Guia de Operacion Biocomand

BioCommand Plus
BioProcessing Software
BEFORE INSTALLATION:
See Chapter 1
MANUAL NO: M1291-0050

Revision A
February 4, 2002
NEW BRUNSWICK SCIENTIFIC CO., INC.

BOX 4005 44 TALMADGE ROAD EDISON, NJ 08818-4005
Telephone: 1-732-287-1200 1-800-631-5417
Fax: 732-287-4222 Telex: 4753012 NBSCO
Internet: http://www.nbsc.com E-mail: bioinfo@nbsc.com
ii
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Users Guide
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INTERNATIONAL OFFICES:
THE NETHERLANDS
New Brunswick Scientific BV
Kerkenbos 1101, 6546 BC Nijmegen
P.O Box 6826, 6503 GH Nijmegen
Holland
Tel: (0)24 3717 600
Fax: (0)24 3717 640
E-mail: sales@nbsbv.nl
BELGIUM
New Brunswick Scientific NV/SA
t Veldeke, 1
B-1970 Wezembeek-Oppem
Belgi/Belgique
Tel: (0)2 731 6787
Fax: (0)2 731 8130
E-mail: sales@nbsnv-sa.be
FRANCE
New Brunswick Scientific SARL
3, rue des Deux-Boules
75001 Paris
France
Tel: (0)1 40 26 47 06
Fax: (0)1 40 26 54 23
E-mail: sales@nbssarl.fr
GERMANY
New Brunswick Scientific GmbH
In Der Au 14
D-72622 Nrtingen
Deutschland
Tel: (0)7022 932490
Fax: (0)7022 32486
E-mail: sales@nbsgmbh.de
UNITED KINGDOM
New Brunswick Scientific (UK) Ltd.
Edison House, 163 Dixons Hill Road
North Mymms, Hatfield, Herts. AL9 7JE
United Kingdom
Tel: (0)1707 275733
Fax: (0)1707 267859
E-mail: bioinfo@nbsuk.co.uk
CHINA (Beijing)
Room 8-3-B
No. 1 Heng Fu Zhong Street
Feng Tai District
Beijing 100070
P.R. China
Tel: 10 6371 0167
Fax: 10 6374 1107
New Brunswick Scientific
CHINA (Shanghai)
Room 1406, Aijian No. 1 Bldg.
Lane 590, WanPing (S) Road
Shanghai 200030
P.R. China
Tel: 21 6481 2658
Fax: 21 6481 2665
E-mail: nbschc@online.sh.cn
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BioCommand Plus
M1291-0050
Users Guide
CAUTION!
This equipment must be operated as described in this
manual. If operational guidelines are not followed,
equipment damage and personal injury can occur.
Please read the entire Users Guide before attempting to
use this unit.
Do not use this equipment in a hazardous atmosphere or
with hazardous materials for which the equipment was not
designed.
New Brunswick Scientific Co., Inc. (NBS) is not responsible
for any damage to this equipment that may result from the
use of an accessory not manufactured by NBS.
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BioCommand Plus
M1291-0050
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Copyright Notice
New Brunswick Scientific Company, Inc.
Box 4005 44 Talmadge Road
Edison, New Jersey 08818-4005
Copyright 2002 New Brunswick Scientific Co., Inc.
All Rights Reserved.
Reproduction, adaptation, or translation without prior written
permission from
New Brunswick Scientific is prohibited.
Disclaimer Notice
New Brunswick Scientific Co., Inc. reserves the right to change
information in this document without notice. Updates to information
in this document reflect our commitment to continuing product
development and improvement.
Manual Conventions
NOTE:
Notes contain essential information that

deserves special attention.
Caution messages appear before procedures

which, if caution is not observed, could result
in damage to the equipment.
CAUTION!
Warning messages alert you to specific
procedures or practices which, if not followed
correctly, could result in serious personal
injury.
WARNING!
Bold
Text in bold face type emphasizes key words

or phrases.
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BioCommand Plus
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WARRANTY
Every Instrument manufactured by the
New Brunswick Scientific Co., Inc. is warranted to be free from
defects in material and workmanship. This apparatus, with the
exception of glassware, lamps and electrodes (where supplied),
is warranted for 1 year against faulty components and assembly and our
obligation under this warranty is limited to repairing or replacing
the instrument or part thereof, which shall, within 1 year after date of
shipment, prove to be defective after our examination. This warranty
does not extend to any NBS products which have been subjected
to misuse, neglect, accident or improper installation or
application; nor shall it extend to products which have been
repaired or altered outside the NBS factory
without prior authorization from
New Brunswick Scientific Co., Inc.
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TABLE OF CONTENTS
1
READ THIS FIRST ..................................................................................1

1.1
1.2
1.3
INTRODUCTION .....................................................................................5
2.1
2.2
2.3
2.4
2.5
2.6
2.7
Creating a New Recipe using Batch Wizard .................................................................................. 27

Expanding a Basic Recipe.............................................................................................................. 33
Alternative Methods to Create a New Recipe ............................................................................... 34
Starting A Batch............................................................................................................................. 40
Batch Summary View .................................................................................................................... 44
INTRODUCTION TO BATCH VIEWS .............................................................47

6.1
6.2
6.3
Cable Connections ......................................................................................................................... 19

Setting Up Computer/Controller(s) Communication ..................................................................... 20
CREATING A RECIPE & STARTING A BATCH.................................................27

5.1
5.2
5.3
5.4
5.5
Workstation Setup.......................................................................................................................... 11
Starting BioCommand Plus............................................................................................................ 14
Workgroup Information ................................................................................................................. 14
Recipes and Batches....................................................................................................................... 15
Starting BioCommand Screen .................................................................................................... 15
Main Menu..................................................................................................................................... 16
Main Toolbar.................................................................................................................................. 17
NBS HARDWARE CONNECTION SETUP ......................................................19

4.1
4.2
Major Features ................................................................................................................................. 5

Product Benefits ............................................................................................................................... 5
How to Use This Manual ................................................................................................................. 6
Organization of This Manual ........................................................................................................... 7
Notation Conventions Used In This Manual .................................................................................... 7
Navigating Through Windows ....................................................................................................... 8
Reference for Item Naming Conventions....................................................................................... 10
BIOCOMMAND PLUS INSTALLATION & SET-UP............................................11

3.1
3.2
3.3
3.4
3.5
3.6
3.7
Before Installing BioCommand Plus................................................................................................ 1

Obtaining a Product Registration Number ....................................................................................... 1
License Agreement Acceptance ....................................................................................................... 2
Trend Views................................................................................................................................... 47
Using the Trend Graph................................................................................................................... 50
Creating Synoptic Views................................................................................................................ 51
CREATING PROGRAMS ..........................................................................57

7.1
7.2
7.3
How to Create a Program ............................................................................................................... 58

User-Defined Loops ....................................................................................................................... 68
More Program Functions................................................................................................................ 69
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SETTING ALARMS & ALERTS ..................................................................71

8.1
8.2
Setting Alarms................................................................................................................................ 71
Setting Alerts.................................................................................................................................. 75
ENDING A BATCH ................................................................................77

9.1
9.2
9.3
9.4
End a Batch .................................................................................................................................... 77

Exiting BioCommand Plus............................................................................................................. 77
Restarting with Active Batches ...................................................................................................... 78
Shutting Down BioCommand Plus ................................................................................................ 79
10 SECURITY FEATURES ............................................................................81

10.1
10.2
10.3
10.4
User-Based Access .................................................................................................................... 81

Entering User Passwords........................................................................................................... 81
Recipe Authorization Levels ..................................................................................................... 85
Creating and Modifying a User List .......................................................................................... 85
11 MAIN SCREEN FUNCTIONS REFERENCE .......................................................91

11.1
11.2
11.3
11.4
11.5
11.6
11.7
11.8
File............................................................................................................................................. 91
Edit ............................................................................................................................................ 92
View .......................................................................................................................................... 93
Tools.......................................................................................................................................... 94
User ........................................................................................................................................... 98
Window ..................................................................................................................................... 99
Help ......................................................................................................................................... 101
Toolbar Description................................................................................................................. 101
12 RECIPE/BATCH FUNCTIONS .................................................................. 103

12.1
12.2
12.3
Creating or Editing Recipes..................................................................................................... 103

Starting a Batch ....................................................................................................................... 121
Altering a Batch in Progress.................................................................................................... 122
13 CREATING & EDITING VIEWS ................................................................ 131

13.1
13.2
13.3
13.4
AutoRefresh Feature................................................................................................................ 131

Program Views ........................................................................................................................ 133
Synoptic Views........................................................................................................................ 146
Trend Views ............................................................................................................................ 150
14 TROUBLESHOOTING ............................................................................ 159

14.1
Troubleshooting Guide............................................................................................................ 159
15 SPECIFICATIONS & SYSTEM REQUIREMENTS ............................................. 161

15.1
15.2
15.3
15.4
15.5
BioCommand Plus Specifications ........................................................................................... 161

System Requirements .............................................................................................................. 161
Network & Communications Requirements............................................................................ 162
Fermentor/Bioreactor Installation............................................................................................ 162
Creating a BioCommand Plus Workgroup .............................................................................. 162
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16 DATA LOG FORMAT ........................................................................... 165

16.1
16.2
16.3
16.4
16.5
16.6
16.7
16.8
16.9
Settings .................................................................................................................................... 166

Changes ................................................................................................................................... 167
Batch Events............................................................................................................................ 169
Reports .................................................................................................................................... 169
Data Logs ................................................................................................................................ 170
Batch Identifications................................................................................................................ 172
User Data................................................................................................................................. 174
Errors....................................................................................................................................... 174
Views Data .............................................................................................................................. 175
17 VIEWING BATCH DATA ....................................................................... 177

17.1
17.2
17.3
17.4
Starting DBViewer32 .............................................................................................................. 177

Existing Batches ...................................................................................................................... 177
Using the Main Data Window................................................................................................. 178
More Batches........................................................................................................................... 187
18 INDEX ............................................................................................ 189
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1.1
READ THIS FIRST
Before Installing BioCommand Plus

BioCommand Plus is copyrighted software and may not be used without a license.
Before you do anything else, read this entire chapter.
The license supplied with your purchase is good for a networked installation at one single
site. Before BioCommand Plus can be used, you will need to obtain a Product Registration
Number from New Brunswick Scientific.
NOTE:
From the time you receive your Product Registration Number, you may use
it to activate BioCommand Plus during a period of two weeks. If you are
not ready to install and activate the software, do not request the product
Registration Number at this time.
The number of Product Registration Numbers that New Brunswick Scientific will issue
against one BioCommand Plus serial number is limited. Be sure you are ready to proceed
with installation before you request a Product Registration Number. Also, be sure to save
the BioCommand Plus serial number in case reinstallation becomes necessary, because a
Product Registration Number cannot be issued without the serial number.
1.2
Obtaining a Product Registration Number

The Product Registration Number can be obtained in several ways:
Online through the worldwide web (the fastest and easiest method to use in most cases)
Through your local NBS sales office, by e-mail, phone or fax
Through our U.S. headquarters, by e-mail, phone or fax
1.2.1
Online Registration
Contact this website: http://www.nbsc.com
Fill out the online Registration Form. You will be asked for:
your name and title
Users Guide
1.2.2
your Institution (the company, institution or organization where you

work)
your institutions street address, city, state or province, and country
your work phone number and e-mail address
the serial number of your BioCommand Plus software, which is found on
the back of the CD case.
Registration at Local NBS Sales Office
Contact your local NBS sales office by telephone, fax or e-mail, and provide
the information listed in Section 1.2.1.
1.2.3
Registration at NBS U.S. Office

Contact NBS headquarters:
by telephone: 1-732-287-1200
by fax: 1-732-4222
by e-mail: bioinfo@nbsc.com
to provide the information listed in Section 1.2.1.

1.3
License Agreement Acceptance

You must also accept the License Agreement below before you can use this software.
NEW BRUNSWICK SCIENTIFIC CO., INC.
LICENSE AGREEMENT FOR BIOCOMMAND PLUS
This is a legal agreement between you, the end user, and New Brunswick Scientific Co., Inc.
By obtaining an installation password and installing this software, you are agreeing to be
bound by the terms of this agreement.
If you do not agree to the terms of this agreement, promptly return the package and the
accompanying items to New Brunswick Scientific.
1.3.1
New Brunswick Scientific Software License

1. Grant Of License
New Brunswick Scientific grants you the right to use the BioCommand Plus software
program (BioCommand Plus) in a networked environment at a single site. You may
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install BioCommand Plus on multiple computers within a single network domain.

You may not install this copy of BioCommand Plus in more than one network domain
at the same time.
2. Copyright
The BioCommand Plus program is owned by New Brunswick Scientific or its suppliers
and is protected by United States copyright laws and international treaty provisions.
Therefore, you must treat BioCommand Plus like any other copyrighted material (e.g.,
a book or musical recording) except that you may make one copy of BioCommand Plus
solely for backup or archival purposes.
3. Other Restrictions
You may not rent, lease or transfer BioCommand Plus. You may not reverse engineer,
decompile, or disassemble BioCommand Plus.
1.3.2
U.S. Government Restricted Rights

The BioCommand Plus software program and documentation are provided with
RESTRICTED RIGHTS. Use, duplication, or disclosure by the Government is subject
to restrictions as set forth in subdivision (b)(3)(ii) of The Rights in Technical Data and
Computer Software clause at 252.227-7013. Contractor/manufacturer is New Brunswick
Scientific Co., Inc./44 Talmadge Road/P. O. Box 4005/Edison, New Jersey 08818-4005.
This Agreement is governed by the laws of the State of New Jersey. Should you have
any questions concerning this Agreement, or if you desire to contact New Brunswick
Scientific for any reason, please write: New Brunswick Scientific Customer Sales and
Service, 44 Talmadge Road, P.O. Box 4005, Edison, New Jersey 08818-4005.
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BioCommand Plus
Users Guide
INTRODUCTION
BioCommand Plus software enhances the capabilities of NBS

bioprocessing equipment. It oversees the independent operation of one or
many NBS process controllers. BioCommand Plus enables centralized
control, monitoring and data acquisition in applications ranging from a
single benchtop laboratory fermentor through arrays of large-scale
production vessels. This software uses industry-standard conventions,
including the familiar terms of Recipe (all of the variables associated with
a fermentation run) and Batch (an active application of a recipe).
2.1
Major Features
2.2
2.2.1
Centralized monitoring and control of one or several fermentors and bioreactors

Network connectivity, so several computer stations can serve as observation and
control centers
Automatic process data recording
Clear synoptic, graphical, pictorial and numerical displays and reports
User programming for automating research and production protocols
Security features
Product Benefits
General
BioCommand Plus is a Windowsbased, network-capable, multibioprocess
supervision program. It is designed primarily for use with New Brunswick
Scientifics fermentation and cell culture equipment, but can be extended to the
control and supervision of other equipment as well. This software uniquely
retains the easy-to-use character of its precursor, AFS BioCommand, while
adding powerful networking; security; 32bit architecture; expanded
programming, enhanced graphing and reporting capabilities; and recipe-based
process control.
We are confident that that the power, flexibility and convenience of this software
will enhance creativity and productivity in laboratory, pilot, and manufacturing
applications.
Users Guide
BioCommand Plus runs under the popular and familiar Windows XP, XP Pro,
ME, 2000, NT and 98 operating systems.
2.2.2
Displays
An intuitive graphical interface for custom Synoptic Views, enhanced graphing
capabilities and custom data reports mean clear and complete process data is
always available.
2.2.3
Security
Automatic data archiving, process alarms and warnings, and assignable batch
authorities lend multiple level security to both process data and the process itself.
List levels are easily maintained and, with proper authority, modified.
2.2.4
Batch Programming: Easy Though Powerful

BioCommand Plus introduces integrated 3-level process programming for
applications where programming can provide superior protocols or convenience.
With easily created time profiles, you can adjust setpoints according to your
specifications based on batch running time. You can also add conditiondependent setpoint adjustments by arranging function blocks in a graphical
workspace.
BASIC programming is available, too, to create user-defined functions. Any and
all of these programming tools can be incorporated in a Control Diagram for
precise batch reproducibility, or for well-defined and controlled experiments.
2.2.5
Application
BioCommand Plus is compatible with all New Brunswick Scientific computercapable products. The number of units supported is limited only by network
capacity.
2.3
How to Use This Manual

We recommend that operators first acquire skill with the controllers, then the software.
The overlap between some BioCommand Plus functions and some controller functions
can steepen the learning curve for those trying to learn both simultaneously.
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Follow the first three chapters carefully to ensure that the software is installed
correctly, and the appropriate interface connects the controlled instrument(s) to the
host computer(s). If you plan to network your installation, you may need the
assistance of networking personnel.
Refer to Chapters 3-8 to set up and complete a first BioCommand Plus run.
As needed, refer to the remaining chapters.
2.4
2.5
2.5.1
Organization of This Manual

Chapters 1-2
Introductory material.
Chapter 3-8
These chapters take the new user from program start-up

through fermentor shutdown in step-by-step tutorial style.
They include sufficient detail to enable further independent
exploration.
Chapters 9-12
Reference chapters containing in-depth explanations of

features.
Chapter 13
A troubleshooting guide to help you diagnose and resolve some

potential difficulties.
Chapters 14-18
Information that is usually not necessary for routine program

operation (product specifications, system requirements,
installation information, data log formats and hardware
connection instructions), but which may be helpful to advanced
users.
Chapter 19
An index to key terms used throughout the manual.
Notation Conventions Used In This Manual

Mouse Notation
Notation
Application
Click
Double Click
Press the left mouse button once.

Press the left mouse button twice, in quick
succession.
Press the right mouse button once.
Press the right mouse button twice, in quick
succession.
Right Click
Double Right Click
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2.5.2
Keyboard Notation
Keys are displayed with their keyboard label between the < and > symbols,
such as <Esc> (Escape) or <Tab>.
Modifier keys (<Alt>, <Ctrl>, <Shift>) which are pressed along with another key
are also shown between the two symbols < and >. The modifier is separated from
the other key by a dash. For example, <Ctrl-D> means that both <Ctrl> (the
Control key, which is labeled Ctrl) and <D> (the key labeled D) must be pressed
simultaneously.
If modifier key(s) are required, press and hold down the modifier(s) while
pressing and releasing the other key. Then release the modifier key(s).
If two modifier keys are required both are shown within the symbols < >, and are
separated by dashes, as <Ctrl-Shift-Esc>.
Function keys are displayed with an F preceding a number: <F1>.
2.5.3
Menu Notation
Menu items are described by the selection sequence that accesses the item. A
dash separates items in the sequence. For example, the Save function under the
File menu is written as File Save.
2.5.4
Window Element Notation
Window names (in the window title bar) are enclosed in double quotation marks,
as Loop Setup Options.
Tab labels are also enclosed in double quotation marks: Recipes.
Data-entry-field names use single quotation marks, as in Loop.
On-screen (virtual) Button captions are enclosed in curly brackets { }.
Navigating Through Windows
2.6
Skip this section if you are very familiar with the Windows Operating System. Those
in need of a review should read on. For more information, consult Microsoft or third
party manuals on the use of your operating system.
The Close Button this button (U) exits the program.
The Maximize/Restore Button the active window can be set to occupy the entire
screen (maximized) or just a portion of the screen with this button (). When the
window is not maximized, it can be resized with the following steps:
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1. Place the cursor over one of the edges or at the corner of the window until the
cursor changes to a double arrowhead.
2. Click the left mouse button and drag the cursor in or out to reduce or enlarge the
window.
The Minimize Button this button () reduces the program window to an icon on the
task bar on the bottom of the screen.
See the sample screen below to locate the Close, Maximize/Restore and Minimize
buttons.
Close
Maximize/Restore
Minimize
Shortcut keys are indicated by an underlined character in a menu item.. From the
Main Menu, press the <Alt> key along with the shortcut key to open that menu item.
While the menu is active, pressing the key associated with the underlined character
is the same as clicking on that menu item. Most of the selection buttons that are
used throughout this program also include shortcut keys.
Many of the windows throughout this program consist of tabbed notebooks. When
the window is first opened, one page of the notebook will be active. The rest of the
pages will be hidden, but their tabs will be visible at the top or bottom of the
window. To change pages in these notebooks, click on the tab for the page you
want; that page will become the active screen.
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10
2.7
Reference for Item Naming Conventions

The BioCommand Plus program uses a system of naming items that is described in this
section. Once a display name is given to a recipe or a batch, that name is used to
identify all items belonging to that recipe or batch. The format for these items is:
display name.Bx:item name.y

where
display name
x
item name
y
2.7.1
is the name given to the recipe or batch

is the number of the batch being used
is the functional name for the item
is the number of the instance of this item
File Naming Conventions

File Name
Extension:
Function:
.RCP
Recipe Files
(contain all information necessary to run a batch)
Batch Files
(contain all logged data, including alerts and
alarms and, where appropriate, offline data)
User Workgroup identification files
(indicating recognized Users and their security
levels)
.BDB
.MDW
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11
BIOCOMMAND PLUS INSTALLATION &

SET-UP
This section guides you through initial program installation, configuration and
startup. This chapter also introduces and defines the terms recipe and batch.
For detailed system requirements and instructions on setting up BioCommand Plus
workgroups, consult Section 15.
3.1
Workstation Setup
The following subsections provide step-by-step instructions for workstations running
Windows 98, NT, 2000 or ME. The Windows 2000 instructions are applicable to
Windows XP and Windows XP Pro. Determine which applies to your system, and
follow the bulleted instruction sequence for that configuration.
Windows 98 Stand-Alone
3.1.1
NOTE:
If you do not know your number, visit the NBS website (www.nbsc.com) to
register your software and to obtain the Product Registration Number.
1. Install BioCommand Plus:
a. Start your computer in Windows 98.
b. Close all programs, including virus detectors, desktop managers and
application toolbars.
c. Insert the CD-ROM in the appropriate drive.
d. You will be prompted to Please enter the Product Registration Number.
Enter the registration number and click on OK.
e. Follow the on-screen instructions to run the installation process. Default
values are recommended for file locations.
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2. NBSHardwareConnection is a program that sets up communications between

the computer and controller(s). Before running BioCommand Plus for the first
time, or whenever attached controllers are changed, run
NBSHardwareConnection as explained in Section 4.
3. Start BioCommand Plus and verify communication with connected
fermentors.
Windows 98 Workstation on a Windows NT Network
3.1.2
NOTE:
1.
2.
3.
4.
5.
Install Microsoft remote registry service.

Enable remote access to the computer in the control panel password screen.
Set network access mode to User-Level Access.
Grant remote access to the registry to the world/everyone.
Install BioCommand Plus:
a. Start your computer in Windows 98.
e. Follow the on-screen instructions to run the installation process.
Default values are recommended for file locations.

fermentors.
Windows NT Workstation Networked or Stand-Alone
3.1.3
NOTE:
1. Make sure Windows NT service pack 5 is installed.
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a. Start your computer in Windows NT. Be sure to log on as a user with
Admin privileges.
fermentors.
Windows 2000, XP & XP Pro Workstation Networked or
Stand-Alone
3.1.4
NOTE:
1. If you are using Windows 2000, make sure the Windows 2000 service pack
5 is installed.
a. Start your computer in Windows. Be sure to log on as a user with
Admin privileges.
Enter the registration number and click on OK
fermentors.
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3.2
Starting BioCommand Plus

After BioCommand Plus has been successfully installed on your computer, it may be
started in any of the usual ways, such as:
3.3
From the
Start button: Click
Start
Programs
NBS
BioCommand Plus
From a desktop shortcut: Double click a shortcut previously placed on the desktop
(refer to a Windows manual)
From the Windows Explorer: double click on BCPLUS.exe in the NBS folder.
Workgroup Information
The first time that the program is executed, you will be asked to enter a default
workgroup file name and location:
Click on {Browse} to locate it:
Then click on {OK}. The Select BioCommand Workgroup window will close.
NOTE:
If this installation of BioCommand Plus is not to be networked, you may
use the file in the BioCommand Plus Install folder created by the setup
program. Otherwise, select the workgroup file that was set up for your
BioCommand Plus workgroup. (See also Creating a BioCommand
Workgroup, Section 15.5)
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3.4
Recipes and Batches

The terms Recipe and Batch appear throughout this manual.
A Recipe is a process description that BioCommand Plus uses to control a fermentation
process. Recipes are created and defined by users. A Recipe is a template that dictates
how the process will proceed. Recipes include initial setpoints for controlled parameters
such as temperature, pH, dissolved oxygen and others. Recipes may also include
programs that alter setpoints at certain times or under specified conditions. Other Recipe
parameters may include display types, data log interval, alarm and limit values, types of
reports to generate, and even which fermentor operators have authority to alter the recipe
itself or the runs derived from it.
Batch refers to a specific fermentation or cell culture run. Every Batch starts from a
Recipe. The same Recipe may be used over and over to run several Batches. Once a
batch has begun, Recipe dictates may be overridden by those operators granted
appropriate authority for the batch.
3.5
Starting BioCommand Screen
Whenever you open BioCommand Plus, you will see the Starting BioCommand screen
represented below (unless you turn it off):
This screen offers six options:
Create a new recipe with Batch Wizard: opens the Wizard which guides you step by
step through recipe creation.
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Open a blank recipe: once you are familiar with BioCommand Plus, you can use this
shortcut to create a recipe, without the Wizard.
Open an existing recipe: one of several ways to access existing recipes.
Extract a recipe from a batch: this use of the Batch Wizard will allow you to create a
recipe used from a previous batchs archive file.
View a batch running elsewhere on the network: this option allows you to look at any
batch that may be running on your network.
Resume a batch running when BioCommand exited: whether it was a power failure, a
PC failure or user error, even though BioCommand Plus was not properly shut down, this
command will allow you to resume computer supervision of an active batch.
3.5.1
Turning the Starting BioCommand Screen Off & On

To prevent the Starting BioCommand screen from appearing in future runs,
click in the white checkbox (Dont show this display on start up), then close the
window.
You can turn it back on by selecting File Start Options from the Main Menu.
The Starting BioCommand screen will open. Click in the box to remove the
checkmark, then close the window (or continue if you wish to use the Wizard).
3.6
Main Menu
The menu items on the main BioCommand Plus screen comprise the Main Menu. Below the
Main Menu is the optional Toolbar. Many of the most commonly used functions that are
available from the Main Menu or its submenus are available by clicking on the appropriate
icon on this toolbar. When the cursor is placed over an icon, a one- or two-word hint
describing the function of that icon is displayed for a short time in a small box beneath the
icon.
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This is the appearance of the Main Screen, under the Starting BioCommand screen, when
the program is started.
3.7
Main Toolbar
The Toolbar may be toggled off from the View dropdown menu if more screen area for
program output display is desired. The figure below indicates the function of each icon on
the Toolbar.
New Batch
View Batch
New Recipe
View Recipe
Batch Wizard
Whats This? HELP
Print
Save
Delete
Paste
Copy
Cut
Standard Windows functions
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NBS HARDWARE CONNECTION

SETUP
This setup program is required to allow your computer, BioCommand Plus, and all
controllers and fermentors in your system to communicate with each other. This
program must be run before you attempt to use BioCommand Plus.
4.1
Cable Connections
Before you run this set-up program, you must make sure that your hardware is
properly cabled.
4.1.1
Required Hardware
The NBS Multi-Controller Adapter (#M1286-0100) and NBS RS-422 cable
(#M1171-8010) included with BioCommand Plus provides communication using
AFS protocol with NBS controller(s), which may be any one or combination of
the following:
BioFlo 110 Primary Control Unit

BioFlo 2000
BioFlo III
BioFlo 3000
BioFlo IV
BioFlo 4000
General Purpose controller
BioFlo 5000
CelliGen Plus
Mobile Pilot Plant
ML-4100 controller
ML-6100 controller
4-20 mA controller
You will need one RS-422 cable per supervised fermentor.

4.1.2
Making Connections
1. Connect the 25-pin connector of an NBS RS-422 cable (#M1171-8010) to the
AFS serial port of one controller.
2. Connect the cable end of the NBS Multi-Controller Adapter (#M1286-0100)
to the other (far) end of the NBS RS-422 cable.
3. Connect the adapter end marked RS-232 to the serial input port of the
computer.
4. If you are using a BioFlo 110 PCU or an ML-6100, make sure the controller is
set to AFS protocol. Consult the controller user guide for instructions. All
other NBS controllers are factory-set to AFS protocol.
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5. Additional controllers may be connected using additional RS-422 cables to

daisy chain from the first controller to the second, and so on.
BioCommand Plus also works with the NBS Interface (see interface box manual
for details).
4.2
Setting Up Computer/Controller(s) Communication
NOTE:
Follow the instructions in this section carefully to ensure that
BioCommand Plus communicates with your hardware.
In order for BioCommand Plus to share information with each of the attached controllers,
you must provide three essential pieces of information to the software:
type of connection (direct/multi-fermentor adapter or NBS BioCommand

Interface)
which computer port is connected to the controller(s)
the unique ID number of each controller.
Use the NBS Hardware Connection Setup program to enter this information.
4.2.1
NBS Hardware Connection Setup

1. Open NBS Hardware Connection Setup by clicking, in succession, on
Start
Programs
NBS
NBSHardwareConnection
2. The program window opens:
3. A few seconds later, the Controller Connection Type window opens:

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4. Click on one option button ( ):
NBS Controller(s) using direct-to-PC connection or the NBS MultiFermentor Adapter. Choose this option if your controller is connected
either (a) via cable directly to the Comm port of your computer, or (b) via
cable to the NBS Multi-Fermentor Adapter (NBS kit number M12918000), which in turn is connected to the Comm port of your computer.
NBS Controller(s) via NBS BioCommand Interface. Choose this

option if you have installed an NBS BioCommand Interface between the
fermentor(s) and the Comm port of your computer.
NOTE:
Anytime you change connection type, to protect you from operator error
the following warning screen will open:
Click on {Yes} to apply the change or {No} to cancel it.

5. Click on {Next >>} to open the Computer Communications window (see
Section 4.2.2).
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4.2.2
Select Comm Port

1. In the Select Comm Port pane, indicate which computer Comm port, 1 or 2,
is connected to your controller(s).
Click here to
change the
number
DO NOT
CHANGE!
2. In the Comm Settings pane, the correct choices are preset for you. Do not
change any of these settings.
3. Click on the {Open Comm Port} button to test the selected Comm port.
4. If you get an error message, it most likely means you have incorrectly
identified the port connected to your controller(s). Change the Select Comm
Port setting, then click again on the {Open Comm Port} button.
5. When the test message indicates no error, click {Next>>} to open the
Controller ID List window (see Section 4.2.3).
4.2.3
Controller ID List
In the Controller ID List, you may enter up to eight ID (identification) numbers
for the controller(s) attached to your computer. ID numbers are electronic
names that allow the software to communicate individually with each of the
attached controllers.
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NOTE:
ID numbers have nothing to do with product, model or serial numbers.

The provided Multi-Controller Adapter or an NBS BioCommand Interface
is required to use more than one controller with BioCommand Plus.
Refer to your fermentor, bioreactor or controller User Guide to learn how to view
the ID number for that specific instrument (see Sample Retrieval of ID Numbers
on the following page). In some older NBS controllers, ID numbers are referred
to as MD or multidrop numbers.
Sample Retrieval of ID Numbers
To obtain the ID numbers for the BioFlo 110, for example:
1. Press the upper right BioFlo 110 touchpad key to display the Setup Screen:
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S
e
t
u
p
NBS BioFlo 110
Version : 0001.01
Config : 1.10
Date: 2/2000
English
Franais
Deutsch
Espaol
http://www.nbsc.com
Use
More
SELECTOR BUTTONS
2. Press the More selector button to display the Systems Detail screen:
S
e
t
u
p
System Details
Unit Base Address: 0
BaseAdd
Unit 1 ID: 0
Unit 2 ID: 1
Unit 3 ID: 2
Unit 4 ID: 3
Comm. Protocol: AFS
Recorder Status: Off
Comm
Recorder
3. Note the four Unit ID number(s).

4. If you have only one vessel, use only the first ID number. Enter that number
in field 1 of the Controller ID List.
5. If you have more than one vessel, enter additional numbers in subsequent
fields of the Controller ID List.
End of Sample Retrieval.
When you have entered the ID numbers in the Controller ID List, click on
{Next >>}. Within a few moments, the Controller Status window opens.
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4.2.4
Controller Status
The Controller Status window indicates the ON/OFF status and available loops in
each controller.
Click
here to
check
entire
loop lists
NOTE:
If the indicated status does not agree with what is observed at the
controller(s), click {<< Back}, confirm the ID numbers, then click {Next >>}
to return to this screen and recheck the status. If the status is still not
correct, check all cable connections, and confirm the operation of each
controller.
When you have confirmed the correct controller status, click {Finish} to exit NBS
Hardware Connection.
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CREATING A RECIPE & STARTING A

BATCH
Follow the steps in this chapter to create a new Recipe (with or without
the help of Batch Wizard), start a Batch from that Recipe, and view the
Batch status using a Batch Summary display. The Recipe, Batch, and
Display in this chapter are minimalist in that they do not invoke the
most powerful or impressive BioCommand Plus capabilities.
Nevertheless, performing the steps in this tutorial will impart a feel to the
new user for how the software works and what it does.
To start a Batch you must either specify a previously saved Recipe or create a new one.
A Recipe must contain at least the following information:
A data recording interval

A data log file name
A list of parameters (loops) identified by name and the controller in which they
reside.
Recipes usually contain more than the minimum required information. The Recipe created in
this section is minimal, but it will be expanded in later chapters. The easiest way to create a
recipe is to use the Batch Wizard; other methods are discussed in Section 5.3.
5.1
Creating a New Recipe using Batch Wizard

In the Starting BioCommand screen (see page 15):
1. Click on the white option button next to Create a new recipe with Batch Wizard (if it is
not already selected)
2. Click on {Continue} or, if you change your mind, Click on {Close} to exit Batch
Wizard.
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If you choose {Continue}, the BioCommand Batch Wizard Introduction screen

opens:
Notice, too, that the New Recipe Setup screen will also open behind it. You will have
access to the Setup screens when you have finished Batch Wizard.
If you do not wish to see this introduction screen when you use Batch Wizard again, click
in the white checkbox next to Skip this screen in the future.
You may use any of the active buttons at the bottom of the screen to obtain help, to cancel
use of the wizard, to move back to the previous screen or to move ahead to the next. If a
button is gray, it is inactive for that screen.
3. Click on {Next>} to move ahead. The BioCommand Batch Wizard Step 1 screen
will appear:
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The default name for the recipe, which appears in the edit box, is Recipe1.
4. If you wish to keep this name, simply click on {Next>}. This is the name that will
appear on the bottom Recipe tab in the Setup view when you finish Batch Wizard. It will
also appear in the title bar of all windows associated with this recipe.
5. If you wish to rename the recipe, enter the new name in the edit box. You may use up to
12 alphanumeric characters, including spaces. Then click on {Next>}. The
BioCommand Batch Wizard Step 2 screen will appear:
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6. Click on the {Select Loops>>} button. The Add/Change Hardware Loop List window
will appear:
7. Click on the {Browse Local Server} button. Wait a moment while BioCommand Plus
searches. The available controller(s) will appear in the left Available Loops pane.
8. Click on the + next to the controller(s) of interest to see the drop-down list of available
loops.
9. If you wish to select all loops from a controller, click on the controller name, then click
on the {>>} button. The controller name (and all its associated loops) will move into the
right, Loops in Batch pane.
10. If you wish to select one loop at a time, click on the loop name, then click on the {>>}
button. The loop name will move into the Loops in Batch pane.
11. When your selections are complete, click on {Close}. You will return to the Step 2
Batch Wizard screen.
12. Click on {Next>}. The BioCommand Batch Wizard Step 3 screen will appear:
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You must assign a Recipe File Name, which is both a file name and its folder location.
Note that every recipe must be assigned the extension .RCP which marks it as a recipe.
13. Click on the {Change Directory/Name} button.
14. The BioCommand Save Files window will open:
15. If this recipe should be available to your network, click now in the check box next to
Shared over the network.
16. To see existing File Name/Folder strings, click on the down arrow () to the right of the
File edit box.
17. Click on an existing File Name/Folder string to bring it into the edit box as a pattern.
You can type over it to create your new name. This will not affect the existing File Name
in any way.
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18. If you wish to find other folders, click on the {Browse} button. The screen that appears
will allow you to explore possibilities (in network if shared, or in your own PC if not),
just as you would with any other Windows -based exploration tool.
19. Create a new one based on this example. Be sure to follow the pattern:
Drive:\FolderName\FileName.RCP (the example shown on the Step 3 screen above is
C:\BCPLUS\BioRcp2.RCP). Normal Windows file-naming conventions apply.
NOTE:
All recipe file names must have the extension .RCP.
Click on {OK}. Your selection will move into the Recipe File name edit box.
NOTE:
When a recipe will be shared over the network, the file name must follow
the pattern: \\ComputerName\FolderName\FileName.RCP
20. Click on {Next>}. The BioCommand Batch Wizard Step 4 screen will appear:
21. After you have read this screen, click on {Next>}. The BioCommand Batch Wizard
Finished! screen will appear:
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22. Click on {Finish}. You will now be in the Setup View for the Recipe you have just
created.
At this point, you have a very basic recipe that is sufficient to start a batch. If you are
ready to do so, see Section 5.4, Starting a Batch, for further instructions. If you wish to
add any or all of the additional features mentioned in Step 4 of the Batch Wizard, see
Section 5.2, Expanding a Basic Recipe, below.
5.2
Expanding a Basic Recipe

At any time (before you start a batch or while a batch is running), you can expand a
recipe using any or all of the features below, which are also mentioned in Step 4 of the
Batch Wizard:
Change the logging interval

Set the Elapsed Fermentation Time format
Add Alarm and Alert settings
Select parameters for trend views
Design synoptic views
Set up control programs
Set security access levels for other users
Modify the hardware loop list
See Section 12.1.4, Time Data Pane

See Section 12.1.4, Time Data Pane
See Section 8
See Section 6.1
See Section 6.3
See Section 7
See Section 10
See Sections 5.3.2 and 12.1.5
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5.3
Alternative Methods to Create a New Recipe

There are a number of ways to create a recipe. The easiest is to use the Batch Wizard, as
outlined in Section 5.1. You can also create the recipe without the Wizard, directly from
the New Recipe Startup screen. There are several ways to access the Wizard, and
several other ways to access the New Recipe Startup screen.
5.3.1
How to Access Batch Wizard

There are two ways to open the Batch Wizard:
On start-up, from the Starting BioCommand screen, click on Create a new

recipe with Batch Wizard
From the Main menu, click on the Batch Wizard icon.
5.3.2
How to Access the New Recipe Startup Screen

There are three ways to open the New Recipe Startup screen:
From the Starting BioCommand screen , click on Open a blank recipe, then
click on {Continue}:
Select File - New Recipe from the Main Menu.
Click on the New Recipe icon on the toolbar.
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After any of the above actions, the New Recipe Setup screen will appear:
1. Click in the Display (Tab) Name: edit box and type the display name for this recipe.
The name may be any combination of up to 12 alphanumeric characters and spaces.
The Owner name is assigned to the logged-on user creating this Recipe and may not
be changed.
2. Click inside the Description: edit box and enter descriptive text as desired. This
Description may be any combination of alphanumerics, spaces, and punctuation
marks.
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3. The default Log Interval is one minute. To change the interval, click the {Change
Interval} button in the Time Data pane. Enter the desired Log Interval in whole
minutes in the edit box, or choose a preset interval from the dropdown list.
4. Select the Time Display Format, either HH:MM:SS (Hours : Minutes : Seconds) or
Decimal Hours, by clicking in the appropriate circle. Decimal format is convenient
for mathematical processing.
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5. Click on the Loops tab. The Add/Change Hardware Loop List window appears.
This window allows you to select loops from any of the attached controllers. Usually
all the loops from a single fermentor are selected. You may choose to include loops
from ancillary equipment, such as a gas analyzer or scale.
6.
Click the {Browse Local Server} button. Controllers that are accessible to
BioCommand Plus appear in the field labeled Available Loops. In the sample
screeen below, loops from two local controllers are available for this recipe:
7. To display the individual loops associated with each controller, click on the + box
to the left of the controller name. The list expands as shown below:
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8. Pressing the {>>} button moves selected loops from the Available Loops pane to
the Loops in Batch pane. Click on a controller name and then click on the{>>}
button to include all the loops from that controller in your recipe, or select an
individual loop from the expanded list and click on the {>>} button to include that
loop in your recipe. Continue until all desired loops are in the right pane of this
window.
9. Use the {<<} button to move loops from the Loops in Batch: list back to the back
to the Available Loops list, if necessary.
10. When all the desired loops are in the Loops in Batch: list, click {Close}. The
Loops page of the Setup View reappears.
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11. The Current Loops pane shows the selected loops. On the left of each line is the
loop name as transmitted to BioCommand Plus by the controller. On the right is
complete loop data in the format [Server Name\Controller Name\Loop Name].
You may change any default loop name to a display name containing a maximum of 10
characters. You may also enter an initial setpoint for each loop in the Recipe. Both of
these options are executed through the Loop Setup Options window.
12. Click on the {View loop details} button. The Loop Setup Options window will open:
A.
B.
C.
D.
E.
Select the loop from the pull-down menu.

Enter a new display name, if desired.
Enter a setpoint, if desired.
Click {Apply}.
Repeat these last four steps for each loop to be changed
13. Click {OK} to return to the Loops tab of the New Recipe Setup window.
The Recipe is now sufficiently complete to start a Batch. Many other Recipe functions are
available, but they are not necessary to start a Batch. They will be covered in later
sections (see Section 5.2 for a cross-reference guide of the most popular features).
Before you start a Batch, however, you need to save the Recipe:
1. Click {Save}. The BioCommand Save Files window will open.
2. Enter a file name in the File edit box, identifying the drive, folder, name, and
extension. Click on the down arrow for sample file names (note that the File extension
must be .RCP and that your default recipe folder is BCPLUS). A typical file name
might be C:\BCPLUS\Recipe1.RCP.
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3. Click {OK}. The New Recipe Setup screen re-appears.

4. Click the {Save} button. At this point you can either close the Recipe window or start
a Batch from this recipe.
5. If you opt to close, the Save Changes window will open. Click on {Yes}.
5.4
Starting A Batch
Before starting a Batch, prepare the fermentor. Be certain that these steps have been
taken:
The fermentor and controller are powered on.

There is media in the vessel.
All appropriate liquid and/or gas addition systems are attached to vessel.
The vessel, media and liquid addition systems have been sterilized as required.
The probes have been calibrated.
All ancillary equipment has been connected, powered on and tested.
Any other procedures that need to be performed prior to starting a culture should be
completed before starting computer supervision and control.
Most users prefer to start the Batch in BioCommand Plus before inoculating. Doing so
sufficiently in advance establishes correct growth conditions according to the Recipe, and
enables confirmation of data logging and other functions before growth begins. The
Elapsed Fermentation Time clock can be reset to zero when inoculation or any other
biologically significant event occurs.
5.4.1
Selecting a Recipe
To start a Batch, you first need a Recipe. There are several ways to select the
desired recipe:
(1) Starting BioCommand Screen
A. Click on Open an existing recipe (see screen below):
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B. Click on {Continue}. The Select File to Open screen will appear (see
sample screen below).
C. Click on the recipe of interest.

D. Click on {Open}. The Select File to Open screen will disappear, and
your selected recipe will be displayed in the View Recipe Setup screen.
You will be able to verify the recipe parameters by cycling through the
tabs. If you wish to modify the recipe, and you have the appropriate
authorization level, see Section 12.1 for more information.
E. Continue in Section 5.4.2 below.
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(2) Main Screen File Menu New Batch

Click on File, then New Batch from the dropdown menu. The Select File to
Open screen will open (see sample above), with the New Recipe Setup screen
shadowed behind it.
(3) Main Screen Toolbar New Batch Icon
Click on the New Batch Icon. The Select File to Open screen will appear (see
sample above), with the New Recipe Setup screen shadowed behind it.
(4) Starting BioCommand Screen to Extract Recipe
This option is handy if you know the Batch File Name but not the Recipe File
Name.
A. Click on Extract a recipe from a batch and then click on {Continue}. The
Select File to Open screen will appear, with the View Recipe Setup
screen shadowed behind it. Note that this Select File to Open screen will
show all available Batch files (*.BDB), instead of recipe files (*.RCP). See
sample screen below:
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B. Select the Batch file of interest, then click on {Open}.

C. The View Recipe Setup screen will open, displaying the recipe (and its
parameters) from the selected batch.
D. Verify the parameters by cycling through the tabs of this screen.
Now that you have selected a Recipe, if you wish to modify parameters for the new
batch, and if you have the appropriate authority level, you may do so at this time. See
Section 12.1 for more information. Note that changing parameters for a Batch does
not alter the Recipe file.
5.4.2
Starting the Batch

1. When you are satisfied with the parameters and ready to start the Batch, click the
{Start Batch} button. The Batch Display Name screen appears:
2. Choose a Batch display name and click OK.

3. The BioCommand Save Files window will open:
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4. To see existing File Name/Folder strings, click on the down arrow (W) to the right
of the File edit box.
5. Click on an existing File Name/Folder string to bring it into the edit box as a
pattern. Type over it to create a unique name for the Batch datafile. This will not
affect the existing File Name in any way.
6. If this file should be available to your network, click in the check box next to
Shared over the network.
NOTE:
All batch file names must have the extension .BDB.
A batch tab with the suffix letter B and the previously selected Batch Display Name
appears at the bottom of the BioCommand Plus screen. Use this tab to select which
Batch to view when several are running.
The batch is now running, as indicated by the Current EFT (Elapsed Fermentation
Time) clock running in the Setup screen.
5.5
Batch Summary View

You can view a text summary of current Batch status by calling up the Batch Summary
View. BioCommand Plus enables many other displays, including synoptic views, trend
graphs, bar graphs, etc., but these must first be specified on the Views page of the Recipe
or Batch setup screens before they are available for use in the batch. (See Sections 6 and
7 for information on other views.)
The Batch Summary view is available by default in all recipes.
There are several ways to display the Batch Summary View:
(1) From the Setup window, click on the Batch name tab at the bottom of the
BioCommand Plus screen.
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(2) From the Main Menu, select View Batch Summary.

(3) From the Setup window, click on the Views tab, then double click on Batch
Summary in the Current Views pane.
The Batch Summary view will open (see sample screen below):
Place your cursor on any edge of the window. When the double-headed arrow ()
appears, drag the edge to open the screen more fully.
Batch Summary View Column Headings

Column Heading
Loop
CV
Units
SP
OU
Mode
Description
Loop Name
Current Value of loop
Measuring Units for Current Value
Loop Setpoint
Controller Output for loop
Control Mode for loop
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INTRODUCTION TO BATCH VIEWS
In BioCommand Plus, trend graphs, bar gauges and the Batch Summary display
combine with BioCommand Plus synoptic display elements to form a virtually
limitless number of possible process viewing screens. Master the easy
BioCommand Plus display tools, and you can create informative, convenient,
appropriate displays, customized to your hardware and process.
6.1
Trend Views
A Trend View is a line graph of fermentation data plotted against time. You may
select up to 8 different data items to plot in real time while the Batch is running.
Each data item is displayed in a unique color so that the plots may be easily
distinguished from each other. A different vertical scale may be assigned to each
plot.
A Trend View can be specified in the Recipe Setup window, or added to the Batch
view after the Batch is running. To create a simple Trend View:
1. From the main menu, select File-View Recipe, or click on the View Recipe icon.
2. Select the Recipe of choice.
3. From the recipe Setup window, select the Views tab (see sample screen below):
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4. Double-click on Trend in the New Views: pane to open the Trend window,
which will look like the sample screen below:
5. Select the Loops tab in the control panel at the bottom of the window. This
changes the control panel to the ControlLoop selection screen, as illustrated
below:
6. Click on the {Setup Loop1} button to open the Select Loop list. These are the
available loops that have been specified for this recipe:
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7. Click on the loop that is desired for the first plot and then click the {OK} button.
This will add the loop name to the ControlLoop window. Click on the {>>}
button to change the control panel to Setup Loop2. This procedure may be
repeated for as many loops as you want to plot, up to a total of 8.
8. Select the Graphs tab on the control panel for the Trend View. The control
panel will change to a screen as shown below.
This allows you to set the high and low limits on the y-axis for each data item that is
to be plotted. Normal Windows editing techniques will allow any of the numerical
parameters to be changed.
You may also edit the Start and End times for the Trend View. Note, however, that
changing either time value will change the value for all parameters plotted.
9. Click on the {>>} and {<<} buttons to step through the selected loops.
10. Click on the Styles tab on the control panel to open a window, as shown below,
that allows the line and plot style for each loop to be set.
The default for each plot is a point-to-point thin line. This may be changed to a
thicker line and to any of the styles shown in the view above. To change the style:
A. Click on the option button next to the desired style and thickness.
B. The {<<} and {>>} buttons may be used to step through the loops to set the
parameters for each.
This completes the design of this simple Trend View. To save it:
11. Right click with the cursor anywhere in the gray area of the lower screen (on
either side of the control panel).
12. Select Save View from the dropdown menu to save the Trend View you have
created.
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13.
Close the window to add this view to the Recipe. It will appear in the
Current Views pane the next time you return to the Views tab.
NOTE:
If the trend graph was entered as part of the New Recipe or View Recipe
function, the trend graph will be available to all batches initiated from
the recipe.
If it was entered from a Batch function, then the trend graph will be
available only in the present Batch.
6.2
Using the Trend Graph

When the Trend View is onscreen, the Main tab should be selected on the control
panel. This will present a screen on the control panel with 8 display windows on it.
Each window, as illustrated in the sample screen below, will display a loop name in
the color of the plot, as long as the cursor is outside the plot area.
If the cursor is moved inside the plot area (i.e., onto the graph), each of these
windows will display the current value for the loop, as illustrated below:
If the Batch is not running, these values will all be 0 (as indicated in the sample
screen above).
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When the view is first entered, the left y-axis will display the name, color and scale
for Loop1, and the right y-axis will be named, colored and scaled for Loop2. In the
above sample, Loop1 (Agit1) is on the left, and Loop2 (pH1) is on the right.
Clicking on the loop name on the control panel Main tab will shift these labels.
With each click the new loop label will replace the current label, first on the left side,
then the right side. It will alternate with each succeeding click.
You can change the Trend View to show a larger graph area by clicking anywhere on
the gray areas of the view. The control panel will reduce to colored buttons, each
representing its assigned loop. Click again in the gray area to return to the tabbed
control panel.
There are many other features available in Trend Views. See Chapter 13, Creating
and Editing Views, for details.
6.3
Creating Synoptic Views

Synoptic Views pictorially represent the physical layout of a fermentation system.
Create a synoptic view by using a toolbar to position icons of fermentation system
components in the display space. Beside these icons, you can place data values and
labels that describe the system and the status of the Batch.
To create a synoptic view:
1. From the main menu, select File-View Recipe, or click on the View Recipe icon.
Select a recipe you created previously.
NOTE:
You can also create synoptic views while a Batch is running, from the
Setup screen.
2. Select the Views tab. This page shows the currently defined views in the left
pane. It shows views that can be defined in the right pane.
3. Double-clicking on Synoptic in the New Views: pane opens the Synoptic
window.
4. A Toolbar appears at the right side of the screen when this window opens and a
new item, Synoptic, is added to the Main Screen menu items, as shown below:
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5. Select Synoptic Design Mode from this menu. A check mark appears beside
Design Mode in the menu and a grid of dots appears on the Synoptic design
screen:
6. Select the vessel icon from the Toolbar (see Section 13.3 for details on the
Synoptic View Toolbar) or select Synoptic Gauges Vessel from the Main
Menu.
7. When you move the cursor onto the synoptic screen, a rectangle will be attached
to the cursor arrow.
8. Move this rectangle to the desired location on the screen and click the left mouse
button to anchor the vessel icon (see sample screen below with vessel icon).
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As illustrated above, the default label Vessel appears with this icon. To change it
to an NBS fermentor name:
A. Double-click on the label (Vessel).
B. Click on the down arrow (W) that appears, to pull down a list of the standard
NBS Fermentation System names (see sample below).
C. Select the desired name by clicking on it.

D. To enter a custom label, type in the new name and press <Enter>.
E. If necessary, you can right-click on this label to use the Delete function.
F. To enable Agitation via this Synoptic View, right click on the Vessel icon to
access the pop-up menu. Select Properties, then select Agit from the Loop
Select Window, then click {OK}. Agit = X (X is the current value) will
appear in the Vessel icon edit box next to the image of the impellers.
A Faceplate is a bar graph display of the Setpoint (SP), Current Value (CV), and
Output Level (OU) for any loop in the recipe.
9. Select the faceplate icon on the Toolbar (see Section 13.3 for details on the
Synoptic View Toolbar) or select Synoptic Gauges Faceplate from the Main
Menu.
Moving the cursor onto the synoptic screen will show a rectangle attached to the
cursor arrow.
10. Move the rectangle to the desired location on the screen.
11. Click the left mouse button to place the faceplate icon there.
12. Click on the bar at the bottom of the faceplate with the right mouse button to open
a submenu.
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13. Click on Properties.

14. The Select Loop window will open, showing a list of the loops available for this
Recipe.
15. Click on the desired loop name.
16. Click on the {OK} button.
17. The bottom bar will turn red, and will also display the name of the loop you
chose:
The above sample shows no active information because no batch is running.

When a Batch is running, the Setpoint (SP), Current Value (CV), and Output Level
(OU) will be displayed as bar graphs. The top of the display will show the actual
value for the loop setpoint, current value, or output level--whichever option button is
selected just below it. It will also identify the control mode for the loop.
The submenu that appears when you right click the loop label bar allows you to
change the setpoint: select Setpoint Change to open the Change Setpoint / Control
Mode window.
You can click on the scale end values for each parameter to change the bar graph
range to values more appropriate to the expected data range. The figure below shows
the Setpoint and Current Value ranges changed for an agitation speed loop:
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The Setpoint and the Current Value scales were changed from 0-100 to 0-1000.
Now add a Flowmeter to the display:
18. Select a Flowmeter from either the menu or the Toolbar (see Section 13.3 for
details on the Synoptic View Toolbar).
19. Place it at an appropriate location on the Synoptic screen; click to anchor it.
20. Right-click on this icon to open a submenu.
21. Select Properties.
22. The Select Loop window will open.
23. Select the loop that this icon will represent. The name and current value of the
selected loop is displayed above the icon:
Now draw a line to connect the flowmeter to the vessel in this simple synoptic
display:
1. Select Synoptic Lines Draw Lines from the Main Menu, or click on the Draw
Lines icon ( ) on the Toolbar.
2. Move the cursor onto Synoptic View screen: it will change to a + shape.
3. Place the cursor at the inside edge of the flowmeter, then click the left mouse
button.
4. Move the cursor toward the vessel icon. As you draw the line, it will be dashed,
not solid, until you anchor it.
5. You may only draw straight lines. If you need to change directions, click the left
mouse button at the end of the line (the dashed line will change to a solid line),
then continue drawing in the new direction. Note that you may only make right
angles.
6. Double-click to anchor the end of the connecting line.
7. Double-click on a blank area of the screen to end the Draw Lines function.
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NOTE:
A line may be drawn only between an output and an input (or vice
versa), not between two outputs or two inputs.
Change the Synoptic View to Run Mode:
1. Click on the Design Mode icon on the toolbar or select Synoptic Design Mode
from the Main Menu.
2. Close the Synoptic View window.
3. The Recipe Setup window will list a new Synoptic view.
The above procedure has created a very simple Synoptic View for the Batch being run,
as shown below:
Note that in this sample, the Faceplate gauge identifies the Agitation loops Current
Value (selected by option button) as 600 and the Control Mode as PID at the top of
the icon. It also displays current values for all three parameters in the bar graphs.
The Flowmeter, which is connected to the Vessel by a short line, identifies Air Flow
at a Current Value of 40. The animation feature of this view will show the impellers
turning in the vessel.
For further information on the features available in Synoptic Views, see Chapter 13
on Creating and Editing Views.
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CREATING PROGRAMS
BioComman Plus has powerful programming tools that can alter setpoints
automatically at specified times, or when specified culture conditions are met.
Programs are useful for implementing feeding strategies, inducing protein
production through temperature shifts or chemical additions, and generally
relieving the operator of having to be present in order to carry out a protocol.
Programs can also calculate values that are not directly measured by probes.
For example, from agitation RPM, the linear speed of the impeller tip can be
calculated, logged, displayed and otherwise utilized in the same ways as a
directly measured loop value.
Programming tools include:
Time Profile Functions, which change setpoints as prescribed by the user according to
elapsed fermentation time
Logical and mathematical function blocks, which are graphic elements with unique
functions such as add, assign a setpoint, compare values, and calculate a value, among others.
User-Defined Function blocks, programmed by the user in the BASIC programming

language.
Programs are created and edited through a Program View. Access a new Program View from
the View tab of the Recipe Setup screen.
Any or all of the programming tools are combined in a diagram that comprises a Program View.
Lines connect program elements, indicating the sequence in which various functions are
performed.
Once a program is running, the Program View can be closed or even deleted without affecting
program operation. (A deleted Program View can be recreated from batch data using the
Extract a recipe from a batch option in the Starting BioCommand screen, accessed by
selecting FileStart Options from the Main Menu.)
Every running program is automatically reevaluated every 10 seconds. This means for
example that a simple program that adds a constant to a setpoint will cause that same constant to
be added repeatedly, resulting in a (nearly) continuous increase in setpoint.
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7.1
7.1.1
How to Create a Program

Open the Program View Window
There are two ways to access the Program View window:
(1) If you are in the main menu, Select Views - New Program
(2) If you are in the Recipe Setup screen:
A. Click on the Views tab. You will see the current defined views in the left pane
and the new views that can be created in the right pane.
B. Double click on Program in the New Views: (right) pane.
When the Program View window opens, a special Toolbar appears at the right side of the
screen (see sample below), and Program appears as a new Main Menu item.
Elements to be used in the program may be obtained by clicking on the appropriate
toolbar icon or by selecting them from the Program menu.
Here are the Program View Toolbar icons:
Input
Setpoint Output
Add
Multiply
Absolute Value
Exponential
Square Root
Totalizer
User-Defined Function
PWM Output
IF
Logical AND
Logical Complement
Draw Lines
Constant
User-Defined Loop
Subtract
Divide
Reciprocal
Natural Log
Limit
Change sign
Time Profile
Comment
Set
Logical OR
Exclusive OR
Select Items
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7.1.2
Example: Automatic Glucose Feed-on-Demand

This simple program relies on a sudden increase in dissolved oxygen to trigger the
addition of glucose through the pump called FEED1. This sample is typical of
programs that use IF-THEN logic. When some condition is met, such programs
change one or more setpoints. In this case, the condition is that dissolved oxygen
(which presumably has a setpoint of 30%) spikes to a value greater than 40%. This
causes the FEED1 pump setpoint to change from 0% to 100% until the DO is restored
to less than 40%, at which time the pump setpoint returns to zero.
In order for this program to work, the depletion of glucose must result in a sudden
decrease in oxygen demand. Also, the control system response must be slower than
the decrease in oxygen demand. Triggers should be tested for validity; do not simply
assume they will work.
Follow the following steps to set up the simple program shown above:
1. Position and configure the If control block:
a. Use the mouse to select the If icon from the toolbar. (Pausing the cursor on
an icon calls up its name.) The cursor changes to indicate the selected icon.
Position an If function block in the workspace by clicking at the location
shown in the diagram above.
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b. Double click on the If control block in the workspace to open the Set
Control Block Parameters dialogue box.
c. Click on the upper Lp>> option button, to open the Select Loop dialogue
box (see below). Select DO2 1 and CV (Current Value). Click on {OK} to
return to the Set Control Block Parameters dialogue box.
CV OPTION
DO2 1 Loop
Name
d. Click on the lower Const option button, and type 40 in the adjacent field.
Select the greater than symbol (>). Click on {OK} to complete the
configuration of the If block.
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2. Position and configure the Set control block:

a. Use the mouse to select the Set icon from the toolbar. The cursor changes to
indicate the selected icon. Position the Set block in the workspace by
clicking at the location shown in the diagram below.
b. Double click on the Set function block to open the Set Control Block
Parameters dialogue box (see below). Select the Const option for the True
field, and type the constant 100 in the True field. Select the Const option for
the False field, and type the constant 0 in the False field.
c. Click on {OK} to complete the configuration of the Set block.

3. Position and configure the Setpt (Setpoint) control block:
a. Use the mouse to select the Spt icon from the toolbar. The cursor changes to
indicate the selected icon. Position the block in the workspace by clicking at
the location shown in the diagram.
b. Double click on the Setpt icon to open the Select Loop dialogue box.
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c. Select the Feed 1 loop. Click on {OK}. Feed 1 appears in the Setpt
control block.
4. Connect the control blocks:

a. Select the Draw Lines icon () on the toolbar, then click inside the right
border of the If block, move the mouse to inside the left border of the Set
block, and click again. This draws a line between the two blocks. If the line
is not sufficiently straight, adjust the vertical position of one of the boxes by
choosing Program Move Block. Drag the block until the line is straight.
b. In similar fashion, connect the Set block to the Setpt block.
5. Click on the Select Items icon ( ), bottom right on the toolbar, to end the Draw
Lines function and to return the cursor to its normal function.
6. If the batch is active, right click on the Setpt oval and select Run from the popup menu. The oval changes from red to green to indicate it is running.
7. To save the program before you close it, right click on the white space in the
program view. Select Save View from the pop-up menu (see sample screen
below).
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The next time you open the Views tab, this program (automatically numbered by
BioCommand Plus) will appear in the Current Views: pane:
New
Program
The program could be enhanced by adding an Elapsed Fermentation Time condition.

By requiring that the EFT be greater than, let us say, 10 hours, initially high values of
dissolved oxygentypical of low cell densitywill be ignored.
Another possibility is to include a time profile, so that when it is triggered the pump
will run at prescribed setpoints for specified times.
7.1.3
Example: Calculation of Impeller Tip Speed

Some programs change setpoints, others calculate values that are not amenable to
direct measurement. This is an example of a program that applies a calculation to
arrive at a result.
The linear speed (in centimeters/second) of the tip of the agitation impeller is
calculated from agitation RPM and the diameter of the impeller. The value could be
useful for scale-up considerations with shear-sensitive cultures.
Tip speed is a multiplication: the rotational speed multiplied by the impeller diameter
(in centimeters) multiplied by the constant (3.142). Since the rotational speed is
reported to BioCommand Plus in revolutions per minute, it must be divided by 60 (the
number of seconds per minute) to convert it to revolutions per second. The general
formula for this calculation is:
TIPSPD = (RPM/60) x diameter x
Using a diameter of 7.5 cm and a value of 3.142 for , the equation becomes:
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TIPSPD = (RPM/60) x 7.5 x 3.142

To draw the program that calculates this equation, which looks like this:
do the following:
1. Position and configure the Input control block:
a. Use the mouse to select the In (Input) icon from the toolbar (you can also
select Program Elements In/Out Input from the Main Menu). Position
the In function block in the upper left corner of the workspace, click to
secure it in place. It becomes an oval control block.
b. Double click on the Input control block to open the Select Loop screen.
Select the CV (Current Value) option and select Agit 1. Click on {OK}. The
Input block is now labeled Agit1.CV.
2. Position and configure three Constant control blocks:
a. Use the mouse to select the k (Constant) icon on the toolbar (or select
Program Elements In/Out Constant from the Main Menu). Position
the function block under the Input block.
b. Double click on the Const block to open the BioCommand Diagram
Editor dialogue box.
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c. Type 7.5 in the edit box, and click on the {OK} button. 7.5 appears in the
Const block.
d. Repeating step a, import a second Const block, and then a third, aligning
them under each other, beneath the first Const.
e. Repeat step b to open the Diagram Editor dialogue box for the second
constant block. Enter 3.142 and click on {OK}.
f. Repeat the same step for the third constant block. Enter 60 and click on
{OK}.
3. Position and configure the User Loop result block:
a. Use the mouse to select the Usr (User-Defined Loop) icon on the toolbar.
Position the Usr function block on the workspace, far right, halfway between
the first and second Const blocks.
b. Double click on the UserLp result block in the workspace to open the
BioCommand Diagram Editor dialogue box. Type TIPSPD in the edit
box. Click on {OK}. The User Loop result block is now labeled
TIPSPD.CV.
Now you have one input, three constants, and one result. They must be connected
mathematically to make the equation work:
4. Add the mathematical functions:
a. Use the mouse to select the multiplication x icon on the toolbar (or select
Program Elements Math Functions Multiply from the Main Menu).
Place the icon between, and to the right of, the Input block and the first
Const block.
b. Place a second multiplication icon between, and to the right of, the first two
Constant ovals, aligning it with the UserLp block.
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c. In similar fashion, place a division icon to the right of the second multiplier,
aligned with the left edge of the UserLp block.
d. Use the Draw Lines tool ( ) to draw a line from the right edge of the
Input block to just above the middle of the first multiplication icon. Left
click to set the line, then continue drawing down to connect with the top of the
multiplier. (Note that all turns when you draw lines are right angles.) Left
click to set the line.
e. In the same manner, draw a line from the right edge of the first Const block
to connect to the bottom of the multiplier. You have now told the program to
multiply the Agit1 current value input by the constant 7.5 (the impeller
diameter).
f. Draw a line to connect the right edge of the first multiplier to the top of the
second multiplier, and add a line to connect the right edge of the third Const
block to the bottom of the second multiplier. Completing this tells the
program to multiply the result of the first multiplication by the constant 3.142
().
g. Now draw a line to connect the right edge of the second multiplier (the result
of the second multiplication) to the left edge of the division icon. Add a line
from the right edge of the third Const block to the bottom of the division
icon. These connections tell the program to divide the result of the second
multiplication (impeller centimeters traveled per minute) by the constant 60
(seconds per minute).
h. Draw a final line from the right edge of the division icon to the left edge of the
UserLp result block. This tells the program that the result of the entire
equation will be the current value of impeller tip speed.
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The UserLp block is red (and is marked OFF) because the program is initially off.
To turn it on:
1. Left click on the UserLp icon. A red border appears around it. Select Program
Run from the Main Menu. The Run Control Diagram window opens:
If you wish, enter a description of the program and/or a comment about its
function in this window.
2. Click on the {Run} button. In the program view, the UserLp block is now green
and says ON.
3. Save the program before you close it:

a. Right click on the white space in the program view.
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b. Select Save View from the pop-up menu.

The next time you open the Views tab, this program (automatically numbered by
BioCommand Plus) will be listed in the Current Views pane:
Previous
Program
New
Program
7.1.4
How to Stop a Program

When a program is running, there is only one way to stop it:
1.
In the Batch Setup screen, click on the Views tab.
2.
In the Current Views: pane, double click on the program name.
For further information on the features available on Program Views, see Section 13 on
Creating and Editing Views. As you have seen, using this simple graphic procedure,
calculations may very easily be entered into process control.
7.2
User-Defined Loops
The Program View function may also be used to create custom programs that may be
used as loops in other portions of the program. Any User-Defined loop created in a and
saved in a custom program will automatically appear on all loop lists that are a part of the
Recipe or Batch being operated on.
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7.2.1
How to Create a User-Defined Loop

Follow the steps outlined in section 7.1.3 above to create a User-Defined Loop. Use
the program view to create the rest of the program in which this new loop will be an
element.
7.3
More Program Functions

For additional information about creating and editing programs, about program functions
and about program icons, see Chapter 12.
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SETTING ALARMS & ALERTS

BioCommand Plus allows you to enter two sets of high and low limits for any or
all of the loops in the Recipe. One set is Alert limits, to inform you that a data
value has exceeded or dropped below normal range. The second set is Alarm
limits, to inform you when a loop value has passed into a dangerous range.
When an alert limit has been reached, the display tab at the bottom of the screen
turns yellow to signal you that an alert has been generated. When a value enters
an alarm range, the tab turns red. There is also an easily accessible Alarm
Summary report that displays any activity beyond the limits you set.
8.1
Setting Alarms
1. From a Recipe or Batch Setup screen, click on the Alarms tab.
NOTE:
First you must select the loops for the Recipe. These settings may be
made as part of the Recipe or added to a Batch while it is running.
If a batch
Is not
running,
this button
will be
labeled
Start Batch
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The Alarms window has two tabs on the bottom, Current Alarm Settings and
Current Alert Settings. This window always opens with the Alarm page active.
To set an alarm for this Recipe:
2. In the first row of the Loop Name column, click on the down arrow (W). A
submenu will open with a list of the loops available for this Recipe:
3. Double-click on the desired loop. That loop name will then appear in the Loop
Name box.
4. Click, in the same row, the box immediately to the right of the loop name, under
Alarm Type. A down arrow (W) will appear at the right side of the box.
5. Click the down arrow to open submenu of two selections for the alarm trigger:
Absolute or Setpoint Deviation.
Double-click on Absolute to generate an alarm if the actual Current Value for

the selected loop exceeds or drops below the absolute limit parameters you
set, independent of Setpoint.
Double-click on Setpoint Deviation to generate an alarm if the actual Current

Value for the selected loop exceeds or drops below the setpoint tolerance you
set. The submenu will close and the alarm type you have chosen will appear
in the Alarm Type box:
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6. Next, enter, in the appropriate edit boxes, the numeric value for the Low (Lo)
Limit and the High (Hi) Limit that will govern the alarm function:
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The availability of the alarm function for each loop may be turned on or off
independently at any time:
1. In the row corresponding to the desired loop, click under the On/Off heading. A
down arrow (W) will appear to the right.
2. Click on the down arrow to open the submenu:
3. Double-click On to activate the alarm, or Off to deactivate it. The selected

action will appear in the box.
4. Click in the Audible On checkbox if you want an alarm sound to be generated
when an alarm is triggered.
NOTE:
A sound card is required to use the Audible option.
5. Repeat the same steps for as many loops as you wish.
6. Click on the {Apply Changes} button. Your alarm settings for the selected
loop(s) are now part of the Recipe or Batch.
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The sample window below shows alarms set for five loops, with the Audible option
enabled:
8.2
Setting Alerts
Setting alerts is exactly the same process as setting alarms, except that you will first
select the Alert Settings window instead of the Alarm Settings window.
NOTE:
First you must select the loops for the Recipe. These settings may be
made as part of the Recipe or added to a Batch while it is running.
1. From a Recipe or Batch Setup screen, click on the Alarms tab.
2. Click on the Current Alert Settings tab on the bottom right of the Alarms screen.
The Current Alert Settings window will open.
3. Follow the steps in Section 8.1 above. The difference is that the parameters you
set in this window will generate alerts instead of alarms.
4. Remember to repeat the process to set alerts for as many loops as you wish.
5. Remember to click on the {Apply Changes} button to save your settings.
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ENDING A BATCH
After a fermentation run has ended, and before exiting the BioCommand Plus
program, perform an End of Batch procedure to close the data log file and to
terminate Batch supervision. Otherwise, exiting BioCommand Plus will be
interpreted as an interruption, and the program will attempt to resume data
logging and control of the same Batch the next time the program is started.
9.1
End a Batch
1. Open the Setup View.
2. Click on the {End Batch} button. A window called End Batch? will open, asking for
confirmation that you do indeed wish to end the Batch.
3. If you wish to terminate the Batch, click on {OK}. If you have made an error or changed
your mind, click on the {Cancel} button to return to the Setup window with no
interruption in Batch operation.
9.2
Exiting BioCommand Plus

If you wish to exit BioCommand Plus without ending all running Batches, an advice window,
Exit with Active Batches, must be acknowledged before the program will close:
Click the {OK} button to exit the program, or click on the {Cancel} button to return to
BioCommand Plus.
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9.3
Restarting with Active Batches

Usually a shutdown with Batches running is the result of an accident, such as power
failure or operator error. Recovery is easy.
1. Restart BioCommand Plus. On restart, you will see the Starting BioCommand
opening Wizard screen. (If you have turned it off, skip to bullet #2.)
Click on the option button to select Resume a batch running when

BioCommand exited.
Click on {Continue}. The Resume Batches window will open (see below).
2. On restart you will see the Resume Batches window immediately if you have
turned off the Wizard:
3. Select the Batch(es) you wish to resume.

4. To reinstate computer supervision of the selected Batch(es), click on the {Resume
Batch} button. The Batch Setup window will open. Expect a brief pause while
the program locates and connects to the hardware. The process will continue as it
was prior to program exit.
5. You may prefer to click on {Details} to directly enter the Batch Setup window for
a selected Batch. This will give you additional options:
Note that this window (see sample below) has two new buttons at the bottom:
{Terminate Batch} and {Resume Batch}.
This option allows you to modify batch parameters before you resume the
batch, or to end the batch.
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NOTE:
If more than one batch is available to be resumed, the Resume
Batches window will return. You may select another batch to resume,
or click on {Exit}. The Resume Batches window can be recalled later
by selecting File-Resume Batches from the Main Menu.
9.4
Shutting Down BioCommand Plus

There are two ways to exit BioCommand Plus:
A. Click the Close icon (U) in the upper right corner of the Main Screen
B. Select File Exit from the Main Menu.
NOTE:
To prevent the loss of data, always exit BioCommand Plus before you
turn off power to the computer.
In addition, always shut down Windows itself in the prescribed manner.
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10
SECURITY FEATURES
BioCommand Plus allows managers to designate access levels for each user.
A Recipe can enforce different batch authorities for different users. If you choose
to secure your BioCommand Plus system, we recommend that you make at least
two users members of the Admin group, to cover the possibility that one member is
unavailable. There is no back door.
10.1
User-Based Access
All members of a workgroups are known as Users. Some of those users may also be
designated as Recipe Creators or as Admins. Recipe Creators have the privilege of writing
new recipes. Admins have full authorization to access and to make changes to any element
under BioCommand Plus control. Each user should be assigned a password to validate that
individuals log-on identification, through which the system recognizes the users access
rights.
10.2
Entering User Passwords

Admin
Recipe
Creators
Other Users
Initially there are no user passwords entered into the program. This means that when you
install and open BioCommand Plus, and each time the program is opened thereafter, you will
be operating in an unsecured mode until a Password is established. If no password is set up,
the system will automatically identify the user as Admin, and because Admin has no preassigned password, the system is open for unsecured use.
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For security, each user of the program should have a personal password that allows that user
to interface with the program up to his/her level of authorization. This will prevent an
unauthorized person from making any operational or functional change.
10.2.1
Setting the First Password

If you are a member of the Admin workgroup (see also Section 10.4 below),
you may enter an initial password. Follow these steps:
1. Select User Change Password from the Main Menu. The Change Password
window will open:
2. Leave Old Password blank.

3. Enter the desired New Password. Note that your password will be displayed as
a string of asterisks (******), so type carefully. This feature is to protect your
password from any unauthorized observer.
4. Confirm the password by carefully typing it again in the Confirm edit box.
Here, too, you will only see ****** as you type.
5. Click {OK} to save your password and to exit this window.
If what you type in the Confirm: box does not match what you entered in the New
Password box, the BioCommand Password error window shown below will
appear:
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1.
2.
3.
4.
10.2.2
Click {OK}. The error window will close.

In the Change Password window retype the new password.
Retype the confirmation.
Click {OK}.
Changing an Existing Password
In order to change a password, you need to know the existing Old Password.
1. Select User Change Password from the Main Menu. The Change password
window will open:
2. Enter the Old Password for the user named at the top of the window (in this
case admin).
3. Enter the desired New Password. As you type, your password will be displayed
as a string of asterisks (******), so type carefully. This feature is to protect your
password from any unauthorized observer.
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4. Confirm the password by carefully typing it again in the Confirm edit box.
Here, too, you will only see ****** as you type.
5. Click {OK} to save your password and to exit this window.
10.2.3
Removing Password Protection

If you do not wish to have password protection to the program for an individual user,
you can clear the password function:
1. Select User Change Password from the Main Menu. The Change Password
window will open (see sample screen above).
2. Enter the old password for the user named.
3. Leave the New Password: and Confirm: lines blank.
4. Click on {OK}.
The password is now blank for the user.
10.2.4
Using Passwords
If passwords have been entered for one or more users, the BioCommand User
LogOn window will appear each time you start the program:
1. Enter the User Name in the Name edit box.

2. Enter the user password in the Password edit box.
3. Click {OK}.
If you enter password incorrectly, the BioCommand LogOn window will appear:
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1. Click Retry for another opportunity to enter the proper password.

2. Click {Cancel} if you wish to enter the program without with limited options
(without the privileges afforded by the password).
10.3
Recipe Authorization Levels
Within each individual recipe, there are five authorization that can be assigned to the users of
that recipe. These levels are:
None This level of authorization has no access whatsoever to the recipe or resulting
batches. This entry is included as a way to remove a users name from the privilege list.
Observer A user with this authorization level can display the different batch views, for
observation only. The Observer cannot make any changes.
Operator This level of user may observe all views, start and stop the batch, and change
setpoints. The Operator may not alter programs, add or remove loops, change
authorization levels or change Alarm or Alert limits.
Supervisor A Supervisor level user has all of the privileges of the Operator, and may
also activate, deactivate and edit control programs. The Supervisor may not add or
remove loops, or access the rights to a recipe.
Manager A Manager has total access to all of the functions of the recipe.
Manager
Supervisor
Operator
None
Observer
10.4
Creating and Modifying a User List

When you create Recipes and Batches, you can also establish the functions that can be
performed by each level of user. Authorized users of the program can be assigned to
different groups with different levels of control.
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The window below shows how the various users and groups are added to the list of
authorized users. The program begins with the three user access groups mentioned
above:
10.4.1
Admins
Recipe Creators
Users
Adding Groups
To add existing groups to the program:
1. From the Main Menu, select User Manage Accounts. The BioCommand
Workgroup User/Group Accounts window will open.
This window functions very much like the Add/Change Loop List window in
Section 5.1.
2. In the Groups: pane (which lists available groups), click on the desired
group name. That group name will then appear in the title of the Members of
pane. A list of its current members will appear inside the pane.
Initially, Admin is, by default, the only member of each group.
10.4.2
Adding Users
To add existing Users to a group:
1. Click on the group name in the Groups pane.
2. Click on the User name in the Users pane.
3. Press the {>>} button to move that user name into the Members of pane.
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The User will now appear as a member of the selected group, and the User will
have the authority level that is assigned to that group.
10.4.3
Removing Users
To remove Users from a group:
1. Click on the User name in the Members of pane.
2. Click on the {<<} button.
That User no longer is a member of that group and will no longer have the level
of authority assigned to the group.
10.4.4
Adding New Users

To add a New User (someone not already listed in the Users pane of the
BioCommand Workgroup User/Group Accounts window):
1. Click on the {Add User} button. The Add new user window will appear:
2. Enter the new User Name. This is the name that will identify this particular
user and will appear in all workgroup lists.
3. Enter a Personal Identifier (PID:) that will be that users unique
identification. This PID must be a group of at least 4, but no more than 20,
alphanumeric characters. Each PID should be recorded elsewhere and kept in
a secure place for possible future reference.
4. Click {OK} to save the entry, or click {Cancel} if you decide not to add this
user.
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5. If no Personal Identifier (PID) is entered, the BioCommand User

Accounts error window will appear:
6. Click {OK}. The BioCommand Workgroup User/Group Accounts window

will reappear without the new user.
7. Follow the above steps again, completing all information, if you still wish to
add the New User.
10.4.5
Adding a New Group

New groups are added in the same way as new users. To add a New Group (one
not already listed in the Groups pane of the BioCommand Workgroup
User/Group Accounts window):
1. Click on the {Add Group} button. The Add new group window will
appear:
2. Enter the new Group Name. This is the name that will identify this particular
group and will appear in all workgroup lists.
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3. Enter a Personal Identifier (PID:) that will be that groups unique

identification. This PID must be a group of at least 4, but no more than 20,
alphanumeric characters. Each PID should be recorded elsewhere and kept in
a secure place for possible future reference.
4. Click {OK} to save the entry.
5. Click {Cancel} if you decide not to add this group.
6. If no PID is entered, an error window will appear. Click {OK}. The
BioCommand Workgroup User/Group Accounts window will reappear
without the new group.
7. Follow the above steps again, completing all information, if you still wish to
add the New Group.
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11
MAIN SCREEN FUNCTIONS

REFERENCE
This chapter provides an overview of the File, Edit, View, Tools, User,
Window and Help menus available from the Main Screen. The Main
Screen also includes an optional toolbar for quick access to several
operations.
11.1
File
The file menu, shown below, provides access to the functions that are used to control
the recipes and batches that may be used for process control with this program:
New Batch creates a new set of Batch parameters.

View Batch views an existing set of Batch parameters.
New Recipe creates a new set of Recipe parameters.
View Recipe views an existing set of Recipe parameters.
Start Options reopens the Starting BioCommand Batch Wizard window.
Local Batches views currently running Batches, local to your PC.
Resume Batches allows you to view the list of Batches still considered open by
BioCommand Plus and offers to resume data collection on any of them.
Print View allows the printing of the current view (Program, Synoptic, Batch
Summary or Trend).
Print Report allows the printing of a report of selected current run parameters,
as specified in the Tools Report Specification.
NOTE:
You can print a report for a batch that is no longer active via the
Database Viewer utility (see Chapter 17).
Exit will close the program and exit back to the Windows operating system.
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11.2
Edit
This selection provides the standard Windows functions that are available in
conjunction with the Windows clipboard. Any item that is selected using normal
Windows selection techniques can be removed from its current location and saved
on the clipboard (Cut), copied from its current location to the clipboard (Copy), or
inserted into the location of the cursor from the clipboard (Paste).
A selected item may also be deleted from the screen without going to the clipboard by
using the Delete selection. The Copy All selection will copy everything on the screen
onto the clipboard. These functions are most useful when designing Synoptic or
Program views.
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11.3
View
This selection provides you with several functions related to the display during
operation of the program, as shown in the sample window below.
Toolbar you can turn the Toolbar display on or off. If there is a checkmark
beside the Toolbar label, the Toolbar will be displayed on the main window. This
is a toggle function: if it is on, clicking on this item will turn it off, and if it is off,
clicking on it will turn it on. See Section 3.7 for further information on the main
Toolbar functions.
New Synoptic View enter the Synoptic View creation and editing function.
New Trend View enter the Trend View creation and editing function.
New Program View enter the Program view creation and editing function.
The following are examples of other selections that may be on this menu. The actual
items will depend on the Batch you are running, or the Recipe you are creating or
modifying.
Setup.1 opens the Batch Setup notebook.

Alarm Summary.1 opens the Alarm Summary screen for the Batch.
Batch Summary.1 opens the Batch Summary screen for the Batch.
Program.1 displays a defined Program View screen.
Synoptic.1 displays a defined Synoptic View screen.
Trend.1 displays a defined Trend View screen.
If two or more of any view types are defined, they will also be listed on this menu,
with increasing suffix numbers; i.e. Trend.2, Trend.3, etc.
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11.4
Tools
The Tools selection contains two options that provide functions that may be used in
conjunction with the rest of the BioCommand Plus program while running a process.
The two options, as shown in the sample screen below, are Report Specification and
Offline Data.
11.4.1
Report Specification Function

This option allows a graphical presentation of the process data to be specified
for printing. The sample screen below shows how the report specification
may be set up:
LOOP NAME
Left Y-Axis
UPPER SCALE
LIMIT
LOWER
SCALE LIMIT
START
TIME (EFT)
LOOP NAME
Right Y-Axis
UPPER SCALE
LIMIT
LOWER
SCALE LIMIT
END TIME
(EFT)
REPORT
SELECTOR
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1. Select Tools Report Specification from the Main Menu. The Batch Report
Specification window (shown above) will open.
2. If you wish, enter a Graph title in the middle edit box, above the graph
template.
3. Click on the down arrow (W) in the left y-axis Loop Name box. From the
dropdown list of available loops, select one.
4. Repeat the above step for the right y-axis Loop Name box.
5. Enter the appropriate Upper and Lower Scale Limits for both left and right yaxes.
6. Use the checkboxes under the Record Selector to select (or de-select) other
information to include in your reports:
Include Batch Events: this report will recap alarms and alerts that have
occurred while the batch was running.
Include Audit Record: this report will recap all changes made while the
batch was running.
Merge Batch Events and Audit Record: this is a single report that
tracks both types of actions chronologically.
7. Enter the Start Time and End Time (EFT) for the data you wish to graph.
You may specify more than one graph for your report. The Record Selector box
below the graph template displays the name of the graph specification you are
creating. This name is automatically assigned by BioCommand Plus; you will not
be able to edit it.
Use the Record Selector arrows ( or ) to step from one graph to another, one
by one. To move more rapidly, use the blocked arrows to move directly to the
first ([) or last ([) graph.
To clear a graph you have already specified:
1. Cycle through the graph templates using the Record Selector to display the
graph you wish to delete.
2. When the graph of interest is onscreen, click on the {Remove} button.
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When you have completed your report specification:

1. Click on the {Close} button or the Close icon (r) at the upper right of the
window. This will automatically save your report specifications as a part of
the Batch.
Another way to view, organize and report data from both active and
terminated batches is to use the Database Viewer utility (see Chapter 17 for
details).
11.4.2
OffLine Data
Data collected by techniques or instruments not connected to the operating
fermentor may be entered into the database for a batch by using this function.
1. While the batch is running, select Tools OffLine from the Main Menu. The
Offline data window will open:
For the time data you enter into the database, there are three time format settings
available. The default time format setting is Calendar, which allows you to input
both date and time of the data reading. EFT means that you will enter the time in
an HH:MM:SS format. Decimal EFT means time recorded as a decimal number.
If you wish to change the time format setting, do Step 2. If not, skip to Step 3.
2. Click on the option button of choice for the Time Format.
3. Enter the time entry.
4. Move to the Comments column: either press the <Enter> key, the right arrow
key (< >) or the <Tab> key, or move the cursor (with the mouse) and click
inside the desired cell.
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5. Enter Comments to describe the data value you are recording.

To make your comments more meaningful, you will probably want to add at least
one more column for the actual data values. The program will treat this new
parameter as a User-Defined Loop; the name you enter here will appear in all loop
lists and reports generated by the database for this Batch.
To add a column, or new parameter:
1. Click on the {New Param} button. The Offline data window will
temporarily disappear as the New Offline Parameter window opens:
2. Enter the name of the new column (use no more than 6 characters) in the edit
box.
3. Click on {OK} (unless you need to {Cancel}). The New Offline Parameter
window will close, replaced by the Offline data window. Your new
parameter will appear as a third column. (See sample screen below.)
4. Repeat the above steps to add other columns. Note that you can move the cell
borders just as you do in a Word table or an Excel spreadsheet.
Now that you have established the records, an offline measured data value can be
added to the database at any time during the running of the Batch.
To enter a new line of data:
1. Move your cursor to the * in the far left column.
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2. Click when your cursor changes to an arrow ( ). A new row will appear,
and your cursor will be positioned in the time column.
3. Enter the new data.
4. If you wish to delete an entry, you can use the {Clear Edits} button as long as
the line is still active.
5. Click on the {Close} button to end the Offline Data function.
11.5
User
The functions provided by this selection (see sample screen below) are:
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11.6
Log On if no user is logged on, this function will allow a new user access to the
program.
Log Off if the currently logged-on user is to cease being the operator, this function
will log that person off, to allow a new user to log on.
Change Password authorized users who have entered a password and are currently
logged on may change their password via this function.
Manage Accounts allows the addition, deletion, and modification of users,
operators, etc. and their level of authorization for the program.
Select Workgroup allows you to switch to another workgroup if there are two or
more sets of workgroups on the computer being used.
Window
Whenever two or more windows are open on the screen within the BioCommand Plus
program, this function allows you to view them in a choice of formats. The available
formats are the standard Windows selections:
Tile Horizontally
Tile Vertically
Cascade
Arrange Icons
Any of the windows may be closed, restored to previous size, or maximized to full
screen size by clicking on the icon, which opens a submenu with selections for
Restore, Maximize, or Close. Double-clicking on the icon will restore that window or
view to its previous size.
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When several windows are open at the same time, selecting Window Tile
Horizontally or Window Tile Vertically will change the screen display. It will be
similar to the one shown below. Each window can be individually selected, resized,
or restored to full screen size.
Selecting Window Cascade will rearrange the screen display, stacking the windows
like a deck of cards. It will resemble the example shown below. Each window can be
individually selected, resized, or restored to full screen size. Clicking on any part of a
window will bring that window to the top of the cascade.
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11.7
Help
This selection provides the standard type of Windows Help functions.
11.8
Contents A list of help topics available.

Search for Help On Provides the option of searching for Help using a key
word or phrase.
About BioCmdPlus Displays a window of information about the BioCommand
Plus program.
Toolbar Description
The Main Screen of the BioCommand Plus program includes an optional toolbar.
This toolbar can be used to initiate several functions within the BioCommand Plus
program, through a single mouse click. When you place your cursor over an icon on
the toolbar, a hint appears to remind you of that icons function.
The toolbar can be toggled on and off:
1. Select View Toolbar from the Main Menu. If the toolbar is on, there is a
checkmark beside Toolbar on the submenu.
2. Click on the checkmark to remove the toolbar from the screen. The checkmark
will also disappear.
3. To redisplay the toolbar, select View Toolbar from the Main Menu.
4. Click in the checkbox to the left of Toolbar.
5. A check will appear in the checkbox, and the toolbar will appear onscreen.
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Below is a picture of the toolbar and its various functional icons:

New Batch
View Batch
New Recipe
View Recipe
Batch Wizard
Whats This? HELP
Print
Save
Delete
Paste
Copy
Cut
Standard Windows functions
NOTE:
Each of these icons performs the same function as the like-named
selection from one of the menus.
The box to the right of the Toolbar displays the name of the currently logged-on user.
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12
RECIPE/BATCH FUNCTIONS
BioCommand Plus allows you to enter a variety of run parameters and save
them for future use without having to re-enter the parameters each time a similar
set-up is desired. There are two components to this function: Recipes and
Batches. A Recipe is a set of parameters that define the fermentation process. A
Batch is a single run based on that Recipe. The same Recipe may be used for
any number of Batches and each Batch starts with a Recipe.
12.1
Creating or Editing Recipes

You can create new recipes or edit existing recipes by using the Batch Wizard. The
Wizard is active as soon as you open BioCommand Plus, unless you have cancelled it.
If it does not appear and you wish to bring it back, select File Start Options on the
Main Menu, or you can click on the toolbar Batch Wizard icon. Refer to Section 4
for instructions on using the Batch Wizard.
You can also create new recipes using the New Recipe function or you can edit
existing recipes with the View Recipe function.
12.1.1
New Recipe Setup Window

Click the New Recipe icon on the Toolbar or select File - New Recipe from
the Main Menu. The Setup window will open:
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This is a dialogue box with 6 tabbed pages. Each page is a new window with
different functions. These pages are:
Recipe for the entry of basic recipe parameters

Loops displays the loops that are available and allows you to select the
loops to be included in this recipe.
Views allows the creation and editing of Synoptic, Trend or Program
views. Also provides an entry to display these views, as well as the
standard views that are included in the program: Alarm Summary, Batch
Summary, and Setup.
Programs provides for the creation and editing of Supervisory Programs
and User-defined Loop Programs.
Alarms allows the setting of Alarm and Alert levels for any of the loops
included in the batch.
User Access allows the setting of user access and rights for this recipe.
See sections 12.1.4 - 12.1.10 for detailed instructions on using the various
tabs.
12.1.2
View Recipe Setup Window

1. Click the View Recipe icon on the Toolbar or select File - View Recipe
from the Main Menu. The Select File to Open window will open first,
listing the existing Recipe files:
2. Select the Recipe of choice: click on its name or type the file name into
the File name edit box.
3. Click on {Open}. The View Recipe Setup window will open.
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This window is the same as the New Recipe Setup window shown on the
previous page. Note, however, that the fields are filled in with the parameters
of the Recipe you selected.
12.1.3
Using the Setup Window

From this point forward, the functions are essentially the same, whether you
are creating a new Recipe or editing an existing one.
The four standard buttons at the bottom of the window are visible at all times,
regardless of which notebook page is displayed. These four buttons are:
{Save As} this function will save the Recipe under a different name than
the original Recipe.
{Save} this function makes your changes to the Recipe parameters
effective for the Batch.
{Start Batch} this function will start a Batch run, using this Recipes
parameters. This button will not be available unless the Recipe contains
enough information to run a Batch.
{Close} This will close the Create Recipe or the View Recipe function.
If you click on {Start Batch} or {Close} but you have not saved the Recipe
changes you have made, the Save Changes window will open:
12.1.4
If you click the {No} button, all of your changes to the Recipe will be lost.
If you click on the {Cancel} button, the program returns to the Create
Recipe or View Recipe function, whichever you were using.
If this is a new Recipe and you click on the {Yes} button, the
BioCommand Save Files window will open. Enter the file name under
which you wish to save the new Recipe.
Recipe Tab
The Recipe page of the notebook (see sample below) contains items that are
considered descriptive of the Recipe:
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File Data Pane:

The edit box in the File Data pane displays the name under which the Recipe
will be saved.
If this window was opened via the View Recipe selection, this box will
contain the name of the Recipe file that was opened.
If, instead, you have created a new Recipe, this box will be blank until you
save the recipe file to disk and you fill in the BioCommand Save Files
window.
If you are going to use an existing Recipe as the starting point for a new
Recipe, click on the {Browse Recipes} button to bring up the Save To
window, as shown above. This window allows you to choose the Recipe
file you wish to use.
You may also use normal Windows techniques to navigate through the
disk folders, to locate the desired Recipe file.
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Recipe Data Pane:

The Recipe Data pane contains three items:
BioCommand Plus supplies the Owner: item, based on the logged-on

user when the Recipe is created.
The Display (Tab) Name: is a descriptive name that you give to the
Recipe. This is the default name that will appear on the tab at the bottom
of the screen when a Batch using the Recipe is active. It is also the default
name suggested for use as the file name for data storage. This item may
contain up to twelve alphanumeric characters.
The Description: item gives you the option of entering text that more
completely describes the function or special features of this Recipe. It
may contain spaces and punctuation marks as well as alphanumeric
characters.
Near the bottom of the window is a pane that contains a sub-notebook with
two tabs, Time Data and Recipe Data, as shown in the sample screen
above.
Time Data Tab:
The Time Data tab allows you to select the time interval between data point
acquisitions.
1. Click on the {Change Interval} button under the edit box. In the Change
Log Interval screen that appears (see below), you have two choices:
Change Log Interval
Save
Save
A. Use the edit box down arrow (W) to open a list of time selections and
choose one by clicking on it.
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B. Enter any number directly into the edit box labeled Log Interval
(Mins). Note that:
If you enter a decimal number greater than one, the program will
round it to the nearest whole minute.
If you enter an interval of less than one, it will be rounded to the

nearest tenth of a minute.
When a Batch is running, this pane also continually shows the Elapsed
Fermentation Time (EFT) in the Current EFT box.
The {Reset EFT} button, which will reset the EFT to zero, is available to you
only when a Batch is running:
1. Click on it at any time during the Batch run. The Reset Eft window will
open:
2. Click the {OK} button if you want to turn the clock back to zero, or click
the {Cancel} button to abort this action.
This tab also allows you to select the format for EFT display. On the far right,
in the pane labeled Time Display Format, there are two selections:
A. HH:MM:SS displays the EFT in the format of hours, minutes, and
seconds (ex: 12:59:03).
B. Decimal hours displays the EFT as a decimal fraction (ex: 12.98).
If it is not already selected, click on the option button next to your format
choice.
Recipe Data Tab:
After a new Recipe is created and saved, the Recipe Data page of the subnotebook (see below) will display information entered while the Recipe was
being created:
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The Recipe File: box displays the file name under which the Recipe is
saved.
Created By: displays the name of the logged-on user who created the
Recipe initially.
The Date: box displays the time and date when the Recipe was created.
Nothing on this page can be edited; it is an information display only.

12.1.5
Loops Tab
The Loops tab opens up the notebook page where the loops to be used in the
Recipe can be selected or modified. There are two panes on this page:
Change Loop List and Current Loops.
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When you open this page, if no loops were previously specified for this
Recipe, the Add/Change Hardware Loop List window will open over it.
This window is used to tell BioCommand Plus where to look for loops that
may be used with this Recipe:
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1. Click on the {Browse Local Server} button to display loops that are
connected only to your PC.
2. Click on {Browse Network Server} to search all workstations connected
to the your PCs network. It will display all of the loops and where they
are located.
The screen shown below is an example of a system that is connected to two
local controllers and one networked controller. Loops that are accessible
through this connection are displayed in the left pane, which is called
Available Loops:.
3. Click on the + box next to the controller name (or double-click on the
controller name). An expanded list will drop down, showing all loops
associated with this controller and therefore available for your Batch:
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NOTE:
Be sure to expand all controller loop lists to see everything available to
you before you complete your selection.
1.
To select all the loops associated with a controller, click on the controller
name, then click the {>>} button.
2.
To select individual loops from one or more controller(s), click on the

desired loop name, then click on the {>>} button.
3.
Each time you select an item and click on {>>}, that item will transfer to
the right pane, Loops in Batch:.
NOTE:
When you expand the controller loop list, the + sign becomes a sign.
To collapse the expanded list, click on the sign. The list will fold back
into the controller name, leaving a + sign again.
To remove a loop from the Loops in Batch pane:
Click on the loop name in the right window pane.
Click the {<<} button. The loop will move back to the left side, which
removes it from this recipe.
4. After all of the desired loops are in the Recipe, click on the {Close} button
to return to the Loops page of the Setup View.
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The loops you have selected will now be listed in the Current Loops pane, in
the following way:
The loop name (default to the controller) appears on the left side of the
window pane.
To the right of the loop name is the location of the loop. The location
is listed in the format of (Server Name\Controller Name\Loop
Name).
You now have the option of assigning new Display Names and initial
Setpoints to the loops for this Recipe. If you do not wish to change the default
controller loop names and setpoints, skip the following steps (5-9):
5. Click on the {View loop details} button or double-click on any loop name.
The Loop Setup Options window will open. This window allows you to
set a Display Name and an Initial Setpoint for each loop.
NOTE:
After each loop is edited, it is necessary to click the {Apply} button to make
the changes effective.
6. To set a loop Display Name that is more meaningful to you than its
controller default name:
Cick in the Display Name: edit box.

Change the name there to any combination of letters, numbers and
spaces, up to a length of 10 characters.
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7. To set an initial setpoint for a loop that is different than its controller
default setpint:
Click in the Initial Setpoint: edit box.

Enter the desired setpoint.
8. Continue editing these parameters for other loops without leaving this
window: click on the down arrow (W) on the right side of the Loop:
edit box, then select the loop name from the dropdown menu.
9. When you have finished editing, click on {Apply}, then click on {OK}.
12.1.6
Duplicating a Recipe
The Loops Tab can also be used to easily duplicate a recipe for use on another
fermentor that is connected to the system:
1. Click on the {Replace loops in this recipe with those from another controller}
icon on the Loops page:
CLICK
HERE
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The Replace Loops In Recipe window (shown below) will open:
2. Click on the down arrow (W) at the right side of the Replace: edit
box.
3. From the dropdown menu, select the controller you want to replace.
4. Now select the new controller from the controller names in the With:
pane.
5. Click on the {Apply} button to effect the change.
6. If there are any loops in the original controller that do not have
equivalents in the new controller, the Error Replacing Loops
window will open to inform you of the discrepancy:
Click the {Yes} button to delete the loop(s) from the loop list.
Click the {No} button to abort the replacement operation.
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After the loop selection process is complete, the Loops page on the Setup
view will resemble the sample shown below:
The Current Loops pane now lists all of the currently selected loops:
On the far left side is the display name of the loop. This will be either the
default name of the loop from the controller, or the name as edited on the
Loop Setup Options screen (see sample below).
The label to the right of the Current Loops pane is the location and
assigned name for each loop. The format for this label is (Server
Name\Controller Name\Loop Name).
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12.1.7
Views Tab
The Views Tab opens the notebook page that allows you to create several
types of views or to open default views established by the program. This page
(see sample screen below) consists of two panes: Current Views: and New
Views:.
Current Views Pane:

This pane lists all of the views that are available by default and those that have
been created for this Recipe. Initially there are three Views which are
standard with each Recipe: Alarm Summary, Batch Summary, and Setup:
The Alarm Summary View is a table summarizing any alarms that are
active while a Batch is running.
The Batch Summary is a table summarizing the loops used in the Batch.
This displays the Loop Name, Current Value, Setpoint, Output Value and
Control Mode.
The Setup View is the notebook you are already using: it contains the six
tabs that open the pages you use to enter parameters for the Recipe and to
control the Batch.
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New Views Pane:

You can use this pane to add a new view to a Recipe or a Batch:
1. Double-click on your choice (Synoptic, Trend or Program) to open the
appropriate design screen. You can then create a new view.
2. Sections 6 and 7 give detailed instructions on how to create and modify
Views and Programs.
12.1.8
Programs Tab
There are two types of programs available for use with BioCommand Plus:
Supervisory Programs and User Loop Programs. Details on how to create
them are given in Section 7 of this manual.
Supervisory programs are designed to control a loop Setpoint through

calculations and logical decisions made on the basis of input values from
other loops, constants, or the EFT.
User Loop Programs are designed to produce an output that has the same
properties as loops in the hardware, in terms of how they may be used by
the program.
Following is a sample of this screen:
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12.1.9
Alarms Tab
BioCommand Plus allows you to enter two sets of high and low limits for any
or all of the loops in your recipe: Alarm limits and Alert limits.
Alarms inform you when a loop value enters a dangerous range. When a
loops value exceeds your preselected Hi Limit or drops below your
preselected Lo Limit, the Alarm display tab (see sample screen below) turns
red to signal a visual alarm. If you have turned the audible alarm on, you will
also hear an alarm signal.
There are three ways to see what triggered the alarm:
A. Select View Alarm Summary from the Main Menu;
B. Click on the Views tab in the Setup view, then click on Alarm Summary
in the Current Views pane;
C. Right click on the Display tab at the bottom of the Setup window.
The Alarm Summary window will open to the Current Alarm Settings page.
Alerts inform you when a loops data value leaves the predetermined normal
range. When a loops value exceeds your preselected Hi Limit or drops
below your preselected Lo Limit, the Alert display tab (see sample screen
above) turns yellow to signal a visual alarm. If you have selected Audible On,
you will also hear an audible alert signal.
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To see what triggered the alert:

1. Open the Alarm Summary using one of the three methods listed above.
2. Click on the bottom right tab, Current Alert Settings, to view any loop(s)
in an alert situation.
See Section 8 for detailed instructions on setting Alarms and Alerts.
12.1.10
User Access Tab

Use this tab to access the window where you assign user authorizations for the
recipe:
1. In the Select User pane of the window (left), click on the down arrow
(W) in the edit box. The list of users for this system will drop down.
2. Click on the desired user name.
3. Underneath, click on the appropriate Access Rights option button to
assign the access rights to this user for this recipe. See the introduction to
Section 10 for an explanation of these various levels.
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4. Click on the {Apply} button. Your selection will appear in the Current
User Access Rights pane.
5. Repeat the above steps for as many users as necessary.
To remove a user from this list:
1.
2.
3.
4.
Select the user name.

Click on None for the access rights.
Click on {Apply}.
The user will be deleted from the list.
The user names available will be those that are entered via the User Manage
Accounts selection from the Main Menu. Details of user restrictions and
privileges can be found in Section 10, Security Features.
12.2
Starting a Batch
NOTE:
There are four ways to start a Batch; whichever method you choose,
each Batch must always begin with a defined Recipe. The options for
starting a Batch are: Batch Wizard, New Recipe, View Recipe and New
Batch.
12.2.1
Batch Wizard
See Section 5.1 to start a batch using Batch Wizard.
12.2.2
New Recipe or View Recipe

You may create a new recipe, modify an existing recipe, or use an existing
recipe following the procedures in Section 4.
When the Recipe has the minimum amount of information needed to
completely define a process, the {Start Batch} button on the bottom of the
window will become available. After you click on {Start Batch}, the program
will ask you for some additional input (see Section 5.4). After you comply,
the Recipe tab on the Setup view will change to Batch, the {Reset EFT}
button will become available, and the {Start Batch} button will become the
{End Batch} button.
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12.2.3
New Batch
NOTE:
Following is a brief recap of New Batch procedures. Be sure to consult
Section 5.4 in detail before starting a new batch.
Aside from using Batch Wizard, you can start a New Batch in two other ways:
A. Select File New Batch from the Main Menu;
B. Click on the New Batch icon on the Toolbar.
The New Batch Setup view window will open, with the Select File to
Open window on top of it. The top window lists the Recipe files that are
currently available for use.
1. Enter the desired Recipe file name in the File name: edit box.
2. Click the {Open} button. The selected Recipe file will be loaded into the
program and the {Start Batch} button will become available.
You may start the Batch immediately, or you may change Recipe parameters
and then start the Batch.
After you click on {Start Batch}, the program will ask you for some
additional input (see Section 5.4). After you comply, the Recipe tab on the
Setup view will change to Batch, the {Reset EFT} button will become
available, and the {Start Batch} button will become the {End Batch} button.
Once the Batch begins to run, operation is the same regardless of which
method was used to start it. The Current EFT box on the Batch page will
start displaying the elapsed time of the process and the View selection from
on the Main Menu will list all of the views that are available at the time.
12.3
Altering a Batch in Progress

When a Batch is started, its parameters are those preset in the Recipe selected, plus
any modifications that may have been made to the Recipe prior to Batch startup.
Most of these parameters may be changed while the Batch is running, essentially by
using the same procedures as those originally used to set them in the Recipe.
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12.3.1
Changing Setpoints
One of the changes most often made during the running of a Batch is the
Setpoint for one or more loops. Bear in mind that only those users who have
Operator, Supervisor or Manager privilege level (see introduction to Section
10 for further details) may change Setpoints.
There are two ways to change the setpoint of a loop: in the Batch Summary
View and in the Synoptic View.
In the Batch Summary View:
1. Open this view by one of the following means:
A. Click on the display name tab at the bottom of the Setup window for
the Batch being run;
B. Select View Batch Summary from the Main Menu;
C. Click on the Views tab in the Setup window, then select Batch
Summary from the Current Views: pane.
2. Once the Batch Summary window is open, double-click anywhere in the
row of the desired loop (Agit 1 in the sample shown below). The Change
Setpoint / Control Mode window will open:
NOTE:
BioCommand Plus cannot change the loop setpoint unless the option
Supv. By BioCommand (Supervised by BioCommand) is chosen in the
Controlled pane of this window.
3. Click on the Supv. By BioCommand option button if it is not already
selected.
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4. Now enter the new setpoint value in the Setpoint edit box.
5. Click on the {OK} button (or press the <Enter> key on your keyboard).
BioCommand Plus will send the new setpoint to the controller; the Batch
Summary window will display the new setpoint value; and you should also
see the Current Value responding to the change in setpoint value.
In the Synoptic View:
Open this view by one of the following means:
A. Select View Synoptic from the Main Menu;
B. Click on the Views tab in the Setup window, then select Synoptic
from the Current Views: pane.
You can change the setpoint for any items displayed on the Synoptic View:
1. Right-click on the loops icon. A submenu will open.
2. Click on Setpoint Change. The Change Setpoint / Control Mode
window will open:
NOTE:
BioCommand Plus cannot change the loop setpoint unless the option
Supv. By BioCommand (Supervised by BioCommand) is chosen in the
Controlled pane of this window.
3. Click on the Supv. By BioCommand option button if it is not already
selected.
4. Now enter the new setpoint value in the Setpoint edit box.
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5. Click on the {OK} button (or press the <Enter> key on your keyboard).
BioCommand Plus will send the new setpoint to the controller; the Batch
Summary window will display the new setpoint value; and you should also
see the Current Value responding to the change in setpoint value.
12.3.2
Changing Control Programs

You may edit the Program View to change control programs while a Batch is
running.
You may also start or stop the Program in either of these two ways:
A. Open the Program View that you wish to modify, then select the
desired action from the Program selection on the Main Menu;
B. Right-click on the Output icon in the Program View, then select either
Run or Stop from the menu.
See Section 7 for more details regarding Program Views.
12.3.3
Changing Process Views

Any of the views created as a part of the Recipe used for your Batch may be
modified or deleted. New views may also be created while the Batch is
running, without interrupting the data acquisition and control functions of the
program.
The techniques for doing this are the same as those used to create a Recipe
and to add Views to it. This process is described in detail in Section 13,
Creating and Editing Views. See also Sections 6, Synoptic Displays and
Other Batch Views and 7, Creating Program Views.
12.3.4
Editing Views
To edit a View, you must first make that view active by one of the following
methods:
A. Select it from the Views option on the Main Menu.
B. Click on the Views tab in the Setup notebook window.
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When the view is displayed, edit it using the techniques described in Section
13 , Creating and Editing Views.
The changes you make to the view become effective immediately, but only as
a part of this Batch; they are not added to the original Recipe that was used to
start the Batch.
12.3.5
Adding Views
To add Views, begin the process by one of the following two methods:
A. Select the Views tab from the Setup notebook, then click on the
desired type of view in the New Views: pane.
B. Select the appropriate item from the View submenu on the Main
Menu.
The Create View window will open, and you can create the view to suit
your needs, using the techniques described in Section 13, Creating and
Editing Views.
The added view(s) will only be a part of the current Batch; the original Recipe
used to start the Batch will not be modified.
12.3.6
Deleting Views
To delete a view from a Batch:
1. Open the desired View from either the Views tab on the Setup view or
from the View selection on the Main Menu.
2. Place your cursor anywhere inside the View.
3. Right click to open a submenu.
4. Click on Delete View in the submenu.
This will clear the View, removing it from the Current Views: pane on the
Views page of the Setup notebook and from the list under the View
selection on the Main Menu.
After this is done, the deleted view will no longer be available to the Batch
being run. The View will only be deleted from this Batch, however; it will
remain part of the original Recipe used to start the Batch.
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12.3.7
Ending a Batch
There is only one way to end a Batch:
1. Open the Setup window.
2. Click on the {End Batch} button.
When you do this, the program will automatically request confirmation before
completing the command:
3. Click on the {OK} button to confirm your desire to terminate the Batch, or
click on the {Cancel} button to save the active Batch from termination.
(The Batch will continue to run until you choose.)
If you cancel, the program will return you to the Setup window with no
interruption in Batch operation.
When you end the Batch, the data logging files and all view windows will
close.
NOTE:
If you exit BioCommand Plus without ending a Batch that is running,
the following window opens before the program shuts down:
Clicking the {OK} button will exit the program and clicking the {Cancel}
button will return to the existing operation. While data logging will
cease if the program is exited, the program remembers the Batch
parameters, so when BioCommand Plus is started the next time, you
will be offered the opportunity to resume the batch.
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If you have not disabled Batch Wizard, you can use the Starting
BioCommand screen (shown below) to resume a batch that was running
when you exited:
Starting BioCommand Plus
_ U
If you have disabled Batch Wizard, the following window will appear as soon
as you start up:
To resume immediately:
1. Click on the {Resume Batch} button. The Batch Setup View window will
open, and there will be a brief period while the program locates and
connects to the hardware.
BioCommand Plus will resume control of the running batch and resume data
logging (from where it was when the program was shut down). The process
will then continue running as it has been prior to the program exit.
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If you prefer to review information about the batch prior to making a decision:
1. Click on the {Details} button. The Setup view window will open:
This screen gives you the option of resuming the batch, modifying the batch
parameters before resuming, or terminating the batch
NOTE:
When you resume a batch which has remained active while BioCommand
Plus was closed, the total EFT for the hardware since the batch was
started will still be accurate. The data log file, however, will have a gap
for the period of time that BioCommand Plus was not controlling the
process.
12.3.8
Changing Data Logging Criteria

The only Data Logging criterion that you may change is the Log Interval.
You may change the interval at any time, even while the batch is running:
1. Open to the Recipe tab or the Batch tab in the Setup view.
2. Click on the down arrow (W) in the Log Interval (Mins) edit box, in the
Time Data pane, and choose a time interval from the dropdown list; or
enter a number directly into the edit box. (See important note below.)
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NOTE:
If you enter a decimal number greater than one, the program will accept
it as entered.
If you enter an interval of less than one, it will be rounded to the nearest
tenth of a minute.
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13
CREATING & EDITING VIEWS
The program sets up the Batch Summary View, which you are not
permitted to change its layout or function. This chapter describes the
details of the creation, use, and editing of the other three views you
may choose to employ with the program.
As has been described previously, there are several ways to view data during a run.
They are:
Batch Summary a tabular list of the loops that are active for the Batch being run with
the current value, setpoint, and output levels for each.
Program View operation of the setpoint controls for some of the loops at the fermentor
can be controlled based on the results of mathematical calculations or logical functions
that use the current value, setpoint, or output level of other loops from the fermentor
interface as inputs. This window allows you to specify these functions in schematic
equation format.
Synoptic View This view allows you to create a schematic picture of some parts of the
physical system and to place data values and labels on the picture to show at a glance
what is happening within the system.
Trend View Many times it is most desirable to view the data plotted as a scientific
graph in real-time. The program allows you to select the data items to plot on the graph,
the scale values to use, and other parameters regarding the plot.
13.1
AutoRefresh Feature
If you enable the AutoRefresh feature for any of the above views, the program will
automatically update the view whenever an operator networked with you makes changes
to that view. If you wish to edit the view yourself, turn off AutoRefresh.
To turn AutoRefresh on:
1. Right click on the batch name tab at the bottom of the Recipe Setup screen. A
submenu will open.
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2. Click on AutoRefresh (see sample screen below).
Click here
A squiggle will appear next to the batch name to indicate that you are in AutoRefresh
mode:
AutoRefresh
is on
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To turn AutoRefresh off:

1. Right click on the batch name tab. The submenu will open.
2. Click on AutoRefresh (which will have a checkmark next to it). The menu will
close, and the squiggle will disappear from the tab.
13.2
Program Views
BioCommand Plus refers to operator-defined programs as views because they are
designed and displayed in a view format. When the Program Views function is
entered, a new item is temporarily added to the Main Menu line across the top of the
screen named Program. All of the functions necessary to create, edit, and control
Programs are available from the Program submenu:
Their functions are:
Run starts running the Program that is active on the screen. If no Batch is
running, this selection will cause the program to start automatically when the
batch is started.
Run All starts running all Programs that are defined for this Batch. If no Batch
is running, this selection will cause the program to start automatically when the
batch is started.
Stop stops running the Program that is active on the screen.
Stop All stops running all Programs that are defined for this Batch.
Elements provides access to most of the functions that may be used in the
definition of a Program. These are also on the Program toolbar.
Line provides the capability of drawing lines to connect the various elements in
the Program. This is also on the Program toolbar.
Erase allows elements and lines to be erased from the Program.
Select All allows you to select all the elements at once in the Program display.
Move Block allows elements to be moved around the screen while maintaining
connections via lines to other elements.
Move Program allows the movement of a group of elements ending in a
Setpoint or User-Loop element as a complete program block. Lines and spatial
relationships between elements are maintained.
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13.2.1
Program View Toolbar

As explained in Chapter 6, all of the functions and calculations for creating
and editing programs are also available as icons on a special Toolbar that
appears on the right side of the window whenever Edit Program View is
entered.
The functions of each item on this Toolbar are shown and described below.
Here are the Program View Toolbar icons:
Input
Setpoint Output
Add
Multiply
Absolute Value
Exponential
Square Root
Totalizer
User-Defined Function
PWM Output
IF
Logical AND
Logical Complement
Draw Lines
Constant
User-Defined Loop
Subtract
Divide
Reciprocal
Natural Log
Limit
Change sign
Time Profile
Comment
Set
Logical OR
Exclusive OR
Select Items
The functions of the Toolbar icons are:
Input a signal or data value to be entered into the program. It may be the Current
Value, Setpoint or Control Output of a loop, a Constant, or the EFT in hours.
Constant will perform the same function as selecting Const from the Input
function mentioned above.
Setpoint output allows the result of a calculation to be applied to the setpoint for
a loop. When you double-click this item, the standard Select Loop window will
open for you to designate the loop to which the setpoint is to be applied.
User-Defined loop allows the Program View function to create a loop to your
specifications. This loop is added to the list of loops available for use by the Recipe
or Batch in which it is created. The output of the program created may be used as
the Current Value of any other loop.
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Add, Subtract, Multiply, Divide, Absolute Value, Reciprocal, Exponential,

Natural log, and Square root are the standard mathematical operations for
modifying program parameters and data values.
NOTE:
The Add and Multiply icons can take as many as three inputs:
For the Subtract (left) and Divide (right) icons, input placement is very
important:
A
+
B
A-B
A/B
The output of the Subtract diagram (above left) will be A - B, and the
output of the Divide diagram (above right) will be A/B.
Limit gives you an opportunity to prevent a program value from exceeding or

dropping below certain values.
Totalizer this is a summing function where the output is (previous output) plus
(input multiplied by the gain factor).
Change sign the output value is the input value multiplied by (1).
User-defined function this allows the entry of a complex user-defined
calculation. After placing this block on the Program View palette, doubleclicking on it will bring up the User-Defined Function Editor window. This
block has four inputs (X1, X2, X3 and X4) and one output (F). The editor
window has a block for you to insert your custom programming operations (see
Section 13.2.4 for details on the user-defined function block).
Time profile allows you to enter a set of conditions whereby certain functions
are performed after the passing of a preset time period.
PWM Output allows you to create a continually recurring, timed signal. When
you import this icon into your view, it has two edit boxes. By typing into each edit
box, you specify the Period (in minutes) of recurrence and the Width or Duty (in
minutes): how long the signal will be on. The program will generate a True output
for the width/duty specified; it will generate a False output the rest of the time. An
excellent application for the PWM output is to program feeding strategies.
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A typical program would tie the PWM output box to a Pump icon, which would be
set with the desired feed value (e.g., 80%). When the PWM output is True, the
pump will feed; when the output is False, no feeding will occur.
Comment allows you to add a brief comment (limited to 32 alphanumeric
characters, including spaces and/or punctuation) to your view. If you choose to
import this icon, even though it has no active effect on the equation you have
programmed, you must tie it into the program to retain it. We suggest that you
position the Comment box between the last mathematical function icon and the
Setpoint/Output icon. Use the Draw Lines function to connect the putput of the last
math function to the input of the Comment box, then draw a line from the output of
the Comment box to the input of the Setpoint/Output icon.
If provides a method whereby you may make a logical comparison between two
items and produce a True or False output based on that comparison.
Set allows you to select between two inputs based on a third logic input. That
is, if the logic input is True, input A is selected, and if the logic input is False,
input B is selected.
Logical AND, Logical OR, Logical complement, and Exclusive OR are the
standard logical functions that their name signifies.
NOTE:
Like the Add and Multiply icons, the Logical AND and Logical OR
icons can take as many as three inputs (and order is not important):
AND
OR
Draw lines - the function for connecting the signal paths of the various functions:
i.e., input to mathematical function, mathematical function output to Setpoint, etc.
The cursor changes to a plus sign when in the draw line mode. Click on the start
point, which must be inside the border of an appropriate item (i.e., one that has
input or output ports), and as you move the cursor, a dotted line indicates where
the line will be. This path will always be orthogonal in two directions. If you
need to change directions, click once to start a new orthogonal line. When you
reach the end point, which also must be an item with an appropriate input or
output port, click the mouse to connect the line to that point. You can then start a
new line, or end the Draw lines function. At any time you can exit this function
by double-clicking the left mouse button. Note that the program will not allow
two output ports to be connected together. If either of two connected items is
moved, it may be moved using the Move Block function to appropriately change
the line between them to maintain the connection.
Select items allows you to abort the Draw lines function.
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Most of these functions are also available from the Elements selection on the Program
menu:
The selections contained within these submenus are:
13.2.2
In/Out allows access to the input and output functions in the top section of the
Toolbar.
Math Functions allows access to the 10 mathematical functions and PWM
Output in the second section of the Toolbar.
Logical Functions allows access to the 6 logical functions in the third section
of the Toolbar.
Special Functions allows access to the 2 special functions (User-Defined
Function and Time Profile) toward the bottom of the second Toolbar section.
Creating a Program
As demonstrated in Chapter 6, to create a Program:

1. Click on the icon that represents the program function you need, or select the item
from the Program menu.
2. Move your cursor into the Program View window. A small box, the size of the
outline of the item, will appear, attached to the cursor.
3. Click to anchor the icon box at the desired location.
4. If you wish to remove an item after it has been placed in the view, click on it. A
red border will appear around the item. Press the <Delete> key. The item will
disappear from the view.
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5. To move an item once it has been anchored, selecting Move Block or Move
Program from the Program menu. The cursor will become a four-headed arrow.
Place the arrow over the item to be moved. Hold the left mouse button down to
grasp the item, and use the mouse to move it to the preferred location. The
Move Block selection maintains the connection(s) you have drawn to any other
elements, while the Move Program selection moves an entire group of blocks (a
program), maintaining both the connections and the spatial relationship between
the elements.
Right-clicking on any element on the program view will open a submenu with 8 items
on it:
The Move Block, Move Program, Run and Stop selections function the same as the
like-named functions from the Program menu. The Cut, Copy, and Paste selections
perform the standard Windows editing functions.
The Properties selection will open up another window to set the characteristics for the
element. This window will vary according to the nature of the element. Furthermore,
it will not have any effect on certain elements, such as the mathematical functions.
Double-clicking on the icon may also open the Properties window.
13.2.3
Icon Element Properties

You can access and use a Properties window for the following:
Inputs For this function, the Set Control Block Parameters window opens
(see sample window below). This allows the input for the selected block to come
from a constant numerical value, the EFT for the Batch, or the Current Value,
Setpoint, or Output level for a loop. Clicking the Const option button will
allow a numerical value to be entered into the edit box. Clicking the EFT
option button will enter the EFT as the input. Clicking the Lp>> button will
open up the Select Loop window and allow you to select the loop for which you
want to use the current value, setpoint, or output level as an input.
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Constant Inputs When you select this item, the BioCommand Diagram
Editor window opens so you can enter the numerical constant. Type the desired
number in the edit box and click the {OK} button to enter the constant into the
program.
User-Defined Function When you select this item, the BioCommand

Diagram Editor window opens for the entry of the name that will be used to
identify this loop. Enter the desired name in the edit box and click the {OK}
button to attach the name to the loop.
NOTE:
This name is limited to 10 alphanumeric characters and must be unique.
If the name of an existing loop is entered, the following window will
open and BioCommand Plus will not allow the name to be used:
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Clicking {OK} will return you to the BioCommand Diagram Editor screen so you
can enter a unique name.
Limit Function When you select this function, the Set Control Block Parameters
window will open (see sample below) so you can enter a high and a low limit value.
As shown in the sample window below, the limit values may be a constant that you
determine, the EFT for the Batch, or the Current Value, Setpoint or Output level for a
loop. Make your selection and enter values as described above under Input. Once
you have entered both limits, click the {OK} button to return to the Program View.
Totalizer Function When you select this item, the BioCommand Diagram
Editor window opens (see sample below) so you can enter the numerical
constant. This constant is the gain value for the Totalizer in reciprocal minutes.
Enter the desired value in the edit box and click the {OK} button.
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13.2.4
Special Functions
The User-Defined Function and Time Profile function are available through the
Main Menu: select Program Elements Special Functions. You can also access
their icons on the Program Toolbar.
User-Defined Function When you select this item, the User-Defined Function
Editor window (see sample below) will open. This function allows up to four
inputs and one output. This editor lets you enter BASIC programming code that
will define the relationship between these items. You enter your program code
after the line UserCode:.
User program
code goes
here
The programming code must be compatible with MicroSoft Visual

BASIC.
There are some functions that are not available for use:
Unavailable to User-Defined Function Block
Declare
Shell
Input
Open
Kill
RmDir
MsgBox
Print
The inputs are variables labeled X1, X2, X3 and X4; the output is a variable labeled F:
Reserved Variables (pre-defined for use in User-Defined Function Block)
X1
X2
X3
X4
F
References the value of the signal connected to Input X1

Assignments to F set the value of the output signal.
F references the value currently assigned to the output signal.
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There are also six pre-defined custom functions:

Custom Functions (pre-defined for use in User-Defined Function Editor)
GetCV(LoopName)1
GetSP(LoopName) 1
GetOU(LoopName) 1
GetEFTHours()2
Save(Register,Value) 2
Retrieve(Register) 2
This command returns the Current value of the

designated Loop.
This command returns the Setpoint of the
designated Loop.
This command returns the controller Output of
the designated Loop.
This command returns the EFT in decimal
hours.
This command saves Value to storage static
register number Register.
This command retrieves the Value stored in
static register number Register.
1 NOTE:
The Loop Name must be enclosed in quotation marks and must match
exactly the loop name in the BioCommand Plus batch, including the
case of each letter.
2 NOTE:
Valid register numbers are 0 through 9. Each function block has
separate and independent static storage registers.
If an error occurs during the calculation, such as a divide-by-zero error, the output
will be automatically set to zero and the function will exit.
Be sure to avoid any type of infinite loop program that will
leave your computer inaccessible as it endlessly attempts
the impossible.
CAUTION!
ESSENTIAL: Once you have finished entering code, click the {Check}
button to verify the syntax of your code entry. A window labeled
NBSDBSvr with a Results label will open: if there are no syntax errors, the label
will say OK; if there are errors, it will read NG.
NOTE:
Never try to run a program with a user-defined function that has not
checked out OK.
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After you have checked and, if necessary, revised and rechecked your code, click the
{OK} button to return to the Program View screen.
Time profile function When you select this item, the Time Profile Editor window
will open. This function allows you to enter an EFT-related alteration of a variable in
the program. The sample screen below shows an example profile that may be used to
adjust the setpoint of the Agitation loop for a Batch. The EFT and Value items are
entered as a standard edit box entry. The Mode entry has two possibilities, Step and
Ramp. Ramp provides a gradual increase or decrease between two points, while Step
effects the desired change at pre-designated intervals:
Ramp:
Step:
Enter an R to specify a Ramp function. Entering any other letter will default to a
Step function.
When the Time Profile is complete, click on the {OK} button to save it to the
Recipe or Batch.
If Function when you select this item, the Set Control Block Parameters
window (see sample below) will open. This function allows magnitude
comparisons to be made between two variables, to produce a True or False output
based on that comparison.
1. In the Enter a constant or click Lp pane, enter one of the two items to be
compared into the first edit box. It may be a constant, the EFT, or a Loops
Current Value, Setpoint or Output Level.
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2. Select the corresponding option button (Const for a constant, EFT for the
elapsed fermentation time, or Lp>> for a loop value).
3. Enter the second of the two items to be compared into the second edit box.
4. Select the corresponding option button.
The four possible comparison types are shown in the pane labeled Comparison.
These comparisons relate the first item to the second: > means that the
function is true if the top item value is greater than the bottom item value.
Similarly, the functions of the other operators are: >= is greater than or equal to,
< is less than, and <= is less than or equal to.
5. Select the option button corresponding to the appropriate type of comparison.
6. When you have entered all of the information, click the {OK} button to return
to the Program view screen.
NOTE:
In the IF function, 0 = False and any number other than zero = True.
Set Function When you select this item, the Set Control Block Parameters
window (as shown below) will open:
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Your Program equation, which feeds the SET function from your IF and/or
AND function(s), will result in either a True or a False output.
In the SET screen above, as you did in the IF screen, enter a constant, an EFT,
or a Loop parameter (Current value, Setpoint or Output Level) for both True
and False operations. The Program will apply the output according to your
instructions.
NOTE:
Be sure to Save the program(s) you create, and to initiate the
program(s) using the Run function.
When your Program View is complete, right-click anywhere on the program view,
except on an icon, and select Save View. The next time you open the Views tab in
the Setup window, you will see your program listed in the Current Views pane.
To run the program, click on the Setpoint icon. When a red box appears around it,
you may initiate the Run function in one of two ways:
A. Right-click on the Setpoint icon, then select Run from the dropdown menu.
B. Select Program Run from the Main Menu.
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13.3
Synoptic Views
When you enter this function, a new item named Synoptic is temporarily added to
the Main Menu line. This menu item has three selections on its submenu, as shown
below:
If the Design Mode selection has a check mark beside it, that function is active and
the view may be edited. No check mark means that the Run mode is active and that
the running Batch will cause the program to display loop values on the Synoptic
View.
When the synoptic view screen opens, it will display the current EFT in the title bar.
Selecting Gauges from this menu will open up a submenu, as shown below:
This list contains all of the icons that may be placed on the Synoptic View.
All of the available functions are also featured on a Toolbar that appears on the right
side of the window when you enter Edit Synoptic View. The functions of each item
on this Menu and Toolbar are shown below:
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Faceplate gauge
Name Tag
Static Label
Input/Output Arrow
Pump
Peristaltic Pump
Vessel
Valve
Flowmeter
Heat Exchanger
Addition Tank
Filter
Draw Lines
Design/Run Mode
13.3.1
Design Mode
To use all of the functions for the placement and customization of the Synoptic View,
the program must be in Design mode:
1. Click on the Design/Run icon on the Toolbar or select Design Mode on the
Synoptic menu. If the Design mode is active, there will be a checkmark beside
the selection on the menu, a dotted grid on the Synoptic View window, and the
Design/Run icon will be highlighted.
2. To place icons on the Synoptic View window, click on the desired icon (or select
the item from the Synoptic menu).
3. Move the cursor into the View window; a small box, appropriate to the size of the
item, will be attached to it.
4. Place the icon in the desired location, then click to anchor it in place.
5. If you need to remove an item after you place it on the View window, click on it.
A red border will appear around the item. Press the <Delete> key to remove the
item from the view.
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6. There will also be resizing points around the periphery of the item. If you move
the cursor one of these points, the cursor changes to a double-headed arrow. You
can resize the icon using standard Windows techniques.
7. You can move any icon by clicking on it, then moving the mouse while you hold
down the left button. Release the button when the item is in place.
NOTE:
Remember that the Edit Synoptic View function must be in Design Mode for
most of the above functions to be available.
If you right-click on an icon that you have placed in the Synoptic View window, you
will open a menu of seven selections for adjusting the characteristics of that item (see
the sample below, a Flowmeter icon).
These selections allow you to do the following:
Properties If you select this item, the Select Loop window will open. This
window lists the loops available in the system; it allows you to select the loop that
pertains to the item involved. You select the loop clicking on it, then you click
{OK} to apply this selection to the item and to return to the Synoptic View
screen. If you click the {Cancel} button, the program will discard the selection
and return to the Synoptic View with no change.
Setpoint Change When you select this item, the Change Setpoint / Control
Mode window for the loop represented by this item will open. In this window,
you can enter the setpoint for the item involved, such as the flow rate for a pump,
etc. The loop must have the Controlled selection set to Supv. By
BioCommand in order to be effective.
Cut, Copy, Paste, and Delete These are standard Windows editing functions.
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The functions of the Gauges items/Toolbar icons are:
Faceplate gauge/Face Plate displays the Setpoint (SP), Current value (CV),
and the percentage output (OU) for a selected loop.
Name Tag places a label on the view which may display the Current Value,
Setpoint or Output level for any loop in the Batch.
Static label/Label allows you to label any part of the view. Place the label at
the desired location on the view and then double-click on the label face. This will
open an edit box entitled Enter label caption. The current label is displayed;
you may alter it using standard editing techniques. When the label says what you
want, press the <Enter> key or click {OK} to exit the edit caption function. The
label will then show the new caption. If you change your mind, click the
{Cancel} button to exit the function. The label caption will default to its previous
reading.
Input/output arrow is used to show the direction of flow associated with
another item on the view.
Pump is a schematic depiction of a standard fluid pump.
Peristaltic pump - is a schematic depiction of a peristaltic pump.
Vessel a representative drawing of a fermentation vessel. This is usually the
first icon you place on the Synoptic View window. There is a label at the top of
the icon that says Vessel. You can change the label: double-click on the label
box to obtain a pull-down arrow (W). Click on the arrow to display a list of
available NBS Systems. Select the appropriate one. This system name will then
appear in the label box; press the <Enter> key to apply this new name. (You can
also change the name by clicking on the label and then typing in a new name.
Press the <Enter> key to save the new name.)
Valve represents a solenoid valve.
Flowmeter/Mass Flow Controller, Heat exchanger, Addition tank/Tank,
Filter are icons that represent the elements that the names suggest.
Draw lines is the function for connecting the fluid paths of the other icons: i.e.,
pump to filter, filter to flowmeter, etc. This function is described in detail
elsewhere in this manual.
Design/Run mode this will toggle the program function between both modes.
The other selection from the Synoptic menu is the Lines function. This contains three
options used for drawing lines to connect the gauge icons in your view: Draw Lines,
Line Color and Line Thickness:
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The Draw Lines selection is the same as the Draw Lines icon on the Toolbar.
The Line Color selection opens another submenu with seven color selections.
The Thickness selection opens up a submenu with three line thickness selections,
numbered 1, 2 and 3. Number 1, which is the default, is the narrowest line and
number 3 is the thickest.
If you right-click anywhere on the Synoptic View screen itself, not on an icon, you
will open a submenu with six selections:
Default View
Save View
Delete View
Print View
Copy All
Paste
These selections have the following functions:
13.4
Default View selects the current view as the Default view.

Save View updates the Recipe or Batch file by saving the current view.
Delete View will delete this view from the Batch or Recipe that is active at the
time.
Print View allows you to print the view currently active on the screen.
Copy All, Paste these are standard Windows editing functions.
Trend Views
The Trend view allows the plotting of up to eight data items in real time on a single
graph. As demonstrated in Chapter 5, each item is plotted in a different color for easy
identification, and each item may be scaled independently. When the batch is active, the
data is plotted at the Log Interval specified in the recipe. Multiple Trend Views may be
created to display more than eight loop items.
The Trend View window is shown below:
The upper graph area is the region where the data is plotted.
There are two y-axis scales visible at any time. Their scale may be changed to be
appropriate for the various loop values that you select for plotting.
The x-axis is a time axis for the Elapsed Fermentation Time (EFT). It initially starts
at zero and is one hour wide. The time scale may be altered to whatever you feel is
appropriate.
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At the bottom of the window is the control panel that is used to set up and modify the
plot, and to display the Current Values for the loops being plotted. In the sample
screen, all of the values are zero because no batch is active.
LEFT Y-AXIS: Scaled & colored
for Agitation Loop
PLOT AREA
RIGHT Y-AXIS:
Scaled & colored for
Air Loop
X-AXIS:
start of
plot EFT
X-AXIS: end
of plot EFT
SLIDER to
change plot
time zones
CONTROL
PANEL
CURRENT VALUE readout
(loop identified by color)
Each of the notebook tabs on this control panel is described separately below.
If you click the cursor in the gray area on either side of the Control Panel, the panel will
change to colored loop buttons, as shown below:
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Normally the active EFT (as a digital clock) is displayed along the x-axis, above the
slider bar. As you move the cursor over any colored button, the name of the loop being
plotted in that color will be briefly displayed in place of the clock. When you click on
the button, the loop name is displayed there (in the sample above, we have clicked on the
red button, so the display reads: CurrentBatch\Agit1), and one of the two y-axes will
be assigned to that loop.
Each additional click, on that button or another one, will alternate from the left side to the
right side of the graph. At any time you can click again in the lower gray area of the
window to return to the main Trend View (with the control panel).
While you are in the colored block view (see sample above), if you click on the small,
white triangle at the lower right corner of the view, the display will change. Now it will
show only the two loops identified by the y-axes on the left and right sides of the graph.
When your cursor is outside the plot area, two small panes separated by the EFT time
clock will identify the loops they represent. Note that each loop name is written in the
color you assigned to it (see sample screen below).
If the cursor is inside the plot area, the panel will show the current values of the two
loops as shown in the sample screen below:
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You can use the slider bar (just below the x-axis) to move the graph display through the
Batch run time record. Place the cursor on the slider, hold the left mouse button down,
and move the mouse horizontally right or left. The plot will move correspondingly
forward or backward through the data. You can also use the arrow keys ( or ) to
move through the time record. For convenience, at any time you can click on the far left
clock readout to return to the 00:00:00 start time.
You can also scroll through the graph using the cursor. As your cursor moves
horizontally within the plot area, click once and hold it. A rolling vertical plot line will
appear under the point of your cursor. The time and current values will read out as you
move the plot line. For easy reference, double click to leave plot lines at desired
intervals.
If you right-click the mouse while your cursor is on the Trend View window but outside
the Control Panel , a submenu with five choices will appear (as shown below):
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The functions of these selections are:
Default View selects this view as the Default view.

Save View updates the Recipe or Batch file by saving the current view.
Delete View removes this view from the Batch or Recipe that is active at the time.
Print View prints the view on the default printer connected to the system.
Zoom allows the time scale of the plot to be changed to a greater (Out) value or
lesser (In) value.
Control Panel: There are four tabs on the Control Panel at the bottom of the Trend
View Screen. They are labeled Main, Loops, Graphs and Styles.
13.4.1
MAIN Control Panel Tab
When a batch is active, the loop panes in this control panel will display the
Current Value for each loop, as long as your cursor is somewhere inside the plot
area. In the sample screen above, all panes display zeroes because no batch is
active. Note that the each value is shown in its loops plot color.
When your cursor is outside the plot area, the loop panes display the loop name,
each in its plot color.
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13.4.2
LOOPS Control Panel Tab

Selecting the Loops tab from the Control Panel changes the display to the
window shown below.
Use this window to assign colors and plot order (1 to 8) to the loops you will be
plotting in this view:
1. Click on the {Setup Loop1} button. The Select Loop window will open.
2. Select the name of the loop you want to see plotted first, and click on {OK} in
the Select Loop window. The loop name will appear in the ControlLoop
box.
3. Click on the {>>} button to move to the next loop. In a new color, the button
will now be labeled Setup Loop2.
4. Repeat the above steps until all loops have been assigned a number and color.
13.4.3
GRAPHS Control Panel Tab

Once the loops have been selected for plotting, it is appropriate to set the plot
scales for each.
1. Click on the Graphs tab:
This checkbox is not available to

your application.
Loop number you

have assigned
Loop name
you have
assigned, in
chosen color
You will automatically be given Loop 1 to work with.

2. Set the low and high limits of the loops y-axis scale by entering numbers in
the Low and High edit boxes.
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3. Click on the {<<} or {>>} buttons to step through each loop, and to set scale
limits for each one individually. As each loop number is selected, the box on
the right of the pane will display the name of that loop.
4. You may also set the x-axis limits here: View Start and View End. The
default values are 00:00 to 01:00.
13.4.4
STYLES Control Panel Tab

You may choose the line width and plot style for each loop in the graph from the
Styles tab selection:
1. There are two line widths available. The thinner line is the default selection;
you will see that its option button is selected. If you wish to change to the
thicker line, click on its option button.
2. Four plot styles are available. Click the option button of the style you choose.
(The seamless point to point graph line is the default choice.)
13.4.5
Modifying a Trend View

1. Return to the Main tab on the Control Panel.
2. Right-click with the cursor over any active loop button to open a submenu of
four items as shown below:
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The functions of these selections are:
Graph Settings this item is not currently functional.

Change Graph Color allows you to change the plot color for the selected
loop and the background color for the entire Trend graph. See details below.
Delete Graph removes the selected loop from the graph
Zoom allows the time scale of the plot to be changed to a greater (Out)
value or lesser (In) value.
When you select Change Graph Color from the above submenu, the following
window opens:
The color you

are going to
change.
Palette of
available
colors.
Choose the desired

option: Line or
Background
Sliders to
custom mix a
color.
Current loop line color
and current
background color.
Selected loop: you are
changing colors for the
plotting of this loop.
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The button-like pane in the lower right corner of the window displays the name of
the loop selected for change.
1. Decide whether you wish to change the plot line color or the plot background
color.
2. Click on the appropriate option button: Set Line Color or Set Background
Color.
3. The pane below the Set Line Color option button displays the color that will
be changed; in the sample screen, it is red. If we had selected Set Background
Color, this pane would be green, as it is in our sample graphs.
4. To change the color, click on the desired color in the palette.
5. If you do not see the color you want, you can custom mix one. Each of the
three slider bars will modify the percentage of one of the three primary colors
that will make up your color:
The top bar controls the amount of red, the middle controls the green, and
the bottom is for blue. Change the proportions of each color by moving
each slider bar to the left (less) or right (more).
The left and right pointing arrows ( and ) on the ends of the slider bar
may also be clicked to move the slider bar in small increments across the
range.
6. The pane below the slider bars displays the current color of both background
and loop plot. As you make changes, the new color(s) will be displayed in
this pane.
The {Cancel} button will remove the last changes you applied.
The {Default} button will return the colors to the original colors defined by the
program.
7. Click the {Apply} button to save and to make effective any color changes you
have made. As you make color changes, they are also displayed on the Trend
View that is on the Main Screen after you click the {Apply} button
NOTE:
You can change the plot background color via any loops Change Graph
Color screen. Of course, that new background color will apply to the plot
graph for all of the loops.
8. Once you have applied your new colors, click the {Close} button to exit this
function.
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14
TROUBLESHOOTING
If you find that BioCommand Plus does not work, or does not respond
properly, there are a few possible reasons you can easily check and
resolve yourself. If the following recommendations do not eliminate your
difficulty, please contact your NBS Representative or NBS Service.
14.1
Troubleshooting Guide
If you encounter any of the following symptoms during initial set-up, or at any
other time while you are working with BioCommand Plus, try the suggested
solution(s) before you call for service:
Symptom
Recipes are not available to the
network.
No feedback is available from

fermentor.
Make sure power is connected.

Check all settings as specified in the system
Set-Up instructions.
Loops 10-16 of ML-6100-type

controller(s) do not appear.
Check version of BClocal (minimum of 2.33

with EPROM Rev. F is required).
Check that both controller ID numbers have
been specified in NBS Hardware Connection.
Data is being logged directly to the server. Set
data to log on the workstation(s) instead, and
transfer the data to the server at a later time.
Change logging interval to a higher number.
Network performance is slow.
Possible Solution
Make sure the recipes are saved to a shared
folder.
Workstation performance is
slow.
There may be too many fermentors on one

workstation. Try reducing to fewer than six.
Communication between the

workstation and the fermentor
has been lost.
Check power to the fermentor.
Fermentor loops are not

reporting.
Make sure that the loops are not engaged in a

batch that is still running.
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Symptom
Certain files do not self-register.
Possible Solution
These files may be running in the
background. Run Task Manager to verify
that the files have stopped, then reinstall
BioCommand Plus.
In Windows NT 4.0, 2000, ME, XP or
XP Pro, make sure that the logged-on user
has administrative privileges on the
computer, then reinstall BioCommand Plus.
If you have encountered a problem not covered in this guide, or if the solutions proposed
above do not resolve your difficulty, please call your NBS Representative or NBS
Service.
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15
SPECIFICATIONS & SYSTEM

REQUIREMENTS
15.1
BioCommand Plus Specifications
Product type
Code
Media
Compatible Operating Systems
Network connectivity
Supported Products
15.2
Bioprocess supervisory software

32-bit
CD-ROM
Windows 98, NT4.0, 2000, ME, XP, XP Pro
Yes
All New Brunswick Scientific computercapable products
System Requirements
15.2.1
Minimum Computer Requirements
PC, 350 MHz Pentium II
128 MB RAM
100 MHz bus
CD ROM
1 GB Hard Drive
1.4MB 3.5 drive
Mouse or equivalent pointing device
Sound card, Operating System-compatible
38 KB RS232 COM port
15 monitor
800 x 600 SVGA, 256 colors
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15.2.2
Recommended Computer
As indicated in Minimum Computer Requirements above, except that we
recommend the following for best performance and user comfort:
15.2.3
PC 1 GHz Pentium IV
256 MB RAM
20GB HD
Larger monitor and higher resolution to suit display requirements
Computer Operating Systems
BioCommand Plus runs on Windows 98, Windows NT 4.0, Windows

2000, Windows ME, Windows XP or Windows XP Pro.
15.3
Network & Communications Requirements

BioCommand Plus works on a single stand-alone workstation, or on a group of
networked workstations. When networked, batches and recipes can be shared and
viewed on multiple workstations. A network adapter card compatible with your
operating system and your network is required.
15.4
Fermentor/Bioreactor Installation
Refer to the appropriate instruction manual(s), or contact New Brunswick
Scientific.
15.5
Creating a BioCommand Plus Workgroup

1. Create, or have the system administrator create, a shared folder on the network
server with full access permissions for all users who will be members of the
workgroup. We suggest USERS as the share name.
2. On any workstation where BCPlus has been installed, there is a file called
BC32USERS.MDW in the BioCommand Plus install directory. Copy it to the
newly created network folder, \\SERVER\USERS\.
3. From a BioCommand Plus workstation, run BioCommand Plus. From the
main menu, select User Select workgroup. Set the workgroup path to point
to BC32USERS.MDW in the network server folder.
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4. Exit and restart BioCommand Plus.
5. From the main menu, select User Manage Accounts.
6. In the account manager diaolog, add a user account for each member of the
workgroup.
7. Determine who, in addition to the Admin user, will be given administrator
access and add the user(s) to the Admins group.
8. Determine which users will be allowed to create recipes and add those users to
the Recipe Creators group.
9. Close the account manager dialog.
10. Select from the main menu User Change Password and enter a password for
the Admin user:
Each user may change his password later.
For each workstation that will be part of the workgroup, repeat the
following three steps:
1. Start BioCommand Plus.
2. From the main menu, select User Select Workgroup. Set the
workgroup path to point to BC32USERS.MDW in the network server
folder.
3. Exit BioCommand Plus.
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16
DATA LOG FORMAT
Batch data is stored in a format compatible with the Microsoft Access database
management program. The figure below shows the list of tables generated for a typical
Batch. Any program that can read Access format data may use the data from a
BioCommand Plus process. The data may be manipulated and displayed in any of the
formats allowed by the database program.
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In addition to the Batch loop data, the database contains all of the parameters that were
used when the Batch was run, no matter what the starting Recipe parameters were. The
contents of the various tables are described in the following sections.
16.1
16.1.1
Settings
AlarmSettings
If you have set alarm parameters for any loops, this table will list them.
The format of this table is very similar to the format of the table you used
to set the alarms in BioCommand Plus.
16.1.2
AlertSettings
If you have set alert parameters for any loops, this table will list them.
The format of this table is very similar to the format of the table you used
to set the alerts in BioCommand Plus.
16.1.3
CascadeSettings
Not used in current version of BioCommand Plus.
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16.1.4
SterilizeSettings
Not used in current version of BioCommand Plus.
16.2
16.2.1
Changes
ChangeRecord
This table lists any changes that have been made during the process of
running the Batch. The ID column consists of consecutive numbers for
each record in the file logged by BioCommand Plus as each action is
recorded. The next column lists the calendar date and time of each action.
The Operator column lists the person responsible for the batch when the
change action occurs. The next column lists the action that was
performed, and the following columns contain data related to the action.
continued
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16.2.2
MgrChanges
This table contains requests for Manager Changes made during the
running of the Batch. This is a temporary storage table until the Batch
Manager Server processes the changes. After that, this table is cleared and
the changes are recorded in the ChangeRecord table (see 16.2.1 above).
16.2.3
OperChanges
This table contains requests for Operator Changes made during the
continued
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16.2.4
SupvChanges
This table contains requests for Supervisor Changes made during the
16.3
Batch Events
16.3.1
BatchEvents
This table lists the time and description of any and all Alarm and Alert
events that occur during the running of a Batch.
16.4
Reports
These tables contain the report specifications that you entered from the Tools
Report Specification menu item. They are used by the Report Printer Module to
print reports of the data.
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170
16.4.1
ReportGraphs
16.4.2
ReportSettings
16.5
16.5.1
Data Logs
Loop Data
The loop data are stored in tables that are individual to each loop. Each
table consists of the log ID number (LG_ID), and the actual data value
(Value). Each loop table will be named Log_[loop name]. The loop
name is the unique display name you have assigned to the loop. In the
sample screen shown below, the name is Log.Agit1.
The log ID number is the number of the data log and is incremented by
BioCommand Plus with each acquisition. The time of each log item can
be determined from the LogTimes table described in section 16.5.2 below.
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16.5.2
LogTimes
This table contains the information that identifies the calendar date and
time that each data log was performed. This data can be used to correlate
the loop log data through the LG_ID parameter.
16.5.3
OfflineData
Any Offline data that you enter while the Batch is running is logged into
this table. The table very closely resembles the window in BioCommand
Plus that you used to enter the data. Any additional parameters that you
added to the Batch via the Tools function will also be shown as another
column in this table.
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16.6
Batch Identifications
The Batch identification tables contain the basic setup information pertaining to
this Batch.
16.6.1
BatchID
The BatchID table is shown below. This table contains the important data
that describes the overall use of the Batch.
16.6.2
Loops
The Loops table lists the loops that you selected for use in this Batch along
with pertinent information about each. This is the information that you
entered into the Batch from the New Batch function prior to starting the
Batch run.
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16.6.3
CurrentStatus
This table holds the most recently acquired data for each loop while a
Batch is running. At the end of a Batch, it contains the last set of data
acquired. All of the data in this table is available in other tables in the
final database, but this table allows remote workstations to access the data
while a Batch is running.
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16.7
User Data
16.7.1
UserAccess
16.7.2
UserLpDiagrams
This table contains the details of any User-defined loops that were a part
of the Batch.
16.8
Errors
The Errors table is the repository for any errors that are reported by the Batch
Manager Server.
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16.9
Views Data
This table is a list of the views that were defined to be a part of the Batch.
It contains the elements that make up the view.
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17
VIEWING BATCH DATA
The Database Viewer utility, installed when you loaded

BioCommand Plus, is a tool that allows you to view data from any
batchcurrently active or previously run. You can use this tool to
organize and present data in a variety of ways. It is a quick and
efficient way to generate reports, to use the Access-compatible
database or to move data into an Excel document.
17.1
Starting DBViewer32
Select
Start
Programs
Nbs
DBViewer 32
There will be a brief DBViewer start-up screen, then the Existing Batches
window will open:
17.2
Existing Batches
In the Existing Batches window, select the desired batch from the list in the
pane, then click on the {OK} button. (If you do not see the batch you want, see
section 17.4 below.) DBViewers data window will open:
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178
Selected
Batch
Dropdown
Menus
Central Data Pane
Batch
Selection
Box
Browse
Button
Settings
Button
Sliders to
scroll through
data
Export to
Excel Button
17.3
Using the Main Data Window

Following are descriptions of the various features of this window.
17.3.1
Browse Button
At any time, you can click on the {Browse} button to access the Browse for
More Batches window:
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This functions the same way as the Browse for Batches window you
have already encountered. To use the More selection for batches not
listed in the window, see Section 17.4 below.
17.3.2
Batch Selection Box

The edit box over the {Browse} button is another way to access available
batch records. Click on the down arrow to open a dropdown menu of
available batch records, then select the batch of interest. All data in the
main data window will update to reflect your new selection. This is a
quick way to toggle between batches.
NOTE:
Some batch data files may not be available to you because you do
not have the appropriate authority level. A warning screen will
appear in such a case to explain why the database will not open.
17.3.3
Settings Button
If you click on the {Settings} button, the DBViewer Settings window
will open:
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Time Log
The Time Log indicates the period of time during which the available data
has been logged.
You can use the Settings pane to select a particular range of records for
review. Naturally. The To Record: entry may not exceed the indicated
Max. Records number.
You can also change the way the logged time is displayed by clicking the
option button for Decimal Hours or Calendar Time instead of the default
hours/minutes/ seconds (hh:mm:ss).
The control loops under BioCommand Plus supervision in the selected
batch can be removed or returned to the Central Data Pane for purposes of
data management.
To select or de-select loops, click on the {Select Loops} button. The
Selected Loops screen opens:
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AVAILABLE
Loop
Records
SELECTED
Loop
Records
To select a loop that is not displayed in the Central Data Pane: single click
on the name and, holding the left mouse button down, carry the record
over to the Selected list; drop it there. You can also double click on the
loop name in the Available loop list, and it will appear in the Selected loop
list.
To remove a loop from the Selected list: single click on the loop name in
the Selected list and, holding the left mouse button down, carry the
record over to the Available pane; drop it there. You can also double
click on the loop name in the Selected loop list, and it will disappear from
that pane.
After you make any changes in this window, click on {OK} to apply them
and to return to the Main Data Window.
17.3.4
Export to Excel Button

Clicking on the {Export to Excel} button will automatically set up a
Microsoft Excel document that contains all of the current data records
displayed in the central pane of the main data window. You will then be
able to manipulate the data records with all available Excel features,
including the creation of graphs.
If you do not want all of the data records in your Excel document, use the
mouse to select the records of choice before you click on the {Export to
Excel} button.
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If you do not have Microsoft Excel, you may use the File Copy
command from the DBViewer Main Menu to place data records on the
Clipboard. Then open a document in the desired program and paste the
records into your document.
Similarly, you may use the File Save As command from the DBViewer
Main Menu to save highlighted data as the file of your choice.
17.3.5
Central Data Pane

This pane displays the data logged from the moment the batch was started
until, (a) for a currently active batch, the moment you opened the
DBViewer or, (b) for a previously run batch, the moment the batch was
ended.
The data is provided in an Excel-compatible format. You can use your
mouse to resize the columns according to your needs, and use the bottom
and right side slider bars to scroll through the records.
In addition to removing and restoring data columns as explained in
Section 4.3.3 above, you can change the order of the columns:
1. Right click on the loop name at the top of the column. The cursor will
change into a hand holding a sheet of paper.
2. Holding the right mouse button down, move your cursor left or right to
the desired location, then release the button. The entire column of data
will now appear where you have placed it.
You may not move the first or second column (data log numbers and Log
Time records).
17.3.6
DBViewer Main Menu

There are three dropdown menus available from the Database Viewer
Main Menu: File, Options and Tools.
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Use the File dropdown menu:
to access the following commands:
Open: This command will open a Browse for More Batches

window.
Print: Use this command to print whatever data records you have
highlighted with the mouse.
Export to Excel: This command has the same function as the {Export
to Excel} button (see Section 17.3.4 above).
Copy: This command allows you to copy selected records to the
Clipboard for transfer to your document of choice.
Save As: This command allows you to save any selected records to
the file name and folder of your choice.
Exit: This is one way to close the DBViewer tool.
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Use the Options dropdown menu:
Open BatchEvents: This command will open the BatchEvents data

table for this batch. The BatchEvents table lists the time and
description of any and all Alarm and Alert events that have occurred
during the period logged. (See Section 16.3.1 for a sample table.)
Open ChangeRecord: This command will open the ChangeRecord
data table for this batch. The ChangeRecord table lists any changes
that have been made during the period logged, when each occurred and
the person responsible for the batch when the change occurred. (See
Section 16.2.1 for more information and a sample table.)
View Entire Database: xxxxx.bdb (where xxxxx.bdb is the name
of the batch on display): Selecting this command will open a window
labeled with the name of the batch (see sample window below).
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In the left pane of this window are icons that represent every Data Log
table available for this batch. These records are stored in a format
compatible with the Microsoft Access database management program.
(See Chapter 16 for details on each Data Log table).
1. Double click on the icon for the desired database. The right pane will
display the logged data:
2. To widen the pane, place your cursor on any edge or corner of the
windowpane; when the cursor becomes a double-headed arrow (),
hold down the left mouse button and drag the edge out until the pane is
the desired size.
3. Use the slider bars to scroll through the data records.
4. Click on U to close this window.
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186
Use the Tools dropdown menu:
Report Specification: This option allows a graphical presentation of the

process data to be specified for printing. See Section 11.4.1 for details,
including a sample report.
Print Report: Selecting this command while the main data window is active
will automatically print a Batch Summary Report.
Convert Database 2.0 to 3.0: If you have data that was logged and saved in
AFS-BioCommand (pre-BioCommand Plus), use this command to convert that
data so it can be read and used by BioCommand Plus.
1. When you click on Convert Database 2.0 to 3.0, a new window will open.
2. Click on the top {Browse} button to locate the old database that you need
to convert.
3. Double click on that database when you find it. It will appear in the
Source File: edit box.
4. Click on the second {Browse} button to open a Save As screen for the
destination and name of the converted database.
5. Click on {OK} to place this new destination & name string in the Dest.
File: edit box.
6. Click on {OK} to start the conversion process.
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Repair a damaged Database: If you encounter a problem reading or using a

database file, other than an issue of authorization level, this tool may help you
to fix the problem.
1. Click on Repair a damaged Database. A new window will open.
2. Use the {Browse} button to locate the problem database file. When you
have selected it, it will appear in the edit box.
3. Click on {Repair}.
4. Close the screen by clicking on {OK}.
17.4
More Batches
The Database Viewer will also give you quick access to data for other, previously
run batches. All data logged while the batch was running is available through the
DBViewer.
1. In the Existing Batches window, either double click on More or select

More and then click on the {Open} button. The Open window will appear,
offering you a full choice of batch histories:
2. To move a batch history into the Existing Batches window, double click on the
batch of interest.
3. Use the More selection and the Open window for as many batches as you
would like to view.
4. When the desired batch is listed in the pane, select it, then click on the {OK}
button. DBViewers data window will open. Refer back to Section 17.3 above.
Users Guide
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18
A
Absolute Alarm, 72
Active Batches
Resuming, 78
Adding New Groups, 88
Adding New Users, 87
Adding User Groups, 86
Adding Users, 86
Adding Views, 126
Alarms, 6, 71, 104, 117, 119, 166
Activating/Deactivating, 74
Alarms Tab, 119
Alerts, 71, 75, 120, 166
AutoRefresh, 131
Turning on, 131
Computer Requirements, 161

Computer/Controller(s) Communication, 20
Confirm Password, 82
Controller ID Numbers
Sample Retrieval of, 23
Controller IDs, 22
Controller Status, 25
Controllers, 5, 6, 37, 111
Copying a Recipe, 114
Copyright Notice, vii
Creating a New Recipe, 34
Creating a Program View, 58
Creating a Synoptic View, 51
Creating a Trend View, 47
Creating User-Defined Loops, 68
Current Alarm Settings, 72
Current Alert Settings, 75
Custom Functions, 142
B
Batch
Definition of, 15
Deleting Views, 126
Ending, 129
Ending a, 77
Icon, 42
Modifying, 122, 129
New, 42, 91, 121, 172
Restart/Resume, 78, 91
Restarting/Resuming, 128, 129
Starting a, 40, 43
Terminate, 78
Terminating a, 77
View, 56, 117
Batch Display Name, 43
Batch Manager Server, 168, 169, 174
Batch Summary, 27, 44, 46, 47, 93, 104, 117, 123, 131
Batch Summary View, 44, 46
Batch Wizard, 15, 27, 121
BatchEvents, 169
BioCommand Interface, 21, 23
D
Data Logging
Changing criteria for, 129
Interval of, 15
Database Viewer
Browse for More Batches, 179
Existing Batches, 177
Exporting Data to Excel, 181
Selecting Batch Data, 177
Starting the, 177
To convert a 2.0 database to 3.0, 186
To open BatchEvents, 184
To open ChangeRecord, 184
To print Reports, 186
To repair a damaged Database, 186
To specify Reports, 186
To view Entire Database, 184
Deleting Views, 126
Disclaimer Notice, vii
Displays, 5, 6, 44, 47, 93
Duplicating a Recipe, 114
C
CAUTION
Symbol for, vii
Changing a Password, 83
Changing a Trend View, 156
Changing Control Programs, 125
Changing Data Logging Criteria, 129
Changing Process Views, 125
Comm Port Setup, 22
Computer Operating Systems, 161, 162
Computer Recommendation, 162
INDEX
Edit Function, 92
EFT, 44, 96, 108, 118, 121, 122, 138, 140, 143, 150
Elapsed Fermentation Time. See EFT
Exiting BioCommand Plus, 77
Extracting a recipe, 42
F
File Function, 91
File Name Extensions, 10
Users Guide
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File Naming Conventions, 10
G
Getting Started, 14
O
Object Naming Conventions, 10
Offline Data
Entering, 96
OffLine Data Function, 96
Old Password, 82
Hardware Connections
Setting up the, 20
Help Function, 101
I
IF Function, 143
International Offices
List of, iii
K
Keyboard Notation, 8
L
License Agreement
U.S. Government Restricted Rights, 3
Limit Function, 140
Local Batches, 91
Log Interval, 15, 108, 129, 150
Logical Function, 137
Loop Data, 54
Loops
Add/Change, 37, 38, 109, 112
Alarms for, 71, 75, 119
Available, 37, 38, 48, 72, 104, 111
Current, 39, 109, 113, 116
in Batch, 38, 112, 117
Setpoints for, 123
Setup Options, 39
User Programs, 118
User-Defined, 68, 134, 174
M
Main Menu, 16
Manual Conventions, vii
Math Function, 137
Menu Notation, 8
Mouse Notation, 7
Multi-Fermentor Adapter, 21, 23
N
Navigating Through Windows, 8
NBSDBSvr Window, 97
Network & Communications Requirements, 162
Network Connectivity, 5, 161
New Password, 82
NOTE
Symbol for, vii
Password
Clearing a, 84
Initial, 82
Removing a, 84
Setting the first, 82
Using a, 84
Print Report, 91
Print View, 91
Product Registration Number
Obtaining a, 1
Program
How to run, 67
How to save, 67
How to start, 67
How to stop, 68
Program Views, 57, 92, 104, 133
Programs
Modifying, 125
Programs Tab, 118
R
Recipe
Browse, 106
Copying a, 114
Creating, 27
Creating a new, 27, 34
Data Pane, 107
Definition of, 15
Description of, 35, 107
Duplicating a, 114
Editing, 103
Extracting a, 42
File naming for, 31
Naming a, 29
New, 50, 91, 103, 106, 121
Renaming a, 29
Replace Loops in, 115. See Loops
Save as, 105
Security features of, 85
Specifying loops for, 30
View, 50, 91, 106, 121
Recipe Tab, 105
Removing Password Protection, 84
Removing Users, 87
Report Specification, 94
Report Specification Function, 94
Restarting with Active Batches, 78
Resume Batch, 16
Resuming a Batch, 78
Running a Program, 67
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S
Saving a Program, 67
Security Features, 6
Select Comm Port, 22
SET Function, 144
Setpoint Deviation Alarm, 72
Setpoints
Changing, 54, 123, 148
Entering initial, 39
Setting initial, 114
Setting Alarms, 71
Setting Alerts, 75
Shutting down BioCommand Plus, 79
Special Function, 137
Special Functions, 141
Specifications, 161
Starting BioCommand Plus, 14
Starting BioCommand Plus Screen, 15, 27, 42
Stopping a Program, 68
Supervisory Programs, 118
Synoptic View, 124
Synoptic Views, 44, 51, 56, 146
System Requirements, 161
T
Table of Contents, xi
Time Data, 107, 129
Time Profile Function, 57, 63, 135, 137, 141, 143
Toolbar
Toggling the, 93
Toolbars, 16, 17, 34, 42, 51, 53, 55, 58, 91, 101, 103,
104, 122, 134, 137, 146, 147, 149, 150
Tools Function, 94
Totalizer Function, 140
Trend Graphs, 47, 50, 131, 150
Changing Background Color, 157
Changing Line Color, 157
Colored Buttons, 151
Graphs Control Panel Tab, 155
Loops Control Panel Tab, 155
Main Control Panel Tab, 154
Marking Specific Times, 153
Modifying, 156
Moving through Time Records, 153
Styles Control Panel Tab, 156
Trend View
Modifying a, 156
Troubleshooting, 159
Turn Off Wizard, 16
Turn On Wizard, 16
U
User Access Tab, 120
User Function, 98
User List
Creating a, 85
Modifying a, 85
User Loop Programs, 118
User Passwords, 81
User-Defined Function, 57, 135, 137, 139, 141
Custom Functions for, 141
Keywords Unavailable for, 141
Reserved Variables for, 141
Using Passwords, 84
V
View Function, 93
Views
Adding, 126
Deleting, 126
Modifying, 125
Views Tab, 117
W
WARNING
Symbol for, vii
Warranty, ix
Window Function, 99
Workgroup
Creating a, 162
Selecting a, 14
Workstations
Setup of, 11
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BioCommand Plus

MANUAL NO: M1291-0050

NEW BRUNSWICK SCIENTIFIC CO., INC.

New Brunswick Scientific

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New Brunswick Scientific

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Notes contain essential information that

Caution messages appear before procedures

New Brunswick Scientific

Text in bold face type emphasizes key words

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New Brunswick Scientific

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READ THIS FIRST ..................................................................................1

Creating a New Recipe using Batch Wizard .................................................................................. 27

INTRODUCTION TO BATCH VIEWS .............................................................47

Cable Connections ......................................................................................................................... 19

CREATING A RECIPE & STARTING A BATCH.................................................27

NBS HARDWARE CONNECTION SETUP ......................................................19

Major Features ................................................................................................................................. 5

BIOCOMMAND PLUS INSTALLATION & SET-UP............................................11

Before Installing BioCommand Plus................................................................................................ 1

CREATING PROGRAMS ..........................................................................57

How to Create a Program ............................................................................................................... 58

New Brunswick Scientific

SETTING ALARMS & ALERTS ..................................................................71

ENDING A BATCH ................................................................................77

End a Batch .................................................................................................................................... 77

10 SECURITY FEATURES ............................................................................81

User-Based Access .................................................................................................................... 81

11 MAIN SCREEN FUNCTIONS REFERENCE .......................................................91

12 RECIPE/BATCH FUNCTIONS .................................................................. 103

Creating or Editing Recipes..................................................................................................... 103

13 CREATING & EDITING VIEWS ................................................................ 131

AutoRefresh Feature................................................................................................................ 131

14 TROUBLESHOOTING ............................................................................ 159

Troubleshooting Guide............................................................................................................ 159

15 SPECIFICATIONS & SYSTEM REQUIREMENTS ............................................. 161

BioCommand Plus Specifications ........................................................................................... 161

16 DATA LOG FORMAT ........................................................................... 165

Settings .................................................................................................................................... 166

17 VIEWING BATCH DATA ....................................................................... 177

Starting DBViewer32 .............................................................................................................. 177

18 INDEX ............................................................................................ 189

New Brunswick Scientific

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READ THIS FIRST

Before Installing BioCommand Plus

Obtaining a Product Registration Number

your name and title

New Brunswick Scientific

your Institution (the company, institution or organization where you

Registration at NBS U.S. Office

to provide the information listed in Section 1.2.1.

License Agreement Acceptance

New Brunswick Scientific Software License

install BioCommand Plus on multiple computers within a single network domain.

U.S. Government Restricted Rights

New Brunswick Scientific

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BioCommand Plus software enhances the capabilities of NBS

Centralized monitoring and control of one or several fermentors and bioreactors

New Brunswick Scientific