
displaying all ligand biosensors 116
displaying from each biosensor 116
viewing
basic kinetic analysis 76
quantitative analysis 41
with no reference subtraction 98
binding data
analyzing (kinetics) 72
analyzing (quantitative) 46
binding data, analyzing 72
Binding Rate Equation, processing parameter 49
binding rate equations

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initial slope 49
R equilibrium 49
Binding Rate, analyzed data 56
binding rates, calculated (figure) 88
binding signal
at Time 1 104
at Time 2 104
biosensor data, viewing specific 122
biosensor number 55
biosensor types, changing (figure) 90
biosensors
selecting (figure) 89
selecting and confirming to analyze (figure) 98
selecting for analysis 71
BR AVG, analyzed data 55
BR CV, analyzed data 56
BR SD, analyzed data 55
By Color, analysis option 107
By Sensor, analysis option 107

C
Calc. Conc., analyzed data 56
calculated binding rates (figure) 88
calculated response at equilibrium 124
Calibrate within plate check box 121
calibration curves 64
Case Sensitive, Advanced Search option 127
Change Password dialog box (figure) 32
Change Password menu 15
Change Project menu 15
Change Well Type menu 90
changing
administrator password 171

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biosensor type (figure) 90

color of user-selected results (figure) 129
constants 178
file type available for selection 28
group settings 174
project settings 176
projects during a user session 31
sample designations 38, 73
sample designations (figure) 38, 73
sample type 85
sample type in the sample plate map (figure) 86
sample type in the sample table (figure) 86
step type (figure) 71
user account password 171
user account settings 170
user password 32
Choose Install Location dialog box (figure) 151, 153
Choose Start Menu Folder dialog box (figure) 151, 154, 157
closing
all experiments 46, 79
application 14
experiment 46, 79
selected experiment (left) or all experiments (right) in the Quantitation or Kinetics folder (figure) 46
closing a kinetics experiment 79
closing a kinetics experiment (figure) 79
COD (coefficient of determination) 124
coefficient of determination 124
color of the biosensor binding curve 123
Color, kinetic analysis result 123
color-coded analysis results
enabling 125
sorted by color (figure) 131
color-coding

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data 128
results by category 129
user-selected results 128
Column, Advanced Search option 126
compliant experiments, generated 27
compliant features for 21 CFR Part 11 26
Conc. (nM), kinetic analysis result 123
Concentration (mM) 104
Concentration avg, analyzed data 56
Concentration CV, analyzed data 56
Concentration SD, analyzed data 56
concentration values, setting 87
confirming
biosensors to be analyzed (figure) 98
reference well is subtracted from the sample wells (figure) 92
connecting Octet instrument to computer 12
Connections to Clients box 182
constant
deleting 178
constants
administrator 176
changing 178
creating 177
viewing 178
Constants Ttab 176
contacting ForteBio technical support 9
contiguous biosensors, selecting (figure) 83
conventions, used in this guide 9
Copy Table to Clipboard, data export option 135
Copy to Clipboard menu 89
copying
binding chart 105
sample plate map 89

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sensor tray map 89

creating
kinetic Settings_DataAnalysis.ini file 111
kinetic Settings_TableInfo.xml file 112
kinetic Settings_WellInfo.xml file 112
new constant 177
new project 175
new user account 168
new user group 173
Settings_DataAnalysis.ini file 58
creating new 175
curve display, customizing 100
curve fitting analysis 72
curve fitting kinetics analysis options
Fitting-Global (Full) 106
Fitting-Local 106
Model 106
Rmax Unlinked option for Global Fitting 107
Steps to Analyze 106
Curve fitting, kinetic analysis type 105
custom reports 134
customizing
binding curve appearance 45, 78
curve display 100
graph appearance 45, 78
graph display 100
Cycle, kinetic analysis result 124

D
data
excluding from analysis 108
Data Acquisition, icon 6
data analysis session, using 36, 68

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Data Analysis User Guide (menu) 16

Data Analysis, icon 6
data color, setting by category 130
data export options
Copy Table to Clipboard 135
described 134
Export Fitting Results 135
Export Table to .csv File 135
in the Analysis window (figure) 134
listed 135
Data Options, view option 118
data processing 98
applying reference subtraction 91
reference subtraction methods 92
Data Selection tab (figure) 36
Data Selection window
displaying experiment summary information (figure) 70
editing sample information, kinetics (figure) 75
editing sample information, quantitative (figure) 40
example (figure) 58
loading an experiment, kinetics (figure) 69
loading an experiment, quantitative (figure) 37
opening an experiment (figure) 37
viewing options (table) 43
data viewing options 121
data, exporting 64
DataAcquisition-CFR-7_0_0_x.exe 150
Define Custom Colors menu 129
defining
replicate groups 51
Delete Constant menu 178
deleting
constant 178

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project 176
user account 170
user group 174
determining
binding rate 56
sample concentration 36
digital signatures, verifying 27
dilution factor 55
discontiguous biosensors, selecting (figure) 83
display options, viewing shortcut menu of 125
displaying
graphics in custom groupings 119
graphs organized into groups 116
license information 16
Octet System Data Acquisition software properties 16
selected step data from a kinetic assay (figure) 85
Dissoc. Loc., kinetic analysis result 123
Dissociation only, analysis option 106
Dissociation, analysis option 107
Do not use alerts, threshold value 61
Dose Response–4PL (Default 48
Dose Response–4PL (Weighted Y) 48
Dose Response–4PL (Weighted Y2) 48
Dose Response–5PL (Default 48
Dose Response–5PL (Unweighted) 48
Dose Response–5PL (Weighted Y) 48
Double Reference
reference subtraction method (figure) 95
reference subtraction method, described 94

E
Edit Group window 174
Edit Legends viewing options

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basic kinetics analysis 77

quantitative analysis 44
Edit Sample Information dialog box (figure) 51
editing
a search 128
alert threshold value 62
experiments 73
processing parameters in the Results window (figure) 41
processing parameters, kinetics 75
processing parameters, quantitative 40
standard concentration information 40, 74
well information 40, 74
Electrical hazard symbol 9
electronic signature of method (.fmf) and data (.frd) files 27
ending
user session 33
equilibrium response 72
equilibrium state data, analyzing 111
estimate of the goodness of the curve fit 124
Event Log (figure) 179
events
listed in the Audit Trail 30
sorting in Audit Trail 30
tracking 179
viewing 30, 179
Events tab 178
Exclude Wells
display option 125
menu 39
Exclude Wells for Analysis menu 91
excluding
data from analysis 108
sample from subsequent analyses 55

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samples from analysis, kinetics (figure) 74

samples from analysis, quantitative 39
samples from analysis, quantitative (figure) 39
wells from analysis, described 91
wells from the biosensor table (figure) 108
Exit (menu) 14
experiment method file 68
experiment method file, loading 14
experiment summary options 136
experiment, quantitation, described 36
experiments
closing all
kinetics 79
quantitative 46
closing one
kinetics 79
quantitative 46
editing 73
loading for analysis, kinetics 68
loading for analysis, quantitative 36
Export Aligned Step (.csv files) menu 83
Export button 135
Export File, Report Point Analysis feature 103
Export Fitting Results, data export option 135
Export Table to .csv File, data export option 135
exporting raw data 83

F
FBServer.exe file 183
file type, changing 28
Fit Curves! button 108
Fitting view
grouped option (figure) 119

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individual option (figure) 117

stacked option (figure) 116
Fitting view and Residual view, stacked option (figure) 116
Fitting view options
Add to Table 117
Auto Scale 116
Full Scale 116
Grouped 116
Individual 116
listed 116
Options 116
Refresh 116
Remove All 117
Report Points 116
Stacked 116
Time (sec) 116
Use__Point Average 117
Y Axis Scaling 116
Fitting-Global (Full) options
By Color 107
By Sensor 107
Fitting-Global (Full), curve fitting kinetics analysis option 106
Fitting-Local options
Full 106
Partial 106
Fitting-Local, curve fitting kinetics analysis option 106
Flip Data viewing options
quantitative analsys 43, 77
flip, analyzed data 55
ForteBio GxP Server 7.0.exe 156
ForteBio GxP Server desktop icon 167
ForteBio GxP Server module, accessing 180
ForteBio GxP Server module, installing 156

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ForteBio technical support, contacting 9

ForteBio Web Site (menu) 16
Full R2, kinetic analysis result 124
Full Scale, Fitting view option 116
Full X2, kinetic analysis result 124
Full, analysis option 106
Fuse symbol 9

G
generating a report 135
graph display, customizing 100
Graph Options, view option 118
Graph Size in Pixels, view option 118
graph, customizing appearance 45, 78
graphical formats 132
graphics, displaying in custom groupings 119
Group Graphs By, view option 118
group settings
viewing 174
Group Type, analyzed data 56
Group View—sensograms sorted by known concentration (figure) 121
Grouped View options
Additional Graphs 118
Data Options 118
Graph Options 118
Graph Size in Pixels 118
Groups Graphs By 118
Legend by 118
Grouped View Options dialog box (figure) 118
Grouped, Fitting view option 116
grouping
results for viewing 118
grouping data

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by color 107
by sensor 107
GxP Server module
accessing 180
restarting 183
testing 182

H
Heat/hot symbol 9
Heterogeneous Ligand model 106

I
icons
Data Acquisition 6
Data Analysis 6
Ignore error in files option 71
Ignore errors in files when loading viewing option
basic kinetics analysis 77
quantitative analysis 43
Include Excluded Traces, Advanced Search option 127
Include Wells
display option 125
menu 39
Include, kinetic analysis result 123
including
sample in subsequent analyses 55
samples from analysis 39
index, analyzed data 55
Index, kinetic analysis result 123
Individual Standards 121
Individual, Fitting view option 116
information, analyzed data 55

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Initial Slope equation 49

Input times after beginning of Association Step 103
installing
Data Acquisition 7.0 21 CFR Part 11 software 150
Data Analysis 21 7.0 CFR Part 11 software 153
ForteBio GxP Server 156
ForteBio GxP Server module 156
interstep correction feature 97
interstep correction features
Align to Baseline 97
Align to Dissociation 97
Invert Selection, display option 126
Iso-Affinity graph
described 133
X and Y axis (figure) 133

K
KD (M), kinetic analysis result 123
kdis (1/s), kinetic analysis result 123
kdis Error, kinetic analysis result 123, 124
kinetc Settings_TableInfo.xml file, creating 112
kinetcs analysis mode 88
kinetic analysis results
Assoc. (Sample) Loc. 123
Baseline Loc. 123
Color 123
Conc (nM). 123
Cycle 124
Dissoc. Loc. 123
Full R2 124
Full X2 124
Include 123
Index 123

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KD (M) 123
kdis (1/s) 123
kdis Error 123, 124
km 124
km error 124
kobs (1/s) 124
kon (1/Ms) 123
kon Error 123
Loading Well Location 124
Report point #1-10 124
Req/Rmax (%) 124
Response 123
Rmax 123
Rmax Error 123
Sample ID. 123
Sensor Info 123
Sensor Location 123
Sensor Type 123
SSG KD 124
table, listed 123
kinetic analysis types
Curve fitting 105
Steady state analysis 105
kinetic assay, displaying selected step (figure) 85
kinetic constants 72
kinetic data
analyzing 106
processing 88
kinetic Settings_DataAnalysis.ini file, creating 111
kinetic Settings_WellInfo.xml file, creating 112
kinetics analysis results 115
Kinetics Batch Mode (menu) 14
Kinetics Batch Mode—Quantitation Batch Mode dialog box (figure) 113

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kinetics experiment
starting 68
km error, kinetic analysis result 124
km, kinetic analysis result 124
Known Conc. 56
kobs (1/s), kinetic analysis result 124
kon (1/Ms), kinetic analysis result 123
kon Error, kinetic analysis result 123

L
launching Octet System Data Acquisition software 12
Legend by, view option 118
license information, displaying 16
ligand biosensor location 103
ligand biosensors, defined 88
Linear Point to Point 48
list options 180
Load Standards menu 49
Loaded Data Directory Tree 37
Loaded Data directory tree 68
loading
experiment for analysis 68
experiment method file 14
Loading Well Location, kinetic analysis result 124
location of the biosensor in the sensor tray map 123
location of the sample well used during the load step of the experiment 124
Lock Application menu 15
locking a user session 32
Logoff menu 15
Lot Number, analyzed data 56
Low concentration threshold, processing parameters
basic kinetics 75
Quantitative Analysis 40

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M
Mass Transport 106
mass transport rate constant 124
matching search term with searchable text 126
mathematical model, generates fitted view 106
Max Residual, threshold value 61
measure of the goodness of curve fitting 124
menu bar, Octet System Data Acquisition software 13
menu commands, listed 14
method files 68
method files, generated 27
Min Sample r2, threshold value 61
Model options
1 to 1 106
1 to 2 Bivalent Analyte Model 106
2 to 1 (HL) Model 106
Mass Transport 106
Model, curve fitting kinetics analysis option 106
modified parameters, saving
basic kinetic analysis 75
quantitative analysis 41
molar concentration of the sample used in the association step 123
multiple kinetic data sets, processing 111
multiple quantitation data sets, processing 57

N
New Group window 173
New Project window 175
new software for 21 CFR Part 11 (new feature) 7
new software for ForteBio GxP Server module (new feature) 7
non-equivalent surface capacity 107
non-specific binding of sample 93

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number of biosensor regeneration cycles 124

numbered order of the curves processed 123

O
observed binding rate 124
Octet instrument labels 9
Octet instrument to computer, connecting 12
Octet RED system
warm-up 12
Octet System Data Acquisition software
launching 12
main toolbar 13
Octet System Data Acquisition User Guide, opening online version 16
Octet system, described 6
opening
Kinetics Batch Mode 14
online Octet System Data Acquisition User Guide 16
Quantitation Batch Mode 14
web browser 16
opening binding curve chart in a separate window
kinetics 78
quantitative 45
Operator, Advanced Search option 126
Options (menu) 14
options for viewing results 99
Options, Fitting view option 116
Order Columns, display option 126
Overlay Standards 121

P
Parallel Reference Sensors
reference subtraction method

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described 93
reference subtraction method (figure) 94
Partial, analysis option 106
plate number 55
preparing samples for quantitation or kinetics experiments 6
printing binding chart 105
Process Data! button 98
processed data
in the sensor summary view (figure) 102
saving 104
processing
data 98
processing kinetic data 88
processing options, listed 137
processing parameters
basic kinetics
Low concentration threshold 75
Read time 75
Zero concentration threshold 75
editing 40, 75
editing in the Results window (figure) 41
Quantitative Analysis
Low concentration threshold 40
Read time 40
Zero concentration threshold 40
Processing window
described 88
Raw Data view selected (figure) 81
Raw Data view, displaying data from a single selected biosensor (figure) 82
Raw Data view, quantitating a selected step (figure) 84
project 175
deleting 176
project administration 175

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project settings
changing 176
viewing 176
Projects tab 175
projects, changing during a user session 31
properties, for Octet System software, displaying 16

Q
Quantatition Batch Mode, opening 14
Quantitate Selected Step menu 83
quantitating raw data
for a selected step (figure) 84
from a selected step, described 83
Quantitation Batch Mode dialog box (figure) 60
Quantitation Batch Mode menu 60
quantitation experiment, described 36
quantitation results report, saving 65
quantitation results reports, exporting data 64
Quantitation window, displaying selected step data from a kinetic assay (figure) 85

R
R equilibrium
binding rate equation 49
steady state kinetics analysis option 110
r2 (COD), analyzed data 56
r2 of the curve fit 56
rate of association 123
rate of dissociation 123
ratio of Req to Rmax 124
raw data
exporting 64, 83
saving 64

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viewing 80
Raw Data view 80
raw Sensograms grouped by known concentration example (figure) 120
Read time, processing parameters
basic kinetics 75
Quantitative Analysis 40
reference biosensors
defined 88
specifying 89
reference buffer wells, defined 88
Reference subtraction average of methods (figure) 47
Reference Subtraction Average of viewing option
basic kinetics analysis 77
quantitative analysis 43
reference subtraction methods
Average Reference Sensors 95
Double Reference 94
Double Reference (figure) 95
for data processing 92
Parallel Reference Sensor (figure) 94
Parallel Reference Sensors 93
Reference Wells 92
Reference Wells (figure) 93
Reference Subtraction option 43
Reference Subtraction options
basic kinetics analysis
All 77
Column 77
Row 77
quantitative analysis
All 43
Column 43
Row 43

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reference subtraction, applying during data processing 91

Reference Well
menu 90
Reference Wells
reference subtraction method 92
reference subtraction method (figure) 93
reference wells
confirming subtraction (figure) 92
specifying (figure) 91
specifying, described 90
Refresh, Fitting view option 116
Remove All, Fitting view option 117
Remove Level, Advanced Search option 127
removing all kinetics experiments from processing (figure) 80
Replicate Group
adding from the Sample Plate Table 54
replicate group, analyzed data 55
Replicate Groups
assigning in the Sample Plate Map 52
assigning in the Sample Plate Table 54
Replicate Groups displayed
in Sample Plate Map (figure) 53
in Sample Plate Table (figure) 53
replicate groups, defining 51
replicates 49
report data types
analysis options, kinetics analysis results (figure) 141
Experiment Summary options (figure) 137
Processing options
processed data (figure) 139
raw data and aligned data (figure) 138
Report Point analysis (figure) 140
sensor tray and sample tray information (figure) 138

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Report point #1-10, kinetic analysis result 124

Report Point Analysis features
Apply 103
Apply All 103
Export File 103
in the Analysis window 102
Input times after beginning of Association Step 103
listed 103
Use 20 point average 103
Report Point Analysis table 102
Report Points
Add to Table 117
Fitting view option 116
Remove All 117
Time (sec) 116
Use__Point Average 117
Report Points view
described 102
processed results (figure) 103
Report Selection form (figure) 136
reports, generating 135
reports, saving 14
Req/Rmax(%), kinetic analysis result 124
Residual view
individual option (figure) 117
stacked option (figure) 116
Residual, analyzed data 56
response calculated from the time window entered in the Steady State Analysis section 123
response maximum 107
Response, kinetic analysis result 123
Response, steady state kinetics analysis option 110
Restart Server console (figure) 184
Restart Server desktop icon (figure) 183

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restarting
ForteBio GxP Server module 183
results table 56
Results table, searching contents 127
Results window for a quantitation experiment (figure) 50
Results window showing standards sample alerts (figure) 62
Results window with calculated binding rates (figure) 88
results, color-coding by category 129
results, grouping 118
results, viewing options 99
returning to kinetics analysis mode 88
returning to the originally configured ForteBio GxP Server module settings 182
Rmax
defined 107
kinetic analysis result 123
Rmax Error, kinetic analysis result 123
Rmax unlinked 107
Rmax Unlinked option for Global Fitting, curve fitting kinetics analysis option 107
running
batch kinetics analysis 113
batch quantitative analysis 60

S
Sample Alert 63
Sample Alert, threshold value 61
sample alerts, applying 63
sample concentration
computed from the standard curve 56
defined 104
sample concentrations, determining 36
sample designations
changing
kinetics analysis 73

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changing, quantatitative analysis 38

sample ID 103
sample ID entered during assay setup 123
Sample ID, analyzed data 56
Sample ID, kinetic analysis result 123
sample location 103
sample plate map
copying 89
defined 56
sample tray map, using 89
sample type
changing 85
sample well location in the sample plate 123
Save All Method Files (menu) 14
Save Analysis Settings menu 59
Save Data Analysis Parameters button—Analysis window (figure) 110
Save Report menu 135
Save Results options 104
saving
all reports 14
analysis results
for each biosensor to a separate text file 135
for selected biosensors to system clipboard 135
analysis settings 57
binding data
for each biosensor to a separate text file 135
for selected biosensors to system clipboard 135
processed data 104
processing parameters 104
quantitation results report 65
raw data 64, 104
results 104
results options 104

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results table to a .csv file 135

standards data 57
Savitzky-Golay filtering 98
scatter plot 132
Search all but keep current selection (implies OR), Advanced Search option 127
Search All, Advanced Search option 127
Search only current selection (implies AND), Advanced Search option 127
search result, defined 126
search term for a single level 126
search, editing a 128
searching
contents of the Results table 127
searching contents of the results table 125
Security menu 15
Security menu commands, listed 15
Select All Rows, display option 126
selecting
adjacent rows, for viewing data 122
analysis results for viewing in the Fitting view and Residual view (figure) 122
biosensors for analysis (figure) 72
biosensors for the analysis 71
biosensors in the Processing window (figure) 89
biosensors to be analyzed (figure) 98
contiguous and discontiguous biosensors in the Sensor location list (figure) 83
experiments and run the batch analysis 113
experiments and running the batch analysis 60
experiments for batch analysis (figure) 61
non-adjacent rows or wells
kinetics analysis 76
quantitative analysis 41
non-adjacent rows, for viewing data 122
sample wells or rows to display in the binding curve graph
basic kinetic analysis (figure) 76

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quantitative analysis (figure) 42

sensors 89
server location 20
standard curve equation 48
Sensor Info, kinetic analysis result 123
sensor location 103
Sensor Location, kinetic analysis result 123
sensor summaries (figure) 139
Sensor Summary view
defined 101
displayed (figure) 102
features 101
sensor tray map
copying 89
using 89
Sensor Tray tab 71
Sensor Type, analyzed data 56
Sensor Type, kinetic analysis result 123
sensor, analyzed data 55
Sensors to be Analyzed box 91
sensors, selecting 89
Server Administration menu 15
server location, selecting 20
Set Color By Group, display option 125
Set Color By, display option 125
Set Color menu 128
Set Color, display option 125
Set Well Data dialog box (figure) 52
setting
concentration values (figure) 87
data color by category 130
setting up administrator account, administrator account, setting up 159
Settings_DataAnalysis.ini file, creating 58

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Settings_DataAnalysis.xml file 111

Settings_WellInfo.xml 111
Settings_WellInfo.xml file 60
shortcut menu of display options, viewing 125
Show All Steps Aligned alignment option 83
Show All Traces viewing options
basic kinetics analsys 77
quantitative analsys 43
Size Columns by Data, display option 126
Size Columns by Title, display option 125
sorting
analysis results by any category 131
results table entries in ascending order 56
results table entries in descending order 56
sorting Audit Trail events 30
specifying
analysis settings 47
reference biosensors 89
reference wells (figure) 91
reference wells, described 90
SSG KD, kinetic analysis result 124
Stacked, Fitting view option 116
standard concentration information, editing 40
standard curve equation 87
standard curve equation, selecing 48
standard error of Rmax 123
standard error of the mass transport rate constant 124
standard error of the rate of association 123
standard error of the rate of dissociation 123
standards alert, applying 62
standards data, saving 57
starting
basic kinetics experiment 68

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user session 24
steady state analysis 72
Steady State Analysis graph
described 134
displayed (figure) 134
Steady state analysis, kinetic analysis type 105
steady state kinetics analysis options 110
Average from 111
R equilibrium 110
Response 110
Steps to Analyze, curve fitting kinetics analysis option 106
Subtraction check box 91
sum of squared deviations 124
symbols
electrical hazard 9
fuse 9
heat/hot 9
system artifacts 93
system drift 92

T
Table Information, batch mode option, kinetics 114
technical support, contacting 9
testing
ForteBio GxP Server module 182
threshold values
Do not use alerts 61
Max Residual 61
Min Sample r2 61
Sample Alert 61
Time (sec), Fitting view option 116
Time 1 (sec) 104
Time 2 (sec) 104

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time range
of the association step data to analyze 107
of the dissociation step data to analyze 107
time, at which the first binding measurement is acquired 104
toggling sample analysis in the Results window 39, 73
Treat Empty Cells as Match, Advanced Search option 127
types of report data included by the Processing options (figure) 141
types of report data including by Processing options (figure) 139

U
Unweighted) 48
Use ”Included” Traces Only check box 118
Use 20 point average 103
Use Entire Step Times, analysis option 107
Use one for all folders, batch mode option
kinetics 113
quantitation 60
Use standards from loaded file check box 49
Use the one in each folder, batch mode option
kinetics 113
quantitative 60
Use the original data folder, batch mode option 60
Use this folder, batch mode option 60
Use__Point Average, Fitting view option 117
user account
deleting 170
user account password, changing 171
user account settings
changing 170
viewing 170
user account, creating 168
user group
creating new 173

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deleting 174
user password, changing 32
user session
ending 33
locking 32
starting 24
user session, changing projects during 31
user-defined annotation that describes the sample 124
user-selected results, changing color (figure) 129
user-specified
ligand biosensor information 103
notes, about the wells 56
standard concentration 56
using
data analysis session 36
sample tray map 89
sensor tray map 89

V
Value, Advanced Search option 126
Verify Digital Signature dialog box (figure) 27
Verify Document menu 15
verifying digital signatures 27
View Audit Trail menu 15
viewing
Audit Trail 29
binding curves
basic kinetic analysis 76
quantitative analysis 41
constants 178
events for a specific project or computer 30
events for a specific user account, project or computer 179
group settings 174

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project settings 176

raw data 80
results, options 99
shortcut menu of display options 125
specific biosensor data 122
user account settings 170
viewing options
basic kinetics analysis
Align X 77
Edit Legends 77
Ignore errors in files when loading 77
in the Data Selection window (table) 77
Reference Subtraction Average of 77
Show All Traces 77
in the Data Selection window (table) 43
quantitative analysis
Align X 43
Edit Legends 44
Flip Data 43, 77
Ignore errors in files when loading 43
in the Data Selection window (table) 43
Reference Subtraction Average of 43
Show All Traces 43
selecting data 121

W
warm-up time 12
web browser, opening 16
Weighted Y2) 48
well concentration 55
well designation 56
Well Information, analyzed data 56
Well Information, batch mode option

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kinetics 113
quantitation 60
well information, editing 40
well location
in the sample plate 56
in the sample plate or reagent plate 123
wells, excluding from analysis 91
Window of Interest (From Start of Step), analysis option 107

X
X-Y graph
described 132
displayed (figure) 132
X-Y graph (figure) 132

Y
Y Axis Scaling
Auto Scale 116
Fitting view option 116
Full Scale 116
Y axis, aligning (figure) 97

Z
Zero concentration threshold, processing parameters
basic kinetics 75
Quantitative Analysis 40

Octet System Data Analysis Software User Guide