Sartorius Stedim Bio PAT SIMCA Ver 13 Manual

User Guide to
Version 13
powered by UMETRICS
85037-541-19 Vers. 06 | 2013

powered by Umetrics
¤ 1992-2009 MKS Umetrics AB, all rights reserved

The software, which includes information contained in any databases, described in this document is
furnished under license agreement or nondisclosure agreement and may be used or copied only in
accordance with the terms of the agreement. It is against the law to copy the software except as
specifically allowed in the license or nondisclosure agreement.
Umetrics patents and trade marks:

OPLS/O2PLS®, SWE-9802229-6, USA-6754543,
OSC®, SWE-0000563-7, USA-6853923
PLS-TREE®, Pending
SEQUENTIAL MODELING, USA-7523384
DESIGN SPACE, USA-8086327
MODDE®, RED - MUP®, VALUE FROM DATA®, OPLS®, O2PLS®, O2-PLS®, OPLS-DA®,
O2PLS-DA™
PLS-TREE™, S-PLOT™, EZinfo®, SBOL®, FABSTAT®, BATCH FINGERPRINT®, SIMCA®.
Sartorius trade marks:

BioPAT®
In this document BioPAT® MODDE, BioPAT® SIMCA and BioPAT® SIMCA-online can be
synonymously read as MODDE ®, SIMCA ® and SIMCA-online ®.
Screenshots may vary from the actual view, depending on the version you are using.
For questions, comments and remarks please send an e-mail to:
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Phone +49.551.308.0
FAX +49.551.308.3289
www.sartorius-stedim.com
Welcome
Welcome to BioPAT® SIMCA-online 13.1.

This is your guide to BioPAT® SIMCA-online and its capabilities. It explains how to use the BioPAT®
SIMCA-online Client and Server and how to configure your system.
This user guide does not include multivariate data analysis or how to use the offline software BioPAT®
SIMCA. For such information, see the book Multi- and Megavariate Data Analysis (ISBN-13: 978-91-
973730-2-9) and the BioPAT® SIMCA user guide.
Content
The user guide is parted into 12 chapters and an appendix.
1. Installation and configuration - Installation and configuration instructions for the BioPAT®
SIMCA-online Client and Server.
2. Introduction to multivariate modeling - Introduction to BioPAT® SIMCA-online and
multivariate modeling and monitoring.
3. Using BioPAT® SIMCA-online - Overview of the steps involved in using BioPAT® SIMCA-
online.
4. File - Description of all commands available on the File tab in the Client.
5. Quick Access Toolbar - Description of feature leaving favorite commands quickly accessible.
6. Home - Description of the most commonly used commands.
7. View - Description of the commands available on the View tab.
8. Tools - Description of plot and list tools.
9. Help - Short description of the Help menu.
10. Project administration - Instructions for the administrator on how to load SIMCA projects and
configure hem for BioPAT® SIMCA-online.
11. Customizing plots - Description of features to customize plots.
12. Maintenance - Description of how to maintain the BioPAT® SIMCA-online system.
Appendix A: General information - Information about error codes, endpoints, interfaces, terminology
and feature changes, and tab and menu reference syntax.
Table of Contents
Installation and configuration 1
Introduction.................................................................................................................... 1
License information ....................................................................................................... 1
What is in the package ................................................................................................... 1
System requirements ...................................................................................................... 1
Installation ..................................................................................................................... 1
DBMaker and DBView ................................................................................................. 4
Configuration of the Server ........................................................................................... 4
Background ......................................................................................................................... 4
Opening the SIMCA-online Server options dialog.............................................................. 4
Paths and directories ........................................................................................................... 4
Parameters to initiate communication with SimApi ............................................................ 5
Miscellaneous settings ........................................................................................................ 5
Introduction to multivariate modeling 7

Introduction to SIMCA-online ....................................................................................... 7
Process data analysis ...................................................................................................... 7
Batch evolution modeling in SIMCA ............................................................................ 8
Reorganization of the 3D table before import ..................................................................... 8
Modeling ............................................................................................................................. 9
Batches with several phases .............................................................................................. 10
Result variables ................................................................................................................. 10
Calculating limits to build control charts .......................................................................... 10
Batch level modeling in SIMCA.................................................................................. 11
Why batch level modeling................................................................................................. 11
Modeling batch level ......................................................................................................... 11
Hierarchical batch models ................................................................................................. 11
The SIMCA approach .................................................................................................. 11
Process data analysis ......................................................................................................... 11
Batch evolution analysis.................................................................................................... 12
Batch level analysis ........................................................................................................... 12
Using SIMCA-online 13

Introduction.................................................................................................................. 13
Preparation ........................................................................................................................ 13
Preparation by the administrator .................................................................................. 13
Server icons ....................................................................................................................... 14
SIMCA-online physical overview ............................................................................... 14
SIMCA-online environment ........................................................................................ 15
Monitoring the model .................................................................................................. 16
To do by the user ............................................................................................................... 16
Plots for monitoring the new continuous data ................................................................... 16
Plots for monitoring the evolution of new batches ............................................................ 17
Plots for predicting results or classifying new batches ...................................................... 18
Differences compared with SIMCA and unsupported features ................................... 18
Terminology ................................................................................................................ 18
Client window .............................................................................................................. 19
Communication with the external system .................................................................... 20
Connection to external database ........................................................................................ 20
SIMCA-online Server handles communication ................................................................. 21
SIMCA-online database stores all data ............................................................................. 21
File 23
Introduction.................................................................................................................. 23
Log in/Log out ............................................................................................................. 23
Configuring network settings ............................................................................................ 24
Open............................................................................................................................. 24
Open workspace........................................................................................................... 25
Print, Print preview, Print setup ................................................................................... 25
Extract .......................................................................................................................... 25
Extract Data - Select Tags ................................................................................................. 25
Extract Data - Select Type ................................................................................................ 26
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BioPAT ® SIMCA-online User Guide
Extract Data - Select Destination ...................................................................................... 26

Administration ............................................................................................................. 27
Project administration ....................................................................................................... 27
Specifying tag out limits ................................................................................................... 27
User administration ........................................................................................................... 28
Server audit trail ................................................................................................................ 31
Server log file .................................................................................................................... 33
Close ............................................................................................................................ 33
SIMCA-online options................................................................................................. 34
SIMCA-online Options General tab .................................................................................. 34
Plot options ....................................................................................................................... 35
Exit SIMCA-online ...................................................................................................... 39
Quick Access Toolbar 41
Introduction.................................................................................................................. 41
Customizing Quick Access Toolbar ............................................................................ 41
Removing buttons from Quick Access Toolbar ................................................................ 41
Adding buttons to Quick Access Toolbar.......................................................................... 41
Moving the Quick Access Toolbar .................................................................................... 41
Minimizing the ribbon ................................................................................................. 42
Home 43
Introduction.................................................................................................................. 43
Batch ............................................................................................................................ 43
Batch evolution plots......................................................................................................... 43
Batch level plots ................................................................................................................ 46
Properties group ................................................................................................................ 48
Regular......................................................................................................................... 53
Worm plot ......................................................................................................................... 53
Scores ................................................................................................................................ 53
DModX ............................................................................................................................. 54
PModX .............................................................................................................................. 54
Hotelling's T2Range .......................................................................................................... 54
Y Predicted........................................................................................................................ 55
Custom plots ..................................................................................................................... 55
Empty instead of plot ........................................................................................................ 55
Properties group ................................................................................................................ 55
View 59
Introduction.................................................................................................................. 59
Data list ........................................................................................................................ 59
Show or hide ................................................................................................................ 59
Project info ........................................................................................................................ 60
Log .................................................................................................................................... 60
Status bar........................................................................................................................... 60
Overview ........................................................................................................................... 60
Plot Details ........................................................................................................................ 62
Tabs ................................................................................................................................... 62
Full screen ......................................................................................................................... 62
Open............................................................................................................................. 62
Configuration audit trail .................................................................................................... 62
Client log........................................................................................................................... 64
Report................................................................................................................................ 65
Window group ............................................................................................................. 68
Save workspace ................................................................................................................. 69
Tools 71
Introduction.................................................................................................................. 71
Select - Marking tool ................................................................................................... 71
Deselecting/unmarking points ........................................................................................... 71
Displaying properties of the item ...................................................................................... 71
Creating contribution plots ................................................................................................ 71
Zoom ............................................................................................................................ 71
Zooming out................................................................................................................. 72
Sort............................................................................................................................... 72
Drill down .................................................................................................................... 72
Contribution plots for batch projects ................................................................................. 72
Contribution plots for regular projects .............................................................................. 79
ii
Table Of Contents
Adding notes ................................................................................................................ 82

Editing notes ................................................................................................................ 83
Deleting notes .............................................................................................................. 83
Create list ..................................................................................................................... 83
Save as ......................................................................................................................... 83
Help 85
Introduction.................................................................................................................. 85
Umetrics on the Web ................................................................................................... 85
Support......................................................................................................................... 85
Project administration 87
Introduction.................................................................................................................. 87
Organize....................................................................................................................... 87
Access rights ................................................................................................................ 88
Add configuration for batch project ............................................................................. 88
Import configuration for the project .................................................................................. 89
Batch node ........................................................................................................................ 89
Batch evolution ................................................................................................................. 90
Batch level ...................................................................................................................... 100
Export the configuration to file ....................................................................................... 104
Add configuration for regular project ........................................................................ 104
Import configuration for the project ................................................................................ 105
Model page...................................................................................................................... 106
Time ranges ..................................................................................................................... 107
Tags ................................................................................................................................. 107
Variable aliases ............................................................................................................... 108
Target values ................................................................................................................... 108
Alarms ............................................................................................................................. 109
Write back ....................................................................................................................... 110
Export the configuration to file ....................................................................................... 112
Starting and stopping the execution ........................................................................... 112
Removing and restoring project configurations ......................................................... 113
Manage data ............................................................................................................... 113
Configuration - view and modify .................................................................................... 113
Repredicting historical batches ....................................................................................... 113
Repredicting data for continuous .................................................................................... 114
Deleting historical batches .............................................................................................. 114
Workspaces ................................................................................................................ 115
Save workspace ............................................................................................................... 115
Delete workspace ............................................................................................................ 115
Customizing plots 117

Introduction................................................................................................................ 117
Mini-toolbar ............................................................................................................... 117
Mini-toolbar for marked items ........................................................................................ 117
Mini-toolbar for formatting ............................................................................................. 118
Mini-toolbar for subplot .................................................................................................. 118
Managing the mini-toolbar .............................................................................................. 118
Show/Hide plot items................................................................................................. 119
Format plot................................................................................................................. 119
Axis ................................................................................................................................. 119
Gridlines.......................................................................................................................... 123
Background ..................................................................................................................... 123
Titles ............................................................................................................................... 124
Legend ............................................................................................................................ 125
Limits and Regions ......................................................................................................... 126
Label Style ...................................................................................................................... 126
Error Bars ........................................................................................................................ 127
Styles ............................................................................................................................... 128
Multiplots ........................................................................................................................ 131
Plot templates............................................................................................................. 131
Saving plot formatting template ...................................................................................... 132
Switching plot formatting templates ............................................................................... 132
Restoring to default plot formatting ................................................................................ 132
Maintenance 133
Introduction................................................................................................................ 133
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BioPAT ® SIMCA-online User Guide
Backup ....................................................................................................................... 133

Restore ....................................................................................................................... 133
Resource management ............................................................................................... 133
What to do? ..................................................................................................................... 133
Appendix A: General information 135

License reminder ....................................................................................................... 135
Error codes when starting the service ........................................................................ 135
Windows error codes....................................................................................................... 135
Service-specific error codes ............................................................................................ 135
Server endpoints ........................................................................................................ 136
SIMCA-online interfaces ........................................................................................... 136
Terminology changes................................................................................................. 136
Discontinued features ................................................................................................ 137
Menu and tab reference syntax .................................................................................. 138
Glossary 139
Index 145
iv
Installation and configuration
Introduction
This chapter describes the installation of SIMCA-online and configuration of the BioPAT® SIMCA-
online Server.
Content
x License information
x What is in the package
x System requirements
x Installation
x DBMaker and DBView
x Configuration of the Server
License information
Before installing the BioPAT® SIMCA-online products, carefully read the license agreement included
with your BioPAT® SIMCA-online software package.
In case you do not fully accept the terms of the license agreement, you should immediately return all parts
of the package to your local supplier.
What is in the package

Your BioPAT® SIMCA-online package holds the following:
x Installation files.
x License file.
x SimApi dll-file when applicable.
x BioPAT® SIMCA-online User Guide (.pdf).
x Readme file.
System requirements
The recommended system requirements for the BioPAT® SIMCA-online Server are:
x Pentium based computer (PC) with a 2 GHz or faster processor.
x 2 GB RAM or more.
x 20 GB available hard disk space.
x Color graphics display with at least 1024x768 resolution.
x Microsoft Windows XP SP3, Windows Vista SP2, Windows 7 SP1, Windows 8, Windows Server
2003 SP2, Windows Server 2003 R2 SP2, Windows Server 2008 SP2, or Windows Server 2008
R2 SP1.
x The x64 version of BioPAT® SIMCA-online requires a 64-bit operating system, a 64-bit SimApi
DLL and a BioPAT® SIMCA-online license that permits it to run on 64-bit Windows.
x SIMCA 13.
Installation
Before installing, verify that the system requirements apply to your system.
1
®
BioPAT SIMCA-online User Guide
Then follow the steps below.

Action Illustration
1. Find the .msi-file, right-click it and select
Open.
2. The first page displays the details of the

software to install and whether it is 32 or 64-
bit.
In the welcome page, click Next.
3. Read the license agreement. To accept,

select the I accept the terms in the
License Agreement check box and click
Next.
4. In the Custom Setup page, if you want to

install the Client only on this computer, click
Next and go to 6.
To change from the default location, click
Browse and change the destination folder.
5. To install the Server (or Client) on this

computer:
1. Click the icon.
2. Select Will be installed on local hard
drive or Entire feature will be
installed on local hard drive.
3. Click Next.
2
Action Illustration
6. The setup program is ready for installation.
Click Install.
While installing a progress bar is displayed.
7. When the installation is completed, click

Finish.
8. When installing the server, the BioPAT®

SIMCA-online Server Options dialog
opens up.
For details about this dialog, see the
Configuration of the Server section later in
this chapter.
9. To be able to run the BioPAT® SIMCA-online Server, import the license-file named
SIMCAonline.$$$, delivered to you, by clicking the Import button in the Paths and directories page
in BioPAT® SIMCA-online Server Options dialog (see illustration in step 8), and browsing for the
file.
10. To use a different SimApi DLL-file than the default, follow the instructions that came with the DLL, or
in some cases simply copy the DLL from the BioPAT® SIMCA-online package to the folder of the
server executable. Then switch SimApi in the SimApi page in the BioPAT® SIMCA-online Server
Options dialog.
Installed programs
Find the program icons, under Start | All Programs | Umetrics | BioPAT® SIMCA-online 13.
x Tools: DBMaker and DBView.
x BioPAT® SIMCA-online Client.
x BioPAT® SIMCA-online Server Options.
x BioPAT® SIMCA-online Server Monitor. Server Monitor opens an icon in the notification
area in the taskbar. Right-click the icon and from the menu start the Server, launch the client,
Server Options and Help.
x BioPAT® SIMCA-online Help.
3
®
DBMaker and DBView

DBMaker and DBView are installed in the same directory as the server.
DBMaker is a small application that can be used to provide data from text or excel-files for testing
purposes. It also supports Write Back. DBMaker is not intended (nor works) for real-world usage on
production data.
The SimApi DLL for DBMaker is installed automatically on the server on a new installation of BioPAT®
SIMCA-online.
No further instructions for running DBMaker and DBView are available in this help.
Configuration of the Server

Background
The BioPAT® SIMCA-online Server handles the data transfer between the BioPAT® SIMCA-online
Client, the BioPAT® SIMCA-online internal database (SDB), and the process database (PDB) and when
present, the historical database (HDB). The last two databases are located in the external system, and the
communication with the BioPAT® SIMCA-online Server is done through the SimApi DLL.
The Server performs all the project management, computation and execution of the multivariate models.
The external system handles the PDB and HDB and runs the I/O drivers connected to the process.
Opening the BioPAT® SIMCA-online Server options dialog

Before starting the Server the first time it has to be configured. The configuration is normally done during
the installation.
To configure, right-click the BioPAT® SIMCA-online Server Monitor icon located in the notification
area in the taskbar and select Server options. Alternatively open the BioPAT® SIMCA-online Server
Options from the Start menu. In the BioPAT® SIMCA-online Server Options dialog the following tabs
are available: Paths and directories, SimApi, and Miscellaneous. Details about these tabs follow.
Paths and directories

Use the Paths and directories page to:
x Enter or change the path to the BioPAT® SIMCA-online database directory, where the copy of
the SIMCA project file is placed when adding a project.
x Click Register to request a license file, if one was not provided with the installation package.
x Import the license file by clicking Import.
x After import, view the details of the imported license file.
x View the current directory for saving the internal configuration file (the file that stores all settings
in Server Options). Clicking the Reset button removes the current server configuration file and
re-configures the server. Note that this affects ALL tabs.
4
Parameters to initiate communication with SimApi

The SimApi DLL for some external databases may need some parameters in order to communicate with
BioPAT® SIMCA-online.
These parameters should be specified in the documentation provided by the supplier of the SimApi DLL.
Select the SimApi in the list and click the Change button to view and modify the settings.
Note that some SimApi DLL may have other means of modifying the settings for the DLL.
Installing SimApi DLLs - interfaces to external systems
See the BioPAT® SIMCA-online interfaces section in Appendix A: General Information to learn how
to install SimApi DLL on your server for use with various external systems from which you want to obtain
data.
Miscellaneous settings
Click an item to display the description and customize the settings as needed.
Log file
Under Log file, change or view, the maximum log file size in kB and minimum severity level to be logged
by selecting Log level. Available log levels are: Debug, Information (default), Warning, Error, or
Critical. Critical is the lowest level and logs the least information. Debug is the highest level and logs the
most information. Each level is cumulative of the lower levels.
x Debug logs in great detail everything that happens including all communication and actual values
read from the external database. Using this setting may slow down the system but provides the
necessary details to know what the server is doing at all times. Recommended by Umetrics online
support as soon as you want to identify problems.
x Information logs login, logout, project added, batch started etc.
x Warning logs incidents, such as a SimApi function being time consuming or a client being
unexpectedly disconnected.
x Error logs errors in the server, such as failing to predict or failing to read from external database.
x Critical logs severe problems that will prohibit you from continuing to run BioPAT® SIMCA-
online, such as project crash or out of memory.
5
®
Server input files

Under Server input files, view or change the path to the Plugin directory.
Active Directory
Under Active Directory settings, specify the authentication server to use if you want your users in
BioPAT® SIMCA-online to be authenticated by servers in your Windows network.
x Host name - Host name of the Active Directory server to connect to.
x Port number - The Active Directory port number to connect to. By default different depending
on whether the SSL encryption is selected or not. If cleared the default port is 389 and if
selected 636.
x SSL encryption - The Active Directory session will use SSL encryption when selected.
x Base - The Active Directory base for creating the users part of the distinguished name.
x Group filter - The Active Directory security group used for filtering the users in the Base.
Server startup and timeout
Under Server startup and timeout, view or change:
x The Listener port - listener TCP port used by the server. Default is 2371.
x The SimApi startup timeout (min). Default 60 minutes.
x The Project DB timeout (min). Default 60 minutes.
x The SimApi call timeout (s). Default is 2 seconds.
x Sound to be played after finished startup and close down. Default is not to play a sound.
x Resume execution is default selected. The execution of models starts automatically if they were
executing when the server was shut down.
x Connection test interval (s) is how often the server should test the client connection. Default is
300 seconds. If the server does not get a response from a client, it will be disconnected and has to
connect and login again to the server.
x Preload projects selected means that project configurations are loaded immediately when the
server starts. When cleared project configurations are loaded when needed, that is when the
execution is turned on or the project configuration is opened.
Processor load
In Processor load you can set a limit in Load warning percent for when to write in the log that “The
processor is working at a high load”. Default is 80%.
Averaging time (s) defines the time in seconds between checking the load. Set a time between 1 - 3600
seconds, default is 60.
6
Introduction to multivariate modeling
Introduction to BioPAT® SIMCA-online

Sartorius-Stedim offline product SIMCA is used to create SIMCA projects (.usp files), and fit models for
your data. SIMCA has no connections to real-time data, and a project can only be used by one person on
one computer at a time.
In BioPAT® SIMCA-online you import the .usp file created in SIMCA, and configure it to be able to
predict new data coming from an external data source. Multiple BioPAT® SIMCA-online clients on many
computers can connect to the same server and monitor how the process behaves.
BioPAT® SIMCA-online is a client-server solution where the server performs all the work, and the client
is used to display the results and to manage the project configurations on the server.
BioPAT® SIMCA-online combines the SIMCA-4000 and SIMCA-Batch On-Line products into one,
handling both continuous and batch data in the same product.
Regular projects, created in SIMCA, imported in BioPAT® SIMCA-online should contain process data.
This means that the model describes the optimal state of the process and the data used for prediction in
BioPAT® SIMCA-online are not logically divided in parts but continuous over time.
Batch projects, created in SIMCA, are built from data that are limited to batches. These batches represent
the optimal state of the batch process and the data used for prediction is logically divided in batches.
For more information about multivariate modeling than found in this chapter, see the SIMCA user guide
and Sartorius-Stedim extensive training catalog.
Content
This chapter describes:
x Process data analysis
x Batch evolution modeling in BioPAT® SIMCA
x Batch level modeling in BioPAT® SIMCA
x The BioPAT® SIMCA approach
Process data analysis

Any investigation of a real process or system is based on measurements (data). Fifty years ago,
measurement devices were expensive and few, and consequently the amount of data, measured on
processes, was limited; a temperature and a pressure here, a flow rate there. The monitoring, display, and
analysis of these few data was relatively simple, and a few running charts of the data provided all available
information about the state of the process.
Today, batteries of sensors and on-line instruments are providing data from all parts of the process in
various forms, often at very short intervals. The masses of data are fed into computers, re-computed into
moving averages (per minute, hourly, daily, weekly, etc.) and displayed and stored.
This change from a situation with few, fairly infrequent measurements, to many, almost continuously
measured variables has still not affected the manner in which process data are treated, potentially leading
to large losses of information. With appropriate multivariate analytical methods, such as Principal
Components (PC) and Projection to Latent Structures (PLS) modeling in the BioPAT® SIMCA software,
the masses of process data can provide easy to grasp graphical information about the state of the process,
and relations between important sets of process variables. These multivariate methods make efficient use
of all pertinent data, with little loss of information.
7
®
Batch evolution modeling in BioPAT® SIMCA

With batch processes, K variables are measured on N batches at regular time intervals. This gives a J x K
matrix for each batch (J time points (X) times K variables). Consequently, a set of N normal batches gives
a 3 way matrix of dimension (N x J x K).
Time
One batch
Batches
Variables
Figure 1. Three-way table of historical data of, for example, N batches with J time points, and K variables. Often the
batches have different length (not shown in the picture) and may also be divided in phases.
This section describes modeling of the batch evolution in BioPAT® SIMCA.
Reorganization of the 3D table before import

To be able to import the dataset, the 3-way data table has to be unfolded to preserve the direction of the K
variables (see figure 2). The resulting matrix has nobs = N x J observations (rows) and K columns. Hence
this matrix, X, has the individual observation as a unit, and not the whole batches.
X Y
Variables
B1 Time
Recorded variables:
Ethanol,
B2 Temperature,
Molasses flow,
Batches B3 NH3 feed,
Air flow,
… Tank level,
pH.
Bn
Figure 2. The three-way matrix of figure 1 unfolded along the batch direction to give a two-way matrix with N x J
rows and K columns. Each row has the data (xijk) from a single batch observation (batch i, time j, variable k).
Reorganization with sub-batches

Sub-batches are present when a batch is divided into multiple parts and individually run through the same
equipment (unit).
Each sub-batch has to be defined as a phase in BioPAT® SIMCA. Therefore, in the case where you have
sub-batches, each sub-batch needs a unique phase id at import.
Sub-batches assumed identical
When the sub-batches should be identical and interchangeable, the phase models must be made identical.
There are a number of ways to avoid that variation in the sub-batches in the workset leads to different
phase models. Currently, none of the ways are easily executed in BioPAT® SIMCA. With small datasets,
all sub-batch data can be copied and included in all phase models of that batch. This is illustrated in Figure
3.
8
3a 3b
Figure 3a and b. 3a displays the three-way matrix unfolded along the batch direction with sub-batches. 3b displays the
permutation to certify that variations in sub-batches will not lead to different models.
The following table explains figure 3:
Original Modified Modification Specifically in Figure 3
term term explanation
Data Permutated The sub- In Figure 3a there are three batches
Data batches have and two phases. Phase 1 has three
been sub-batches while Phase 2 has no
permutated so sub-batches.
that each sub- Now, let's look at Batch 1: in Figure
batch is 3b, through the permutation, each
included in each sub-batch (Sub-batch 1, 2, and 3) has
phase once. been combined with each phase ID
(Phase 1:1, 1:2, 1:3) leading to three
unique batch IDs (Batch 1:1, 1:2, 1:3).
For Phase 2, no permutation is
necessary, therefore Phase 2 is only
present in the first batch (Batch x:1).
Real Modified Each sub-batch In Figure 3a, there are two phases,
Phase ID Phase ID has to be Phase 1 and Phase 2. In Figure 3b
imported as a there are four phases Phase 1:1, 1:2,
phase, and 1:3, and 2, so that all sub-batches
therefore needs have unique phase IDs.
a unique phase
ID.
Real Modified After To let each sub-batch be included in

Batch ID Batch ID permutation of each phase once, this demands 3x3
the sub- unique batch IDs.
batches, the
Batch IDs must
be unique
before importing
in BioPAT®
SIMCA.
Modeling
When importing the dataset in BioPAT® SIMCA and no maturity (y-variable) has been specified, an
index y-variable starting at 0 is constructed representing the "relative local batch time".
The default model, after completed import in BioPAT® SIMCA, is a PLS model for the centered and
scaled X and "relative local batch time", y if no other y was specified. If a maturity variable, recorded
relative to the start of each batch, was defined as y, that variable will be used as y by default.
9
®
When fitting the batch PLS model, “Autofit” will stop when 85% of X has been explained, but will also
give at least 3 components (not exceeding N/2). This is necessary in order to ensure that much of the X-
matrix is "explained". This results in an (nobs x A) score matrix, T, plus PLS weight and loading matrices
W and P (of dimensions K x A).
Batches with different length
Alignment of data is done differently depending on configuration of the time/ maturity variables. For
batches of similar length the impact is small. The default y configuration aligns the batch length by cutting
the longer batches at median (or average) batch length. Batches that are shorter than the median (or
average) batch are filled up with the last value up to the median batch length.
The used length in average batch is the shorter of the median batch length and the average batch length
rounded down.
Batches with several phases

When batches have several phases, observations are organized in classes, one class for every phase.
Separate PLS class models are fitted for every phase.
Result variables
The score matrix T is a good summary of X, and PLS focuses this summary on y (local time). Hence the
first column of t (t1) will contain strong contributions of those X-variables that vary monotonically with y,
i.e., either increase or decrease with time. The second component (t2) is an aggregate mainly of those
variables that change “quadratically” with time, i.e., first go up to a maximum, and then decrease, or first
go down, and then up. The third component catches the variables having a cubic behavior, etc.
The value of "local time" predicted by the PLS model (with the number of components determined by
cross-validation ), ypred, is very suitable as a "maturity index" that can be used to indicate how far the batch
has evolved, if it is ready for termination, etc.
Calculating limits to build control charts

To monitor the evolution of new batches, one calculates the typical evolution trace of a normal batch. This
is in short done as follows:
1. Reorganization: First the scores of the batch evolution model are chopped up and reorganized so
that the scores of one batch form one row vector (t1 followed by t2, followed by t3, etc.) in a
matrix ST. This matrix has N rows (one per batch) and A x J (AJ) columns from the A score
vectors and the J "time points" per batch. When batches have phases, the scores of each batch are
collected from the different PLS phase models.
t1
Average Avg + 3 sd
Batch
StDev Avg – 3 sd
Time
Figure 4. The score values for each batch are arranged as row vectors below each other, giving
an N x (J x A) matrix, ST. Above we see only the first part of ST corresponding to the 1.st
component (t1). From this matrix one calculates the averages and standard deviations (SD:s) of
the matrix columns, and then control intervals as the averages r 3 SD.
2. Calculating tolerance limits for control charts: Now the matrix ST is used to derive minimum
and maximum tolerated values at each time point (j) of tj1, tj2, tj3…, tjA from the column averages
and standard deviations of ST, as indicated in figure 4. In MSPC one would typically use
tolerance intervals of the average r 3 SD at each time point. Hence, we now have for each score
vector an average trace with upper and lower tolerance limits.
The corresponding actions are done when building the control charts for Predicted Y, DModX, and
Hotelling's T2Range.
10
Batch level modeling in BioPAT® SIMCA

Why batch level modeling
Batch level modeling may be advantageous in the case that the measurement of Y is laborious and time
consuming, and one wishes to make an initial fast quality assessment before the real Y is available. This is
often the case in biotechnological production, where extensive analysis and testing of the final products is
made before acceptance (or rejection).
The batch level model also allows the full interpretation of the batch data. Groups of batches may be
discovered, outliers will be found, etc. Critical time periods will be indicated by "periods" of large
weights, loadings, and VIP values. Analogously, important factors in the initial conditions will stand out.
The "ideal" evolutionary trace corresponding to a desirable Y-profile can be deduced, and so on.
Modeling batch level

The objective of batch level modeling is to make a model of the whole batch in order to understand how Y
is influenced by the combination of batch conditions and the batch evolution. This model will be based on
(when available) the batch conditions (Z), the evolution trace matrix ST, and when applicable the
properties and quality of the completed batch (Y), as shown in figure 5. The resulting model is used to
predict Y for new batches from their batch conditions and their evolution traces.
In the case that Y-values do not exist, the X-matrix can still be used to develop a PC model. This is the
same type of model as the X-part of PLS in the batch evolution model. The difference is that in PCA the
scores (T) are calculated to give an optimal summary of X, while in PLS this optimality is somewhat
relaxed to make T scores better predictors of Y. The PC model can then be used to classify new batches as
normal (similar = well fitting to the PC model) or non-normal (far from the model).
X Y
Back Scores t1, t2, t3 Final

ground or Results
Data original variables Data
Z ST
Figure 5. The data for batch level modeling. Each row has the data from one batch. The left matrix contains data
describing initial conditions. The middle matrix contains the unfolded scores (or original variables or summary
variables) which describe the evolution of each batch. The optional right matrix (Y) contains the responses, the
properties of the complete batch such as yield, purity, activity, etc.
Hierarchical batch models

With batch level datasets you can fit hierarchical models of the whole batch, for different levels of
completion:
x One model for each phase and component in the batch evolution model.
x One model for each phase.
x Sequential models covering parts of the batch completion, for example for 25%, 50%, 75% and
100% completion.
These models can predict the final batch quality or classify the batch, before the batch is finished.
The BioPAT® SIMCA approach

The BioPAT® SIMCA project is the basis of the multivariate monitoring, describing the behavior of the
process for good batches/optimal process behavior. In BioPAT® SIMCA-online, you load projects,
previously developed in BioPAT® SIMCA.
For batch data the BioPAT® SIMCA approach includes analysis and monitoring of the batch data in two
steps (levels): batch evolution analysis and batch level analysis.
Process data analysis

The model consists of optimal process behavior data.
The steps in modeling and monitoring:
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1. Modeling the data in BioPAT® SIMCA.

2. Predicting results of new process data in BioPAT® SIMCA-online.
x Predictions: As the process is evolving, the data for monitoring are derived from
applying the model to data from the external system and making predictions.
x Plots: Worm, Score, Hotelling’s T2Range, and DModX are displayed with limits. For
PLS models, predicted Y plots are displayed.
x Classify or predict result: You can classify the data as good or bad or predict their final
quality.
x Contribution plots: If the values are outside the limits, contribution plots indicate
which variables together are related to the deviations.
Batch evolution analysis

A batch evolution model, BEM, has many observations per batch.
Modeling the batch evolution consists of:
1. Modeling the evolution of batches in the BEM in BioPAT® SIMCA.
2. Monitoring the evolution of new batches in BioPAT® SIMCA-online.
x Predictions: The batch evolution data of new batches, as they are evolving in real
time, are projected on to the model plane or model planes (for batches with phases) of
the batch evolution model developed off-line. This results in predicted scores
(coordinates in the model plane), together with the distance between the new points and
the model plane, DModX, and predicted maturity.
x Control charts: The predictions are plotted on control charts with limits calculated from
the workset. These charts indicate whether the new batches are evolving normally or not.
x Contribution plots: If the values are outside the normal ranges, contribution plots based
on the x-values of the average batch or the residuals (DModX) indicate which variables
together are related to the deviations.
Batch level analysis

A batch level model, BLM, has one observation per batch.
Modeling the whole batches consists of:
1. Modeling the whole batches in the BLM in BioPAT® SIMCA.
2. Predicting results of whole new batches in BioPAT® SIMCA-online.
x Predictions: As the batch is evolving, the data for monitoring the whole batch are
derived from unfolding and aligning scores, original variables (raw data), or statistics for
the original variables of the batch evolution data (raw data statistics).
x Plots: Score, Hotelling’s T2Range, and DModX for the whole batch are displayed with
limits. For PLS models, predicted Y plots are displayed.
x Classify or predict result: You can classify the finished batches as good or bad or
predict their final quality. If you have made hierarchical models of the batch level at
different percentage of completion, you can classify or predict the final quality of new
batches as they are evolving when they reach the percent of completion of the models.
x Contribution plots: If the values are outside the limits, contribution plots indicate
which variables together are related to the deviations.
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Using BioPAT® SIMCA-online
Introduction
BioPAT® SIMCA-online version 13 is an execution module for models built with SIMCA version 13, in
this user guide referred to as SIMCA. BioPAT® SIMCA-online is designed as a client-server application.
BioPAT® SIMCA-online reads data from the process (referred to as external system or external database)
at regular intervals through supported interfaces.
BioPAT® SIMCA-online executes multivariate models, thereby projecting new data, in real time, on to
the model plane. This results in coordinates in the model plane, together with the distance between the new
points and the model plane, DModX. The real time display of these results allow for an efficient
monitoring of online process or batch data.
Preparation
Before using BioPAT® SIMCA-online you must develop a project in SIMCA. This is done by building
the models, for batch project batch evolution models and optionally batch level models, from data
representing good process or batch behavior.
For details on creating projects, see the SIMCA user guide.
Content
x Preparation by the administrator
x BioPAT® SIMCA-online physical overview
x BioPAT® SIMCA-online environment
x Monitoring the model
x Differences compared with SIMCA and unsupported features
x Terminology
x Client window
x Communication with the external system
Preparation by the administrator

Before monitoring projects in the Client the following steps have to be conducted by the administrator.
Step Action How More
1. Starting the BioPAT® SIMCA-online Server
BioPAT® Monitor is found on the start menu,
SIMCA-online or if it is already running in the
Server Monitor. notification area in the taskbar
2. Starting the Right-click the BioPAT® SIMCA- If the message displayed is

BioPAT® "Service start failed", see the
online Server Monitor icon , in
SIMCA-online section Error codes when
the taskbar notification area, and
Server. starting the service in
select Start BioPAT® SIMCA-
Appendix A: General
online Server. A User Account
information.
control prompt may be displayed
asking for administrative prilieges to
start the server. The icon then
changes into the BioPAT® SIMCA-
online - Running icon , and a
message is displayed stating
"Service start succeeded".
3. Starting the Start the Client from the start menu.

BioPAT® This can be done on the server
SIMCA-online
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Step Action How More

Client. computer or on another computer.
4. Logging on as Select the server to connect to. Use For more, see the Log in/Log
administrator. the button next to the server to set out section in the File chapter.
up servers to connect to. Log on as The Connect dialog is opened
Administrator with its password automatically when starting
(default is empty). Click Connect. the client.
5. Adding a Add the SIMCA project and For more, see the Add
project. configure it from File | configuration for batch
Administration | Project project and Add
administration. configuration for regular
project sections in the
Project administration
chapter.
6. Starting the In the Project Administration For more, see the Starting
execution. dialog, select the configuration and and stopping the execution
of the project section in the
click the play button.
chapter.
7. Adding users Add user accounts and their For more, see the User
privileges by clicking File | administration section.
Administration | User
administration.
Now the project can be opened from any client connected to the server.
Note: To stop the server, right-click the BioPAT® SIMCA-online Server Monitor icon , in the taskbar
notification area, and click Stop server.
Server icons
The Server Monitor icon shows the state of the BioPAT® SIMCA-online service.
Icon Description
The server is not running. Icon before starting and after stopping the server.
The server is pending. Icon during starting and stopping of the server.
The server is running and regularly checks for new data.
The server has not been installed.
®
BioPAT SIMCA-online physical overview
The BioPAT® SIMCA-online Server is running on a specific server computer. The server has copies of
the SIMCA projects, and executes those, making multivariate predictions, for new data that the server
obtains from a Data Source. To get the data from the data source the server uses a SimApi DLL. The
server also stores all predictions locally on disk on the server.
Clients connect to the server to view how the process evolves, by interacting with plots, etc.
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Using BioPAT ® SIMCA-online
Figure 7. The BioPAT® SIMCA-online implementation.
®
BioPAT SIMCA-online environment
This subsection describes the different pieces of software that make up the BioPAT® SIMCA-online
environment:
Client – the software you use to view the execution of the models, the predictions, any alarms and such.
Also used by administrators to import projects and set up configurations on the server. The client is the
software that contains the user interface to interact with the server.
There can be many clients running at the same time on different computers, all connecting to the same
server.
Server – there is one server running on one computer which uses data from its data source to predict new
results using the BioPAT® SIMCA-models. These results can then be displayed in the Client. You never
use the BioPAT® SIMCA-online Server directly, you always work with it through the client software or
any of the utilities listed below, for managing the server:
Server Monitor – a small icon and menu in the notification area in the taskbar of the server computer. It
can be used to start and stop the server and provides quick access to the server log. The server monitor is
optional, and doesn’t need to run, because the server is running as a service which can be started or
stopped as other windows services.
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Server Options – a small application that is run on the computer running the server. It is used to make
settings controlling how the server runs; what folders to use, what SimApi's to use, and to specify the
license file.
In addition there are two programs that are used for demo or testing purposes:
DBMaker –a demo data source, see the DBMaker and DBView subsection.
DBView –a small tool to view data from DBMaker and from the internal databases of the BioPAT®
SIMCA-online Server, see the DBMaker and DBView subsection.
Monitoring the model

BioPAT® SIMCA-online handles both regular (continuous) and batch projects in the same product.
However, since batch projects need particular settings, as in SIMCA offline, they also need special
configuration when they are added to BioPAT® SIMCA-online. Furthermore, different plots and different
functionality are available in the ribbon interface for regular and batch projects. For more about this, see
the Add configuration for batch project and Add configuration for regular project sections in the
Project administration chapter and the Batch and Regular sections in the Home chapter.
Once the administrator has started the execution, the model starts to execute, i.e. read data in real time, at
the specified interval, and computes the scores. For batch projects the new data is first used for predictions
using the batch evolution model and then, as data becomes available, for the batch level models.
To do by the user
The table lists what the user needs to do in order to monitor a project.
Step Action For more
1. Open a configuration known to the Server, in For more, see the Open
the Client. section in the File chapter.
2. Open plots. The plots are available on the For more see the Home
Home tab. chapter.
3. Open contribution plots. When time points or For more, see the Drill
batch points fall outside the limits, create down section in the Tools
contribution plots. chapter.
Plots for monitoring the new continuous data

The new data points, read from the external system, are inserted into the model, giving predicted values. If
you only want predictions under certain conditions, use Prediction conditions to define when to predict.
Worm plot
The predicted values of the score line plot displaying t1 vs. t2, where the most recently predicted
observation is displayed with a symbol that is larger than the other symbols. This plot also displays the
Hotelling's ellipse, and workset observations, indicating whether the process is evolving normally or not.
DModX, Hotelling's T2Range, and Y Predicted trend plots
The predicted values of DModX, Hotelling's T2Range, and YPred values are plotted in trend plots. These
plots indicate whether the process is evolving normally or not.
Contribution plot
If values are found outside the normal ranges, contribution plots based on the x-values of the average or
the residuals (DModX) indicate which variables together are related to the deviations.
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Plots for monitoring the evolution of new batches

The batch evolution data for new batches, read from the external system, are inserted into the PLS model,
giving predicted values. When batches have phases, the phase condition has to be defined for the correct
PLS phase model to be used to predict the t scores of that phase.
Score, DModX and Hotelling's T2Range control charts
The predicted values of the score t1 to ta, DModX, and Hotelling's T2Range values are plotted in control
charts, with limits derived as described previously (trace level). These charts indicate whether the batches
are evolving normally or not.
Predicted maturity control chart
The PLS model also gives predicted values of y (local time or maturity variable). Plotting ypred vs. yobs
gives an indication of whether the batches are developing too quickly (over-mature, ypred > yobs) or too
slowly (under-mature, ypred < yobs).
Contribution plot
If values are found outside the normal ranges, contribution plots based on the x-values of the average
batch or the residuals (DModX) indicate which variables together are related to the deviations.
Batch evolution plots background
Batch evolution plots display a plot grid with many plots in the same window when there are units, phases,
or sub-batches in the model. When the process includes several units, the plots for each unit are displayed
beneath each other when the Layout selected is Units, see figure 6.
Figure 6. This is an example of how BioPAT® SIMCA-online presents units, unit groups, and sub-batches in a batch
evolution plot.
In the table, the notation in Figure 6 is explained.
Unit Units Sub-batches Phases
Group
G G1, G2, G3. One sub-batch. In BioPAT® SIMCA- Phase 1
online, each unit has to have at and 2.
least one sub-batch. Therefore the
single sub-batch in this unit is
denoted Sub-batch 1 in the figure.
D D1 and D2. Sub-batch 1 and 2. Phase 3

and 4.
C One unit. In One sub-batch. In BioPAT® SIMCA- Phase 5.

BioPAT® SIMCA- online, each unit has to have at
online, each unit least one sub-batch. Therefore the
group has at least single sub-batch in this unit is
one unit. The single denoted Sub-batch 1 in the figure.
unit in this unit
group is denoted C1
in the figure.
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Plots for predicting results or classifying new batches

The batch evolution data must first be read by the server, and fitted to the PLS model to get the predicted
scores. These scores get appended row wise to the batch conditions (Z) if present, once the batch (or with
hierarchical models the model) is completed in batch evolution. The batch level PLS, PCA, and
hierarchical models are used to predict quality of the final batch (Y), or classify the batch as normal good
batch or bad batch. These plots are found in the Batch level plots group.
Score scatter plot
The Hotelling’s T2 ellipse, by default at the 99% confidence interval, is drawn around the batch points in
the batch level score scatter plot. When a batch is outside the ellipse limit, this indicates that this batch has
some variables that are larger or smaller than the average batch.
DModX
When a batch is projected onto the model, BioPAT® SIMCA-online computes also the distance of that
batch to the model, DModX. DModX is proportional to the RSD (Residual Standard Deviation) of that
batch in the X space. Larger DModX than the warning level indicates something unusual about the batch
(different from the others) that was not captured by the model.
Hotelling's T2Range
For a given observation (batch) the Hotelling’s T2Range is a combination of all the scores (t) for the
selected components. Hence this plot is a summary of all the batch variables for the selected components
and displays how far away from the center (target) the batch is along the PC model hyper plane. When a
batch is outside the critical limit, this indicates that for this batch, the data vector has some variables that
are larger or smaller than the average batch.
Predicted Y plots
The Predicted Y plots are displayed with confidence limits. Unusually large or small values in comparison
with the others are interesting to display in a contribution plot.
Contribution plot
Contribution plots of points found outside the limits illustrate which variables differ between the marked
point and average. When opening a contribution plot for a variable that is a score, the batch evolution
contribution plot can be created by double-clicking the score variable.
Differences compared with SIMCA and unsupported features

BioPAT® SIMCA-online, unlike SIMCA, typically receives data from the data source observation by
observation (whereas SIMCA already has ALL data available when modeling). This fact, and that some
functionality of SIMCA isn’t meaningful in an online scenario, means that there are number of features
available in SIMCA that are unsupported in BioPAT® SIMCA-online or just executed differently. See the
list below for details.
x A batch that meets the conditions for conditional exclude is available in BioPAT® SIMCA-
online but with missing instead of values.
x Generated variables that take into account future observations are not supported.
x Generated variables that take into account results from other models are not supported.
x Generated variables that lag variables.
x Date/Time variables are read as missing.
x Hotelling's T2Range is unavailable for OPLS models.
Some features previously available in SIMCA-Batch On-Line or SIMCA-4000 are unavailable in
BioPAT® SIMCA-online. See the Discontinued features subsection for details.
Terminology
This section describes the basic terminology of BioPAT® SIMCA-online.
Project – a Sartorius-Stedim SIMCA Project (USP-file), containing the models you want to execute on the
BioPAT® SIMCA-online server. Projects are uploaded (automatically copied) to the server from the client
and then configured. For batch projects only one batch evolution model, BEM, may be present in the
imported project. The single BEM may include several phases and the project may also include several
batch level models, BLM.
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Configuration – or project configuration, is a specific instance of a SIMCA project configured to take

data from certain tags in your data source, have specific alarms, and a range of other settings. A
configuration can be executing the model for new data from the data source or it can be stopped (i.e. not
reading new data). You can have multiple configurations for the same BioPAT® SIMCA project. The
configurations, for one particular SIMCA project, are managed independently from each other and can
have totally different settings. The only thing they share is the same BioPAT® SIMCA project.
Batch node – a node in the data source that contains the names, start and stop times for batches.
Execution – used for continuous configurations (non batch data) defined as follows: An execution starts
when play-button for that configuration is clicked, and ends when the stop-button is clicked. Thus if the
configuration’s execution is started and stopped multiple times, it will result in multiple executions in the
Overview window in the BioPAT® SIMCA-online client. The execution is also stopped when the server
is stopped.
Repredict data – the process of reading data from the data source again, and then repredicting it. This
effectively first deletes data, then reads it again, and then finally predicts it again.
Delete predicted data – the process of deleting already predicted data for a configuration.
Alarms – alarms are triggered when certain user specified conditions are met. Alarms are used so that the
user can be aware that something might have gone wrong with the process. Alarms can be displayed in
plots as symbols, in the Plot Details window, the Report window, and in the Overview window which
shows the global alarm state per model if alarms have been triggered. Only one alarm of a specific type
(for a certain condition) can be triggered at the same time. Triggered (active) alarms can be reset
(acknowledged). This means that the same alarm can be triggered again. These multivariate alarms are
specified during the project configuration. Multivariate alarms use special trigger rules configured for
them, which means that they are not triggered immediately when data is outside a limit, but rather after a
certain number of observations outside the limits.
Univariate Alarms on x- or y-variables can be specified in the Target values page in the project
configuration. They are always triggered at first value outside the defined limits.
Client window
The BioPAT® SIMCA-online client consists of the ribbon tabs, the Quick Access Toolbar, the help menu,
tabs, and dockable windows. Plots and lists are displayed in the unused area between ribbon, dockable
windows and status bar in client window.
Note: You can have several clients open on the same computer.
The table describes the parts of the client window.

Item Description Default More info
position
Ribbon Displays the tabs File, Top of the screen. File, Home,
Home, View, and Tools View, Tools, and
and the Help menu. Help chapters.
Quick By default displays a few Toolbar positioned Quick Access

Access commonly used commands at the top above the Toolbar chapter.
Toolbar for easy access. Can be tabs.
customized to hold your
favorite commands.
Tabs Tabs to switch between Bottom of the Tabs section in

open project configurations. screen. the View
chapter.
Dockable The dockable windows are: The Overview and Show or hide
windows Project info, Log, Plot Details section in the
Overview, and Plot windows are placed View chapter.
Details. to the right, while
the others are
placed to the left.
<empty The area where the plots Center of the Plots sections in
area> are displayed. screen. the Home
chapter.
Figure: Explanation Client window for batch.
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Figure: Explanation Client window for continuous.
Communication with the external system

In order to monitor BioPAT® SIMCA project data, BioPAT® SIMCA-online requires access to an
external system, i.e. the process data, to read data and make predictions using the models. Process data
comes from an interface (software) accessing the process databases on-line in real time.
Connection to external database

BioPAT® SIMCA-online connects to the external database via a SimApi, and samples the data in real
time.
The process system, which we refer to as the external system, has a process database, PDB and often an
historical database, HDB.
x The PDB is similar to a process buffer and contains only the current values of all the process
variables.
x The HDB stores the historical values of the process variables.
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BioPAT® SIMCA-online Server handles communication

The BioPAT® SIMCA-online Server handles the communication with the external system - process PDB
and HDB. The BioPAT® SIMCA-online Server samples the PDB at regular intervals, the phase execution
time, to extract the current value of the batch process.
BioPAT® SIMCA-online database stores all data

The batch data read by BioPAT® SIMCA-online as well as result variables computed by the model
(output variables such as scores, distance to the model, predicted values, etc.), of both batch evolution
models and batch level models, are stored in the BioPAT® SIMCA-online database, SDB (internal
database created by BioPAT® SIMCA-online). The location of this database is specified in the BioPAT®
SIMCA-online Server Options application on the first tab.
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File
Introduction
On File tab the following is available:
x Log in/Log out and connect to server.
x Open project configurations and workspaces
x Print, Print preview, Print setup
x Extract data from the external database
x Administration with Project administration, Out limits, User administration, and Server log.
x About BioPAT® SIMCA-online to display program and license information, version number,
and copyright information.
x Close to close the current configuration.
x BioPAT® SIMCA-online options to view and change settings.
x Exit BioPAT® SIMCA-online to close the client.
x Recent files list with both recently opened project configurations and workspaces, with the
possibility to pin favorites.
Log in/Log out

When you start the Client the first time, it will automatically try to connect to a Server running on the
same computer (the default Server). If the Server is running on a different computer, or the Server has not
been started, the connection fails. You must then use File | Log in to connect to a Server.
To manually connect to a server, click File | Log in. In the Log in dialog, click the arrow to see the list of
servers known to the Client (i.e. you have specified their network settings). Default is the Server you were
connected to last. Select one and click Connect.
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Note: If the client is connected to a server and you want to switch servers, click File | Log out and then
connect to the new server. Clicking Log out closes all open projects and disconnects from the current
Server.
See the Configuring network settings subsection next on how to add, remove, and configure the Server.
Configuring network settings

In the Configure Network Settings dialog you can add new servers, remove servers, and configure the
server port.
Note: The server port has to be the same in the client as in the server configuration. The default server
port is 2371.
To open the Configure Network Settings dialog, click File | Log in, then in the Log in dialog click the
browse-button to the right of the Server box.
Adding new server
To add a new server, click the Add button. The Server Settings dialog opens with the default settings.
Removing server
To remove a server, mark it and click the Remove button.
Editing the server configuration
To change the configuration of a server, mark the server and click the Edit button. Use the Server
Settings dialog to change the description, port number, and network address of the marked server.
New server available
When done adding, removing or configuring the servers, click OK in the Configure Network Settings
dialog. In the Log in dialog, note that the names of all servers, including any new server, are displayed in
the list of configured servers. Select the desired server and click Connect.
Note: The client port is dynamic and set by the operating system.
Open
To open a project configuration or workspace known to the Server, click File | Open. In this dialog all
project configurations and saved workspaces are listed.
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File
For a project configuration to be known to the Server, it must have been added and configured in the
Project Administration in the Client.
For a workspace to be available, it must have been saved, either in the Project Administration dialog or
by clicking Save workspace in the Windows group on the View tab.
To close a project click File | Close, or right-click the project tab and click Close.
Open workspace
To open a workspace, in the Workspaces section, mark the workspace and click Open.
The Workspaces section is positioned below the Configurations section.
Print, Print preview, Print setup

The standard print utilities are available by clicking File | Print.
Print preview is unavailable for lists.
Extract
To extract data to spreadsheet or file, click File | Extract and click through the wizard.
The only difference between extracting to spreadsheet and extracting to file is the last page where you
select how to extract. When extracting to file you can select to save as (*.dif) DIF Files (*.dif), Text Files
(*.txt), or Matlab 4.x Files (*.mat).
There are three pages in the wizard:
x Extract Data - Select Tags
x Extract Data - Select Type
x Extract Data - Select Destination
Extract Data - Select Tags

The external database holds only raw data, no calculated vectors. On the first page you must select which
tags you want to extract data from in the external database:
1. Under Data Sources all data sources currently known are listed.
Mark a node to view which tags are available.
2. The tags of the selected node appear under Tags to the right of the data sources.
Mark the wanted tags and click the down-arrow.
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3. The selected tags are displayed in the Selected Tags list.
Extract Data - Select Type

To select which type of data and the time period including interval:
Data
Description Settings
type
Current The last observation received
No settings.
data from the external database.
From date/time and To date/time.

All observations (batch
Sampling interval also has to be
Historical evolution or regular) with a
specified and should be the same as the
data time stamp within the range
database. Number of points is updated
specified.
automatically using the other settings.
Batch condition data with a From date/time and To date/time.

Batch
time stamp within the range Number of points is updated
data
specified. automatically using the other settings.
Then use the Time section to specify the range and sampling interval.
Hint1: To change the date, click the arrow to display the calendar.
Hint2: To change the time, start with the To time, position the cursor on the hours or minutes or seconds,
and use the up and down arrows in the dialog or on your keyboard.
Extract Data - Select Destination

Select whether to extract to list or file by:
x Leaving Extract to list.
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File
x Clicking Extract to file and specifying the file to extract to. The path to the file is then displayed
in the Path field.
Administration
Use Administration to access:
x Project administration
x Out limits
x User administration
x Server audit trail
x Server log
Note: If you cannot see the Server log in the backstage menu, click the small arrow at the bottom of the
backstage.
In the Project Administration dialog the projects and configurations currently known to the Server are
listed and an administrator with configure management permissions can do the following:
1. Add, configure, and remove batch project configurations and regular project configurations.
2. Start and stop the execution of a project configuration.
3. Repredict and delete predicted data.
4. Save workspaces.
For details, see the Project administration chapter.
Specifying tag out limits

Out limits for tags define the valid range of a tag. Outside these limits, the value of a tag is set to missing.
To add an out limit, click the Add tag-button and select the tag to add the out limit for (see below).
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Then enter the out limit values.
Managing the out limits

To exclude a tag and replace it with missing, select Yes in the Exclude column for that row. This can be
useful when an instrument is malfunctioning.
To include the tag again, select No in the Exclude-column.
Turn on or off the usage of out limits by selecting/clearing the Use out limits check box.
Note: Out limits are global and independent of configurations and take action before the data reaches the
clients.
Shortcut menu
You can copy, paste, and delete the values in the spreadsheet using the shortcut menu.
Right-clicking and clicking Print prints the spreadsheet.
User administration
For a BioPAT® SIMCA-online client to connect to the BioPAT® SIMCA-online Server, the user must
first log in to the server using a user name and password.
The Server keeps lists of users allowed to log on to the server, groups of users, and their rights to perform
various tasks. By default the account Administrator is created with an empty password. This account has
full rights to the server and can import projects and create configurations on the Server.
Note: It is recommended practice that the password for the Administrator account is changed from the
default.
After installation of the software, the administrator has to set up other user accounts with passwords for
the individuals that will use the system. These new users may have other permissions, for example cannot
delete projects from the server or cannot add new users.
Adding users with roles and group belonging is done using the tabs:
x Users
x Groups
x Roles
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File
Users page
The Users page in the User Administration dialog displays the users present in the system, which groups
the marked user is a member of and the role the user has.
By default there is one user, the Administrator which is member of the groups Everyone and
Administrators.
To add a new user, do as follows:
1. Click New.
2. Enter the User name and password, for a Normal user or a Domain user. A normal Normal
user is authenticated by BioPAT® SIMCA-online using the specified password. A domain
Domain user is authenticated using Active Directory services. When selecting to add a domain
user, the Distinguished name needs to be specified.
3. Click OK and in the Users page, specify the groups the new user should be a member of.
4. Repeat this procedure as needed.
In case you misplace the master administrator password, contact Sartorius-Stedim support.
Groups page
The Groups page in the User Administration dialog displays the groups present in the system and which
members the marked group has.
By default there are two groups, Everyone and Administrators, both with one member: Administrator.
To add a new group, do as follows:
1. Click New.
2. Enter the new group Name in the Add Group dialog and click OK.
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Using groups
When groups have been specified, access rights can be specified using the Access rights button in the
Project Administration dialog.
Note: Access rights is only available for folders.
Roles page
The Roles page in the User Administration dialog displays the available roles and their permissions.
By default there are two roles present, Administrator and User, and the possible Permissions:
x alarm management - alarms can be reset.
x configuration management - the Project administration is available for adding and updating
configurations.
x extract data - extracting data using File | Extract.
x note management - notes can be added and removed.
x out limits - out limits can be specified.
x purge configurations - configurations can be permanently removed.
x user administration - can add/remove users, change/add/remove roles and groups of users and
modify permissions.
x workspace management - can add and remove workspaces.
By default the Administrator has all the permissions and the User has none.
Change permissions for the marked role by selecting or clearing the Permission check boxes.
To add a new role, do as follows:
1. Click New.
2. Enter the new role Name in the Add Role dialog and click OK.
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File
Server audit trail

The server audit trail records events on the server. Here all events in the Server audit trail are listed with
details about the event.
Note: All events are accompanied by date and time. All events but the first 4 in the list below are
accompanied by a session ID. Project ID includes the project name.
Event Description Event details

The audit trail may have
1. audit_integrity_warning
been compromised.
The application name,

2. server_starting The server is initialized.
version and platform.
x The path and name

of the used server
ini-file including ini-
file content.
x SimApi name and
path.
x License information
including license
3. server_started The server has started. number, user,
company, features
and expiration date.
x Local server
information
including port and
network address.
x Database directory
path.
4. server_stopped The server has stopped.
FolderID,
The folder <folder name>
5. folder_created ParentFolderID,
has been created.
FolderName

6. folder_deleted FolderID
has been deleted.

FolderID,
7. folder_renamed has been renamed <new
NewFolderName
folder name>.

8. folder_moved has been moved to <parent FolderID, ParentFolderID
folder ID of new position>.
The access rights to

folder_group_access_gra <folder name> have been
9. FolderID, GroupID
nted granted for the current
group.
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The access rights to
folder_group_access_rev <folder name> have been
10. FolderID, GroupID
oked revoked for the current
group.
The user has commenced

ProjectID,
11. project_created the import of a BioPAT®
ParentFolderID
SIMCA project.
<project name> has been

12. project_deleted ProjectID
deleted.
<project name>,which was

13. project_restored previously deleted, has ProjectID
been restored.
<project name>,which was

14. project_purged previously deleted, has ProjectID
been permanently deleted.
A BioPAT® SIMCA project

has been imported and
15. project_initialized ProjectID
copied. A unique project ID
has been assigned.
<project name> has been ProjectID,

16. project_moved
moved to <folder name>. ParentFolderID
A new configuration has

been created defining how ConfigurationID,
17. configuration_created a BioPAT® SIMCA project ParentProjectID,
should be handled in ConfigurationName
BioPAT® SIMCA-online.
<configuration name> has

18. configuration_deleted ConfigurationID
been deleted.
<configuration name>,
19. configuration_restored which was previously ConfigurationID
deleted, has been restored.
<configuration name>,
which was previously
20. configuration_purged ConfigurationID
deleted, has been
permanently deleted.

ConfigurationID,
21. configuration_renamed been renamed
NewConfigurationName
<configuration new name>.
ConfigurationID, version
22. configuration_updated and comment added to
been changed.
summary.
A workspace has been

23. workspace_created WorkspaceName
created.
A workspace has been

24. workspace_deleted WorkspaceName
deleted.
<workspace name> has

WorkspaceName,
25. workspace_renamed been renamed <workspace
NewWorkspaceName
new name>.
A new user role has been

26. role_created created in the User RoleID
Administration.
A user role has been

27. role_deleted RoleID
deleted.
<permission ID> has been

28. role_permission_granted RoleID, PermissionID
granted for <role name>.
<permission ID> has been

29. role_permission_revoked RoleID, PermissionID
revoked for <role name>.
<user name> has been

30. user_created UserID
added to the user list.
31. user_deleted <user name> has been UserID
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File

removed from the user list.
The password for <user

32. user_password_changed UserID
name> was changed.
The user role for <user

33. user_role_changed name> was changed to UserID, RoleID
<role name>.
The distinguished name for

user_distinguished_name UserID,
34. <user name> was
_changed DistinguishedName
changed.
<group name> has been

35. group_created GroupID
added to the groups list.
<group name> has been

36. group_deleted deleted from the groups GroupID
list.
A user has been added to a

37. group_user_added GroupID, UserID
group.
A user has been removed

38. group_user_removed GroupID, UserID
from a group.
The Use Out Limits check

box was selected in the
39. out_limits_enabled
File | Administrators | Out
limits dialog.
The Use Out Limits check

40. out_limits_disabled
box was cleared.
The out limits were

41. out_limits_updated Settings
updated.
<user name> has logged

42. user_session_started
on to the server.
<user name> has logged

43. user_session_ended
off the server.
For details about the interface, see the Audit trail toolbar features subsection in the View chapter.
Server log file

The Server log displays information about the server the Client is connected to. The content of the Server
log file depends on the severity level selected in the Server options Miscellaneous settings.
To open the server log file, you need to have configuration management permissions. Open it by clicking
File | Administrator | Server log.
Close
To close the current project in the BioPAT® SIMCA-online Client, click File | Close.
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BioPAT SIMCA-online options
In the BioPAT® SIMCA-online Options dialog various options for the Client are available. An
explanation to each option is displayed at the bottom of the window when an option is clicked. The options
are organized in two tabs:
x General
x Plot options
BioPAT® SIMCA-online Options General tab

In the BioPAT® SIMCA-online Options General tab various options for the Client are available. An
explanation to each option is displayed at the bottom of the window when an option is clicked.
The options available are:
Paths
Ini file – view or change the Client Ini file path.
Log file
Log file size (kB) – view or change the maximum Client Log file size.
Log level - view or change the minimum severity Log level for messages that should be written to the
client log file.
Server log file
Max display size (kB) – view or change the Max display size which is the maximum log file size that
will be displayed. If the log file exceeds the limit, the last max size part will be displayed.
Text editor - View or change the current Text editor when opening the log file.
Miscellaneous
Info tip show level - View or change the Info tip show level, which is the minimum importance level of
server messages to the Client, also shown as info tips.
Startup - Select what to do on Startup: (a) Show Connect to BioPAT® SIMCA-online Server dialog
(default), (b) Show Empty Environment which results in that the client does not connect to the last server
and does not display the Connect to Server dialog box.
Interface
Tabs – view or change whether the tabs are configurations or windows:
x One tab per window– to view all open windows as tabs.
x Grouped (default) – to view all open project configurations as tabs. Using this mode one tab for
each project configuration is displayed.
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File
Rolling view – When enabled, rolling view behaves as a screen saver, and is activated after a given
number of seconds (default 60) if the user doesn’t move the mouse or press a key on the keyboard. When
Rolling view is selected the client will loop through all open workspace tabs at a given interval, by default
15 seconds.
Audit trail comparison tool

To see what differs between two versions of the configuration, use the Audit trail comparison tool:
x In File comparison utility select the file comparison utility to use. ExamDiff is automatically
installed and the default. For more about ExamDiff, visit
http://www.prestosoft.com/edp_examdiff.asp.
x The Command line parameters content specifies the command line parameters sent to the file
comparison utility. Change this according to the documentation of the specified File comparison
utility if changed from the default utility. $File1 and $File2 are expanded to the full paths of the
files to compare.
The comparison tool is opened by clicking the Compare button after marking one or two versions in the
configuration or server audit trails. When marking only one version, clicking the Compare button
compares with version 1.
Plot options
Use File | BioPAT® SIMCA-online options to view or change:
x Limit settings in Plot defaults.
x Batch control chart settings in Plot defaults - batch evolution.
x Batch level plot defaults in Plot defaults - batch level.
x The Identifiers to be listed in plots and lists
x The Batches box content in the Properties group.
Plot defaults
Plot defaults general for regular project models, BEM and BLM are found in the Plot defaults section.
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Show alarm limits

To display the alarm limits specified in the project configuration, in the plots for which alarm limits were
specified, select the Show alarm limits check box.
Read how to specify alarm limits in the Alarms for batch evolution and Alarms for batch level sections
in the Project administration chapter.
Show control limits
For continuous, select the Show control limits check box to display DCrit, T2Crit, Hotelling's ellipse, and
standard deviation in the relevant plots.
Show annotation
To display notes for points or batches for which a note has been added, select the Show annotations check
box.
Plot defaults - batch evolution

The Plot defaults - batch evolution section holds default settings for visualization of the batch evolution
model control charts.
Layout
In the Layout box, select to default display the batch evolution control charts by Units or by Phases. See
also the Layout box section in the Home chapter.
Automatic zooming
Select the Automatic zooming check box to automatically zoom in the subplot displaying the phase of the
currently active batch. Note that this option requires that Phases is selected in the Layout box. Note that
automatic zooming cannot be selected in the properties of the individual plot.
Show recent batches
Select to display respective not display recent batches by selecting respective clearing the Show recent
batches check box.
How many batches are considered recent is specified in the configuration.
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File
Show target values

Select the Show target values check box to display the target values specified in the project configuration,
in the plots for which target values were specified.
Read how to specify target values in the Specifying Target Values section in the Project administration
chapter.
Show subheader
Select the Show subheader check box to display the subheaders for all plots in multiplots.
Plot defaults - batch level
The Plot defaults - batch level section holds settings for visualization of the batch level plots.
Layout
In the Layout box, select for the plots to display Individual models or Combined by default.
Show recent batches
Select to display respective not display recent batches by selecting respective clearing the Show recent
batches check box.
Show significance limits
Select to display the significant limits in the score scatter plot, DModX plot, and Hotelling's T2Range plot
by selecting the Show significance limits check box.
Significance level
In the Significance level field enter the significance level to use in the score scatter plot, DModX plot, and
Hotelling's T2Range plot.
Show standard deviation limits
Select to display the standard deviation limits in the score plot displaying one component by selecting the
Show standard deviation limits check box.
Number of standard deviations
In the Number of standard deviations field, enter the number of standard deviations to display in the
score plot displaying one component.
Show subheader
Select the Show subheader check box to display the subheaders in all plots.
Identifiers
Select the way you want variable and batch identifiers to be displayed in plots and lists. The details of the
variable and batch IDs are displayed in the header row.
Variable ID
For regular projects
x In the Variable ID box select:
a. One of the available IDs to display the primary or secondary ID as in BioPAT® SIMCA.
b. Alias to display the Alias specified in the project configuration.
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x Use the Start at and Length fields to define which part of the names to display.
For information about how to specify aliases, see the Tags page in Configure dialog subsection in the
Project administration chapter.
Batch evolution
In the Batch evolution section
x In the Variable ID box select:
a. One of the available IDs to display the primary or secondary ID as in BioPAT® SIMCA.
b. Alias to display the aliases specified in the project configuration.
For information about how to specify aliases, see the Phase tags page in Configure dialog subsection in
the Project administration chapter.
Batch level
In the Batch level section
x In the Variable ID box, select:
a. One of the available IDs to display as listed in the dataset spreadsheet in BioPAT®
SIMCA.
b. Phase to display the phase ID.
c. Maturity to display the maturity of the variable. When the batch level holds summary
variables, the maturity is the name of the function, for instance MIN or MAX.
d. Source to display the source of the batch level variable, for instance t[1] or variable id.
Batch ID
For batch level plots displaying the batch ID, use the Start at and Length fields to define which part of
the identifiers to display.
Batches box
The active batches are always by default displayed.
In the Batches box section, select the batches to be displayed in the Batches box in the Properties group
on the Home tab:
1. Active batches are always displayed.
2. Select whether to Include recent batches. The number of batches considered recent is specified
in the configuration.
3. Select whether to Include workset batches. When the Include workset batches check box is
selected the button is available. Click the browse-button and select which of the workset
batches to display. By default all workset batches are included.
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File
Selecting which workset batches to display

Clicking the browse button opens a dialog displaying all workset batches available. All batches are by
default selected.
To exclude batches, clear the Select all check box and then clear the check boxes of the batches to
exclude.
Note: Multi selection is available in the Select Batches dialog. Consequently, if you mark several batches
and then select or clear one of them, all marked batches will be selected or cleared.
®
Exit BioPAT SIMCA-online
To close the BioPAT® SIMCA-online Client, click File | Exit BioPAT® SIMCA-online.
39
Quick Access Toolbar
Introduction
The Quick Access Toolbar is by default positioned at the top above the tabs and allows you to have your
favorite commands easily accessible. The Quick Access Toolbar is standard in Windows software with
ribbons.
The Quick Access Toolbar in BioPAT® SIMCA default displays the following features:
x Open (Ctrl+O) - to open a configuration or workspace.
x Project administration - to open the Project Administration dialog.
x Copy (Ctrl+C) - to copy the active plot or selection.
Customizing Quick Access Toolbar

You can add buttons to and remove buttons from the Quick Access Toolbar and also reposition the Quick
Access Toolbar to below the ribbon.
Quick Access Toolbar menu
Quick Access Toolbar shortcut menu
Removing buttons from Quick Access Toolbar

To remove a button from the Quick Access Toolbar use one of the following methods:
x Right-click the button and click Remove from Quick Access Toolbar.
x Click the arrow to the right of the available Quick Access Toolbar buttons and clear the relevant
check box.
Adding buttons to Quick Access Toolbar

To add a button to the Quick Access Toolbar, right-click the button on the ribbon and click Add to Quick
Access Toolbar.
Moving the Quick Access Toolbar

To position the Quick Access Toolbar closer to the workspace you can select to position it below the
ribbon by clicking the Show Below the Ribbon in the Quick Access Toolbar menu. Click Show Above
the Ribbon to move it back to its original position.
41
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Minimizing the ribbon

To maximize the workspace you can minimize the ribbon so that it folds away like a menu.
The Minimize the Ribbon command is available:
x When you right-click a button in the Quick Access Toolbar.
x In the Quick Access Toolbar menu.
x When you right-click a button in the ribbon.
42
Home
Introduction
The Home tab holds the commands most commonly used. On the Home tab you can:
x Create plots for batch and regular projects.
x Change the properties of the active plot in the Properties group.
x If you have the right privileges: View or update the configuration, Repredict data, and Delete
predicted data in Manage data. For details, see the Modifying configuration section in the
Project administration chapter.
All plots, except for the variable plots, display predicted values.
Batch
On the Home tab, view/update the configuration, select the plots to display, and change the properties of
the open plot. All plots, except for those displaying individual variables, display predicted values.
There are four groups on the Home tab:
x Manage with Configuration, Repredict data and Delete predicted data. Only available for
users with configuration management permissions.
x The Batch evolution plots group with the available batch evolution plots.
x The Batch level plots group with the available batch level plots.
x The Properties group which allows changing the properties of the active plot.
Batch evolution plots

In the Batch evolution plots group, find the control charts: Scores, DModX, Hotelling’s T2, Variable,
and Y Predicted. The Dual Variable Plot is found by clicking the Variable menu.
Batch evolution plots display active and historical batches and the appropriate limits for the respective
plots. Batches with observations outside the limits are in some way different from the workset batches.
Score
Batch Evolution control chart for the scores (T) of the active batches. The default is to display scores for
the first component, t[1].
43
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Displaying triggered alarms

When alarms have been defined, triggered alarms are displayed as described in the Alarm visualization
section in View chapter.
For more, see the Plot defaults subsections in the BioPAT® SIMCA-online Options section in the File
chapter.
DModX
Batch Evolution control chart of the distance to the model, DModX, after the last component.
Hotelling’s T2Range
Batch Evolution control chart of Hotelling’s T2Range. The default is to display from component 1 to the
last component.
Variable
Batch Evolution control chart of the individual variables. By default the first variable available is
displayed.
Use the Variable box in the Properties group on the Home tab to switch variables.
44
Home
Dual variable
Batch Evolution control chart of two variables. By default the first and second variables available are
displayed.
Use the Variable boxes in the Properties group on the Home tab to switch variables.
The plot is opened by clicking Variable and then Dual Variable in the Batch evolution plots group on
the Home tab.
Y Predicted
Batch Evolution control chart of predicted maturity (Y).
Empty instead of plot

When the space where you expected a plot is empty, the reason is one of the following:
x There is no data to display.
x The plot cannot be displayed since some of the necessary variables and/or components are
missing. Can happen for subplots.
x The x-axis annotation is too large.
To switch variable or component, use the Properties group.
45
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Batch level plots

In the Batch level plots group on the Home tab, find Scores, DModX, Hotelling’s T2, Variable, and Y
Predicted.
The Score Scatter plot can be opened from the Score menu and the All Y Predicted plot from the Y
Predicted menu.
The batch level plots by default display the completed batches (Recent Batches) in a plot grid with one
plot for each model. Using the Layout box, the plot can be displayed one for each plot type so that the
prediction for each model is displayed for each batch. See also the Layout box for batch level subsection
later in this chapter.
With hierarchical models or partial models, you can also display the active batches as they are still
evolving in the batch evolution level. Without hierarchical or partial models, active batches are
unavailable in the batch level plots.
Scores
The Batch Level Score plot is a scatter plot of a score vector; scores for the first component are shown by
default, t[1].
The plot can be displayed Combined (default) and as Individual models using the Layout box to switch.
Figure: Batch Level Score plot Combined
Score scatter plot

The Batch Level Score Scatter plot displays the scores. The default is to display t[1] vs. t[2].
When Individual models is selected the Hotelling’s T2 ellipse (99%) is also displayed.
Figure: Batch Level Score Scatter plot Combined
The plot is opened by clicking Score and then Score Scatter in the Batch level plots group on the Home
tab.
DModX
The Batch Level DModX plot is a scatter plot displaying the distance to model after the last component.
DModX is proportional to the RSD (Residual Standard Deviation) of batches in the X space.
Figure: Batch Level Distance to Model X plot Combined
46
Home
Hotelling’s T2
The Batch Level Hotelling’s T2Range plot is a scatter plot displaying the distance from the origin in the
model plane (score space) for each selected batch. The default is to display from component 1 to the last
component.
Figure: Batch Level Hotelling's T2Range plot Combined
Variable plot
The Batch Level Variable plot is a scatter plot displaying the selected variable. By default the first
variable in the variable list is displayed.
Use the Variable box in the Properties group on the Home tab to switch variables.
Figure: Batch Level Variable plot Combined.
Y Predicted
The Batch Level Y Predicted plot is a scatter plot, default displaying the predictions of the first y-
variable.
Figure: Batch Level Y Predicted plot Combined.
47
®
The confidence intervals displayed in this plot were derived from Jack-knifing. For details about Jack-
knifing, see the BioPAT® SIMCA user guide.
All Y Predicted
The Batch Level All Y Predicted plot displays the predictions of all y-variables in the same plot. The
predictions of all y-variables are displayed for each batch in this plot.
Figure: Batch Level All Y Predicted plot.
The plot is opened by clicking Y Predicted and then All Y Predicted in the Batch level plots group on
the Home tab.
Properties group
Use the Properties group to change the relevant parameters of the plot, such as variables, components,
batches and layout.
Access the properties by using the arrow keys on your keyboard. Pressing:
x UP and DOWN switches the component or variable in the first property box for the next or
previous.
x RIGHT and LEFT switches the content of the second property box for the next or previous.
x PAGE UP and PAGE DOWN switches the content of the third property box for the next or
previous.
Customize the display of the active batch plot by
x changing the properties in the displayed boxes
48
Home
x opening the Properties dialog using one of the methods described in the Plot Properties section
later in this chapter.
For other and more customization, see the sections Plot Properties later in this chapter and Format Plot
in the Customizing plots chapter.
Note: The selected change will affect only the active plot. If you want to customize the default settings for
the plots, click File | BioPAT® SIMCA-online options.
Batches box
Select from the Batches box the batches to display in the active plot. The Batches box is available for all
plots for batch evolution and batch level models.
Batches box content

In the Batches box, find the groups Active Batches and Recent Batches (historical) and the list of named
selected batches. For the batch level score scatter plot there is also a group named Workset Batches to
enable displaying all workset batches with one click.
Beneath these groups, the Active Batches, Recent Batches and Workset Batches are listed.
Reference batches
To display certain workset or historical batches as reference batches, along with the active batches, select
them in the Batches box under the respective headers. Named batches selected in the Batches box are
displayed until cleared. So to continue to display a certain active batch, click the Batches box and select
the batch from the list.
Note: Any specific batch selected from the Batches box is referred to as a reference batch. You can select
to display several reference batches.
Customizing Batches box

The content of the Batches box can be customized in the Batches box section in the BioPAT® SIMCA-
online options dialog. For details see the Batches box subsection in the BioPAT® SIMCA-online
options section in the File chapter.
The number of batches considered recent is specified in the Time ranges page in the Configure dialog.
Selecting components
In plots displaying scores or T2Range you can select for which components to display the plot. In the Y-
axis/From/To box in the Properties group on the Home tab; all score vectors available for the active plot
are listed.
In the table, the first column shows the plots for which the components can be changed and the second
column contains the available boxes.
Plot Boxes to select components from
Score plots Y-axis
Score Scatter plot for batch X-axis and Y-axis

level
Hotelling’s T2Range Plots From and To
The component to display for the Distance to Model X plots cannot be changed. The DModX plot is
always displayed after the last component of the model. The Y Predicted plot is displayed using all
components.
49
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Selecting variables
When the active plot is a Variable plot, or a Y Predicted plot from batch level, the Variable box displays
the list of available variables.
When the active plot is a Dual Variable plot for a batch evolution model, an additional variable box,
Variable 2, displays the list of available variables.
Click the Variable box and select the desired variable.
Properties group for the Variable plot and Y Predicted plot.
Layout for batch evolution plots

In the Layout box, select whether to view the plot by Phase or by Unit (default).
When displaying the plot by Phase the phases are displayed one after the other from left to right in the
model order.
When displaying the plot by Unit the cells are displayed to visualize the system at hand.
See also the Plot defaults - batch evolution subsection in the BioPAT® SIMCA-online options section
in the File chapter.
Layout for batch level plots
In the Layout box, select whether to view the plot as Individual models (default) or Combined in one
plot.
When the plot displays Individual models (subplots), the predictions for each batch level model are
displayed in one plot.
When displaying the plot Combined, the plot is reorganized to display the predictions for all models for
each batch. The batches are displayed on the x-axis, one after the other from left to right, in the order the
batches were executed.
See also the Plot defaults - batch level subsection in the BioPAT® SIMCA-online options section in the
File chapter.
Individual models
Combined
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Home
Plot Properties
Use the Plot Properties dialog to customize what is displayed in the current plot.
The Plot Properties dialog the current plot is opened by:
x clicking the plot and clicking Properties in the mini-toolbar.
x clicking the Properties group dialog dispatch launcher on the Home tab or
x right-clicking the plot and clicking Properties.
The Plot Properties dialog can have the following tabs: Select batches, Plot options and Selected
observations (contribution plot only).
These tabs are described in the sections that follow.
For other customization, see the section Customizing plots chapter.
Note: The selected change will affect only the active plot. If you want to customize the default settings for
the plots, click File | BioPAT® SIMCA-online options.
Plot options
The Plot options tab has a number of options depending on the open plot. .
Show alarm limits
To show or hide the alarm limits of the current plot, select or clear the Show alarm limits check box. To
show or hide the alarm limits by default, see the BioPAT® SIMCA-online options section in the File
chapter.
Note: When displaying plots by clicking in the Overview window, the created plots always display the
alarm limits.
Show annotations
To display an envelope icon for points or batches for which a note has been entered, select the Show
annotations check box.
Read how to specify notes in the Add note subsection in the Tools chapter.
Show subheader
To hide or display the subheaders in the subplots, the Show subheader check box has to be cleared or
selected.
Control limits for batch evolution plots
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In Control limits, select the limits to display: +3, +2, +1, -1, -2, -3 std. dev. (standard deviations), Average
(batch). Default is to display +3 standard deviations and the Average. The current selection is displayed on
the header row.
To add/change limits to choose from, see the Control limits subsection in the Project administration
chapter.
Show significance limits for batch level plots
Select to display or hide limits in the current plot by selecting or clearing the Show significance limit
check box. To change the significance level from the default 0.01, enter a new value in the Significance
level field, available when the Show significance limits check box is selected
This feature is available for the batch level DModX and Hotelling's T2Range plots.
Show standard deviation limits for batch level score plot
Select to display or hide limits in the batch level score plot by selecting or clearing the Show standard
deviation limits check box.
To change the number of standard deviations, by default '3', enter a new number in the Number of
standard deviations field, available when the Show standard deviation limits check box is selected.
Plot options for Contribution
In the Plot Properties dialog of the Contribution plot there is a Selected observations page, a Plot
options page with the Sort feature described here and for continuous a Time page.
By default the contribution plot is not grouped nor sorted.

To sort the contribution plot:
1. Select the Sort check box.
2. Select Absolute Value (default), Value, or Name.
Select batches
By default the most recent historical batches are plotted in the background. The number of recent batches
displayed is specified in the Time ranges page in the Configure dialog.
Change which batches are displayed in the current plot by specifying a new time range in the Select
batches tab in the Plot Properties dialog.
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Home
Selected observations
Contribution plots are displayed for one point/group of points versus another point/group of
points/average.
In the case with groups, use the Selected observations page to see which points were included in the
group.
Regular
On the Home tab, view/update the configuration, select the plots to display, and change the properties of
the open plot. All plots, except for those displaying individual variables, display predicted values.
The number of observations displayed is specified in the Configure dialog on the Time ranges page.
There are four groups on the Home tab:
x Manage with Configuration and Repredict data. Only available for users with configuration
management permissions.
x The Trend plots group with the available predefined trend plots.
x The Custom plots group with the fully customizable trend and scatter plots.
x The Properties group which allows stepping backwards and forwards or pause the active plot.
Worm plot
The Worm Plot displays:
x Scores, default t1 vs. t2, as a line plot.
x Head (larger circle) of the worm (line).
x The workset observations.
x Hotelling’s T2 ellipse.
Scores
Trend plot displaying scores (T). The default is to display t[1].
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DModX
Trend plot of the distance to the model, DModX, after the last component.
From the DModX menu, the trend plots for DModX+, PModX and PModX+ can be displayed.
PModX
Trend plot of the probability that each point belongs to the model. Available both for regular PModX and
PModX+.
Display the PModX and PModX+ plots by clicking DModX and the respective vector name.
Hotelling's T2Range
Trend plot of Hotelling's T2Range. The default is to display from component 1 to the last component.
For OPLS this plot is unavailable.
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Home
Y Predicted
Trend plot of observed and predicted y-variables. By default the first y-variable is displayed.
See also the Data vectors and Plot options subsections later in this chapter.
Custom plots
Use Trend and Scatter to create plots using any combination of vectors. Trend and Scatter are found in
the Custom plots group on the Home tab for regular projects.
When clicking Trend or Scatter a dialog opens allowing you to select which vectors to plot.
Identifiers are displayed according to plot defaults in BioPAT® SIMCA-online options.
Note: To switch component or variable, click the (blue) number/variable ID and select another one.

Properties group
The Properties group for continuous processes contains the stepping buttons and the Pause button.
Pausing affects only the current plot and not the execution as such. Stepping is done in steps of 10% of the
total window length.
The Plot Properties dialog the current plot is opened by:

x clicking the plot and clicking Properties in the mini-toolbar.
x clicking the Properties group dialog dispatch launcher in the Home tab or
x right-clicking the plot and selecting Properties.
Plot options
Specify whether to show limits and annotations in the Plot Options page.
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Note: Changes in options in the Plot Properties dialog apply to the current plot only. When opening a new
plot, the Properties settings are reset to default. To change for future plots, change in Plot options in the
File | BioPAT® SIMCA-online Options dialog.
Show alarm limits

To show or hide the alarm limits of the current plot, select or clear the Show alarm limits check box. To
show or hide the alarm limits by default, see the BioPAT® SIMCA-online options section in the File
chapter.
Note: When displaying plots by clicking in the Overview window, the created plots always display the
alarm limits.
Show control limits

Select to display or hide limits in the plots by selecting or clearing the Show control limits check box.
Depending on plot, the relevant critical limit or standard deviation limits are displayed.
Show annotations
To display an envelope icon for points or batches for which a note has been entered, select the Show
annotations check box.
Read how to specify notes in the Add note subsection in the Report section in the View chapter.
Plot options for Contribution
In the Plot Properties dialog of the Contribution plot there is a Selected observations page, a Plot
options page with the Sort feature described here and for continuous a Time page.
By default the contribution plot is not grouped nor sorted.

To sort the contribution plot:
1. Select the Sort check box.
2. Select Absolute Value (default), Value, or Name.
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Home
Selected observations
Contribution plots are displayed for one point/group of points versus another point/group of
points/average.
In the case with groups, use the Selected observations page to see which points were included in the
group.
Data vectors
In the Data vectors page you can change vectors to display, remove vectors, add new vectors, and change
components. .
Actions available:
x Remove all vectors by clicking the Delete All-button in the header.
x Remove a vector by clicking the delete-button.

x Add a vector by clicking the new-button at the bottom of the list.
x In the Type column, change the displayed vector by clicking the vector and selecting a new
vector in the list that expands.
x In the Vector column, change components or variables by clicking the blue item to change.
x In the Vector column, display all components or variables by right-clicking the blue item and
clicking Expand.
Time
In the Time page you can select to display a specific interval in time by changing the From and To dates
and times. This applies only to the current plot.
The default is to Automatically update to show the latest available data on the server.
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View
Introduction
On the View tab, find following features:
x Data list.
x Show/Hide group with Project info, Overview, Log, Plot details, Status bar, Tabs and Full
screen.
x Open group with Configuration audit trail, Client log, and Report.
x Window arrangements in the Window group including Save workspace.
Data list
The data in the internal database can be listed by clicking Data list on the View tab.
In the dialog that appears, select the data to display in the spreadsheet using the From and To date and
time fields. For batch projects you can also select among the batches listed for the specified interval.
In the table below, the content of the tabs in the created list are described.
Sheet What is listed
Batch Evolution Original measured variables plus the computed parameters, scores,
Data DModX, etc available in the selected batch evolution model.
Batch Level Original measured variables plus the computed parameters, scores,
Data DModX, etc available in the selected batch level model.
Batch Condition Batch condition variables.

Data.
Local Centering Local centering data used in the selected batch evolution model.
Data
Continuous Original measured variables plus the computed parameters, scores,

Trend Data DModX, etc available in the selected model.
Show or hide
The Show or hide group includes the following features:
x The dockable windows Project info, Overview, Log and Plot details.
x The Status bar check box.
x The Tabs check box.
x Full screen
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Project info
The Project info dockable window displays, the project name, the projects original location, the time the
project was added to the Server, and whether the execution is On or Off for each open project.
The Project info dockable window is opened by selecting the Project info check box in the Show or hide
group on the View tab.
Log
The Log dockable window displays:
x Administrator actions, such as log on or off.
x Project failures, such as failing to initialize, to connect, or to create a data source.
x If the processor works at high load, this is also logged here.
x A license reminder message when the license is about to expire.
The Log dockable window is opened by selecting the Log check box in the Show or hide group on the
View tab.
Status bar
The Status bar, found at the bottom of the screen, displays a description, coordinates, and connection
status for the server.
In the table, see which type of information and where in the Status bar it is displayed:
Action Position Displays
Marking a menu item Left The description of a menu item or button. When nothing is marked
(for ex. File | Print) the Status bar displays 'Ready'
or hovering over a When holding the cursor over Print.
button.
Hovering in a plot. Middle The coordinates of the cursor in a plot.
None. Right The user currently logged on and the status of the connection to the
server (Connected/Disconnected/Server busy).
Overview
The Overview dockable window displays the status of the active batch or execution.
The header row displays the batch ID/execution start time, and current overall status for the
batch/execution: OKAY and green when no alarm has been triggered, WARNING (yellow) and
CRITICAL (red) when the respective alarm has been triggered.
Below the header row the Start and Stop times are displayed. If the batch/execution is still active, the stop
time is Active.
Each model is represented by a color coded box with its model number and title, or for phases, phase ID.
The box is green when there is an active batch or execution but no alarm has been triggered, yellow when
a warning alarm has been triggered, red when a critical alarm has been triggered, and uncolored before
data has reached that model.
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View
The progress of an active batch can be followed through these color coded boxes to completion.
Note: For phases with normalized maturity, alarms are displayed during the evolution of the batch, but
are not final until after phase completion.
When clicking one of the models, Reset alarms, Display triggered alarms and Display configured
alarms are displayed.
Reset alarms returns the color for the model to green until the next alarm is triggered.
Display triggered alarms opens the triggered vectors zoomed in on the subplot with the triggered alarm
for the model. These plots also display the specified alarm limits, warning limits in yellow and critical
limits in red.
Display configured alarms opens plots displaying all alarms specified in the configuration. These plots
also display the specified alarm limits, warning limits in yellow and critical limits in red.
In the Alarm visualization section next, see details about the visualization of the alarms.
See also the Adding alarms section in the Project Administration chapter.
Alarm visualization
When alarms are specified, triggered alarms are displayed in:
x Overview window.
x Plots displaying the vector with the specified alarm.
x Plot Details window when a plot with a triggered alarm is active.
x The Report window.
The table describes the color coding and symbols displayed concerning alarms.
Alarm Overview window color Plot, Plot Details and
Report
No alarm triggered and the Uncolored Plots display nothing, Plot Details
model is not executing displays No alarms or notes and the
Report displays:
No alarm triggered and the Green Plots display the default plot
model is currently symbols, Plot Details displays No
executing alarms or notes and the Report
displays:
Alarm triggered due to Yellow The triggered point displays a yellow

point outside a warning
warning sign:
limit (Lo/Hi).
Resetting the alarm results in that
the symbol changes to:
Alarm triggered due to Red The triggered point displays a red

point outside a critical limit
circle with a cross.
(LoLo/HiHi).
Resetting the alarm results in that
the symbol changes to:
Note: After resetting an alarm the Overview window again displays a green box while the plots, Plot
Details window and the Report display the symbol for reset alarms.
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Plot Details
The Plot Details dockable window displays all triggered alarms and all notes present in the active plot.
In the Plot Details window you can reset alarms and edit notes by double-clicking the respective rows.
You can also delete notes by marking and pressing DELETE.
Tabs
To display or hide tabs for all open project configurations or windows, on the View tab, in the Show or
hide group select the Tabs check box.
Whether the tabs show project configurations or all windows depends on the settings in File | BioPAT®
SIMCA-online Options under the Interface header in the General tab.
The tabs are color coded signaling status. In the example below:
x The left configuration is not receiving data, thus the tab is uncolored.
x For the middle one a critical alarm was triggered, thus the tab is colored red. When a warning
alarm has been triggered the tab is colored yellow.
x The right configuration is running and no alarms have been triggered, thus colored green.
When selecting to display the individual windows, all windows are colored according to the description
above for the configuration they were created from.
Full screen
To maximize the plot area, leaving only the minimized ribbon and the plot area, on the View tab, click
Full screen. To return to normal, again click Full screen.
Open
The Configuration audit trail, Client log, and Report are all available in the Open group on the View
tab.
Configuration audit trail

In BioPAT® SIMCA-online the Audit trail is always turned on. The actions and incidents listed in the
table are recorded in the audit trail with time and date stamp:
Open the audit trail by clicking Audit trail in the Open group on the View tab. The audit trail of the
current configuration is then opened.
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<configuration name>
UserSessionID, Version
has been updated to
1. configuration_updated number and comment
version <version
added to Summary
number>.
The execution of
UserSessionID,
2. execution_started <configuration name>
ExecutionID
has started.
The execution of
UserSessionID,
3. execution_stopped <configuration name>
ExecutionID
has stopped.
The execution of
4. execution_resumed has resumed (started ExecutionID
again after being
stopped).
The execution of
was interrupted, for
5. execution_aborted ExecutionID
instance error when
reading from external
data source.
6. repredict_started Repredict has started. ExecutionID
7. repredict_stopped Repredict was stopped. ExecutionID
8. batch_started <batch ID> has started. BatchID
9. batch_finished <batch ID> has finished. BatchID
<batch ID> has been

10. batch_deleted UserSessionID, BatchID
deleted from the server.
<batch ID> has been

discarded. Happens
11. batch_discarded BatchID, Reason
when a batch is not read
to completion.
<phase name> has

12. phase_started BatchID, PhaseNumber
started.
<phase name> has

13. phase_finished BatchID, PhaseNumber
finished.
UserSessionID, Severity,
NoteID, note text and point
A note has been created
14. note_created ID (Batch ID, Phase
at with <content>.
Number, time point) added
to summary.
NoteID, note text and point
<note ID> has been
15. note_deleted ID (Batch ID, Phase
deleted.
Number, time point) added
to summary.
<note ID> has been NoteID, note text and point
16. note_updated updated to hold ID (Batch ID, Phase
<content>. Number, time point) added
to summary.
17. alarm_triggered The alarm <triggered TriggeredAlarmID,

alarm ID> has been Severity, vector, point ID
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triggered for <vector>. (Batch ID, Phase Number,
time point) added to
summary.
TriggeredAlarmID,
The alarm <triggered
Severity, vector, point ID
alarm ID> has been
18. alarm_elevated (Batch ID, Phase Number,
elevated to critical for
time point) added to
<vector>.
summary.
UserSessionID,
TriggeredAlarmID,
The alarm <triggered Severity, vector, point ID
19. alarm_reset alarm ID> has been (Batch ID, Phase Number,
reset for <vector>. time point) and user
entered reset-comment
added to summary.
In the audit trail, use the toolbar to organize, select range, compare configuration versions, view
configurations, roll back to a previous version of a configuration and filter search.
The table describes the different features available for batch and regular projects.
Toolbar features Result
Organize - see the Organize in the audit trails subsection later in this chapter.
Select the event to start from. Negative values indicate how many
From
events backing up from the value in To to back up.
To The last event displayed. Last means the last event at all times.
Updates the audit trail window. Has to be clicked to update after

Refresh
changes in the From and To fields.
Displays what differs between the two marked versions of the

configuration using a File comparison utility. When only one version is
Compare
marked, the comparison is made versus version 1. For options, see the
BioPAT® SIMCA-online Options - General topic.
Opens the marked version of the configuration. No changes can be

View configuration
made in the dialog.
Roll back Creates a new version with the content of the marked version.
The content of the audit trail is filtered to only display rows matching the
Filter field
filter field.
Organize
In the Organize button the following features are available:
x Show system events - In addition to showing regular events, system events are displayed.
x Show details - Displays details of the events currently displayed in the audit trail.
x Field chooser - displays the columns currently not displayed in the audit trail. Drag headers from
the Field chooser to the audit trail to add columns. To remove a column, drag the header down
from the header row.
x Copy - is available when something is marked in the audit trail and then copies the selection.
x Select all - selects all contents of the audit trail thus allowing all contents to be copied.
x Expand all groups - expands all groups when some or all collapsed. Groups are created by
dragging a header to the area above the headers.
x Collapse all groups - collapses all groups in the case when some or all are expanded. Groups are
created by dragging a header to the area above the headers.
Client log
The Client log lists information such as:
- Connection/disconnection to server.
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- Log level specified in BioPAT® SIMCA-online options.

- Days until license expires.
The Client log is available in the Open group on the View tab.
Report
The Report displays a summary of all triggered alarms and notes, in the current configuration for the
selected time period/batches.
In the Report you can reset alarms and add, edit and remove notes.
Note: After resetting alarms or adding/editing/removing notes, you have to refresh to see modifications.
The table describes the features available in the report.

Report features Description
Toolbar features See the Report toolbar features subsection.
Saving of the report Can be done by printing it to pdf or copying to clipboard.
Drag a column header above the header row to group by that property.
Group The report for batch configurations is grouped by batch and model by
default.
The shortcut menu allows you to:

x Select more/other columns in Columns.
x Group by this field adding a group to the group area.
x Hide column to not display the right-clicked column.
Shortcut menu x Sort ascending according to the right-clicked column.
x Sort descending according to the right-clicked column.
x Copy the selection.
x Select all items in the report.
x Print the content in the report.
The Report is available in the Open group on the View tab.

Report toolbar features
In the Configuration audit trail and Server audit trail use the toolbar to organize, select range, display
plots, reset alarms, and add/modify notes.
The table describes the different features available for batch and regular projects.
Toolbar features Result
Organize - see the Organize subsection later in this section.
1. Click Select batches/Select time range

Select batches 2. Specify the From and To dates and times.
Select time range 3. For batch projects, mark the batches to
display in Available Batches and click ->.
Plots displaying the triggered alarms marked in the

Display triggered alarms
Report are opened.
See the Reset alarms subsections later in this

Reset alarm
section.
See the Add note and Adding note to

Add note, Edit note, Delete note batch/phase/model subsections later in this
section.
The content of the report is filtered to only display

Enter filter text here
rows matching the filter field.
Refresh Updates the Report window.
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Adding notes
Notes can be added to a point marked in a plot or in the Report as follows:
x Plot: mark a point and click Add note:
x in the mini-toolbar,
x in the Marked items group on the Tools tab or
x on the shortcut menu.
x Report: mark the row and click Add note in the toolbar or in the shortcut menu.
When adding a note the following dialog appears.
In the Add Note: Specify Severity and Text dialog, select the Severity level, and enter the text for the
note in the Comment field.
The Severity levels available are: Low, Medium (default), or High where they result in different note
symbols in the plot, in the Plot Details window, and in the Report:
x Low -
x Medium -
x High -
Editing notes
To modify a note use one of the following methods:
x In the plot, mark the point with the note and click Add note.
x In the Report, mark the note and click Edit note in the toolbar.
x In the Plot Details window, double-click the note.
Deleting notes
To remove a note use one of the following methods:
x Mark the note in the Report and click Delete note in the toolbar.
x In the Plot Details window, mark the note and press DELETE on your keyboard.
Adding Note in Note wizard
Notes can also be added to a batch, phase model, batch level model or observation using a wizard in the
Report.
To add a note to an entire batch:
1. In the Report mark a row that does not relate to maturity.
2. Click the Add note-button.
3. In the Add Note: Select Note Type window, select Batch, Phase/Model, or Observation.
a. With Batch selected you must select a batch.
b. With Phase selected you must select a batch and a phase or batch level model.
c. With Observation selected you must select a batch, a phase, and an observation.
4. After stepping through the wizard making selections according to step 3 the Add Note: Specify
Severity and Text page opens allowing you to enter severity and text. For more about this page,
see the Add note subsection earlier in this chapter.
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Reset alarms
Triggered alarms can be reset in three places:
x In the Overview window by clicking the model with the triggered alarm and clicking Reset
alarms in the menu.
x In the Plot Details window by double-clicking the triggered alarm.
x In the Report by marking a triggered alarm row and clicking the Reset alarms button in the
toolbar.
In the Reset Alarms dialog the user must enter a text in the Comment field to enable the Reset button.
Alarm symbols after resetting:

x Warning level:
x Critical level:
Organize
In the Organize button the following features are available:
x Show alarms - results in that all alarms triggered during the time period are displayed. By default
selected.
x Show reset alarms - results in that triggered alarms during the time period that were reset are
displayed. By default selected.
x Show phases/models with no alarms - displays all phases and models for the time period even if
no alarms were triggered and no notes added for them. By default selected and only available for
batch models.
x Show notes - displays all added notes for the time period. By default selected.
x Field chooser - displays the columns currently not displayed in the Report. Drag headers from
the Field chooser to the Report to add columns. To remove a column, drag the header down
from the header row.
x Copy - is available when something is marked in the Report and then copies the selection.
x Select all - selects all contents of the Report thus allowing all contents to be copied.
x Expand all groups - expands all groups when some or all collapsed. Groups are created by
dragging a header to the area above the headers.
x Collapse all groups - collapses all groups in the case when some or all are expanded. Groups are
created by dragging a header to the area above the headers.
x Save layout - saves the current column headers and groups as the default for next time the report
is opened.
x Load saved layout - opens the saved layout for column headers and groups.
x Restore default layout - removes any customization of the layout and displays the Umetrics
default layout.
Note: Save layout does not save changes to the selection in Organize.
Report columns description

The columns in the Report window are described in this subsection.
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To add columns, use the Organize | Field chooser from the toolbar, or Columns on the shortcut menu. To
remove columns, just drag the column from the header row.
The default layout is different depending on whether the project is batch or regular, but the columns
available are the same.
Column Description and illustration
Icon signaling severity:
- a HiHi/LoLo alarm was triggered, then reset:

Severity
- a Hi/Lo warning was triggered, then reset:
- a note was added, here displayed with increasing importance:
Icon signaling importance:
- no alarms were triggered or there is a note of low importance :

- a warning alarm was triggered or a medium importance note was added:
Importance nothing.
- a critical alarm has been triggered or a high severity note has been added:
- reset alarm:
Icon signaling which type of event has happened:
Type - an alarm:
- a note:
Model Model name from SIMCA, for instance "M1, Process under control".
Vector Vector that the alarm was triggered in, for instance 'YPred'.
Observation Time the alarm was triggered or note was added.
Batch specific
Batch Batch ID from the external database
Maturity The maturity value at the triggered alarm or note.
Batch start time Start time, in the external database, for the batch.
Batch stop time Stop time, in the external database, for the batch.
Phase start time Start time, in the external database, for the phase.
Phase stop time Stop time, in the external database, for the phase.
Window group
The Window group contains the window commands Cascade, Tile horizontally, Tile vertically, Close,
Save workspace and Switch windows. Clicking the Window group dialog box launcher opens the
Arrange Windows dialog.
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Save workspace
The configuration of the Client's open projects and plots can be saved as a workspace. All workspaces are
saved on the Server. Workspaces can be opened by any user, while only an administrator with
workspace management permissions can save or delete workspaces.
To save a workspace, open the projects and plots that you want the workspace to contain, on the View tab,
in the Window group, click Save workspace, give the workspace a unique name, and then click Save.
Note: Only open configurations and plots are saved in workspaces.
See also the Workspaces section in the Project administration chapter.
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Tools
Introduction
The Tools tab holds the buttons: Select, Zoom, Zoom out, Sort, Drill down, Add note, Create list, and
Save as.
Select - Marking tool

The Select-button is used to select which type of marking to use.
Click the small arrow below the button and click the type of marker from the menu. The available marking
types are:
x Free-form selection: Allows marking to take any shape (default).
x Rectangular selection: Marks in a rectangular shape.
x Select along the X-axis: Marks as a vertical bar.
x Select along the Y-axis: Marks as a horizontal bar.
Note: To keep the marked points marked, while marking new points, hold down CTRL. The marked points
then belong to the same group of marked items.
Deselecting/unmarking points
To deselect points in a plot, click a white area in the plot.
To deselect points in a list, mark the first row.
Displaying properties of the item

When positioning the cursor on an item in a plot, the marker behaves as a pointer and displays the name
and coordinates of the observation or variable.
Creating contribution plots

With any marker:
1. Double-click an observation in a score plot for instance. The contribution plot opens, comparing
the variable values of the selected observation to the average of all the observations in the
workset. This plot indicates why the selected observation is different from the average.
2. Click the first observation, and then double click the second observation. The resulting
contribution indicates why the first observation differs from the second.
For more about creating contribution plots, see the Drill down section in the Tools chapter.
Zoom
To zoom in a plot, click the Zoom tool in the Zoom group. By default Zoom in is selected.
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Use the Zoom menu to select the type of zoom from the drop down menu:
x Zoom in: Magnifies a rectangular region
x Zoom X: Magnifies a region along the x-axis
x Zoom Y: Magnifies a region along the y-axis
x Zoom subplot: Magnifies a subplot in a multi-plot display.
Then mark the desired region, or subplot, of the plot to zoom.
Note: With any zooming type selected, double-clicking a subplot automatically zooms the subplot.
Zooming out
Click Zoom out to revert zoom to original scale in the steps taken when zooming.
Sort
The contribution column plots can be sorted ascending or descending.
To sort
1. Open the contribution plot.
2. On the Tools tab, click Sort.
The resulting plot is sorted by absolute value with the largest absolute column to the left.
By clicking the Sort arrow, you can select to:
x Sort by absolute value (default when clicking Sort) - see above.
x Sort by value - leaving the plot sorted with the largest positive column to the left and the
smallest value to the right.
x Sort by name - leaving the plot sorted alphabetically using the displayed variable ID.
x Original sort order - reverting the sorting to standard order, that is, the variables are displayed in
the same order as the BioPAT® SIMCA workset.
Drill down
The Drill down button becomes available in the Marked Items group, on the Tools tab, after marking one
or more points.
The table lists, the different results possible when using the Drill down button.
Marked points Drill down result
Time points for regular or batch A contribution plot.
evolution.
Batch points in batch level. A contribution plot of the points vs. average batch.
Contribution column for regular A variable plot.

or batch evolution.
Score (t) contribution column in A batch evolution contribution plot.

batch level.
Contribution column for a batch A batch level variable plot.

condition in batch level.
Contribution column that is not A batch evolution variable plot.

score and not a batch
condition, in batch level.
Contribution plots for batch projects

When a time point or batch point deviates from the expected, a contribution plot displays which variables
that have contributed to the deviation.
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Tools
In the table, the types of contribution plots available are listed.

Plot type Using Drill down
One point compared Mark a point and click the Drill down button.
to the average.
One point compared Click on one point and then on the other. Note that they are
with another point. marked in different colors. Click the Drill down button.
A group of points Mark all points in the group by circling them or by holding down
compared to the the CTRL key and clicking the points. Then click the Drill down
average. button.
One point compared Mark all points in the group by circling them and then click the
to a group of points. single time point (without holding down the CTRL key). Click
the Drill down button.
A group of points Mark all points in the first group by circling them or by holding
compared to down the CTRL key and clicking the points. Then mark all points
another group of in the second group by circling them or by holding down the
points. CTRL key and clicking the points. Click the Drill down button.
Note: When marking a group of points and then clicking Drill down, the Select Observations dialog
opens. To not include all points when calculating the contribution plot, clear the relevant boxes.
Contribution plots not available

The following contribution plots cannot be created in BioPAT® SIMCA-online batch projects
x Contribution plots of time points in different phases or sub-batches in batch evolution.
Display a contribution or variable plot
To display a contribution or variable plot, use one of the following methods:
x Double-click the point or column.
x Mark and click Drill down in the mini-toolbar.
x Mark and on the Tools tab, in the Marked items group, click Drill down.
x Mark, right-click, and click Drill down.
Marking first one point or group and then another, in a score or y predicted plots, results in a contribution
plot of the first marking vs. the second marking.
When marking in a contribution plot of a regular or batch evolution model, and using the Drill down, the
result is a variable plot.
When marking in a batch level contribution plot, where the model was built from score variables from the
batch evolution model, the resulting plot is a batch evolution contribution plot.
Contribution plot for time points outside the limits
For batch evolution models, the active batches are projected in control chart plots as they are evolving.
When a batch time point is outside the limit, this indicates that at this time point the batch data vector has
some variables that are larger or smaller than the variable of the average batch computed from the
workset in BioPAT® SIMCA offline.
Contribution score plots
When a point is found outside the limits, double-click the selected time point to display the contribution
plot.
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The contribution plot displays the difference between the variables of the active batch at the selected time
point and the variables of the average batch at that same time point, weighted by the loading p of the
corresponding dimension.
Trend plot of the variable

Double-click the variable with the large value in the contribution plot to display the dynamic trend plot of
that variable. This plot is also updated in real time as the active batch evolves.
Contribution DModX plots

When a time point has a DModX or DModX+ outside the critical limit, double-click the time point to
display the contribution plot.
The contribution plot shows the variables residuals for the selected time point weighted by the variable
importance in the model RX.
Trend plot
Double-click a variable to display its trend plot.
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Tools
Contribution Hotelling's T2Range plots

When the value for Hotelling's T2Range is outside the limit, double-click the time point to display the
contribution plot.
The contribution plot shows the deviations for the selected time point weighted by the loading p of the
corresponding dimensions.
Trend plot
Contribution Y Predicted plots

When a time point in the Y Predicted plot is outside the limits, double-click the time point outside the
limits to display the contribution plot.
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The contribution plot shows the deviations for the selected time point weighted by CoeffCS.
Trend plot
Contribution plot of the difference between batches at a selected time point

To display the contribution plot between the active batch at a selected time point and a reference batch, do
the following:
1. Select the reference batch from the Batches box.
2. Mark the two points by clicking one, and then the other.
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Tools
3. Click Drill down in the Marked items group on the Tools tab.
4. Double-click the variable if you want to display the trend plot.

Contribution plot for batch points outside the limits
When the last observation of a new batch or model has been read from the server, the batch level
observation for that batch is created and the batch is displayed in the batch level plots.
When a batch point is positioned outside the limit, this indicates that the batch differs from the batches
used in the workset in BioPAT® SIMCA offline.
When a batch is found outside the ellipse in the score scatter plot, mark the batch, and click the Drill
down button to display the contribution plot.
The batch level score contribution plot shows the difference in the X variables between the selected batch
and the model center, weighted by the loadings p[1] & p[2] for PCA and w*[1] & w*[2] for PLS.

Double-click the deviating batch in the DModX plot to display the contribution plot.
The batch level DModX contribution plot shows the variable residuals for the selected batch weighted by
the variable importance in the model RX.
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Double-click a deviating batch in the Hotelling's T2Range plot to display the contribution plot.
The batch level Hotelling's T2Range contribution plot shows the deviations for the selected batch
weighted by the loading p of the corresponding dimensions.

When a value is large or small in comparison with the others in the Y Predicted plot, this indicates
something unusual about that batch.
Double-click the batch to display the contribution plot.
The contribution plot shows the deviations for the selected batch weighted by CoeffCS.
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Tools
Batch evolution contribution from batch level contribution

When the variables in the batch level model are scores from the batch evolution model, the variables
displayed in the batch level contribution plots are scores, t1, t2 etc over the evolution of the batch. Double-
clicking a score column in the batch level contribution plot then opens the batch evolution contribution
plot.
The plot displayed here was created by double-clicking a column in the Batch Level DModX Contribution
plot found in the section Contribution DModX plots subsection earlier in this chapter.
Contribution plots for regular projects

When a point deviates from the expected, a contribution plot displays which variables have contributed to
the deviation.
In the table, the types of contribution plots available are listed.
Plot type Using Drill down
One point compared Mark a point and click the Drill down button.
to the average.
One point compared Mark one point and then the other. Note that they are marked in
with another point. different colors. Click the Drill down button.
A group of points Mark all points in the group by circling them or by holding down
compared to the the CTRL key and clicking the points. Then click the Drill down
average. button.
One point compared Mark all points in the group by circling them and then click the
to a group of points. single time point (without holding down the CTRL key). Click the
Drill down button.
A group of points Mark all points in the first group by circling them or by holding
compared to down the CTRL key and clicking the points. Then mark all points
another group of in the second group by circling them or by holding down the
points. CTRL key and clicking the points. Click the Drill down button.
Note: In the DModX contribution plot, the columns indicate the deviations from the normal correlation
structure (model), NOT from the average point or another reference point. The dominating columns
indicate which variables deviate most from the correlation structure, and the sign of the column (down =
minus and up = plus) indicate in which direction the variables deviate.
Display a contribution or variable plot

To display a contribution or variable plot, use one of the following methods:
x Double-click the point or column.
x Mark and click Drill down in the mini-toolbar.
x Mark and on the Tools tab, in the Marked items group, click Drill down.
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x Mark, right-click, and click Drill down.

Marking first one point or group and then another, in a score or y predicted plots, results in a contribution
plot of the first marking vs. the second marking.
When marking in a contribution plot of a regular or batch evolution model, and using the Drill down, the
result is a variable plot.
When marking in a batch level contribution plot, where the model was built from score variables from the
batch evolution model, the resulting plot is a batch evolution contribution plot.
Contribution plot for deviating points
The points in the process are projected in plots as they are evolving. When a time point deviates from
normal behavior, this indicates that at this time point the data vector has some variables that are larger or
smaller than the variable of the average computed from the workset in BioPAT® SIMCA offline.
Independent of which type of contribution that is being created, when more than one point is marked (a
group is marked) the Select Observation dialog opens enabling revision of the selection.
Contribution plot of the difference between selected time points

To display the contribution plot between a selected point and another point:
1. In the relevant plot, mark the two points by clicking one, and then the other.
2. Mark and then click Drill down in the Marked items group on the Tools tab.
3. Double-click the variable if you want to display the trend plot.
When a point deviates, double-click the selected time point to display the contribution plot.
The contribution plot displays the difference between the variables of the marked point and the variables at
the workset average, weighted by the loading w* of the corresponding dimension.
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Tools

When a time point has a DModX that deviates, double-click the time point to display the contribution plot.
The contribution plot shows the variables residuals for the selected point weighted by the variable
importance in the model RX.
Note: When DModX+ is displayed in the plot, the resulting plot is a plot displaying Hotelling's T2Range
and DModX since these plots reveal which of the two, if not both, is responsible for the deviating
observation.

When the value for Hotelling's T2Range deviates, double-click the time point to display the contribution
plot.
The contribution plot shows the deviations for the selected time point weighted by the loading w* of the
corresponding dimensions.
Trend plot
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When a point in the Y Predicted plot deviates, double-click it to display the contribution plot.
The contribution plot shows the deviations for the selected point weighted by CoeffCS.
Note: For models with only one y-variable, w*[1] is used as weight in the contribution plot.
Adding notes
Notes can be added to a point marked in a plot or in the Report as follows:
x Plot: mark a point and click Add note:
x in the mini-toolbar,
x in the Marked items group on the Tools tab or
x on the shortcut menu.
x Report: mark the row and click Add note in the toolbar or in the shortcut menu.
When adding a note the following dialog appears.
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Tools
In the Add Note: Specify Severity and Text dialog, select the Severity level, and enter the text for the
note in the Comment field.
The Severity levels available are: Low, Medium (default), or High where they result in different note
symbols in the plot, in the Plot Details window, and in the Report:
x Low -
x Medium -
x High -
Editing notes
To modify a note use one of the following methods:
x In the plot, mark the point with the note and click Add note.
x In the Report, mark the note and click Edit note in the toolbar.
x In the Plot Details window, double-click the note.
Deleting notes
To remove a note use one of the following methods:
x Mark the note in the Report and click Delete note in the toolbar.
x In the Plot Details window, mark the note and press DELETE on your keyboard.
Create list
The data in each plot can be displayed as a list with tabs by clicking Create list on the Tools tab. This list
includes data for dynamic limits.
For multiplots, the data from each subplot is found in a tab named by the phase ID.
Note: Creating a list can also be done by pressing CTRL+L or right-clicking the plot and clicking Create
list.
Save as
On the Tools tab, click Save as to save the active plot or list to a specific file name and path.
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Plots can be saved as Bitmap files (*.bmp), EMF files (*.emf), JPEG files (*.jpg), or PNG files (*.png).
Lists can be saved as DIF Files (*.dif), Matlab Files (*.mat), or Text Files (*.txt).
To save a plot:
1. Display it and make sure it is active.
2. On the Tools tab, click Save as. The Save Plot dialog is displayed.
3. In the Size box you can choose between
- Custom
- A) 600x375 (Suitable for portrait (A4, US Legal, etc.))
- B) 300x300 (Square, fits two side by side)
- C) 600x600 (Square)
- D) 755x465 (Suitable for PowerPoint, one per slide)
- E) 755x270 (PowerPoint, fits two above and below)
- F) 370x465 (PowerPoint, fits two side by side)
- G) 800x600 (4:3 format)
- H) 1024x768 (4:3 format)
- I) 1280x720 (16:9 format, HD 720)
- J) 1920x1080 (16:9 format, HD 1080)
- Original size
4. In the dialog select the Keep aspect ratio check box to keep the proportions of the plot as on the
screen (Original size) or according to a predefined plot size.
5. Click OK when done.
6. Select location, file name, and file type. Click Save.
To save a list:
1. Display it and make sure it is active.
2. On the Tools tab click Save as. The Save dialog is then displayed.
3. Select location, file name, and file type. Click Save.
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Help
Introduction
The Help menu holds the standard help menu commands. Clicking the ?-button opens the help file, as
does clicking Help | View help.
Sartorius-Stedim on the Web

If you have an Internet connection, you can visit the web page of Sartorius-Stedim (www.Sartorius-
Stedim.com) to get the latest news and other information by clicking Sartorius-Stedim on the Web on
the Help menu.
Support
Click Help | Support to open the Support page on the Sartorius-Stedim website.
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Introduction
In the Project Administration dialog, opened by clicking File | Administration | Project
administration, the projects and configurations currently known to the Server are listed. Users with
configure management privileges can view and change the settings of the Project Administration
dialog.
In the Project Administration dialog, the following features are available:

x Organize with Show deleted items, New folder, Delete, Rename, and Save workspace
allowing flexible organization of configurations.
x Upload BioPAT® SIMCA project to import the BioPAT® SIMCA project and add project
configurations for BioPAT® SIMCA-online. The Configure dialog is automatically opened after
selecting a SIMCA project.
x Save workspace to save the currently open project configurations and plots as a workspace. Only
available when no folder, project or configuration is marked.
x Access rights for folders. Permissions to access folders and their content can be specified per
group.
x Restore and Purge projects and configurations. After a project or configuration has been deleted
it can be restored, which means that it returns as it was, or it can be purged, which means that it is
permanently deleted.
x Open/Close depending on whether the marked project configuration is currently open or not. See
also the Open subsection in the File chapter.
x Add configuration, see the Add configuration for batch project and Add configuration for
regular project sections.
x Manage data with Configuration, Repredict data and Delete predicted data.
Organize
In Organize the following features are available:
x Show deleted items - Displays also deleted items that have not been purged.
x New folder - Create a new folder and group configurations/workspaces as desired.
x Delete - Delete the marked configuration or workspace.
x Rename - Rename a configuration, workspace or folder.
x Save workspace - Save the currently open project configurations and plots as a workspace.
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Access rights
The Access rights feature controls which folders group members can see and open.
To specify access rights, mark a folder and click Access rights.
Note: Permissions are controlled by the role specified for the individual user in the User administration
dialog.
Add configuration for batch project

To import a new batch project and configure it:
1. Click Upload BioPAT® SIMCA project (available when a project or the Type: Configurations
line is marked).
2. Select the BioPAT® SIMCA project and click Open. The configuration wizard opens.
When loading a BioPAT® SIMCA project, the following files are created specific to that project:
x Static information of the BioPAT® SIMCA project (.solproject).
x A copy of the BioPAT® SIMCA project (.usp).
When adding a configuration for a batch project, the following files are created:
x Current project and configuration id (.solconfig).
x Current configuration settings and history plus audit trail content (.solconfig.db).
x Databases for local centering for each phase (_LC_Pn.db and _LC_Pn.sbdb).
x Databases for the results for each phase and sub-batch combination (_LL_Sn.db and
_LL_Sn.scdb).
x Databases for the results for each batch level model (_UL_Mn.db and _UL_Mn.sbdb).
x Databases for batch conditions (_BC.db and _BC.sbdb).
The configuration wizard for a batch project includes the following pages:
Import configuration - to import an already created configuration-file.
Batch node - to specify the batch node of the current configuration.
Batch evolution - to specify Execution interval.
Time ranges - to specify scanning time period in search of incomplete batches and time range that
specifies a batch as recent.
Unit groups - to specify how the process is set up.
Phase conditions - to specify phase and sleep conditions and the batch tag.
Phase tags - to associate the variables to the correct tags in the database.
Variable aliases - to optionally specify aliases to display in plots.
Local centering - to specify the tag supplying local centering information.
Target values - to specify target and limits for specific variables to display in plots and trigger univariate
alarms.
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Control limits - to specify default limits in the batch evolution plots.

Alarms for batch evolution - to specify multivariate alarms for the batch evolution models.
Alarm triggers for batch evolution -to specify trigger event.
Write back - to specify batch evolution information to be written back to the database.
Batch level - to specify which batch level models to include.
Batch conditions - to specify tags for batch condition variables.
Alarms for batch level - to specify multivariate alarms for the batch level models.
Write back - to specify batch level information to be written back to the database.
Export configuration - to save the configuration to file.
Import configuration for the project

If you have a BioPAT® SIMCA-online configuration file you want to use, click the Import configuration
button, in the Import configuration page, and select the .bcg-file.
After importing the configuration file, the Description section displays the name of the selected
configuration file warnings if there are obvious mismatches between the selected project and the imported
configuration file.
To start configuring, or view/modify the configuration in the case where you have imported a
configuration file, click Next.
To save the configuration for import, on the Export configuration page of the Configure wizard click the
Export configuration button and specify where to save it and under which name.
Importing configuration file from previous version
You can import a .bcg-file from a previous version. However some configurations are not imported.
When converting a SIMCA-P+ batch project with both observation and batch level, the converted project
will rename the batch level models. For instance, in the previous version the batch level model could be
M1, in BioPAT® SIMCA 13 a batch level model can never be M1.
Thus, when importing a .bcg-file created in a previous version, the batch level model settings are not
imported, nor are export settings (write back) or execution intervals for phases.
Batch node
The batch node contains information about start and stop times of the batches.
On the Batch node page, select the node that contains information about the active and historical batches
of the project you are configuring. Then click Next.
If no node is listed here you need to check the SimApi configuration, see the subsection Parameters to
initiate communication with SimApi in the Configuration of the Server section in the Installation and
configuration chapter.
Nodes that are unavailable in the external system are displayed in red. If the external system was started
after the server, stopping the server and restarting it might solve the issue.
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The Batch identifier filter field enables batch selection by batch ID. For instance, if the Batch ID contains
the recipe used by the batch, entering that recipe will result in using this selection of batches in the
predictions in BioPAT® SIMCA-online.
Wild card symbols '?', and '*' are allowed in specifying batch IDs. For example “?LH*” selects batches
with IDs such as SLH2 or QLHSW, etc.
Batch evolution
Specifying execution interval for phases
When there are phases in the project, you have to specify the execution interval for each phase in the
Batch evolution page.
The unit of the Execution interval is seconds.
The execution interval is the sampling interval of the BioPAT® SIMCA-online Server, i.e. how often the
Server samples the PDB for batch data and executes the models.
Note: The execution interval in BioPAT® SIMCA-online must be the same as the sampling interval used in
the SIMCA model.
After filling in all execution intervals, click Next.

Time ranges
Catch-up
Catch-up can be performed if a batch was started but not finished, while running BioPAT® SIMCA-
online.
In the Catch-up time range field, enter the time in minutes (default), hours, or days that BioPAT®
SIMCA-online should retrieve in the database in search for uncompleted batches. Leaving the default '0'
disables the catch-up function.
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When enabling the catch-up function by entering a time allowance, the recommendation is to enter a value
that is twice the length of the average batch.
Recent batches
The value in the Recent batch time range field defines batches that are considered recent batches and
thus are displayed when selecting the Recent batches check box in the Batches box and in the Overview
window.
Unit groups
A unit group is a process step, for instance a granulator. The unit group contains one or more identical
units. Each unit is a physical equipment/machine/vessel that processes a batch or sub-batch. A sub-batch
is a part of a batch. Sub-batches are present when an entire batch cannot be processed in a single unit.
Each batch passes through one or more phases.
When a unit group is marked use the Add unit group, Remove unit group and Rename unit group
buttons to organize the unit groups.
When a unit is marked, use the Add unit, Remove unit and Rename unit buttons to organize the units.
If some part of the batch process separates batches in sub-batches, right-click and click Show sub-
batches.
When there are phases in the project, you have to specify in which unit and sub-batch the phase will be
executed by selecting the respective phase check box in that unit group or sub-batch.
Note: Expand all or Collapse all unit groups by right-clicking the dialog box.
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When all unit groups, units, and sub-batches have been defined and phases selected, click Next.
Phase conditions
In the Phase conditions page, the tags in BioPAT® SIMCA-online must be connected with the
corresponding tags in the server. For phases, this includes defining all phase conditions.
The following needs to be connected and configured:
x Batch Identifier Tag with the batch identifying variable (Batch ID).
x Optionally Sleep Condition.
x Phase Conditions.
Configuring phase and sleep conditions
The phase conditions have to be configured to enable prediction using the correct phase model. Optionally
you can configure sleep conditions to not include nor display observations satisfying the entered sleep
condition expression.
In the example here, GranulatorPhase1 is running when the G1:Granulator1Phase (the first phase
condition tag) text is equal to P1.
For each phase, mark the phase and click the Configure-button to open the configure condition dialog.
1. In Tag name, select the tag holding the trigger or part of the trigger.
2. Select the type of trigger in Logical expression and enter a value in the Value field.
3. Click the And, Add, or Or button and note that the selected tag trigger is displayed in the
Expression field.
4. Repeat 1-3 to add another condition. If the phase should be triggered when both expressions are
true, click the And button. If the phase should be triggered when either one of the expressions is
true, click the Or button. Under Expression the complex expression is displayed.
5. When done click OK or Next.
Adding sleep triggers is done in the same manner, using the dialog displayed here:
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After cross referencing all tags, click Next.

Configure condition dialog explanation
The configure condition dialog works as follows.
Logical expression box
In the table, the available logical expressions are listed.
Logical Triggers when Use when

expression
Value equal The numerical tag value equals A phase is running when a
to the value entered in Value. variable equals a certain value.
Value not The numerical tag value does A phase is running when a
equal to not equal the value entered in variable does not equal a certain
Value. value.
Value less The tag value is smaller than A phase is running when a
than the value entered in Value. variable decreases below a
certain value.
Value less The tag value is smaller than, A phase is running when a
than or equal or equal to, the value entered variable decreases to or below a
to in Value. certain value.
Value greater The tag value is greater than A phase is running when a
than the value entered in Value. variable increases above a certain
value.
Value greater The tag value is greater than, A phase is running when a
than or equal or equal to, the value entered variable reaches or increases
to in Value. above a certain value.
Text equal to The tag value equals the text A phase is running when a
entered in Value. variable equals a certain text.
Text not The tag value does not equal A phase is running when a
equal to the text entered in Value. variable does not equal a certain
text.
Text starts The tag starts with the text A phase is running when a
with entered in Value. variable starts with a certain text.
Text ends The tag ends with the text A phase is running when a
with entered in Value. variable ends with a certain text.
Text contains The tag contains the text A phase is running when a
entered in Value. variable contains a certain text.
Value field
In the Value field, enter the value that triggers the phase.
And and Or buttons
When using more than one logical expression to trigger a phase:
x Click the And button when both expressions have to be true to trigger the phase.
x Click the Or button when either expression being true triggers the phase.
Expression field
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In the Expression field, the currently added trigger expression is displayed. In addition standard
mathematical and some logical operations are available by typing in this field. For more, click the question
mark.
Phase tags
On the Phase tags page, each variable of each phase from SIMCA has to be associated with the correct
variable from the database.
By default the tag associations are done for <All Phases>. Select a single phase if you want the
associations to apply to that phase only.
To associate:
1. Mark the cell
2. In the list of notes, mark the correct node
3. In the Tags list, double-click the variable.
For all methods to associate tags, see the Associating tags subsection next.
Use Tag filter field above the Tags list to search in the variable list.
Use the shortcut menu to facilitate the association.
After associating variable IDs from the BioPAT® SIMCA models with the tags in the external database,
click Next.
Associating tags
The variables are associated by clicking the cell in the spreadsheet, and then entering the name by one of
the following methods:
1. Double-clicking the variable from the database in the Tags list. Alternatively, right-clicking the
variable in the Tags list and clicking Associate tag.
2. Typing the name.
3. Pasting the name.
Using the Tag filter field
The Tag filter field, found above the Tags list in the dialog, is not case sensitive, meaning that a and A are
perceived as the same character. Typing in the Tag filter field instantly loops the available variables in the
Tags list to match each new character, leaving all variables matching the string marked.
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Shortcut menu
Use the spreadsheet shortcut menu to Copy, Cut, Paste, Select all, Find and replace, Add prefix, or
Add suffix.
Variable aliases
In the Variable aliases page you can optionally specify alternative IDs for your variables.
Note: Identifiers entered in the Alias column are by default displayed in plots and lists.
Local centering
When a phase in your offline model has used local centering, i.e. the variables for batches in that phase
have been centered with values read from a file at import, you can specify tags containing new values for
these variable centers on the Local centering page.
Mark the empty cell in the Tag column and associate with the appropriate variable in the Tags list.
Batches with no values for local centered variables, are centered using the average value for that variable
in the workset.
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Target values
On the Target values page, enter low, target, and high limits in the Lo Limit, Target, and Hi Limit cells
respectively. These limits will be displayed in plots but do not trigger alarms when the Alarms cell is left
empty.
Note: For batch projects with phases, you must select for which phase the target values should be
displayed/trigger alarms. By default the target values are displayed/triggered for <All Phases>.
Alarms
Use the Alarms column to let the Target values page not only specify limits to display in plots but also
univariate alarms. You can select:
x Missing - the alarm is triggered when missing value is read for the variable.
x Outside - the alarm is triggered when the read value is either below the Lo Limit or above the Hi
Limit.
x Outside or missing - the alarm is triggered when a missing value is read or the read value is
either below the Lo Limit or above the Hi Limit.
Control limits
In the Control limits page, select which limits to default display in all batch evolution control charts. The
Variable box has a list of the batch evolution variables and a <Default> entry. The limits that you specify
as default will apply to all batch evolution control charts where you have NOT specified individual limits
for the displayed variable.
If you want more, or other, levels than +/- 1, 2, 3 standard deviations, e.g. also 1.5 standard deviations,
click the Add button and enter the limit.
To remove one of the added limits, click the Remove button and type the limit to remove.
Note: Only user added limits can be removed.
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Limits for specific variables

To specify which limits to be displayed for a specific variable, select the variable in the Variable box,
then select the desired limits in the Control limits box.
Note: You can always switch limits in an open plot by right-clicking it and selecting Properties.
Alarms for batch evolution

The Overview window normally displays all batches in green. By configuring alarms, the color of a batch
or phase can be changed to yellow (warning) or red (critical) when the values of specific batch vectors fall
outside a set of predefined limits for a certain number of observations in the batch. In the plots, triggered
alarms are illustrated using a colored alarm symbol.
There are two degrees of limits: Lo Limit and Hi Limit representing the lower severity (warning), and
LoLo Limit and HiHi Limit representing the higher severity (critical). For each vector in each phase, you
can define any combination of limits.
This section describes batch evolution alarms. For details about batch level alarms, see the Batch level
alarms section later in this chapter.
Vectors
The table below shows the vectors for which alarms can be added.
Vector Component Default Limit
DModX No component. +3 and 4 standard deviations.
t One specific component. ±3 and 4 standard deviations.
T2Range From and To components. T2Crit at 0.05 and 0.01 significance

level.
Note: Univariate alarms can be added for individual variables in the Target values page.
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Adding an alarm
1. In the Phase box, select a phase or leave <All phases> selected.
2. Select Vector and, when applicable, component.
3. Set the Hi Limit and/or HiHi Limit. The Lo Limit and LoLo Limit are automatically filled in as
the negatives of the Hi Limit and HiHi Limit. The HiHi limit must be numerically larger than
the Hi limit.
4. Click Add and note that the alarm is added to the list in the dialog.
Removing an alarm
Mark the alarm, and click Remove.
Updating an alarm
Mark the alarm, change the settings, and then click Update. Update is only available for specific phases,
not for <All phases>.
Note: An alarm can be added for each component for t and for each component combination for T2Range.
Alarm triggers
After specifying the alarms in batch evolution alarms the Alarms page, the Alarm triggers have to be
specified.
Triggers are events that activate the alarm. There are two types of triggers:
x Consecutive activates when X observations in a row are outside the limit.
x Total activates when Y observations are outside the limit during a phase.
The default values for X and Y are 3 and 10 respectively. To change these values, enter new values in the
Consecutive and Total columns.
Note: Alarm triggers cannot be left empty when alarms have been specified.
Write back
The PDB can retrieve the current values of all output variables (computed by the model) for storage in the
HDB. When you configure the PDB you must define blocks for the output variables you want to connect.
The PDB is a global database so if you are executing several projects you will have, for example, per
project, DModX for the batch evolution and batch level models. In the PDB you should give these
DModX from different projects unique names.
In the Write back pages for the batch evolution and batch level respectively define which predictions,
limits and information to automatically export to the process database.
Figure: Write back page for batch evolution. The page is identical for batch level but Phase is Model.
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Connect the vectors to the tags as follows:

1. In the Vector box select the vector to export.
2. When applicable, select the relevant component or variable in the From, To, Component, and
Variable boxes.
3. Click the Add button.
4. Associate the appropriate tag to the added item.
For more about how to connect to the tags, see the Associating tags section earlier in this chapter. Use the
Tag filter field to help you find the desired tag. See also the shortcut menu to facilitate the association.
Result variables for batch evolution
Available prediction results that can be exported for batch evolution are:
Name in dialog Description Result exported
Predictions
DModX Distance to Model DModXPS
t Scores tPS
T2Range Hotelling's T2Range T2RangePS
YPred Predicted Y YPredPS
Maturity Observed maturity YVar(as WS) treated as the y in the model.
Limits
T2RangeCrit Critical limit for T2Range T2Crit for significance level 0.01.*
DModXAverageBatch DModX for average batch DModX for average batch.
DModXStdDevBatch Standard deviation for Standard deviation for DModX.

DModX
T2RangeAverageBatch T2Range for average batch T2Range for average batch.
T2RangeStdDevBatch Standard deviation for Standard deviation for T2Range.

T2Range
TAverageBatch Scores for average batch t for average batch.
TStdDevBatch Standard deviation for Standard deviation for t.

scores
YPredAverageBatch Y Predicted average batch YPred for average batch.
YPredStdDevBatch Y Predicted standard Standard deviation of YPred.

deviation
Information
AlarmStatus Batch evolution alarms 0 when no alarm was triggered.
1 when one or more warning alarms were
triggered.
2 when one or more critical alarms were
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triggered.
BatchID Batch identifier BatchID for the active batch.
ConfigurationName Configuration name Configuration name, by default project name

plus model title.
ConfigurationUniqueID Configuration identifier Internal project configuration identifier.
ModelID Model identifier Model in the BioPAT® SIMCA project, for ex

M1.
ModelNumber Model number Model number for the model.
PhaseID Phase identifier Phase ID from the SIMCA project.
PhaseNumber Phase number Phase number in the SIMCA project.
ProjectName Project name BioPAT® SIMCA project name.
ProjectUniqueID Project identifier Internal project identifier.
SineTime Variable used to signal that Sine of the current time. Results in values
the server is running. ranging between -1 and 1.
*Always 0.01 significance level.

To export alarms, associate the alarms for each unit and phase with the appropriate external variable.
Vector box content
Batch level
On the Batch level page, select which batch level models you want to include.
Under Batch level model prediction in the lower part of this dialog, select when to predict for the batch
level models. You can select to:
x Predict at model finish
x Predict at model finish and repredict at batch finish
x Predict at batch finish
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Batch conditions
When the offline batch level model has batch conditions, there is a Batch conditions page in the wizard.
Associate the batch condition tags in the Batch condition page, by marking the empty cell in the Tag
column and associating it with the appropriate variable in the Tags list.
Alarms for batch level

The Overview window normally displays all batches in green. By configuring alarms, the color of a batch
or phase can be changed to yellow (warning) or red (critical) when the values of specific batch vectors fall
outside a set of predefined limits. In the plots, triggered alarms are illustrated using a colored alarm
symbol.
This section describes batch level alarms. For details about alarms for batch evolution models, see the
Alarms for batch evolution section earlier in this chapter.
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There are two degrees of limits: Lo Limit and Hi Limit representing the lower severity (warning), and
LoLo Limit and HiHi Limit representing the higher severity (critical). For each vector in each model, you
can define any combination of limits.
Vectors
The table below shows the vectors for which alarms can be added.
Vector Component/Variable Default Limits
DModX No component. DCrit at 0.05 and 0.01 significance
level.
t One specific component. ±3 and 4 standard deviations.
T2Range From and To components. T2Crit at 0.05 and 0.01 significance

level.
YPred Selected variable. ±3 and 4 standard deviations.
Note: Alarms cannot be added for batch level variables.
Adding an alarm
1. In the Phase box, select a phase or leave <All phases> selected.
the Hi limit.
Removing an alarm
Updating an alarm
Mark the alarm, change the settings, and then click Update.
Note: An alarm can be added for each component for t, for each component combination for T2Range,
and for each y-variable for YPred.
Write back
The PDB is a global database so if you are executing several projects you will have, for example, per
project, DModX for the batch evolution and batch level models. In the PDB you should give these
DModX from different projects unique names.
In the Write back pages for the batch evolution and batch level respectively define which predictions,
limits and information to automatically export to the process database.
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Figure: Write back page for batch evolution. The page is identical for batch level but Phase is Model.

Variable boxes.
Result variables batch level and regular
Available prediction results that can be exported for batch level and regular are:
Predictions
t Scores tPS
YPred (available when Predicted Y YPredPS.

applicable)
Limits
DCrit Critical distance for DModX DCrit*.
TMean Center of the hotelling's Average of the score vector for the selected
ellipse in the score scatter component.
plot.
TCrit The radius of the hotelling's TCrit for the selected component.
ellipse in the score scatter
plot.
TStdDev Standard deviation of t. Standard deviation of t.
T2RangeCrit Critical distance in the T2RangeCrit* is the critical limit in the

Hotelling's T2Range plot. Hotelling's T2Range-plot.
Information
AlarmStatus Batch level alarms 0 when no alarm was triggered.
triggered.
triggered.
BatchID Batch identifier BatchID for the active batch. (batch only)
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plus model title.

M1.

To export alarms, associate the alarms for each model with the appropriate external variable.
Vector box content
Export the configuration to file

On the last page of the wizard, click the Export configuration-button to export the configuration to file
(.bcg).
This is useful when adding more than one project with a similar configuration.
To save the configuration to file after completing the configuration, see the Configuration subsection later
in this chapter.
Add configuration for regular project

To import a new regular project and configure it:
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1. Click Upload BioPAT® SIMCA project (available when a project or the Type: Configurations
line is marked).
2. Select the BioPAT® SIMCA project and click Open. The configuration wizard opens.
When loading a BioPAT® SIMCA project, the following files are created specific to that project:
x Audit trail for the project (.audit).
x Static information of the BioPAT® SIMCA project (.solproject).
x A copy of the BioPAT® SIMCA project (.usp).
When adding a configuration for a regular project, the following files are created:
x Audit trail for the configuration (.audit).
x Configuration settings for audit trail (.bcg).
x Current configuration settings (.solconfig). This file is the internal configuration file and cannot
be imported when configuring another project.
x Database for triggered alarms and notes (.solconfig.db)
x Database for the results for the model (_Mn.db and _Mn.scdb)
The configuration wizard for a regular project includes the following pages:
Import configuration - to import an already created configuration-file.
Model - to specify model, execution interval and prediction condition.
Time ranges - to specify the time range displayed in the Overview window and in plots.
Tags - to associate the variables to the correct tags in the database.
Variable aliases - to optionally specify aliases to display in plots.
Target values - to specify target and limits for specific variables to display in plots and trigger univariate
alarms.
Alarms - to specify multivariate alarms.
Write back - To select project results and limits to send to external database.
Export configuration - to save the configuration to file.
Import configuration for the project

If you have a BioPAT® SIMCA-online configuration file you want to use, click the Import configuration
button, in the Import configuration page, and select the .bcg-file.
After importing the configuration file, the Description section displays the name of the selected
configuration file warnings if there are obvious mismatches between the selected project and the imported
configuration file.
To start configuring, or view/modify the configuration in the case where you have imported a
configuration file, click Next.
To save the configuration for import, on the Export configuration page of the Configure wizard click the
Export configuration button and specify where to save it and under which name.
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Importing configuration file from previous version

You can import a .bcg-file from a previous version. However some configurations are not imported.
When converting a SIMCA-P+ batch project with both observation and batch level, the converted project
will rename the batch level models. For instance, in the previous version the batch level model could be
M1, in BioPAT® SIMCA 13 a batch level model can never be M1.
Thus, when importing a .bcg-file created in a previous version, the batch level model settings are not
imported, nor are export settings (write back) or execution intervals for phases.
Model page
Use the Model page of the configuration to specify model, execution interval and prediction condition.
The settings in the Model page are described in the table below.
Setting Description
The selected model using the model number and title from the BioPAT® SIMCA
Selected model
project file.
The execution interval is how often process data tags are read.
Execution interval Enter the desired execution interval. Recommended is to use the execution
interval of the BioPAT® SIMCA project.
Prediction condition, when used, specifies the condition under which predictions
will be performed. When the prediction condition is not fulfilled, there is no
prediction result.
Leaving Prediction condition empty results in continuous predictions of all
incoming data.
Click the button to the right of the Prediction condition field and in the
Configure Prediction Condition dialog:
1. Click the Tag name field button and select the tag to enter the condition
for.
2. Select a Logical expression and enter a value in the Value field.
3. Click Add/And/Or as desired.
Prediction condition When clicking OK the condition is automatically added to the Prediction
condition field.
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Time ranges
The values in the fields in the Time ranges page specify catch-up, what is displayed in the Overview
window and in the plots.
x The Catch-Up time range value specifies the time period (backing up from current) that will be
predicted if the execution is stopped and then resumed. If the Catch-Up time range value is '0',
predictions will only be made for current values when the execution resumes.
x The Default plot time range value specifies the time range displayed in the plots.
x The Overview time range value specifies the time range displayed in the Overview window.
These values can be changed as desired but the fields may not be left empty.
Tags
On the Tags page, each variable from the BioPAT® SIMCA model has to be associated with the correct
variable from the database.
To associate: Mark a (red) cell and double-click the variable in the Tags list.
For all methods to associate tags, see the Associating tags subsection next.
Use the Tag filter field at the bottom of the page to search in the variable list.
Use the shortcut menu to facilitate the association.
After associating variable IDs from the SIMCA models with the tags in the external database, click Next.
Associating tags
The variables are associated by clicking the cell in the spreadsheet, and then entering the name by one of
the following methods:
1. Double-clicking the variable from the database in the Tags list. Alternatively, right-clicking the
variable in the Tags list and clicking Associate tag.
2. Typing the name.
3. Pasting the name.
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Using the Tag filter field

The Tag filter field, found above the Tags list in the dialog, is not case sensitive, meaning that a and A are
perceived as the same character. Typing in the Tag filter field instantly loops the available variables in the
Tags list to match each new character, leaving all variables matching the string marked.
Shortcut menu
Use the spreadsheet shortcut menu to Copy, Cut, Paste, Select all, Find and replace, Add prefix, or
Add suffix.
Variable aliases
In the Variable aliases page you can optionally specify alternative IDs for your variables.
Note: Identifiers entered in the Alias column are by default displayed in plots and lists.
Target values
On the Target values page, enter low, target, and high limits in the Lo Limit, Target, and Hi Limit cells
respectively. These limits will be displayed in plots but do not trigger alarms when the Alarms cell is left
empty.
Note: For batch projects with phases, you must select for which phase the target values should be
displayed/trigger alarms. By default the target values are displayed/triggered for <All Phases>.
Alarms
Use the Alarms column to let the Target values page not only specify limits to display in plots but also
univariate alarms. You can select:
x Missing - the alarm is triggered when missing value is read for the variable.
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x Outside - the alarm is triggered when the read value is either below the Lo Limit or above the Hi
Limit.
x Outside or missing - the alarm is triggered when a missing value is read or the read value is
either below the Lo Limit or above the Hi Limit.
Alarms
The Overview window displays each model in green. When configuring alarms, the color of a model
changes to yellow (warning) or red (critical) when the values of a specific model fall outside a set of
predefined alarm limits for a certain number of observations.
In the plots, triggered alarms are illustrated using a colored alarm symbol.
Triggers
Triggers are events that activate the alarm. There are two types of triggers:
x Trigger 1 activates when X observations in a row are outside the limit.
x Trigger 2 activates when Y observations are outside the limit.
The default values for X and Y are 3 and 10 respectively. To change these values, enter new values in the
Triggers section of the Alarms window.
Note: Trigger fields cannot be empty.
There are two levels of limits: Lo Limit and Hi Limit which are warning, and LoLo Limit and HiHi
Limit which are critical. For each vector, you can define any combination of limits. The Lo limits are
automatically filled in as the negatives of the Hi limits.
Vectors
The table below shows the vectors alarms can be added for.
Vector Component/Variable Default Limit
DModX No component. DCrit at 0.05 and 0.01 significance level.
DModX+ No component. DCrit at 0.05 and 0.01 significance level.
PModX No component. 0.01 and 0.05.
PModX+ No component. 0.01 and 0.05.
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Vector Component/Variable Default Limit

t One specific component. + 3 and 4 standard deviations.
T2Range From and To components. T2Crit at 0.05 and 0.01 significance level.
YPred Y-variable. + 3 and 4 standard deviations displayed in

real values.
Note: Univariate alarms can be added for individual variables in the Target values page.
Adding an alarm
1. Set the trigger values in the Triggers section (or use the default settings).
the Hi limit.
Removing an alarm
Updating an alarm
Mark the alarm, change the settings, and then click Update.
Note: An alarm can be added for each component for t, for each component combination for T2Range,
and for each y-variable for YPred.
Write back
The PDB is a global database so if you are executing several models you will have, for example, one
DModX per model. In the PDB you should give these DModX from different models unique names.
In the Write back page, define which predictions, limits and information to automatically export to the
process database.

Variable boxes.
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Result variables batch level and regular

Available prediction results that can be exported for batch level and regular are:
Predictions
t Scores tPS
YPred (available when Predicted Y YPredPS.

applicable)
Limits
DCrit Critical distance for DModX DCrit*.
TMean Center of the hotelling's Average of the score vector for the selected
ellipse in the score scatter component.
plot.
TCrit The radius of the hotelling's TCrit for the selected component.
ellipse in the score scatter
plot.
TStdDev Standard deviation of t. Standard deviation of t.
T2RangeCrit Critical distance in the T2RangeCrit* is the critical limit in the

Hotelling's T2Range plot. Hotelling's T2Range-plot.
Information
AlarmStatus Batch level alarms 0 when no alarm was triggered.
triggered.
triggered.
BatchID Batch identifier BatchID for the active batch. (batch only)

plus model title.

M1.

To export alarms, associate the alarms for each model with the appropriate external variable.
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Vector box content
Export the configuration to file

On the last page of the wizard, click the Export configuration-button to export the configuration to file
(.bcg).
This is useful when adding more than one project with a similar configuration.
To save the configuration to file after completing the configuration, see the Configuration subsection later
in this chapter.
Starting and stopping the execution

When logged on as administrator of the program, you can start and stop the execution by marking a project
configuration and clicking the play and stop-buttons respectively in the Project Administration dialog,
opened from File | Administration | Project administration.
Projects can execute in the background without being opened.
Depending on whether a project is executing or not, the status according to the buttons is displayed to the
left of the configuration name.
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- the configuration is not executing.

- the configuration is executing.
- the configuration is repredicting but not executing.
- the configuration is repredicting while executing.
- the configuration is unavailable.
Removing and restoring project configurations

To remove a project or a configuration from the Server, mark it in the Configurations section, in the
Project Administration dialog, and press the DELETE-button on your keyboard. If you answer Yes in
the displayed dialog, the project/configuration will no longer be displayed in the dialog.
After deleting the project or configuration you can restore it by marking it and clicking Restore.
To permanently delete, click Purge. Then the project/configuration and all associated files will be
removed from the Server, while the original BioPAT® SIMCA .usp files remain.
To be able to purge projects and configurations you need to have purge configurations permissions.
Manage data
The Manage data button includes:
x Configuration - open the current configuration.
x Repredict data - to repredict selected batches or the specified time range for continuous.
x Delete predicted data - to delete selected batches.
These features are available for users with configuration management privileges only, and in the
following locations:
x Manage on the Home tab.
x Manage in the Project Administration dialog.
Configuration - view and modify

You can modify previously added project configurations. Before modifying a project, the execution has to
be stopped.
To re-configure a project:
1. Log on as a user with configure management privilege.
2. If the project is executing, File | Administration | Project administration and click the stop-
button for the project configuration you want to update. Make sure the configuration is marked
and not executing, then click Manage.
3. Start the re-configuration.
In the Configure dialog, all pages from the configuration wizard are available as tabs. For more about
these tabs, see the sections Add configuration for batch project or Add configuration for regular
project earlier in this chapter.
Note: The configuration done on the Batch evolution, Unit groups, and Batch level pages for batch and
Model for regular cannot be modified. To make such changes, add a new configuration for the project.
Repredicting historical batches

When the BioPAT® SIMCA-online server is turned off, it does not receive any data for new batches. If an
entire batch has passed while the server has been turned off you can use Repredict data to monitor that
batch once the server is running again.
Note: Repredicting batches can take a while and the server may become unresponsive.
To repredict do as follows:
1. Enter the From date/time and To date/time that contain the (missed) batches.
2. Click the Show batches button.
The batches that match the specified time limits are displayed with their start and stop times and
current status. The status can be:
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a. Missing - The batch has not been predicted.

b. Repredicting - The batch is currently repredicting.
c. Predicted - Predicted results exist for the batch.
d. Workset duplicate - A batch with the same name exists in the workset and cannot be
predicted.
3. In the list, select the (missed) batches.
Note: To multiselect, mark and press <SPACE>.
4. Click the Repredict button.
Note: All batches within the date/time range will be displayed when clicking the Show batches button,
including batches already displayed in plots. However, the batches may display different status.
Repredicting data for continuous

When the BioPAT® SIMCA-online server is turned off, it does not receive any data. Use Repredict data
to monitor the data not predicted once the server is running again.
Note: Repredicting data can take a while and the server may become unresponsive.
To repredict do as follows:
1. Enter the From date/time and To date/time that specifies the time range to repredict.
2. Click the Repredict button.
Note: All data within the date/time range will be predicted when clicking the Repredict button, including
data already displayed in plots.
Deleting historical batches

Historical batches can be deleted from the server. After deleting a batch, it can no longer be displayed in
plots or lists.
To delete historical batches, click the Delete Batches tab, select the batches to delete, and click the Delete
button.
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Note: To multiselect, mark and press <SPACE>.
Workspaces
A workspace holds information about the Client's open projects and plots. This selection can be saved as a
workspace. All workspaces are saved on the Server and can thus be opened by all clients connected to the
Server. Workspaces can be opened by any user, while workspace management privilege is needed to save
or remove workspaces.
Save workspace
To save the current selection of projects and plots as a workspace, on the View tab, in the Window group,
click Save workspace.
Alternatively use the Project Administration dialog:
1. With the Type: Workspaces section active.
2. Click Save workspace.
Delete workspace
To remove a workspace from the server:
1. On the View tab, in the Window group, click Save workspace.
2. Mark the unwanted workspace.
3. Press DELETE, or click the Organize button and click Delete.
Alternatively use the Project Administration dialog:
1. Mark the unwanted workspace in the Type: Workspaces section.
2. Press DELETE, or click the Organize button and click Delete.
Note: No lists are saved in workspaces.
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Customizing plots
Introduction
The plots in BioPAT® SIMCA-online can be customized using Properties or Format Plot.
Commonly used features in the Format Plot dialog can be accessed from the mini-toolbar. The Format
Plot dialog can be opened from the mini-toolbar or by right-clicking the plot. Applying and organizing the
templates saved using the Format Plot dialog is done from Plot templates on the shortcut menu.
Properties or Plot Properties can be opened by right-clicking the plot or by clicking the Properties
group dialog box launcher. The content of the (Plot) Properties dialog is described in the sections
describing the Properties group on the Home tab for batch and regular respectively.
Content
This chapter describes the following features:
x Mini-toolbar - for quick access to common commands regarding the content or marking in the
plot.
x Show/Hide - to quickly show/hide text outside the plot area.
x Format plot - customize plots using Format Plot. Changes in Format Plot can be saved to a
template.
x Plot templates - save, load and manage the plot templates.
Mini-toolbar
When you click or mark points the mini-toolbar automatically appears. The mini-toolbar helps you to
customize the attributes of the plot, create contribution plots and to add notes to marked points. It also
appears with the menu when you right-click.
To hide the mini-toolbar, see the Managing the mini-toobar subsection.
Mini-toolbar for marked items
Mini-toolbar for marked items: (cogwheel appears only when right-clicking)
Note: When clicking a symbol, that symbol is marked and the mini-toolbar for marked items appears.
Features available when marking items are described in the table.

Mini-toolbar button Description
Opens a contribution/variable/T2Range&DModX plot. For details,
Drill down.
see the Drill down section in the Tools chapter.
Opens the Add note dialog. For details see the Add note
Add note.
subsection in the Tools chapter.
Mini-toolbar options When right-clicking the marking, the cogwheel appears allowing you
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Mini-toolbar button Description

to select the behavior of the mini-toolbar. For details see the
Managing the mini-toolbar subsection later in this section.
Mini-toolbar for formatting

The mini-toolbar contents change when you click on different items in the plot.
When no other mini-toolbars are available the standard mini toolbar is displayed. This mini-toolbar
contains the Format Plot and Properties commands as well as commands to toggle zooming and
selecting modes.
Mini-toolbar for formatting, after clicking a text-field in the plot or an empty area:
Mini-toolbar for formatting:
Features available when clicking in plots are described in the table.
Click in plot area Mini-toolbar features in order of appearance

An empty area in the plot area. Format Plot, Properties and zooming.
A line. Format Plot dialog, line width, style, and color of that specific line
when the Marked items mini-toolbar is not enabled..
A limit. Format Plot dialog, line width, style, color and fill color of that
specific line. The last button allows saving the current settings as
default for the limit type.
Features available when clicking in the legend are described in the table.
Click in legend Mini-toolbar features in order of appearance
Symbol Format Plot dialog, hide series, symbol style, size and color.
Format Plot dialog, hide series, line width, style, and color of that
Line
specific line.
Column Format Plot dialog, hide series, color.
Features available when clicking in a text box are described in the table.
Click in text box Mini-toolbar features in order of appearance
Any text box (header, footer, axis Format Plot dialog, hide selected, font face, font size, grow font,
title, etc.) shrink font, bold, italic, font color and save as default style.
Mini-toolbar for subplot
Mini-toolbar for subplot that zooms in or out depending on current plot state:
Managing the mini-toolbar

The mini-toolbar is always displayed with the menu when right-clicking. Clicking the cogwheel of this
mini-toolbar opens the Mini-toolbar options where you can select to:
x Show mini-toolbars - the appropriate mini-toolbar is displayed when clicking in the plot. When
cleared the mini-toolbars are only displayed above the shortcut menu.
x Enable 'Format Plot' mini-toolbar - when clicking on text, lines etc. the plot, common plot
formatting features/commands/buttons are displayed.
x Enable 'Marked Items' mini-toolbar - when marking points, the drill down and add notes-
button are displayed.
x Enable 'Zoom Subplot' mini-toolbar - when the plot has subplots, this mini-toolbar shows up in
the upper right corner of each subplot.
Figure: Default mini-toolbar options.
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Customizing plots
Mini-toolbar for formatting, after clicking a text-field in the plot when Enable 'Format Plot' mini-
toolbar was selected in the Mini-toolbar options:
Show/Hide plot items

To quickly show/hide the Header, Footer, Legend, Axis titles, Axes, or Timestamp, right-click the plot,
click Show/Hide and select/clear the relevant items. When done, click outside the menu or click Done at
the bottom of the menu.
Maximize plot area is also available here. Maximize plot area hides everything but the plot area.
Format plot
Use the Format Plot dialog to change the most common attributes of the axes, plot area, and header and
footer.
To open the Format Plot dialog right-click the plot and click Format plot. This dialog can also be opened
by clicking a plot and then clicking the Format plot button in the Mini-toolbar or double-clicking on the
axes, axis titles, header or on the footer.
To save the new settings, click the Save Settings button in the settings dialog, or right-click the plot and
click Plot templates | Save as default.
Axis
The properties under the Axis node apply to the selected axis: Axis X, Axis Y, Axis Y2 (second Y-axis)
etc.
In the Format Plot dialog, Axis node, click:

x The respective axis to customize the scaling of the selected axis, annotation rotation etc. Leave
the node marked to introduce changes for all axes.
x Axis General to access the following pages:
1. Axis General to customize color, width and other properties of all axes.
2. Tick Marks to select how to display major and minor tick marks.
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3. Axis Font to customize the font of the axis annotation.

4. Title Font to customize the font of all axis titles.
Individual axes
The content for the individual axes is described in the table below:
Field/button Displays Result after entering a new value and
name clicking Apply
Axis
Show axis Default selected. If cleared, that axis is not displayed.
Minimum Start point for the selected The new start point is used for the selected axis.
axis when the values are
displayed in regular order. For
time-variables the page is
adjusted, see the Time axis
subsection.
Maximum End point for the selected axis The new end point is used for the selected axis.
when the values are displayed
in regular order.
Auto adjust Default selected. If cleared, enables the Step size field.
scales for
suitable limits
and step size
Step size Default disabled. The entered value defines the major tick mark
spacing for the selected axis.
Reverse axis Default cleared. If selected, the scale is displayed with the highest
number to the left and the lowest to the right.
Annotation
Rotation Default No Rotation. Selecting 90 degrees displays the annotation
turned 90 degrees.
Title
Show title Default selected. If cleared, the axis title is not displayed.
Title The vector name. The new title. Title changes cannot be saved.
Note that the distance between the tick marks is constant.
When you have more than one series in a plot, you can select to display more than one y-axis. For more,
see the Multiple Y axes subsection later in this chapter.
Time axis
The content for the Axis X and Axis X Title pages for a time variable is described in the table below:
name clicking Apply
Time Axis section
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Customizing plots

name clicking Apply
Show axis Default selected. If cleared, that axis is not displayed.
Minimum Start point in time units. The new start point is used for the selected axis.
Change by typing in the field.
Maximum End point in time units. Change The new end point is used for the selected axis.
by typing in the field.
Auto adjust Default selected. If cleared, enables the Step size field.
scales for
suitable limits
and step size
Step size Default disabled. The entered value defines the major tick mark
spacing for the selected axis.
unit The unit of the step size. Switching between units updates the step size
automatically.
Format section
Time format Default ISO 8601, YYYY-MM- The entered time format specifies the annotation on
DD HH:mm:ss. the marked time axis.
Axis X Title tab

Rotation under Default No Rotation. Selecting 90 degrees displays the annotation turned
Annotation 90 degrees.
Show title Default selected. If cleared, the axis title is not displayed.
under Title
Title The vector name. The new title. Title changes cannot be saved.
Note that the distance between the tick marks is constant.
Axis General
In Axis General the following features are available and are applied for all axes:
x Axis Color and Width.
x Always recalculate scales - when selected all axes are autoscaled. Clearing it makes the current
ranges of the axes stick even if the vector displayed is switched except when the new vector range
goes outside the minimum or maximum.
x Show arrows - when selected the arrows are displayed at the end of the axes.
x Arrow Color - Automatic here means the same as the axis color.
x Annotation Color and Distance from axis.
x Axis title Color.
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Tick Marks
Use the Tick Marks page to specify how the tick marks should be oriented and how long they should be.
Under Major tick marks and Minor tick marks the same boxes are available:
x Tick mark type - where None is no tick mark, Outside is to have the tick mark outside the axis,
Inside is to have the tick mark inside the axis and Cross is to have the tick mark on both sides of
the axis.
x Tick mark size is the length of the tick mark.
Font
Use the respective font pages, to select the Font, Font style, Size, and Effects for the annotation, title, etc.
Section Description
Font Displays the currently selected font. Click another font to switch.
Displays the current font style. Select to display the text Regular (default), Bold,
Font style
Italic, or Bold Italic.
Size Displays the current size. Select another size as desired.
Preview Displays a preview of the expected text according to the selections above.
Anti aliased Allows selecting to display the text Anti aliased or not.
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Customizing plots
Section Description
check box
Gridlines
Use the Gridlines page to customize the gridlines and grid stripes. The gridlines are placed on the major
tick marks. Grid stripes are the areas between the gridlines, where every second such area can be colored.
Note: Gridlines and grid stripes can be specified individually for Vertical and Horizontal. Specification
using the node applies to both.
The following is available:

Option/Box/Field Description
No gridlines No gridlines are displayed when No gridlines is selected.
Gridline When selecting Gridline you can select to display the lines Solid, Dashed,
Dotted, Dash dot or Dash dot dot.
Gridline Color The color of the grid, by default gray.
Width The width of the gridlines.
No grid stripes No grid stripes are displayed when No grid stripes is selected.
Grid stripe Solid fill When selecting Solid fill the grid stripes are displayed in the selected color.
Grid stripe Color Displays the current color and allows selecting a new color.
Grid stripe Gradient When selecting Gradient fill you can select to display the stripes Horizontal,
fill Vertical, Forward diagonal, Backward diagonal, Radial, Horizontal bar, Vertical
bar.
Grid stripe Color 2 Displays the current color and allows selecting a new second color for
Gradient fill.
Background
The Background node controls the attributes of the background displayed in the plot.
Note: The background fill and border can be specified individually for the Window area and Plot area.
Specification using the node applies to both.
The table describes the available options:

Fill
No fill No background is displayed when No fill is selected.
Sold fill When selecting Solid fill the background is displayed in the selected color.
Gradient fill When selecting Gradient fill you can select to display the background Horizontal,
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Vertical, Forward diagonal, Backward diagonal, Radial, Horizontal bar, Vertical
bar.
Color Displays the current color and allows selecting a new color for the background.
Color 2 Displays the current color and allows selecting a new second color for Gradient
fill.
Border
No border No border around the background area is displayed when No border is selected.
Solid line When selecting Solid fill, the background is displayed in the selected color.
Color Displays the current color and allows selecting a new color for the border.
Width The width of the border.
Titles
Use the Format Plot dialog to customize the items available in the Titles node. When customizing, the
changes apply to the selected item, Header/Footer/Timestamp/Subheader.
Note: Changing color, font and size of the Header/Footer/Timestamp/Subheader can be done directly in
the plot by clicking and using the mini-toolbar for formatting.
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Customizing plots
On the Titles page:

x Select to hide or show by selecting or clearing the Is Visible check box.
x Select where to display the title in the Anchor box, when applicable.
x Customize the text displayed by changing or typing in the field.
x Align the text right, center, or right by clicking the appropriate alignment button.
x Customize the color of the text in the Text color box.
x Customize the background color by clicking the Background color box.
x Select to display a border by selecting the Is visible check box in the Border section. With it
selected you can customize Color, Margin (to the text) and Width of the border.
On the Font page you can select the Font, Font style, Size, and Effects. See also the Font subsection
earlier in this chapter.
Legend
The Legend page controls the attributes of the legend, such as placement, color, and border.
Placement section
Show legend The legend is displayed when the Show legend check box is selected.
Position By default the legend is positioned Top right. To change from the default, click one
of the available placement options.
Orientation The orientation is by default Vertical. Horizontal is the other option.
Text alignment Alignment of the text in the legend is by default Left. Right and Center are the
other options.
Color section
Text color By default the text is black.
To customize text color of the legend, click the Text color box.
Background color The default background color is white.

To select another color, click the Background color box.
Border section
Is visible By default the border is not displayed. To display the border around the legend,
select the Is visible check box.
Color To customize the border color of the legend, click the Color box in the Border
section.
Margin To specify the margin to the text, change the value in the Margin field.
Width To increase or decrease the width, enter a new number in the Width field.
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Limits and Regions

There are a number of limits available in plots in BioPAT® SIMCA-online, for instance the ellipse in the
score scatter plot, the DCrit limit in the DModX plot etc. Additionally there are regions, such as the
background active batches for a batch level plot with partial models.
The attributes of the limits and regions can be modified individually for each limit and region type under
the Limits and Regions node in the Format Plot dialog, in the respective Region Style pages. The
Region Style page is described in this section.
For multiplots, the limit pages are positioned last in the Format Plot dialog under Plot 1, Plot 2, Plot 3,
etc.
For batch evolution plots, the limit pages are positioned under Styles.
Customizing Limits and Regions
The selected limit or region can be customized in the Region Style page.
Feature Description
Line
Style Select between the available line styles.
Width Increase or decrease as desired.
Color Displays the current color and allows selecting a new color.
Fill
Type Select to fill the area Over or Under the limit, or select No fill.
Select the fill to be Solid or Gradient. Selecting Solid enables the Color 1 box and selecting
Style
Gradient enables the Gradient, Color 1 and Color 2 boxes.
When selecting Gradient you can select to display the fill Horizontal, Vertical, Forward
Gradient
diagonal, Backward diagonal, Radial, Horizontal bar, Vertical bar.
Color 1 Displays the current color and allows selecting a new color.
Displays the current color and allows selecting a new color. Available when the Style is
Color 2
Gradient.
Font tab - see the Font subsection.
Label Style - see the Labels subsection.
Label Style
The Labels pages control the attributes of the displayed plot marks. Color, alignment, font and rotation
apply to all labels in a given series.
The tabs available in the Labels node, Label Style, Font and General, are described in the table.
Label section in Label Styles
Position The default position of the label in reference to the point is Right To position the
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Customizing plots
label in another direction, click the Position box and make a new selection.
Offset The offset defines the distance between the label and what it labels in the direction
of the selected Position.
To increase or decrease the distance between the label and item, enter a new
value in the Offset field.
Rotation The default rotation of the labels is 0. To rotate the label, enter a new value in the
Rotation field. Note that this field is unavailable when Avoid overlapping labels
has been selected in the General tab.
Color section in Label Styles

Text color Displays the current color of the text in the label and allows selecting a new color.
Automatic displays the text in the same color as the symbol fill.
Background color The background color of the label is default transparent. To select a color, click the
Color box and make the selection.
Border section in Label Styles

Is visible By default, no border for the label is displayed. To display a border around the
label select the Is visible check box.
Color Displays the current color of the border and allows selecting a new color.
Margin The margin between the text and the border can be customized in the Margin
field.
Draw connection Draw connection line is by default cleared. Selecting it will display a thin line
line between the label and its point.
Font tab - see the Font subsection.
General tab
Avoid overlapping With Avoid overlapping labels selected, point labels will try not to overlap each
labels other. A high specified limit in the Limit field in combination with many labels can
be quite time consuming.
Error Bars
The Error Bars page controls the attributes of the error bars displayed in the Y Predicted plot for batch
level plots.
The settings available are:
x Is visible - hides the error bars when cleared.
x Color of the error bars - by default black. To display the error bars in any other color, click the
Color box.
x Line width of the vertical and horizontal lines. To display wider error bars, enter a new number
in the field.
x Error bar width is how wide the horizontal line is compared to the column.
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Styles
In the Styles node the attributes of the series, and for batch evolution plots limits, can be customized.
The available pages in the Styles node, different depending on which plot is open, are:
x Category coloring
x Marking Style
x Line Style
x Fill Style - See Customizing limits Fill section.
x Y-Axis
x Font
Category coloring
In Category coloring you can specify colors for the batches.
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Customizing plots
Marking style
In the Marking Style page you can change the marking colors by marking and selecting a new color in the
color box to the right.
Symbol Style
The Symbol Style page controls the attributes of the symbols displayed in the plot.
Shape The shapes of the series can be changed by:
1. Marking a series.
2. Selecting a new shape in the Shape box.
With None selected, no symbols are displayed.
Size To increase or decrease the size, enter a new number in the Size field.
For the Worm plot for continuous, the size of the head of the worm is sized
proportionally.
Fill
No fill Results in symbols transparent inside the outline.
Solid fill Displays the color selected in Color.
Gradient fill Allows you to select to display the symbol with a gradient fill of type Horizontal,
Vertical, Forward diagonal, Backward diagonal, Radial, Horizontal bar, Vertical
bar.
Color Displays the current color. To display another color, click the Color box, and then
select a new color.
Color 2 Displays the current second color for Gradient fill and allows selecting a color.
Outline
No outline No outlining contour of the symbols.
Solid line The outline of the symbol is displayed.
Color Color of the outline. Automatic results in an outline in the same color as the
symbol but in a darker shade.
Width Width of the outline.
Glow
Use glow When selected an area outside the outline is colored for a glowing effect.
Color Color of the glow. Automatic results in the same color as fill color.
Width Width of the glow.
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Line Style
The Line Style page controls the attributes of the lines displayed in the plot.
Pattern Change the pattern of the line by clicking the Pattern box and selecting another
pattern.
The available types are: Solid, Dashed, Dotted, Dash dot, and Dash dot dot.
Color To display another color, click the Color box, and then select a new color.
Smoothed line Select Smoothed line (Bezier) to smooth out the edges of the line.
(Bezier)
Note: Filling is available in the Fill Style tab. See the Customizing limits subsection for details.
Column and Column Style

The Column and Column Style pages control the attributes of the columns displayed in the plot.
The Column page, found above the Styles node, displays the current Column width and allows adjusting
it.
The Fill and Border options are described in the Symbol Style subsection earlier in this chapter; Border
is there named Outline
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Customizing plots
Multiple Y axes
When you have more than one series in a plot, you can select to display more than one y-axis and linking
it to one of the series.
To display multiple y-axes:
1. Click the Styles node and click the series you want on the second y-axis.
2. Click the Y Axis tab.
3. In the Attach to Y Axis box, select Axis Y2.
Steps 1 - 3 can be repeated for more series.
Multiplots
For multiplots there are Plot nodes beneath the Styles node, named Plot 1, Plot 2, etc.
In these plots specific nodes the Sub Title and Plot area of the individual plots can be customized as
described in Titles and Background respectively.
Plot templates
The Plot templates command on the shortcut menu holds features pertaining to handling of the templates.
The following features are available and described in this section:
x Load described in the Switching plot formatting templates subsection.
x Save as and Save as default described in Saving plot formatting template subsection.
x Open templates folder - opens the folder holding the templates when clicked.
x Restore default settings described in Restoring to default plot formatting subsection.
The Format Plot dialog itself is described in the self titled section earlier in this chapter.
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Saving plot formatting template

After customizing the plots using Format Plot you can save the settings of some attributes, such as fonts,
gridlines, symbol type etc, to a template.
To save a template, with the plot open, right-click the plot, click Plot template and then, under the Save
template header click Save as default or Save as and specify a name.
Note: Only the formatting available in the current plot is saved to the customized plot formatting
configuration. All other formatting will remain default. This means that formatting of headers, footers etc.
apply to all plot types (e.g. scatter, column, line) while default line color, default symbol shape are plot
specific and need to be specified with that plot type open.
Switching plot formatting templates

After having added customized plot formatting templates, these templates can be selected by right-clicking
the plot, clicking Plot template and then selecting it under the Load template header.
After loading a new template, that template is applied to the open plot and future plots.
Restoring to default plot formatting

To restore to the Umetrics default plot formatting template, with the plot open, right-click the plot, click
Plot template and then, under Manage templates click Restore default settings.
Clicking Restore restores the Default plot formatting to the Umetrics default plot formatting and switches
to it.
Under the Manage templates header you can also select to Open templates folder to view and delete
templates.
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Maintenance
Introduction
This chapter contains instructions and routines for the administrator on how to maintain the BioPAT®
SIMCA-online system.
Content
Backup and restore
Resource management
Backup
1. Stop the server.
2. Backup the database directory and subdirectories.
3. Backup the configuration file.
4. Backup the license file.
5. Backup the plugin directory.
6. Backup the SimApi files and settings.
7. Start the server.
Restore
1. Stop the server.
2. Restore the database directory and subdirectories.
3. Restore the configuration file.
4. Restore the license file.
5. Restore the plugin directory.
6. Restore the SimApi files and settings.
7. Start the server.
Resource management
Several data structures are used by BioPAT® SIMCA-online for keeping information about predicted
results, their identifiers and when they executed, triggered alarms, added notes and such. Over time these
data structures grow in size. These data structures are stored in a database that increases over time,
sometimes to an unsustainable level.
It is therefore important to include regular checks on available disk space on the server computer.
What to do?
When the available disk space becomes low, you have to free up disk space on your computer.
To free disk space, you may remove project configurations or delete historical batches.
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Appendix A: General information
License reminder
A license reminder will be issued and written to the log dockable window once a day starting 60 days prior
to license expiration. The last 10 days prior to license expiration a tooltip will also be displayed once a
day.
Error codes when starting the service
Windows error codes

Error 3: The system cannot find the path specified.
Possible The installation of the BioPAT® SIMCA-online service is incomplete.

cause:
Solution: Reinstall from installation package.
Error 5: Access denied.
Possible Application does not have sufficient permissions to complete the operation.
cause:
Solution: Start application as administrator.
Error The service did not start due to a logon failure.

1069:
Possible The Windows password for the selected user is incorrect.

cause:
Solution: In Control Panel, click Administrative Tools, and then Services. Locate the BioPAT® SIMCA-
online Server service, right-click and click Properties. Click the Log On tab, and enter the correct
password for the specified account.
Service-specific error codes

Error 42: General error code often referring to the initialization of the SimApi. When running the demo-
version, this means that DBMaker needs to be started before the server.
Solution: For more information, review the server log file, or if the log file does not exist, the Windows
event log. The server log file is named SIMCAonlineserver.log and positioned in the database
folder specified in the Server configuration page Paths and directories.
Error The path to the configuration file is unavailable.

1001:
Possible The server configuration has not been done.

cause:
Solution: Open BioPAT® SIMCA-online Server Options from Umetrics | BioPAT® SIMCA-online 13
and review the settings.
Error The path to the database directory is unavailable.

1002:
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Service-specific error codes

Possible The server configuration has not been done correctly.
cause:
Solution: Open BioPAT® SIMCA-online Server Options from Umetrics | BioPAT® SIMCA-online 13,
tab Paths and directories and review the settings.
Error The path to the SimApi file is unavailable.

1003:

cause:
tab SimApi and review the settings.
Error There is a problem with the license file.

1004:
Possible The license has expired or the license file cannot be found.
cause:
tab Paths and directories. Click the Import button and browse to the license file.
For more information, review the server log file, or if the log file does not exist, the Windows
event log. The server log file is named SIMCAonlineserver.log and positioned in the database
folder specified in the Server configuration page Paths and directories.
Error Could not create the log file.

1005:
Possible The account the database directory used for the server has too low permissions.
cause:
tab Paths and directories and review the settings.
Error The network settings are unavailable.

1006:

cause:
tab Network Settings and review the settings.
Server endpoints
TCP/IP is the only supported protocol. The default port is 2371.
®
BioPAT SIMCA-online interfaces
BioPAT® SIMCA-online is available with an interface to OPC, OSIsoft PI, ODBC, AspenTech IP21 and
more. Please contact you sales representative for more information.
Terminology changes
With the rearrangement of BioPAT® SIMCA-online into ribbons, features were moved, some renamed,
others found obsolete. In this section the basic terminology changes are listed in alphabetical order of the
previous version terminology.
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Appendix A: General information
SIMCA-Batch On-Line
BioPAT® SIMCA-online
SIMCA-4000
Autocolor Autoformat
Active Batches dockable window Overview dockable window
Alarms dockable window Overview dockable window
Batch level Batch level, BL
Batch level project (model) Batch level model, BLM
BM BEM. BM includes BEM and optionally BLM.
Default plot action Drill down on the Tools tab.
Distance to Model, DModXPS,

DModX, DModX+
DModXPS+
Hotelling’s T2Range Hotelling’s T2, Hotelling's T2 Range
Observation level Batch evolution, BE
Observation level project (model) Batch evolution model, BEM
PS-vectors, for example The letters PS in the vector name of the predicted
DModXPS vectors is no longer displayed.
Recent Batches dockable

Overview dockable window
window
SIMCA-P+ BioPAT® SIMCA
The features of the toolbars have been split to

Toolbars different parts of the software, some are available
on the Home tab, others on the Tools tab.
Discontinued features
Discontinued features when comparing BioPAT® SIMCA-online 13 to SIMCA-Batch On-Line 3.4 and
SIMCA-4000 12 are:
x Four overview plots - the plots can be opened one by one and tiled. Use workspaces to specify
project configurations and plots to open.
x Plots displaying model results: Score Plot, Loading Plot, Variable Importance Plot (VIP), and
Coefficient Plot.
x Insert plot label.
x Coordinate reader - The Status Bar displays the plot coordinates.
x Regression line.
x Shewhart, EWMA and CUSUM Control Charts.
x Administrator Message.
x Connected Clients.
x Server Info dockable window - info available in the Project Info and Log windows and in the
Status bar.
x Lag Multiplier in the configuration of projects. When the sample time between consecutive
observations in BioPAT® SIMCA offline was different from the online execution time, you
could use the Lag Multiplier field to address this. In BioPAT® SIMCA-online the sampling and
execution times have to correspond.
x Model Description in the configuration of projects. To alter the name of a configuration from the
default (project: model title), in the Project Administration dialog, right-click the configuration,
click Rename and introduce the change.
x Averages box allowing removal of average and normalization of batch evolution plots.
x Time Sync setting. Was deemed unnecessary.
x Show Overview Status – select to show the status of all open projects in the Active Batches
dockable window. Currently displayed by coloring the project configuration tab.
x Grouping of observations in combination with sort for contribution plots.
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x Workset observations can no longer be hidden in for regular (continuous) projects.

x Scaling of plots for regular projects to 0-1, previously available in the Properties dialog Scale
page, was discontinued.
x Connect to Last Server on Startup was discontinued. The Log in dialog is displayed when
opening the Client.
x Alarm zones for continuous.
x Manually specifying contribution weight for continuous.
x Dynamic, automatically updated, lists for continuous.
x Prediction list for continuous.
x Repredict and catch-up for continuous.
x Delete predicted data for continuous.
x Adaptive predictions for continuous..
x The following features in the Active Batches and Recent Batches dockable windows:
1. Open Projects Overview - showed the overall status of all open projects.
2. Observation Level Overview and Batch Level Overview - showed the status of the
overall status of the current project for the respective batch project types. These two are
combined in one, just showing the overall alarm status of the configuration in the color
of the configuration tab.
3. Unit Overview - unavailable, the models are just displayed in the order in BioPAT®
SIMCA.
4. Individual observation level overview - unavailable, the models are just displayed in the
order in BioPAT® SIMCA.
5. Create DModX Plot and Create Score Plot were deemed unnecessary.
6. Shortcut menu.
Menu and tab reference syntax

In this user guide we use the following syntax when referring to the File tab commands:
x Click Tab | Command. An example: Click File | Print.
x On the Tab tab, click Command. An example: On the File tab, click Print.
x Click Command on the Tab tab. An example: Click Print on the File tab.
In this user guide we use the following syntax when referring to tab commands/buttons:
x On the Tab tab, in the Group group, click Command. An example: On the View tab, in the
Window group, click Save workspace.
x Click Command, in the Group group, on the Tab tab. An example: Click Save workspace in
the Window group on the View tab.
x Click Tab | Command | Menu item. An example: Click View | Close | Close all windows.
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Glossary
A
Active batches: The Active Batches (previously named current) are the batches that are being predicted by the server
currently. The active batches are displayed as they are evolving in the batch evolution control charts and in the
Overview window. After completion, batch or model wise, active batches are also displayed in the batch level plots.
Note: when repredicting a batch it will also briefly show up as active during the time it is being predicted.
Automatic classification: Option available in previous versions. In the current version there is no automatic
classification. Phase belonging of new observations is identified using the phase condition.
Average batch: The average batch is the average at each time point, computed over all batches in the model.
B
Batch hibernation: Batch hibernation was available in a previous version. In the current version, batch hibernation is
only available between phases when a phase condition for any phase not yet has been fulfilled.
Batch node: The batch node contains information about start and stop times of the batches. The batch node is created and
updated by the external system.
Batch process: A batch process is a finite duration process. The batch starts, evolves, and stops.
C
Catch up: The model reads all observations since the last execution or since the specified time point.
Class: A class is a subset of similar observations from a dataset.
Concurrent batches: The ability to run and monitor several batches at once.
Contribution: The contribution is a measure of the differences in variable values between two observations. The
differences are normally weighted by model loadings or modeled variability.
Critical limit: When points are found outside the critical limit the resulting product is likely to be of poor quality.
Cross-validation: In cross-validation, parameters are estimated on one part of a matrix and the goodness of the
parameters tested in terms of its success in the prediction of another part of the matrix.
Current batches: See Active batches.
D
Data source: See SimApi.
Dataset: A dataset is the base of all multivariate data analysis, often also called a data matrix. It is made up of values of
several different variables for a number of observations. The data are collected in a data matrix (data table) of N rows
and K columns, often denoted X. The N rows in the table are termed observations. The K columns are termed
variables.
Dependent variables: See Y-variable.
Discriminant analysis: Discriminant analysis is a method for allocating observations to one class of a given set of classes
by means of a decision rule based on a function of the data. The function is derived from data for a reference set of
individuals where it is known which class each individual belongs to.
E
Endpoint: See Port.
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F
Factor: Factor is a term often used in experimental design. It signifies controlled and varied variable. Also a term for one
model dimension in factor and bilinear models. See also: X-variable.
Factor analysis: Factor analysis has an aim similar to PCA, but assumes an underlying model with a specified number of
factors which are linear combinations of the original variables. The analysis is more concerned with 'explaining' the
covariance structure of the variables rather than with 'explaining' the variances.
H
HDB: HDB is the abbreviation for Historical DataBase. The HDB contains observations from the past.
Hi limit: Hi and Lo limits are used as warning limits. This means that when the process is inside these limits it is under
control.
HiHi limit: HiHi and LoLo limits are used as critical limits. This means that when the process is outside one of these
limits it is out of control.
Historical batch: A historical batch is a batch that was not part of the workset of the model, was previously monitored,
has finished, and sits in the database.
L
Least squares estimate: The least squares estimate is a method to estimate model parameters by minimizing the sum of
squares of the differences between the actual response value and the value predicted by the model.
Lo limit: Hi and Lo limits are used as warning limits. This means that when the process is inside these limits it is under
control.
Loading vector: The loading vector is the direction coefficients of a PC or PLS component axis.
LoLo limit: HiHi and LoLo limits are used as critical limits. This means that when the process is outside one of these
limits it is out of control.
M
Missing value: Missing values are elements in a data matrix without defined values. As a rule of thumb, each observation
and variable should have more than five defined values per principal component. Observations (or variables) with
missing values that show up as outliers should be treated with suspicion.
Model: A model is: 1) An approximation of reality. A good model preserves all properties of interest. 2) A hyperplane,
with limited extension, that approximates the variable space spanned by a class of observations.
MSPC: Multivariate Statistical Process Control. The use of multivariate methods to characterize the state of a process
with respect to known states. The state is determined from model score plots and distance to model plots. See also:
SPC.
Multivariate analysis: Multivariable analysis is a group of statistical methods, which are appropriate when
measurements are made on several variables for each of a large number of individuals or observations.
Multivariate data: Multivariate data consist of observations on several different variables for a number of individuals or
observations. Indeed, the vast majority of data is multivariate, although introductory statistics courses naturally
concentrate on the simpler problems raised by observations on a single variable.
N
NIPALS: Non-linear Iterative Partial Least Squares
O
Observation space: The space spanned by the observation vectors of a data matrix. Each variable vector is represented as
a point in that space.
Outlier: An outlier is a batch or time point found outside a critical limit, e. g. DCrit.
140
Glossary
P
Partial Least Squares: Partial Least Squares Projection to Latent Structures. See PLS.
Partial models: In workset of the batch level model, where the batch evolution model has phases, there is a ’Create
partial models for each phase’ box. After selecting this box, the models fitted are cumulative over the phases. That is,
the first model contains the first phase, the second the first and second phases, etc. and the last contains all phases.
PC: Principal Component. A PC is a one model dimension of a PC model. Often also used as a term for the scores t.
PC modeling: Principal Component modeling. PC modeling is: 1) The use of PCs to define a model. 2) The
approximation of a matrix by a model, defined by averages and a relatively small number of outer vector products.
The components can often be used in place of the original variables for plotting, regression, clustering and so on.
PCA: Principal Component Analysis. PCA is the technique for finding a transformation that transforms an original set of
correlated variables to a new set of uncorrelated variables, called principal components. The components are obtained
in order of decreasing importance, the aim being to reduce the dimensionally of the data.
PDB: PDB is the abbreviation for Process DataBase, a database in the external system.
PLS: Partial Least Squares Projection to Latent Structures. PLS is a generalization of PCA where a projection model is
developed predicting Y from X via scores of X. Can also be seen as a generalized multiple regression method that can
cope with multiple collinear X and Y variables.
Port: The communication channel that is used by the server and client. Also named Endpoint. BioPAT® SIMCA-online
uses TCP ports.
Prediction set: A dataset used together with an established model in order to obtain model predictions for each of the
observations in the set. See also Test dataset.
Predictor variable: See X-variable.
Principal component: See PC.
Principal component analysis: See PCA.
Principal component modeling: See PC modeling.
Principal factor analysis: See: Principal component analysis.
Projection: 1) The act of projecting. 2) Something that has been projected, i.e. the 'picture' of orthogonally projected
points on a line, plane or hyperplane.
Projection methods: Projection methods are a group of methods that can efficiently extract the information inherent in
MVD. They give results that are easy to interpret because they can be presented as pictures. Such methods are
efficient for pattern recognition, classification, and predictions. The most commonly used methods are PC and PLS
modeling.
Projection point: The projection point is a point, along a line or in a plane or hyperplane (created by approximating data
in k-space as a low dimensional hyperplane), which is closest to the original point.
Projection to Latent Structures: See PLS.
PS: Prediction Set. Denotes that the vector displays results for predictions.
R
Recent batches: Recent Batches are the most recent batches that have finished executing. The time range that defines
recent batches can be modified in the Time ranges page of the project configuration for each project.
Reference batch: A reference batch is any historical or workset batch that you select to display alongside the active
batches. You select a reference batch by marking it in the Batches box. A reference batch is by default displayed as
line without symbols alongside the active batches.
Reference dataset: The term 'Reference dataset' is used for datasets with known properties and origin, often used to
define models. Synonyms: Calibration dataset, Training dataset, Workset.
Regression: In mathematics Y is called a function of X, but in statistics the term regression of Y on X is generally used to
describe the (sound, approximate) relationship.
Regression analysis: Regression analysis is the fitting of an equation to a set of values. The equation predicts a response
variable from a function of regressor variables and parameters, adjusting the parameters such that a measure of fit is
optimized.
141
®
Residual: The residuals are the left-over; un-modeled part of a dataset; the mismatch between the observed and modeled
values.
Response variable: See Y-variable.
S
Score: The score is: (1) The distance from the origin, along a loading vector, to the projection point of an observation in
K- or M-space. (2) The coordinates of a point when it is projected on a model hyperplane.
Score vector: The score vector is the observation coordinates along a PC or PLS component axis. Scores for all
observations for one model dimension (component).
SDB: SDB is the abbreviation for BioPAT® SIMCA-online DataBase. SDB is the internal database created by BioPAT®
SIMCA-online to store results.
Selected batch: See Reference batch.
SimApi: Short for BioPAT® SIMCA Application Programming Interface. A data source and a programming interface for
data access specified by Umetrics. Version 2 is the latest version used by BioPAT® SIMCA-online.
SimApi DLL: An implementation of the SimApi for a specific external system. Used by BioPAT® SIMCA-online to
obtain data from the external system. Sartorius-Stedim provides the DBMaker SimApi DLL for demo purposes, and
there are implementations for OPC, PI, ODBC.
BioPAT® SIMCA: The Sartorius-Stedim offline software used to create projects to use in BioPAT® SIMCA-online. See
the System requirements section for version.
Singular value decomposition: See: Principal component analysis
Sleep: Sleep is used to inform BioPAT® SIMCA-online of skipped observations. Sleep was used in versions before 3.0 of
SBOL to inform SBOL of skipped phases.
SPC: Statistical Process Control. The behavior of a process is characterized using data when the process is operating well
and is in a state of control. In the monitoring phase the new incoming, measured, data are used to detect whether the
process is in control or not. See also: MSPC.
Sub-batch: When a batch is partitioned into several physical parts, each part is a sub-batch.
Sublot: See sub-batch.
T
Tag: Tag is another name for variable.
TCP/IP: TCP/IP is the standard internal protocol. BioPAT® SIMCA-online uses TCP.
Test dataset: See Prediction set.
Trend plot: Variable plot that is displayed over time.
Trigger: An act or event that initiates a reaction such as raising an alarm.
U
Unit: A unit is a physical equipment/machine/vessel that processes a sub-batch.
Unit group: A unit group is a process step, for instance a granulator. The unit group contains one or more identical units.
W
Warning limit: When points are found outside the warning limit the process has left its controlled state and some
parameters should probably be adjusted.
Workset: The workset contains the batches used to build models in SIMCA. Synonyms: Training dataset, training set.
Workspace: A workspace consists of one or more open project configurations and the positioning of all open plots as
arranged when the workspace was saved.
X
142
Glossary
X-variable: X-variables are used to 'explain' the variation in the dependent variables (y). Synonyms: predictor variables
or explanatory variables.
Y
Y-variable: Y-variables are modeled as dependent on other variables. These other variables are often named predictor
variables or X-variables. Synonyms: dependent variables, response variables.
143
Index
145
A Catch-up ....................................... 130
Adding Changing
Alarms............................. 140, 147, 159 Color ...............................................174
Note .................................... 96, 97, 120 Configuration ..................................166
Project .............................................125 Classifying new batches ................. 29
Unit groups .....................................131
Workspaces .....................................168 Client window................................. 31
Administrator preparation ............... 22 Close project configuration............. 37
Alarm Color
Adding batch evolution ...................140 Background .....................................181
Adding batch level ..........................147 Customization .................................174
Adding for regular...........................159 Combined ....................................... 72
Alarm triggers for BEM ..................142
Coloring ............................................88 Communication parameters .............. 7
Displaying triggered alarms ..............62 Configuration
Export ............................. 143, 149, 162 Audit trail ..........................................91
Show limits .......................................74 Export ..................................... 151, 164
All Y Predicted Plot ........................ 69 Import ..................................... 128, 153
Loading ................................... 128, 153
Associating tags .................... 136, 156 Saving ..................................... 151, 164
Audit Trail ................................ 46, 91 Server ..................................................6
Axis ...................................... 175, 178 Configuring
Network settings ...............................36
B Old project ......................................166
Phase conditions..............................132
Background................................... 181 Project ..................................... 127, 152
Batch Server ..................................................5
Box....................................................70 Connect
Box in BioPAT® SIMCA-online options57 batch conditions to tags ...................146
Classification ....................................29 local centering to tags .....................138
Conditions .......................................146 output variables to the process database142, 148,
Data visualization..............................11 161
Deleting...........................................168 SIMCA variables to tags .................135
Evolution...........................................12 tags and configuring phase conditions132
Model selection ...............................145 to Server ............................................36
Monitoring ........................................26
Node................................................129 Context menu................ 137, 157, 171
Repredict .........................................166 Contribution plot batch evolution
Batch evolution Difference between .........................111
Contribution plots ...........................107 Display .................................... 106, 116
Overview...........................................87 DModX ...........................................108
Plots ..................................................62 Hotelling's T2Range........................109
Properties ..........................................74 Score plot ........................................107
Y Predicted .....................................110
Batch filter .................................... 129
Contribution plot batch level
Batch level Display .................................... 106, 116
Alarms.............................................147 DModX ...........................................113
Combined ..........................................72 Hotelling's T2Range........................113
Contribution plots ...........................112 Score plots ......................................112
Layout box ........................................72 Y Predicted .....................................114
Model selection ...............................145
Overview...........................................87 Control charts
Properties ..........................................81 Defining ..........................................139
Variables ......................................... 115 Limit calculation ...............................16
Box Control Tags ................................. 132
Batches ..............................................70 Create
Components ......................................71 Contribution plot ..................... 106, 116
Layout ...............................................72 List ..................................................121
Variable.............................................72 Variable plot ........................... 106, 116
Button Critical limit.......................... 140, 147
Add note.............................. 96, 97, 120
Drill down .......................................105 Customizing
Starting, stopping execution ............164 Plots with Format plot .....................174
Zooming in, out...............................104 Plots with Properties ................... 74, 81
C D
Catchup ................................. 130, 155 Databases
146
Index
Directory .............................................6 Header................................... 174, 182

HDB ..................................................33
PDB ..................................................33 Help menu .................................... 123
SDB ..................................................33 Hi Limit ................................ 140, 147
DBMaker .......................................... 5 Hierarchical batch models .............. 18
DBView ............................................ 5 HiHi Limit ............................ 140, 147
Default Port .................................. 201 Historical batch deletion ............... 168
Default Properties ........................... 52 Hotelling's T2 Range
Defining Contribution plot ............. 109, 113, 118
batch conditions ..............................146 Plot ........................................ 63, 67, 79
control chart limits ..........................139
I
Delete
Initiate communication ..................... 7
Historical batches ............................ 168
Project configuration .......................165 Installation ........................................ 2
Workspace ......................................168
Interface
Deleting Option page .......................................51
Historical batches ............................ 168 To external system ..........................201
Project configurations .....................165
Workspace ......................................168 L
Diagnostics ................................... 106 Layout box ...................................... 72
Directories ........................................ 6 License
File ......................................................6
Disconnect ...................................... 36 Info......................................................1
Display a contribution or variable plot106, 116 Reminder.........................................199
Distance to Model Limits
Contribution plot ............. 108, 113, 118 Alarm ...................................... 140, 147
Plot ........................................ 63, 67, 78 Calculate control charts .....................16
In options .................................... 54, 55
DModX Lo, LoLo, Hi, HiHi ................. 140, 147
Contribution plot ............. 108, 113, 118
Specify variable out limits ................41
Plot ........................................ 63, 67, 78
Line Style...................................... 191
Dockable windows ............. 86, 87, 90
Lo Limit ................................ 140, 147
Drill down ............................. 105, 106
Load warning percent ....................... 7
Dual Variable.................................. 64
Local centering tags ...................... 138
E Log File ...................................... 7, 51
Empty plot .......................... 65, 69, 81
Log in/Log out ................................ 36
Environment ................................... 24
LoLo Limit ........................... 140, 147
Error codes.................................... 199
M
Execution
Interval .................................... 130, 154 Magnify ........................................ 104
Start .................................................164 Maintenance ................................. 197
Stop.................................................164
Marker .......................................... 103
Exit ................................................. 58
Menu reference syntax .................. 204
Export
Alarms............................. 143, 149, 162 Minimizing the ribbon .................... 60
To external database ....... 142, 148, 161 Mini-toolbar
To spreadsheet or file ........................38 Formatting.......................................172
External database communication142, 148 Managing ........................................173
Marked items ..................................172
Extract data ..................................... 38 Subplot ............................................173
F Miscellaneous page..................... 7, 51
File tab ............................................ 35 Modeling
batch evolution ............................ 12, 15
Find ............................... 136, 137, 157
batch level .........................................17
Footer .................................... 174, 182 why batch level .................................17
Format Plot ................................... 174 Monitoring
evolution ...........................................27
H project ...............................................26
HDB................................................ 33 Multiple Y Axes ........................... 192
147
®
N New ......................................... 127, 152

Old ..................................................166
New
batch classification ............................29 Project DB Max Time....................... 7
project configuration ............... 127, 152 Properties
Not available ....................... 65, 69, 81 Batches ..............................................70
Components ......................................71
Notes ................................. 96, 97, 120 Layout ...............................................72
Plot Properties dialog ........................74
O BioPAT® SIMCA-online options .....50
ODBC ........................................... 201 Variable.............................................72
What is ........................................ 70, 81
Open
Overview window .............................87 Properties group
Project configuration .........................37 Batch .................................................70
Workspace .............................. 101, 168 Continuous ........................................81
Plot Properties dialog ........................74
Organize
In Project Administration dialog .....126 Protocol......................................... 201
In the audit trails ...............................94
In the Report .....................................98 Q
OSI PI ........................................... 201 Quick Access Toolbar .................... 59
Outliers ........................... 17, 107, 116 R
Overview window........................... 87 Real time on-line batch data ........... 33
P Re-configuring old project ............ 166
Partial models ................................. 18 Removing
Historical batches ............................ 168
Paths ........................................... 6, 51 Project configuration .......................165
PDB ................................................ 33 Workspace ......................................168
Phase conditions ........................... 132 Reorganization of table before import13

Phase tags ..................................... 135 Report ............................................. 94
Physical overview ........................... 24 Repredict............................... 166, 167
Plot Reset alarms .................................... 97
Batch evolution plots ........................62 Result variables....... 16, 143, 149, 162
Batch level ........................................65
Combined ..........................................72 Rolling view ................................... 51
Default batch evolution .....................54
Default batch level ............................55
S
Drill down .......................................105 Save
Formatting.......................................174 As ....................................................122
Labels................................................56 Configuration .......................... 151, 164
Options ............................ 74, 75, 82, 83 Plot formatting ........................ 193, 194
Regular..............................................77 Workspace .............................. 101, 168
Templates ........................................ 193
Save as .......................................... 122
Plot labels ....................................... 56
Score
Plot options ..................................... 52 Contribution plot ............. 107, 112, 117
Plot templates ............................... 194 Plot ........................................ 62, 66, 78
Pop-up menu ................. 137, 157, 171 SDB ................................................ 33

Port ............................................... 201 Select batches ................................. 76
Predict batches ................................ 29 Sequential models ........................... 18
Predicted Maturity Server
Contribution plot .............................110 Administration .......................... 41, 125
Plot ....................................................65 Audit trail ..........................................46
Configuration ......................................5
Preparation by administrator........... 22 Endpoints ........................................201
Print ................................................ 38 Installation ..........................................2
Log file........................................ 50, 51
Print preview .................................. 38
Several phases................................. 15
Print setup ....................................... 38
Shortcut menu ....................... 137, 157
Processor load ................................... 7
Significance level ........................... 55
Project administration ............. 41, 125
SimApi
Project Configuration Call timeout.........................................7
148
Index
Configuration ......................................7 Audit trail ..........................................93

Max time .............................................7 Report ...............................................95
Parameters...........................................7 Status bar ..........................................87
BioPAT® SIMCA approach ........... 18 Tools tab ....................................... 103
BioPAT® SIMCA-online interfaces201 U
BioPAT® SIMCA-online options .. 50 Unit groups ................................... 131
General..............................................51
Plot options .......................................52 Unsupported features ...................... 30
BioPAT® SIMCA-online Server.. 2, 5 User administration......................... 42
Groups page ......................................44
Sleep condition ............................. 132 Roles page .........................................45
Sleep trigger.................................. 132 Users page .........................................43
Sort ............................................... 105 Using
BioPAT® SIMCA-online .................21
Specify Tag filter ................................. 136, 157
Alarms............................. 140, 147, 159
Limits ................................................74 V
Variable out limits.............................41
Variable
Start Aliases.....................................137, 157
Client ................................................22 batch evolution ..................................64
Execution ........................................164 batch level .........................................68
Server ................................................22 display plot.............................. 106, 116
Status bar ........................................ 87 Dual plot ...........................................64
from contribution ............ 106, 115, 116
Stop Identifiers ..........................................56
Execution ........................................164
Server ................................................22 View by phase ................................ 72
Sub-batches..................................... 13
Subplot
Empty.................................... 65, 69, 81
Subheader .........................................74
Zoom ...............................................104
Switch plot formatting .................. 194
Symbol Style ................................ 190
System requirements......................... 2
T
T2 Range
Plot ........................................ 63, 67, 79
Tabbed mode ............................ 86, 90
Tabs
Description ........................................90
Interface ............................................51
Tag
Association.............................. 136, 156
Batch condition ...............................146
Condition dialog..............................134
Local centering ...............................138
Page in Configure dialog.................156
Phase conditions..............................132
Phases .............................................135
Tag filter field ....................... 136, 157
Target values......................... 138, 158
TCP/IP .......................................... 201
Terminology ................................... 30
Time........................................ 84, 177
Time ranges .......................... 130, 155
Title ...................................... 174, 182
Toolbars
149
®
Worm plot ....................................... 77

W
Warning limit................ 140, 147, 159 Y
Window group .............................. 100 Y Predicted
Workbook Plot ........................................ 65, 68, 80
Interface ............................................51
Tabs ..................................................90 Z
Workspace Zoom
Open..................................................37 Automatic .........................................54
Save ................................................101 In and out ........................................104
150
Sartorius Stedim Systems GmbH
Robert-Bosch-Str. 5–7
34302 Guxhagen, Germany
Phone +49.551.308.0
Fax +49.551.308.3289
www.sartorius-stedim.com
Copyright by
Sartorius Stedim Biotech GmbH,
Goettingen, Germany.
All rights reserved. No part of
this publication may be reprinted
or translated in any form or by any
means without the prior
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Stedim Biotech GmbH.
The status of the information,
specifications and illustrations
in this manual is indicated by
the date given below.
Sartorius Stedim Biotech GmbH
reserves the right to make changes
to the technology, features,
specifications and design of the
equipment without notice.
Status:
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Sartorius Stedim Biotech GmbH,
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Welcome to BioPAT® SIMCA-online 13.1.

Introduction to multivariate modeling 7

Using SIMCA-online 13

Extract Data - Select Destination ...................................................................................... 26

Adding notes ................................................................................................................ 82

Customizing plots 117

Backup ....................................................................................................................... 133

Appendix A: General information 135

What is in the package

Then follow the steps below.

2. The first page displays the details of the

3. Read the license agreement. To accept,

4. In the Custom Setup page, if you want to

5. To install the Server (or Client) on this

7. When the installation is completed, click

8. When installing the server, the BioPAT®

DBMaker and DBView

Configuration of the Server

Opening the BioPAT® SIMCA-online Server options dialog

Paths and directories

Parameters to initiate communication with SimApi

Server input files

Introduction to BioPAT® SIMCA-online

Process data analysis

Batch evolution modeling in BioPAT® SIMCA

Reorganization of the 3D table before import

Reorganization with sub-batches

Real Modified After To let each sub-batch be included in

Batches with several phases

Calculating limits to build control charts

Batch level modeling in BioPAT® SIMCA

Modeling batch level

Back Scores t1, t2, t3 Final

Hierarchical batch models

The BioPAT® SIMCA approach

Process data analysis

1. Modeling the data in BioPAT® SIMCA.

Batch evolution analysis

Batch level analysis

Preparation by the administrator

2. Starting the Right-click the BioPAT® SIMCA- If the message displayed is

3. Starting the Start the Client from the start menu.

Step Action How More

The server is running and regularly checks for new data.

The server has not been installed.

Figure 7. The BioPAT® SIMCA-online implementation.

Monitoring the model

Plots for monitoring the new continuous data

Plots for monitoring the evolution of new batches

D D1 and D2. Sub-batch 1 and 2. Phase 3

C One unit. In One sub-batch. In BioPAT® SIMCA- Phase 5.

Plots for predicting results or classifying new batches

Differences compared with SIMCA and unsupported features

Configuration – or project configuration, is a specific instance of a SIMCA project configured to take

The table describes the parts of the client window.

Quick By default displays a few Toolbar positioned Quick Access

Tabs Tabs to switch between Bottom of the Tabs section in