User Manual BX V293

BioXpert V2
Supervisory Control
&
Data Acquisition Program
USER MANUAL
Software Version 2.93 (Compatible with Microsoft Windows Vista)
May 2009
Contents
WHAT IS BIOXPERT V2 ........................................................................................................................................................ 3
What you should know .............................................................................................................................................................. 3
Hardware and software requirements ........................................................................................................................................ 4
THE LOGICAL STRUCTURES .............................................................................................................................................. 5
The logical structure of one BioXpert V2 ................................................................................................................................. 5
The logical structure of multi-fermentor system ....................................................................................................................... 6
INSTALLATION OF BIOXPERT V2 TO HARD DISK ......................................................................................................... 7
BioXpert's command line options.............................................................................................................................................. 7
Starting the BioXpert V2 ........................................................................................................................................................... 7
Starting the BioXpert V2 the very first time ............................................................................................................................. 8
WHAT IS WHAT? .................................................................................................................................................................... 9
Variables ................................................................................................................................................................................... 9
Cultivation protocol ................................................................................................................................................................... 9
Cultivation data ....................................................................................................................................................................... 10
Installation protocol ................................................................................................................................................................. 10
Desktop of the BioXpert V2 .................................................................................................................................................... 11
WHAT YOU CAN DO ........................................................................................................................................................... 12
Recalculate DEMO.FRM file .................................................................................................................................................. 12
Run new cultivation using standard batch protocol ................................................................................................................. 12
BIOXPERT'S COMMANDS .................................................................................................................................................. 13
The menu bar ........................................................................................................................................................................... 13
The system menu commands................................................................................................................................................... 13
The file menu commands ........................................................................................................................................................ 14
The data editor menu commands ............................................................................................................................................. 15
The chart menu commands ...................................................................................................................................................... 16
The run menu commands ........................................................................................................................................................ 16
The control laws menu commands .......................................................................................................................................... 17
The install menu commands .................................................................................................................................................... 17
The window menu commands ................................................................................................................................................. 18
The help menu commands ....................................................................................................................................................... 18
HOW TO START BIOXPERT V2 ......................................................................................................................................... 19
The New Cultivation or Recalculation dialog ......................................................................................................................... 19
The New User dialog ............................................................................................................................................................... 20
Open cultivation protocol and data .......................................................................................................................................... 20
The File Selection dialog ......................................................................................................................................................... 20
DATA EDITOR ...................................................................................................................................................................... 22
The Cultivation Description dialog ......................................................................................................................................... 22
The Variables Status dialog ..................................................................................................................................................... 23
The New Variable dialog ........................................................................................................................................................ 24
The Edit On-line Variables dialog and the Edit Off-line Variables dialog .............................................................................. 25
The Off-line Time Schedule dialog ......................................................................................................................................... 26
The Calculate Data dialog ....................................................................................................................................................... 27
The Edit Constants dialog ....................................................................................................................................................... 28
The Edit Formulas dialog ........................................................................................................................................................ 29
The Substrates Characteristics dialog and the Products Characteristics dialog ....................................................................... 31
The Representation Mode of Curves dialog ............................................................................................................................ 32
The Import Data dialog ........................................................................................................................................................... 33
DISPLAYING DATA ON THE CHART WINDOW ............................................................................................................. 34
The Variable(s) in Y-axis dialog ............................................................................................................................................. 34
The Time or Variable in X-axis dialog .................................................................................................................................... 35
The Scaling Settings dialog ..................................................................................................................................................... 35
The Chart Options dialog ........................................................................................................................................................ 36
The Chart Pictures dialog ........................................................................................................................................................ 37
The Select Font dialog ............................................................................................................................................................. 38
May 2009
BioXpert V2 user manual page 1
DATA PRINT, EXPORT AND IMPORT............................................................................................................................... 39

The Print Options dialog ......................................................................................................................................................... 39
The Import ASCII File dialog ................................................................................................................................................. 40
The Export Data Format dialog ............................................................................................................................................... 42
CONTROL LAWS .................................................................................................................................................................. 43
The Manual Setpoint dialog .................................................................................................................................................... 43
The Profiles dialog .................................................................................................................................................................. 43
The Control Algorithm dialog ................................................................................................................................................. 44
The Internal Control Variables dialog ..................................................................................................................................... 46
The Control Interval for Profiles and the Control Interval for Algorithms dialog ................................................................... 47
Description of control statements ............................................................................................................................................ 47
ON-LINE SESSION ................................................................................................................................................................ 51
The Warning dialog at the time of open the protocol .............................................................................................................. 51
The Cultivation Parameters dialog .......................................................................................................................................... 52
The On-line Session ................................................................................................................................................................ 52
The Alarm Warning dialog ...................................................................................................................................................... 55
The Alarm Control dialog ....................................................................................................................................................... 56
The On-line Measured Variables dialog .................................................................................................................................. 56
INSTALL DEVICE AND CHANNELS ................................................................................................................................. 57
The Devices dialog .................................................................................................................................................................. 57
The Communication Interface between PC and Fermentor dialog .......................................................................................... 58
The AD/DA Card Test dialog.................................................................................................................................................. 59
The COM Settings dialog ........................................................................................................................................................ 59
The On-line Variables Setup dialog ........................................................................................................................................ 60
The Linear Calibration dialog ................................................................................................................................................. 62
The Signal Unit dialog ............................................................................................................................................................ 63
INSTALL BRAUN OR SARTORIUS DCU ........................................................................................................................... 64
Installation ............................................................................................................................................................................... 64
The Devices dialog .................................................................................................................................................................. 65
Passwords ................................................................................................................................................................................ 65
On-line variables setup dialog ................................................................................................................................................. 66
Manual control set point .......................................................................................................................................................... 67
Communication check ............................................................................................................................................................. 68
Limitations .............................................................................................................................................................................. 68
GRAPHIC WINDOW ............................................................................................................................................................. 69
The Graphic Setup dialog ........................................................................................................................................................ 70
The Variable for Graphic dialog.............................................................................................................................................. 71
MULTI-FERMENTOR SYSTEM .......................................................................................................................................... 72
The Run Manager dialog ......................................................................................................................................................... 72
The Fermentor Numbers dialog ............................................................................................................................................... 73
The Starting Time and Interval dialog ..................................................................................................................................... 74
The Edit Starting Parameters dialog ........................................................................................................................................ 75
The End On-line Sessions and Close BioXperts dialog........................................................................................................... 76
MESSAGES ............................................................................................................................................................................ 77
Error messages ........................................................................................................................................................................ 77
Warning messages ................................................................................................................................................................... 79
Index........................................................................................................................................................................................ 81
May 2009
WHAT IS BIOXPERT V2
BioXpert V2 is a program with
expert system features running in
the Microsoft Windows XP or Vista
environment developed for a real
time on-line, and off-line data
processing and fermentation process
control. It has a special user
definable installation module for
coupling different fermentors to the
PC. BioXpert V2 has a built in
editor and library of equations for
the analysis of data for batch, fedbatch and continuous cultivation
procedures. Interpolation of data by
cubic spline can be used throughout
for carrying out calculations,
activated just by one click.
Practically all functions are
accessible from the main window
(screen) of the program through the
mouse driven graphical interface.
BioXpert V2 has special utilities for the exchange of data files with other fermentation and spreadsheet
programs. The data (tables and figures) can be printed out in ready-to-publish form.
From the very beginning the BioXpert V2 was designed as an on-line (real time) tool for a fermentor with a
curious scientist beside of it being very much interested in as final as possible immediate analysis of the current
fermentation. The aim was to finish a cultivation experiment with the ready-to-publish data in the printed form.
These requirements needed to develop the editor and library of the equations used for the calculations of
derived growth characteristics but also to the extensive use of spline interpolation of both, off-line and online data. The above mentioned features have proved to be especially helpful in using a very powerful new
method of cultivation of cells - the A-stat.
We tried to make the logical structure of the program opaque and the interface user-friendly. An experienced
user of Microsoft Windows should be able to use the program immediately without looking for the manual.
What you should know

The BioXpert V2 runs in Microsoft Windows XP and Vista. To use the BioXpert V2, you must know how to
operate this Operating System. This manual assumes you are already familiar with Microsoft Windows XP /
Vista. As minimum you should know:
how to use the mouse
how to activate, move and size the windows
how to select options and files from menus, list boxes and dialog boxes
May 2009
Hardware and software requirements

You must have MS-Windows XP or Vista installed on your computer. To run BioXpert V2 your computer
should have the following:
processor pentium
64 MB RAM at least
pagefile size is 3 times the available memory (192 MB at least)
color monitor (EGA, VGA, MVGA, SVGA, etc.)
mouse
hard disk
A printer is optional. All peripherals, including a mouse, monitor, and printer are supported through MSWindows V2. Although the BioXpert V2 is designed for on-line fermentation control it can be successfully
used also for fermentation control in off-line mode or just for analysis of fermentation data. BioXpert V2 can be
coupled with fermentation system through AD/DA board and serial port.
May 2009
THE LOGICAL STRUCTURES

The logical structures of one BioXpert V2and multi-fermentor system are showed in that chapter.
The logical structure of one BioXpert V2

BioXpert V2 is coupled to fermentor(s) through specially designed Interface module. The interface device is
described, input/output channels defined and calibrated in a separate window. All installation information is
saved in an initialization file (FERM1.INI - the initialization file for the first fermentor) and it could be used in
further cultivation experiments. This file is open on invoking the cultivation mode of the program. The signals
collected by Interface module (ON-LINE data) are used together with values of CONSTANTS and OFF-LINE data in
data processing. The Data editor is designed for definition of data processing procedures. The Chart module
is designed for graphic representation of data. Once developed the cultivation and data processing procedures
can be saved in a protocol file (*.FRM) and used in following cultivations. It is also possible to import data
(from MFCS etc) and to export the data (to Excel etc).
FERM*.INI
F
E
R
M
E
N
T
O
R
Interface
on-line
variables
settings
calibration
coefficients
device
descriptions
Cultivation protocol and data

Control Laws
Data editor
profiles
on-line data
off-line data
constants
formulas
alarm control
spline data
substrates
products
algorithms
Data
setpoints
on-line
measured data
off-line data
constants
Keyboard
May 2009
Installation protocol
for one fermenteor
Chart
Y-scale
X-scale
settings
header
names
*.FRM
Data and protocol
*.FOR
formulas only
*.FCL
Control laws only

(profiles and
algorithm s)
*.BMP
*.W MF
Export
picture
*.TXT
*.SLK
Export
data
*.TXT
Im port
on-line data
*.FOM
On-line session
m essages
The logical structure of multi-fermentor system

BioXpert V2 can be coupled to multi-fermentor systems. In that case several independent BioXpert V2
programs are running simultaneously.
Fermentors with BioControllers
Connecting cables
PC with MS-Windows
There are some ways to couple the fermentor and computer physically. You can connect each fermentor (with
Bio controller) to the several COM port (using RS232 serial interface) or all fermentors to the one COM port
(using RS422 or RS485 serial interface). There are maximum four COM ports available in the BioXpert.
To use more fermentors or other devices, which are coupled to the RS232 port (for example the mouse), you
have to connect the fermentors through the multiplexer. To connect all fermentors to the one COM port without
multiplexer you must use the external device between fermentors and computer (for example microMAC). At
this case the variables channel numbers must be different for the fermentors.
On-line access (reading present values and writing set-points) to the fermentors are organized in consecutive
order. One access to the one Marubishi fermentor takes maximum 10 seconds. Access time depends on number
of fermentor channels (on-line variables) and number of set-points. For example, using on-line access interval 1
minute for all fermentors, you can run maximum six fermentors simultaneously.
May 2009
INSTALLATION OF BIOXPERT V2 TO HARD DISK

The BioXpert V2 is installed automatically by the installation program. Insert the CD or USB stick into the PC
and run the SETUP.EXE .
BioXpert V2 is ready for work in off-line mode. For installation in on-line mode the fermentor must be
connected to the computer, and respective interface defined (see Install Device and Variables section).
BioXpert's command line options

You can specify the protocol and data immediately for the BioXpert icon in the BioXperts folder using the
properties. Then the format is the following:
ferm.exe [ username ] [ -r / -ci ] [ filename ]
where:
username
is subdirectory from BioXpert main directory
-r
recalculation mode (default option)
-ci
cultivation mode where i is the fermentor number (default i = 1)
filename data filename for recalculation and protocol filename for cultivation mode
Examples:
ferm.exe tom -r demodata
ferm.exe anne -c2 batch
Starting the BioXpert V2

You can start the BioXpert V2 from:
Start menu
BioXperts folder
Windows Explorer
How to add the BioXpert V2 icon to the BioXperts folder:
activate the BioXperts folder
choose File New Shortcut menu item
press Browse button in the Create Shortcut window
choose the FERM.EXE from BioXperts main directory and then click OK button in the Browse window
add command line options to Command Line, if desired
select a suitable name (BioXpert 1 for example) in the Select a Title for the Program window
How to duplicate the BioXpert V2 icon to the BioXperts folder:
activate the BioXperts folder
make copy from existing icon
select a suitable name (BioXpert 2 for example) for new icon
choose File Properties menu item
add command line options to Target in the Properties window, if desired
You can install several icons with different command line options for convenient use of BioXpert V2 (for
example, you can have separate icons of BioXpert V2 for different fermentors in the BioXperts folder).
How to add the personal folder for different BioXpert icons to the desktop of Windows:
click with the mouse right button on the desktop
choose New Folder menu item
select a suitable name (My BioXpert for example) for the new folder
open this folder and add BioXperts icons
May 2009
Starting the BioXpert V2 the very first time

Before you run BioXpert V2 first time, you must type your name and your company name (at the time of
installation). Later this names are used in the application in the About window and in the printout paper.
May 2009
WHAT IS WHAT?
Now you get information about the several types of the variables, cultivation protocol, data, and installation
protocol.
Variables
variables are cultivation parameters, which are connected with physical device: AD/DA card and serial
port are supported. On-line measured variables are variables measured on-line from fermentor. On-line
controlled variables are variables which send values to fermentor. All on-line variables have the same on-line
time scale. For example pH, Temperature, O2 and CO2 concentrations in the exhaust gas, dissolved oxygen,
feeding pumps etc. are on-line variables.
ON-LINE
variables are cultivation parameters which, are measured manually and introduced during the
fermentation or during recalculation. All off-line variables have the same off-line time scale. For example
fermentor volume, substrates and products concentrations, optical density etc. are off-line variables.
OFF-LINE
CONSTANTS are cultivation parameters, which do not change during fermentation or change step-wise.
For example the O2 and CO2 concentrations in the inflow gas, normality of alkali, normality of acid etc. are
constants.
are cultivation parameters, which are calculated on the basis of on-line variables, off-line variables,
constants, and other formula variables according to the defined formula. For example the dilution rate, growth
rate, respiratory coefficient, carbon recovery etc. are formulas.
FORMULAS
SUBSTRATES
are on-line variables, off-line variables, constants or formulas, which have been created for
substrates.
PRODUCTS
are on-line variables, off-line variables, constants or formulas, which have been created for products.
Cultivation protocol
Cultivation protocol and data are stored in a file (extension is always FRM). You can use the same protocol in
several cultivation sessions. If you started a new cultivation, the old data is deleted.
Cultivation protocol includes:
organism name
cultivation comments
start and end moments (date and time) of cultivation
on-line variables calibration coefficients
list of on-line measured variables (identifier name, comment, scale unit name)
list of on-line controlled variables (identifier name, comment, scale unit name)
list of off-line measured variables (identifier name, comment, scale unit name)
list of constants (identifier name, comment, scale unit name)
list of formulas (identifier name, comment, scale unit name)
lists of substrates and products names
list of variables names, which have buttons in the Variable window
on-line and off-line time intervals
alarm settings
control laws (set-points by profiles and by algorithm)
May 2009
Cultivation data
Cultivation data includes:
on-line variables (measured and controlled) and off-line variables data points
constants and their changes
spline parameters for on-line and off-line variables
variables scale ranges
Chart window picture settings (list of variables displayed in the Chart window)
Installation protocol
Installation protocol for each fermentor is stored in the file, which is named FERMi.INI, where i is the number
of fermentor. It means that each fermentor has its own on-line variables with own calibration constants. You
can use serial interface and AD/DA card at the same time.
Installation protocol includes:
fermentor number (included in the file name)
serial port device (device protocol, serial port number, number of channels)
AD/DA card device (AD/DA card, main address, number of physical input and output channels)
list of on-line measured and controlled variables (name, comment, scale unit name, minimum and maximum
values, precision, counter flag)
calibration data for AD/DA card channels
If you started BioXpert in the CULTIVATION mode, the on-line variables are read from the installation protocol
file, for RECALCULATION mode all the variables read from the cultivation protocol and data file.
May 2009
Desktop of the BioXpert V2

BioXpert V2 desktop includes Chart window, Variables window, Chart Values window, On-line Session
window and Status bar.
Chart window
Variables window
Menu bar
Caption bar
Status bar
On-line Session window
Chart Values window
Caption bar includes program name: BioXpert (Demo added to the demo version), program mode:
Recalculation, Cultivation OFF-LINE and Cultivation ON-LINE, and data filename. If you started BioXpert in
the CULTIVATION mode, the fermentor number is inserted to the caption bar and to the caption of all dialogs and
messages. ON-LINE means that the On-line Session window is opened.
Chart window includes several curves in the specified scales and plotting options (use Chart | Options menu
command). Use mouse left button on the Y-scales area to change scales, X-scale area to change X-axis (time or
variable), header lines area to change options, and curves area to zoom in the time scale and to view values in
the Chart Values window. Use mouse right button on the curves area to zoom out the time scale.
Variables window includes important (often used) on-line and off-line variables and formulas buttons.
The four mode exist for clicking mouse left button on the variables buttons:
display curve in the Chart window immediately
select variables that will be displayed in the Chart window after double clicking this mode button
change curves presentation mode (straight lines between measured points, splined curve, etc)
change variables settings (data points, comments, formulas, etc)
Use mouse right button to change variables settings in the case of all modes.
Chart Values window includes a list of variables and their values, which are displayed in the Chart window.
Use mouse left button on the Chart window curves area or use Elapsed time edit control and E button to view
curves values exactly in the Chart Values window list box.
On-line Session window includes information about on-line session. The string '(before starting)' in the On-line
Session window caption means, that start moment is coming soon (start line is drawn in the Chart window in
red). All on-line data is deleted at the start moment. The current time, elapsed time and the last update (reading
and sending data from fermentor) time are displayed. You can also change the control laws and alarm settings
during the cultivation session from that window.
Status bar includes 'Ready' word in the wait state, 'Wait' word for waiting, or menu command description. Some
information messages also appear in the Status bar (opening, saving file etc.).
May 2009
WHAT YOU CAN DO

This is a short description how you can recalculate existing cultivation data and make a new cultivation.
Recalculate DEMO.FRM file

Choose 'DEMO' user name, choose RECALCULATION mode and press Ok button in the New Calculation and
Recalculation dialog (File | New menu command).
Choose 'DEMO.FRM' file for open cultivation protocol and data in the File Selection dialog (File | Open
menu command).
Use variables buttons in the Variables window for viewing several variables in the Chart window. Press the
mouse left button for viewing pointed variable in the Chart window (Chart | Y-axis menu command) and
the mouse right button for editing the pointed variable (Data editor | On-lines, Data editor | Off-lines, Data
editor | Formulas menu commands).
Use Data editor and Chart menu commands to edit cultivation protocol, cultivation data and chart.
Print Chart window picture and cultivation protocol and data to printer (File | Print menu command).
Run new cultivation using standard batch protocol

Choose 'DEMO' user name, choose CULTIVATION mode, choose fermentor number 1, and press Ok button in
the New Calculation and Recalculation dialog (File | New menu command).
Open standard batch cultivation protocol (File | Open standard Batch menu command).
Install device (Install | Device menu command), by default AD/DA card used.
Install on-line variables and calibrate it (Install | Variables menu command), default settings are done.
Define control set-points (Control laws | Profiles menu command) by profiles.
Define control set-points (Control laws | Statements menu command) by algorithm.
Start the new cultivation (Run | Begin menu command). Enter the comments in the Cultivation Description
dialog. Choose the on-line access interval, starting moment and data file (measured data are saved) in the
Cultivation Parameters dialog. Press Ok button to start.
Use Data editor and Chart menu commands to edit cultivation protocol and data and chart.
Print Chart window picture and cultivation protocol and data to printer (File | Print menu command).
May 2009
BIOXPERT'S COMMANDS
After starting, the BioXpert draws the screen containing the caption bar, menu bar, desktop area, and status bar.
The menu bar will show the system menu, File, Data editor, Chart, Run, Control laws, Install, Options, and
Help menus. The desktop includes Chart window and Variables window.
The menu bar

System menu box
Caption bar
Minimize box
Maximize box
Menu bar
The menu bar is the second upmost line after caption bar on the screen containing menu names. The first menu,
called the system menu, has no name and is represented by a small symbol on the leftmost side of the caption
bar. The menus contain all main commands of BioXpert. They are opened (pulled down) by holding down the
Alt key and pressing the underlined letter of the menu. System menu is activated by Alt-spacebar. You can also
access the menu bar by using a mouse. You perform your selections in menus by using the arrow keys and
pressing Enter at the command of your choice or by clicking the mouse button on the selected command.
Greyed menu items are inactive and can not be selected.
The system menu commands
Restore
Restores the window size after the BioXpert is maximized or minimized. Same as click the
Restore box (window is maximized and Restore button is exist instead of Maximize box) with
mouse left button to move a window to the previous size.
Move
Move window location on the screen. Same as use the mouse on the caption bar.
Size
Change window size. Same as use the mouse on the sizing borders.
Minimize
Minimize the window to its minimum size (icon). Same as click the Minimize box with mouse
left button.
Maximize
Maximize the window to its maximum size (full screen). Same as click the Maximize box with
mouse left button.
Close
Terminates the BioXpert program. The short-cut key for System | Close is Alt-F4.
Switch To
Switch to Task List (A Window that shows all the applications you have running and lets you
switch among them). The short-cut key for System | Switch To... is Ctrl-Esc.
May 2009
The file menu commands
To open, save, export, import and print out the cultivation protocol and data. The cultivation protocol and data
are placed in the same file. The file extension is 'FRM' for all BioXpert files.
New
Opens a New Cultivation or Recalculation dialog to choose user name, fermentor number and
program mode. The current protocol and data are deleted. In CULTIVATION mode the Variable
window is filled with on-line variables read from selected fermentor initial file (FERMi.INI, i
is fermentor's number).
Open Standard Open standard Batch (BATCH.FRM), Fed-batch (FEDBATCH.FRM) or Continuous

(CONTIN.FRM) cultivation protocol.
Open
Opens a File Selection dialog where you can select the cultivation protocol and data file to
open. After selection file, the Variable window is filled with variables buttons read from that
file. You can open same files for cultivation mode and recalculation mode.
Save
Saves the current cultivation protocol and data. If you have opened a file (the file name exists
in the caption bar), then the content of that file is updated with no further questions asked. If
you have created a new file, a File Selection dialog appears and you can enter a name for the
new cultivation protocol and data, then the current cultivation protocol and data is saved to
that file.
Save as
Opens a File Selection dialog where you can enter a name for the currently used cultivation
protocol and data. The current content of the cultivation protocol and data is then saved to that
file with no further questions asked.
Export Chart
Opens a File Selection dialog where you can enter a name for picture of Chart window. Then
the picture is saved as bitmap (file extension is BMP) or as windows metafile (file extension is
WMF). You can use those pictures to edit in the other programs (PaintBrush, CorelDraw etc.).
Export Data
Opens a Export Data Format dialog where you can choose file format (SYLK or ASCII) and
variables that will be exported. Then the File Selection dialog opens where you can enter a
name for selected data. Then the data is saved in SYLK or ASCII format (file extension is
SLK or TXT). The data is saved in off-line time scale. You can use those files in the MSExcel.
Import
Opens a File Selection dialog where you can enter ASCII file name for import data in the online time scale. Then the Open ASCII File dialog opens where you can choose the relations
between the variables in the file and variables in the current cultivation protocol and first data
line. All current on-line data is deleted.
Print
Prints the cultivation protocol, data, installation protocol and Chart window picture in the
ready-to-publish form to the default printer. To change printer use Control Panel in the
Program manager.
Run Manager
Opens a Run Manager dialog where you can start and end on-line sessions and close
BioXperts.
May 2009
Exit
Terminates the BioXpert program.
The data editor menu commands
Create, delete and edit on-line variables, off-line variables, constants and formulas. Add, edit and spline data.
Set substrates and products. The quick way to edit variables is click the mouse right button on the variable
button in the Variables window.
New data
Deletes all data in measured variables (on-lines and off-lines), constants changes and
calculated formulas curves. No more changes.
On-lines
Opens an On-line Variables dialog to add, delete and set on-line variables. Enter and change
variables values.
Off-lines
Opens an Off-line Variables dialog to add, delete and set off-line variables. Enter and change
variables values.
Constants
Opens a Constants dialog to add, delete and set constants. Enter and change constants values.
You can change constants values during cultivation (step-wise).
Formulas
Opens a Formulas dialog to add, delete and set formulas.
Substrates
Opens a Substrates Characteristics dialog to add, delete and set substrates characteristics.
Products
Opens a Products Characteristics dialog to add, delete and set products characteristics.
Show mode
Opens a Representation of Curves dialog to spline measured curves (on-line and off-line
variables only), add/delete measured data point marks, add/delete lines between measured
data, etc.
Status
Opens a Variables Status dialog to set variables status. Add, delete and change variables.
Description
Opens a Cultivation Description dialog to enter the cultivation organism name and comments
and to view the start and end moment of cultivation and calibration coefficients for on-line
variables.
Import
Opens a Data Import dialog to get data of one variable from the all running BioXperts and
shows the imported curves to the Chart window.
May 2009
The chart menu commands
Reset
Unselects all variables from the Chart window. It is a quick way to remove all variables.
Redraw
Refreshes the Chart window.
Copy
Copies the Chart window picture to the clipboard. It is a quick way to use this picture in other
program. For example use Edit | Paste command in the PaintBrush program.
Pictures
Opens a Chart Pictures dialog to add current Chart window settings, to delete and view
existing pictures.
X-Axis
Opens an X-axis dialog to choose time or variable to the Chart window and set scale.
Y-Axis
Opens a Y-axis dialog to choose variables to the Chart window. The quick way to choose
variables is click the left mouse button on the variable button in the Variables window.
Scaling
Opens a Scaling dialog to change scale representation.
Options
Opens a Chart Options dialog to choose grid, marks, zero lines and y-axis placing on the Chart
window.
Show Names
Creates and removes variables names windows (variables in the Y-axis). Use this command
before printing. Move the names to the suitable place and printer plots the names in the same
place.
Font
Opens a Select font dialog to change font in Chart window. Use this option before printing
Chart window.
The run menu commands
New
May 2009
Starts some actions before measurement is actually started:

Opens a Cultivation Description dialog to enter organism name and comments.
Opens a Cultivation Parameters dialog to enter on-line time interval, start moment and
name for the file, where measured values are stored during the measurement.
Creates the On-line Session window to start new cultivation and deletes all current data
before measuring.
Continue old
Opens a Cultivation Parameters dialog to enter on-line time interval and name for the file,
where measured values are stored during the measurement. You can use the same file to
continue measuring. Then the On-line Session window is created to continue old cultivation.
End
Ends or breaks the on-line session.
Alarm
Opens an Alarm dialog to add and remove variables alarm control.
Test
Opens a Test dialog where you see the on-line measured values by each 2 seconds.
The control laws menu commands
Manual setp.
Opens a popup menu of control variables to change setpoint for selected variable (in the
Manual Setpoint dialog). Activated manual setpoint disables the corresponding profile and
algorithms.
Profiles
Opens a Profiles dialog where you can specify the on-line control variables set-points by
curves. Three modes are enabled to represent curves: constant, straight line, cubic spline.
Statements
Opens a Control Algorithms dialog where you can specify the on-line control variables setpoints by algorithm.
Open
Opens a File Selection dialog where you can select the control laws (profiles and statements)
file (*.FCL) or cultivation protocol file (*.FRM) to open. After selection file, the Open
Control Laws Options dialog opens where you can select which control laws you want open
and delete old profiles and statements, or not.
Save as
Opens a File Selection dialog where you can enter a name for the currently used control laws
(profiles and statements). The current control laws are then saved to that file with no further
questions asked.
The install menu commands
Devices
Opens a Devices dialog where you can choose AnalogDigital/DigitalAnalog (AD/DA) cards
and serial ports with communication protocol which you will use.
Variables
Opens a Variables Setup dialog where you can connect the on-line variables with the
corresponding physical input and output channels. In this dialog you can calibrate the
AD/DA channels also.
Graphic
Opens a Graphic Setup dialog where you can choose picture, variables, updating interval etc
for Graphic window.
May 2009
The window menu commands
Show chart
Brings a Chart window to front on the desktop of BioXpert.
Show on. sess.
Brings a On-line Session window to front on the desktop of BioXpert.
Show variables Creates and hides a Variables windows. The buttons are created in the New Variable dialog
(use Data editor | Status command and Change button). Variables window includes on-line
variables, off-line variables and formulas which Button check box in the New Variable dialog
is checked.
Show chart val. Creates and hides a Values window. Values window includes list box with variables in the Yaxis and their values at the specified time in the Elapsed time edit control. Click mouse left
button in the curves area in the Chart window or enter the value into the Elapsed time edit
control and use E button in the Values window, then the variables values are showed in the list
box. Value 'NA' in the list box means an unknown value.
Show graphic
Creates and hides a Graphic window.
The help menu commands
Index
Opens a Help window that displays the list of all Help topics available for the BioXpert.
Keyboard
Opens a Help window that displays the list of keyboard topics. Keyboard topics contain tables
of keys and their functions in the BioXpert.
Using Help
Opens a Help window that displays the introductory topic about how to access and use Help.
About
Opens a window displaying logo bitmap, installer and company name, and information about
memory, disk space and mathematical co-processor.
May 2009
HOW TO START BIOXPERT V2

To start BioXpert V2 from BioXperts folder move the tip of the pointer onto (point) the BioXpert icon and two
times quickly press and release (double click) leftmost mouse button. Your monitor displays the BioXpert logo.
At first you must select user name and program mode.
The New Cultivation or Recalculation dialog
mini scroll bar
Select user name, program mode and fermentor number. For create new user use New User button.
List of user names
This list box contains user names that exist. Select one of them.
Home
Home directory for selected user. The data is saved to this directory by default.
Mode
Choose Cultivation radio button to run cultivation session or Recalculation radio

button to recalculate old cultivation data or make off-line fermentations (all on-line
variables are off-line variables; physical connection between fermentor and PC
does not exist).
Fermentor no.
Choose the fermentor number (from 1 to 9999). Use mini scroll bar to change
number. The number is important only in the CULTIVATION mode and multifermentor systems.
New User
Press this button to open a New User dialog to enter new user. After Ok the new
user name is added to the list box.
Ok
Press this button to close this dialog deleting all old cultivation protocol and data (if
exist). In the CULTIVATION mode all on-line variables are read from install protocol
file (FERMi.INI, where i is fermentor number).
Cancel
Press this button to close this dialog without changes. If you are first time in that
dialog you exit from BioXpert.
Help
Press this button to open a Help window with text about this dialog.
The user name is subdirectory of main directory (where ferm.exe is placed) and if you want to rename or delete
it, you must use the MS-Windows Explorer.
For example the DEMO user name is selected and CULTIVATION mode is choosen.
May 2009
The New User dialog
Name
Enter the new user name. The user name can include letters (A...Z), digits (0...9)
and underline symbol (_). The first character must be letter and maximum length is
8 characters.
Ok
Press this button to close this dialog. The new subdirectory is created in the
BioXpert main directory.
Cancel
Press this button to close this dialog without changes.
Help
For example the 'toomas' user name is created. There are not difference between lower-case and upper-case
letters.
Open cultivation protocol and data

After selecting user name and program mode, an empty Chart window and Variables window (in the
CULTIVATION mode the installed on-line variables buttons appeared in the Variables window) will appear. Now
you can make a completely new cultivation protocol (use Data editor menu commands) or use predefined
protocols. Use File | Open Standard Batch (Fed-batch or Continuous) menu command to use standard protocol.
The standard protocols are default protocols installed by BioExpert.
Use File | Open menu command to use custom cultivation protocol and data. Before opening custom protocol or
old cultivation data, the File Selection dialog is opened.
The File Selection dialog
Drives
May 2009
Select the necessary drive from the list box. After changing drive the Directories
and Files list boxes are filled again. Double click the mouse left button on the drive
icon to rebuild the Directories list box.
Directories
Select the necessary directory from the list box. After changing directory the Files
list box is filled again.
List Files of Type
Select the type of files from the combo box. The files of selected type will be listed
to the files list box.
File Name
Enter the file name or string (includes '*' or '?' symbols) to select the group of files
in Files list box.
Select the file from the list box. The same file name appears in the File Name edit
control and the last update time, size of file and some BioXpert file comments
appear under the edit control. Double click the left mouse button on the file name to
open (save) file.
Ok
Press this button to close this dialog. The selected file is loaded (saved).
Cancel
Help
To get better acquainted with BioXpert you are welcome to open a demonstration file. Directory tree highlights
your home directory. The list of files in demo directory is displayed. Select demo.frm. The short description
of the file: Cultivation of Saccharomyces cerevisiae is displayed on the window. Use Ok button to open this
file. The message Opening file... is displayed on the Status bar. When file is loaded the message Ready
appears and you can start the data processing.
May 2009
DATA EDITOR
Although the Data Editor menu commands are especially designed for off-line processing of the cultivation
data, they can be successfully applied for recalculation and for final data representation. Data editor allows you
to create, delete and change variables, edit variables values, formulas, set substrates and products. The
cultivation protocol and data always have a description.
The Cultivation Description dialog
Organism
Enter the cultivation organism name to edit control. The maximum length is 128
characters.
Comments
Enter the cultivation comments to multi-line edit control. Use Ctrl-Enter to make
new line.
Start (date and time)
Displays the start date and time of the current cultivation.
End (date and time)
Displays the end date and time of the current cultivation.
Ok
Press this button to close this dialog with saving the organism name and comments.
Cancel
More
Press this button to open a Calibration Coefficients dialog to view the information
about the set-up of fermentation system and calibration constants.
Help
May 2009
The Variables Status dialog
In that dialog you can create new variables, delete existing variables (not measured or not analyzed) and change
variables mode (get from one list box and put to other) and settings. Four list boxes includes all cultivation
variables.
On-lines
Off-lines
Constants
Formulas
Imported
List of on-line measured and controlled variables.

List of off-line variables.
List of constants.
List of formulas.
List of imported variables.
Select one variable from list boxes for delete or change. Under the list boxes you see the selected variables
name, mode, comment and scale unit name. The asterisk character '*' in the list boxes before the variable name
means that the button is drawn in the Variables window. The character 'S' or 'P' after the variables names means
that the variable is SUBSTRATE or PRODUCT.
New
Press this button to open a New Variable dialog. Enter the new name, comments
and mode and the new variable appears to the according list box. In the
CULTIVATION mode you can't add a new on-line variable in that dialog. It is
possible only by Install | Variables menu command.
Delete
Press this button to delete the selected variable from list box. The places of
formulas that include deleted variable are replaced with '0' character.
Change
Press this button to open a New Variable dialog filled with selected variables
settings. You can change names, mode, etc.
Done
Press this button to close the Variables Status dialog. All changes are saved.
Help
For example the off-line variable 'eth' (ethanol) is selected. This variable has a button in the Variables
window and it is a PRODUCT.
May 2009
The New Variable dialog
Create new or change existing variable. Choose status and other settings.
Name
Enter or change the variable identifier name. The name will include letters, digits
and underline symbols '_'. The first character must be a letter. Special symbol '#' or
'$' is added to the name for constants (substrates or product characteristics) and
formulas which are calculated for all substrates or formulas.
Scale unit
Enter or change the variable scale unit name. Maximum length is 12 characters.
Comment
Enter or change the variable comment. Maximum length is 63 characters.
Status
Choose variables status from combo box. There are four modes: ON-LINE, OFF-LINE,
CONSTAV2 and FORMULA.
Subs/Prod
Choose the Substrate for

button for other variables.
Button
Check the check box, when the button is drawn to the Variables window.
Ok
Press this button to close New Variable dialog with adding or changing the
variable.
Cancel
Press this button to close the New Variable dialog without changes.
Help
May 2009
SUBSTRATES,
Product for
PRODUCTS and
None radio
The Edit On-line Variables dialog and the Edit Off-line Variables dialog
Add, delete, and change off-line variables and their values. The main function of this dialog is to introduce new
data during the run or recalculation.
There are differences between the Edit On-line Variables dialog and the Edit Off-line Variables dialog:
you can change time scale (extra sampling points) for off-line variables.
you can't add and delete on-line variables (the Install | Variables menu command is recommended).
you can't change the on-line data
Table
List of on-line (off-line) variables with their values. The first line includes the
names of variables. The second line includes the scale unit names of variable (you
can edit). The first column includes the time points. The time is shown in the
hour:minute format. Select the cell in the off-line variables table and enter the
value. For unknown value enter 'NA' or empty the cell.
Comments
Enter the comments of the selected variable.
New
and mode and the new variable appears to the according table.
Delete
Press this button to delete the selected off-line variable from the table. The places of
formulas that includes deleted variable are replaced with '0' character.
Calculate
Press this button to open the Calculate Variable dialog. Recalculate the selected offline variable's data points.
Copy
Press this button to copy the values of selected variable (entire row) to the
clipboard. It is a quick way to use this data in other program. For example use Edit |
Paste command in the MS-Excel program.
Timing
Press this button to open the Off-line Time Schedule dialog. Change off-line time
points.
Done
Press this button to close this dialog. All changes are saved.
Help
For example the value of the glucose 'glc' at time 20:30 is 3.2 mCmole/l.
May 2009
The Off-line Time Schedule dialog
Add irregular time points, delete and change off-line time points.
Default interval (min)
Enter the default off-line points interval by minutes. When adding new points this
interval is used.
Time Points
List of existing off-line time points. Select one of them to delete.
Time
Enter the time (hour:minute) to edit control for adding and inserting new time point
to the list.
Insert
Press this button to insert new time point (in the Time edit control) to the list.
Delete
Press this button to delete selected time point. All the off-line variables data of this
time point are also deleted.
Done
Press this button to close this dialog. All changes are saved. If Keep rest check box
is checked, then the latest time points (previous time point + default interval) are
not changed.
Help
If you have taken samples at unusual time point (for example 5:30 instead of full hours), or if you would like
to change the default interval of time points use this dialog. The default interval is 60 minutes.
May 2009
The Calculate Data dialog
Value
Recalculate the on-line and off-line measured variables.

Operation
Choose +, -, *, / or clear 'auto zero' operation.
Side
Choose left radio button for operator on left side of Value, or right for right side.
Time
Enter the minimum and maximum time to the edit controls. Only the data between
the selected time range are calculated. Press the All button to set the all time range
of selected variable to the edit controls.
Value
Enter the value for calculation to the edit control. The 'NA' is used for unknown
value.
Ok
Press this button to close Calculate Data dialog. All the data from the selected
variable are calculated by chosen operation and side.
Cancel
Press this button to close Calculate Data dialog without changes.
Help
Use Clear 'Auto Zero' operation for counter type data, there the data point (auto zero point) coming rapidly to
near the zero (the counter is full). This operation result is continuously rising curve.
Source curve:
Result curve:
For example, you have measured acetate concentration in g/L, but in formulas you need the data in mC-molar
units. To correct the value you have to divide the measured values by 30.0. Select in the Edit Off-line Variables
dialog the variable ace and then press Calculate button. Choose division ('/') and left side and enter 30 into the
Value edit control. Press Ok button and new values of the ace appear in the off-line variables list.
May 2009
The Edit Constants dialog
Define the cultivation variables which do not change during cultivation or change step-wise.
Table
List of constants. The first column includes the names of constants. The second
columns includes the constants values (you can edit). The third columns includes
the scale unit names of constant (you can edit). The fourth column includes the
comments (you can edit).
New
and the new variable appears to the table.
Delete
Press this button to delete the selected constant from the table. The places of
formulas that includes deleted constant are replaced with '0' character.
Done
Help
The constant has a form:

value0 value1(time1) value2 (time2) etc.
where
value0 is the constant value at the time moment 0:00
value1 is the constant value at the time moment time1
value2 is the constant value at the time moment time2
Time points must be in the incremental order and have time format (hours:minutes). For unknown value enter
'NA' or empty the cell of table.
For example pump rate will be changed at a certain time point by typing in the table a new value of the new
pump rate and in the parenthesis the respective time:
22.3 25.1(12:00) 12.0(14:00)
The last pumping rate value 12.0 will be maintained from the 14-th hour of cultivation till the end of the
cultivation.
May 2009
The Edit Formulas dialog
This dialog is designed for the calculation formulas using the values of on-line and off-line variables, constants,
and other formulas. The BioXpert has got three different sets of formulas for batch, fed-batch and continuous
cultivations respectively. In demo file 'DEMO.FRM' the formulas are designed for processing of continuous
cultivation data.
Table
List of formulas. The first column includes the names of formulas. The second
columns includes the formulas (you can edit). The third columns includes the scale
unit names (you can edit).
For substrate
List of substrates or products (For products). Only for formula variables which are
created for substrates and products.
Comments
Enter the comments of the selected formula.
New
and the new variable appears to the table.
Delete
Press this button to delete the selected formula from the table. The places of
formulas that includes deleted formula are replaced with '0' character.
Open
Opens a File Selection dialog where you can select the formulas file (*.FOR) or
cultivation protocol file (*.FRM) to load formulas. You can delete currently used
formulas before the selected formulas file is loaded.
Save as
Opens a File Selection dialog where you can enter a name for the currently used
formulas. The current formulas are then saved to that file with no further questions
asked.
Items
View the enabled formula items: cultivation variables, operators and functions.
Enabled variables names List of all variables, whish are used in the formulas. Selected variable identifier
name appears to the table (after caret position).
Operators and functions Lists of operators and functions, which are used in the formulas. Selected operator
or function appears to the table (after caret position).
NA is 0 for + and -
May 2009
Check this check box to set the unknown value (NA) to 0 in the calculating + and operations. For example:
3 + NA = 3
3 + NA = NA
check box is checked

check box is unchecked
Done
Help
Formula will be simple or master type. Master formula is formula for all substrates or products. Master formula
must be include # (for substrates) or $ (for products) symbol in the end of the identifier name. Two master
variables S# and P$ are created to present substrates and products. After you create the master formula the
simple formulas for each substrates or products are generated. For example:
Master formula is Sf# = S# * V
Two substrates are
ace and glc (alias names are S_ace and S_glc)
Simple formulas
Sf_ace = S_ace * V and
Sf_glc = S_glc * V
Feedback in the formulas is not supported. For example next group formulas are wrong:
a = f1(b); b = f2(c); c = f3(a)
where f1(b) is formula including variable b etc.
Formula must be arithmetic expression and includes:
operators: +, -, *, /, ( )
functions:
rate (simple variable) - variables rate by each minute
integrate (simple variable) - square between curve and zero-line by each minute
total (master variable) - sum of all substrate or product dependent variables
ln (simple variable) - natural logarithm
variables names
numeric constants
For example, the CO2, rate (CO2) and integrate (CO2) are displayed in the next picture.
For example, to differentiate the biomass concentration select the place where to type in FORMULA box, scroll
the Operators list box until you find rate (, select it , scroll the Variables list box to find X, select X and select
) from Operators list box. If you are familiar with the operators and variables used in BioXpert you can enter
the formula through keyboard. If the undefined operator or variable is used an error message will be displayed.
May 2009
The Substrates Characteristics dialog and the Products Characteristics dialog
Characteristic
V l
List
List of substrates or products. Select the variable to set characteristics.
Characteristics
List of selected substrates or products characteristics. Select the characteristic

constant to edit.
Value
Enter the characteristic value to the edit control in the constant form.
Unit
Enter the characteristic scale unit name to the edit control.
Comment
Enter the characteristic comment to the edit control.
Replace
Press this button to save characteristic value, unit and comment.
New
Press this button to open a New Variable dialog. Add new substrate or product to
the List.
Delete
Press this button to delete selected substrate or product.
Change
Press this button to open a New Variable dialog filled with selected substrate or
product. Change names.
New ch
Press this button to open a New Variable dialog. Add new substrate or product
characteristic (the last symbol in the name is # or $) to the Characteristics list box.
The same characteristics for other substrates or products are created also.
Delete ch
Press this button to delete selected characteristic. This command deletes also same
characteristics of other substrates or products.
Done
Help
On-line and off-line variables, constants, and formulas have to be "sorted" into two groups - and are designated by S or P, respectively, in the Variables Status dialog.
SUBSTRATES
or
PRODUCTS
First is for the substrate definition and the second is for the definition of substrate characteristics like
concentration in the feeding medium Fa#, molecular weight MW#, number of carbon atoms in molecules NC#.
For example enter the molecular weight of glucose. Press New Ch button. Type MW# into Name box,
molecular weight into Comment box and press Ok button. The MW_glc is displayed in the Characteristics
list. Select MW_glc and type 180 into Value edit control and press Replace button.
May 2009
Substrate and product characteristics can be defined only through this dialogs. The introduction of substrate and
product marking by # and $ and use of C-molar representation enables to write carbon balance equations for
unlimited number of substrates and products.
The Representation Mode of Curves dialog
The calculation of several important fermentation parameters like growth rate, biomass production and
substrate(s) utilization rate includes differentiation. If we interpolate the experimental points linearly (by
straight lines) the result may be quite hard to interpretate. Therefore, BioXpert suggests to use this dialog.
List
List of on-line and off-line variables.
Spline
Straight lines
Constant
Sum
Press this button to calculate spline between measured points.

Press this button to connect measured points with straight lines.
Press this button to connect measured points in the constant mode.
Press this button to sum all measured points.
The straight lines between measured points are drawn in the black pen. The splined,
constant or sum curve are drawn in the red pen.
Convergence criterion
Relative weight
Enter the number to edit control for convergence criterion to change spline
function. Value 0 means that splined curve is drawn trough all the measured points.
For large values (over 1000) a straight line is drawn.
Enter the relative weight for all points by percents to the edit control.
Respline
Press this button to recalculate the splined curve with new spline parameters.
No marks, No lines
Press this buttons to view selected curve without marks and without lines between
marks.
X-axis is...
Press TIME button to select time or Variable button to select variable to the Xaxis. You can select only variable, which is selected to the X-axis of the Chart
window.
Done
Press this button to close this dialog. All changes are saved. The formulas, which
includes resplined variables will be recalculated.
Help
IMPORTANT! If variable is splined, the formulas use the splined points.
May 2009
You may change the spline function by selecting two spline parameters convergence criterion and relative
weight of all points (%)'. Change the values of those parameters and press Respline button until the line drawn
through the points is adequate.
The Data Import dialog
Name of variable...
Choose variable to import. Combo box includes on-line, off-line variables and
formulas of selected BioXperts.
To
The data will be imported to the current BioXpert.
From
List of others running BioXperts which are marked with numbers. Select one or
more BioXpert(s) to import data. After the curve is imported, this number is added
to the name of chosen variable.
Ok
Press this button to close this dialog with importing the data of chosen variable
from selected BioXperts. The new variables will be created and filled with
imported data. The name of variable will be consist with chosen name and number
from the list of running BioXperts. After closing this dialog the imported curves
will be drawn to the Chart window and buttons will be appeared to the Variables
window.
Cancel
Press this button to close this dialog without importing data.
Add
Opens a File Selection dialog where you can select the cultivation data file
(*.FRM). After the data file is selected the new BioXpert starts and selected data
will be loaded.
Help
May 2009
DISPLAYING DATA ON THE CHART WINDOW

The data curves will displayed in the Chart window.
Curves area
Header lines
Y-scale area
X-scale area
Select variables for the Y-axis using the buttons in the Variables window or Chart | Y-axis menu command.
Select time or variable for the X-axis using the X-scale area in the Chart window or Chart | X-axis menu
command.
Choose scaling using Y-scale and X-scale area or Chart | Scaling menu command.
Change screen options using header lines area or Chart | Options menu command
Zoom time scale using curves area or Chart | X-Axis menu command
The Variable(s) in Y-axis dialog
On-lines measured
On-lines controlled
Off_lines
Constants
Formulas
Imported
Lists all types of variables. Select any variables, which you want to see in the Yaxis in the Chart window.
Ok
Press this button to close this dialog. After the Chart window is redrawn with
selected Y-axis.
Cancel
Help
May 2009
The Time or Variable in X-axis dialog
List
List with TIME and all variables, possible on the X-axis. Select time or variable,
which you want to see in the X-axis in the Chart window.
Manually scale range
Check this check box to view the time or variable in the preset scale and enter the
scale range of the selected time or variable to the edit controls. For unchecked
check box the scale is calculated automatically.
Keep width
Check this check box to fix width of x-scale during on-line session. The x-scale
will be shifted automatically right by half of width, when the time exceeds the
maximum of x-scale.
Ok
Press this button to close this dialog. After that the Chart window is redrawn with
selected X-axis. If the variable is selected, then all variables, chosen to the Y-axis,
will be drawn relative to time.
Cancel
Help
The Scaling Settings dialog
List of variables
List with all variables, possible on the Y-axis. Select variable to change scaling.
The symbol '*' means, that the variable has manual scale.
Number of spaces
Enter the number of spaces between scale numbers.Use mini scroll bar to change
the number.
May 2009
Manually scale
Check the Manually scale check box to view the variable in the manual scale. By
default the scale is calculated automatically.
Scale range
Enter the scale range of the selected variable to the edit controls.
Ok
Press this button to close this dialog. After that the Chart window is redrawn with
defined scaling.
Cancel
Help
For example the dissolved oxygen consumption has the scale from 0 to 50.
The Chart Options dialog
Header (two lines)
Enter the Chart window picture header lines.
X-axis name for time
Enter the Chart window picture X-axis name for time scale.
Decimal time
Check the Decimal Time check box to use decimal time format. Otherwise the time
has hour:minute format.
Zero-lines
Check the Zero-lines check box to view the zero lines, when the variable has the
positive and negative scaling.
Scale units
Check the Scale units check box to view the scale units.
Grid
Check the Grid check box to view the grid.
Marks
Check the Marks check box to view the sample points (for the off-lines variables
only). When the Different check box is checked the marks are circles, asterisks,
diamonds etc., otherwise all the marks are circles.
Y-axis
Choose the Y-axis placing in the Chart window:

left side
all axis are drawn in the left side
left-right side axis are drawn in the left and right sides
not present
axis are not present
first for all
use one axis (by first variable)
Ok
Press this button to close this dialog. After that he Chart window is redrawn with
selected options.
May 2009
Cancel
Help
The Chart Pictures dialog
You can save the Chart window pictures to view them later.
List of pictures
List of Chart window pictures. Select one picture to view or delete. Double click
the left mouse button on the picture name to view.
Current picture name
Enter the current picture name to the edit control for adding to the list.
View
Press this button to close this dialog. The Chart window is redrawn with selected
picture.
Add
Press this button to add current picture to the list with entered picture name.
Delete
Press this button to delete selected picture from the list.
Done
Press this button to close this dialog. All changes are saved. The Chart window is
not redrawn.
Help
May 2009
The Select Font dialog
You can choose the font for the Chart window. The same font is used in the printer for printing Chart window.
Choose face name, size and style.
Face name
List of font face names.
Size
Enter the font size from keyboard or choose from list box.
Style
The Bold, Italic, Underline, and Strikeout styles are available.
Ok
Press this button to close this dialog. After that he Chart window is redrawn with
selected font.
Cancel
Help
May 2009
DATA PRINT, EXPORT AND IMPORT

You can print data, Chart window picture, cultivation protocol and installation protocol. To change printer use
Printers folder from Start menu Settings Printers. Use Chart | Names menu command to set variables names to
the curves area. Those names are printed in the same places to the paper.
You can export data to the other programs:
in the SYLK format to the MS-Excel. Data are exported in the off-line time scale.
in the ASCII format. Data are exported in the off-line time scale.
in the bitmap format to the PaintBrush, CorelDraw etc. The current Chart window picture is exported.
You can import the data from other programs. The data is read from file in the on-line time scale.
The Print Options dialog
Printer
The selected printer and printer port are displayed.
Font for text
Choose the font's face and size for protocols and data. The font for chart picture is
same as in the Chart window.
Print
Choose what you want print out. There are four possibilities:
1. Print Protocol
The cultivation comments, times and all variables with settings are printed.
2. Print Data
Check the On-lines check box to print all on-line variables data in the on-line time
scale. Check the Off-lines check box to print all off-line variables data in the offline time scale. Check On,Off-lines check box to print all on-line and off-line
variables in the off-line time scale. Check the Fixed number of columns check
box and enter the number of columns of the variables to according edit box to print
variables to the manually fixed number of columns. Otherwise number of columns
is calculated automatically (all width of page is used).
3. Print Chart picture
Print current picture of the Chart window. Check the With data check box to print
variables (drawn on the Chart window) data in the off-line time interval. Check the
By curve area check box to placing the picture by curves area, otherwise the
measurements are done by full Chart window picture. Enter the Left and Top
margins and Width and Height sizes to the according edit controls. All margins
will done in millimeters. Press Default button to set default numbers to the edit
controls (10, 10, 180, 100 for picture and 50, 10, 100, 100 for curves area). Enter
the curves Line Width to the edit control in the device units. Uncheck the With
titles check box to print picture without variables names, scale unit names and
May 2009
header. Check the With filename check box to print current data filename above
the picture. Check the All with marks check box to print marks for all variable's
curves. For off-line variables the marks will be printed by off-line timescale, for
other variables the marks will be printed every 10 millimeters.
4. Print Install protocol
The information about the physical interface device (AD/DA chart and serial port),
all on-line variables with settings are printed.
Setup
Press this button to open Printer Setup dialog. Choose the settings for selected
printer.
Ok
Press this button to start printing. The BioXpert Print Request window is opened.
Press Cancel button to cancel the printing job.
Cancel
Help
The Open ASCII File dialog

To import on-line variables data use File | Import menu command. After the import file is selected (File
Selection dialog), this dialog is opened. Three steps are supported:
STEP 1 Select on-line variables names line from File list box.
Ok
Press this button to go to next step.
Cancel
Help
May 2009
STEP 2 Set connections between on-line variables in the ASCII file and in the BioXpert.
ASCII File Variables
List of on-line variables in the ASCII file and connections with variables in the
BioXpert. Select the variable for adding and deleting relations.
System Variables
List of on-line variables in the BioXpert. Select the variable to couple with selected
ASCII file variable.
Del Rel
Press this button to delete selected relation.
New Var
Press this button to open a New Variable dialog to add new on-line variable.
Ok
Press this button to go to next step.
Cancel
Press this button to go to previous step.
System | Close
Use the System menu to close this dialog without changes.
Help
STEP 3 Select first data line and enter time interval.
File
May 2009
Select first data line from file list box. The first line corresponds to the 0 time point.
Time Interval
Enter the time interval in the file by minutes. Use micro scroll bar to change the
interval.
Ok
Press this button to close this dialog. All previous on-line data is deleted.
Cancel
Press this button to go to previous step.
System | Close
Use the System menu to close this dialog without changes.
Help
The Export Data Format dialog

To export data use File | Export | Data menu command. First this dialog is appeared.
Format
Choose SYLK or Text format.
Variables
Choose On-lines variables data, Off-lines variables data, Constants and Formulas
values.
Time interval
Choose On-line to write data in the on-line time scale, Off-line to write data in the
off-line time scale, or Other to write data using the custom interval by minutes.
Time range
Choose All to write all data or From to write data in the selected time range (by
hours:minutes).
Ok
Press this button to close this dialog. Then the File Selection dialog opens where
you can select the file name. The choosen variables data will be exported by the
choosen format.
Cancel
Press this button to close this dialog without exporting data.
Help
May 2009
CONTROL LAWS
To control the cultivation parameters (pH, temperature, pumps, etc.) the options of manual setpoint, profile and
statements (control algorithms) are available. Manual setpoint will sent to fermentor immediately after pressing
OK button in the Manual Setpoint dialog. Setpoints by profiles and statements will sent to fermentor in each
control interval.
The Manual Setpoint dialog
Manual
Check the Manual check box and enter the desired setpoint value. To activate the
control by profiles and statements uncheck this button.
Ok
Press this button to close this dialog and send value to fermenter.
Cancel
Help
The Profiles dialog
Maximum limit
Current time
Graph
The control interval for set-points by profiles is equal with on-line reading intervals (minimum 1 minute) or
custom interval (minimum 1 second).
List of variables
May 2009
List of on-line controlled variables. Select the variable to set profiles.
Points
List of profile points. The list includes time and value pairs. Select the pair to delete
it.
Time, Value
Enter the point to the time (by format hours:minutes) and value edit controls.
+, -, -All
Press these buttons to add new point, delete selected point and delete all points.
Graph
Graph includes profile curve, scales and minimum and maximum limits (red pen).
Use left mouse button to add new point and right mouse button to delete profile
point. Use Line Mode to connect the profile points. Green line points to the current
moment during the on-line session.
Scaling
Enter the axis bounds to the Time and Variable edit controls.
Precision
The values precision, installed in the Setup Variables dialog is displayed.
Interval
The control interval for profiles (chosen in the Control Interval for Profiles dialog)
is displayed by format minutes:seconds mode, where mode is R (equal with reading
interval), C (custom interval) and C+ (custom interval with synchronization with
reading moment).
Line Mode
Choose line mode for connecting the profiles points. Use Constant mode for
advancing by leaps and bounds profiles, Line mode for straight lines and Spline
mode for cubic spline.
Done
Interval
Press this button to open the Control Interval for Profiles dialog to change the
control interval for profiles.
Help
The Control Algorithm dialog
Name
May 2009
Enter the name for algorithm.
Control interval
The control interval for statements (chosen in the Control Interval for Algorithms
dialog) is displayed by format minutes:seconds mode, where mode is R (equal with
reading interval), C (custom interval) and C+ (custom interval with synchronization
with reading moment).
Table
The table includes control statements. The first column includes line order numbers.
The second column includes statements. The third and the fourth column includes
starting and ending time (by format hours:minutes) of the calculating statement.
The default values of the starting and ending time of the calculating statements are
start of cultivation and end of cultivation. Start and end time in the group line are
default values for all group.
+, -, C, P, U
Press these buttons to insert new empty line, delete selected line, copy text from
selected line and column to buffer, paste text from buffer to selected line and
column, undo the last overwriting.
Statements
List of types of the statements:

IF ... ELSE ... ENDIF
IF statement
variable = expression
set value to variable
- nr, nr, ...
disable lines during solving
+ nr, nr, ...
enable lines during solving
GOTO nr
goto line
STOP
ends the calculation of statements
-new group
#
comment line
Expression includes variables, functions and operators, which are in the Variables
list box, in the Functions list box and in the Operators list box.
Selected statement, variable identifier, function or operator appears to the table
after the caret position.
Check
Press this button to check the statements syntax.
Variables
Press this button to open the Internal Control Variables dialog to view and change
values of internal variables. Before you using this button, check the syntax for
updating the list of internal variables.
Interval
Press this button to open the Control Interval for Algorithms dialog to change the
control interval for all statements.
Reset
Press this button to reset all statements.
Items
Press this button to view the enabled statement items: variables, functions,
operators.
Done
Press this button to close this dialog. All changes are saved and statements syntax
are checked.
Help
May 2009
The Internal Control Variables dialog
Internal control variables are temporary variables, which used only in the control algorithms. They have only
the last value (no history). By default the first value is 0. For example var = var+1 means that the value of var is
greater by 1 in the every next interval.
List
The list of internal control variables. Choose the variable to change the value in the
edit box. The initial value is 0.
All to 0
Press this button to set the values of all variables to 0.
All to NA
Press this button to set the values of all variables to NA.
Ok
Press this button to close this dialog with changes.
Cancel
Help
May 2009
The Control Interval for Profiles and the Control Interval for Algorithms dialog
Reading interval
Choose this radio button to calculate profiles (control statements) each time after
the on-line variables are measured.
Custom
Choose this radio button to enter (or use mini scroll bar) the custom control interval
to edit box by format minutes:seconds. Check the Synchronize with reading
moment check box to calculate profiles (control statements) additionally in the
each reading interval (custom control interval must be smaller than reading
interval). The on-line variables values are saved every reading interval. Use left
mouse button to change seconds and right mouse button to change minutes.
Ok
Cancel
Help
Description of control statements

Algorithm consists of several statements (if, activity, goto, semaphore, stop). One statement must be written in
the one line (exclude IF statement, where IF and ENDIF part must be written in the other line). All statements
are dependent on the time specified in the third and the fourth column in the table. The statements will be
calculated at the time moment between begin and end time (from the beginning of cultivation and by format -hh:mm). When there are no starting and ending time specified, the default values of the starting and ending time
of the calculating statements are start of cultivation and end of cultivation. Start and end time in the group line
are default values for all group.
The statements will be calculated line by line and up to down.
The interval of calculating formulas is on-line session interval (same as in the On-line Session window) or extra
interval (by format minutes:seconds). It means that minimum control interval could be 1 second.
The new group line includes in the beginning at least two minus signs (--). Use several groups for calculating
statements in the different times.
The comment line begins with # sign.
When the result of the expression is NA and it is set-point for the fermentor, the fermentor parameter will be set
to the manual mode (MAN mode).
May 2009
STATEMENTS
1. IF STATEMENT
IF expression
statement_11
statement_12
...
ELSE
statement_21
statement_22
...
ENDIF
ELSE part is optional.
Condition of the IF statement is TRUE , when the value of the expression is not zero and not 'NA'. When the
condition is TRUE the statements statement_11, statement_12 are calculated, otherwise the statements
statement_21, statement_22 are calculated.
For using semaphore statements, the calculating is different:
IF line
ELSE line statements, which are calculated
disabled
disabled
statement_11, statement_12, ...
disabled
enabled
enabled
disabled
when the condition is TRUE all this statements are calculated, otherwise
the statements statement_21, statement_22 are calculated.
2. ACTIVITY
variable = expression
When the variable is on-line output variable, the set-point (value of expression) is sent to the fermenter
immediately after the expression is calculated.
3. GOTO
GOTO nr
The next statement, which will be calculated, is statement nr.
4. SEMAPHORE
+nr, nr, ...; -nr, nr; ...
Semaphore consists of sublists separated by semicolon. Sublist consists sign and list of statement numbers nr.
Minus sign means, that all statements in the sublist are disabled and not calculated at the current interval and
next intervals. Stements are enabled and should be calculated after the sublist with plus sign is calculated. When
the group line is disabled/enabled, the all group is disabled/enabled.
5. STOP
STOP
This statement disables the sending set-points to the fermentor. To continue you must break the on-line session
(Run | Break menu command) or enable the on-line controlled variables (use Enable all button to enable all
variables or Enabled check box to enable choosen variable in the On-line Session window) .
May 2009
EXPRESSIONS
Expression consists arithmetic, boolean and relational operators, functions, bounds, variables and constants.
Following table includes operators and their precedence and comments. The #1 category has the highest
precedence; category #2 (Unary operators) takes second precedence, and so on to the OR operator, which has
lowest precedence. The operators within each category have equal precedence. The Unary (category #2),
operators associate right-to-left; all other operators associate left-to-right. When at least one value of operand is
NA, the result is always NA.
# Category
Operator
Comments
1. Highest
()
[]
Function call and bounds

Time subscript
2. Unary
NOT
-
Logical negation
Unary minus
3. Multiplicative
*
/
%
Multiply
Divide
Remainder (modulus) For example: 13%5=3
4. Additive
+
-
Binary plus
Binary minus
5. Relational
<
<=
>
>=
Less than
Less than or equal to
Greater than
Greater than or equal to
6. Equality
=
<>
Equal to
Not equal to
7. Logical
AND
NAND
Logical AND
Logical AND with negation
8. Logical
OR
NOR
Logical OR
Logical OR with negation
9. Logical
XOR
XNOR
Logical OR
Logical OR with negation
Following table includes results of logical operations (result = a operator b):

a
b
AND NAND XOR XNOR OR
NOR
0
0
1
1
0
1
0
1
0
0
0
1
1
1
1
0
0
1
1
0
1
0
0
1
0
1
1
1
1
0
0
0
Following table includes common functions and extra functions for Marubishi fermentors:
Function
Result
Extra function Meaning
exp (x)
power (x, y)
log (x, y)
log10 (x)
ln (x)
sin (x)
cos (x)
tan (x)
max (x, y)
min (x,y)
abs (x)
May 2009
exp (1) = 2.71828...

power (2, 3) = 8
power (27, 1/3) = 3
log (2, 8) = 3
log10 (1000) = log (10, 1000) = 3
ln (2.71828) = 1
sin (3.14159 / 2) = 1
cos (3.14159 / 2) = 0
tan (3.14159 / 4) = 1
max (3, -5.7) = 3
min (3, -5.7) = -5.7
abs (-3.5e3) = 3500
pv (var)
sv (var)
p (var)
nsb (var)
cp (var)
fs1 (var)
ms1 (var)
fs2 (var)
ms2 (var)
present value
set point value
proportional band
non sensitive band
control period
full stroke
minimum stroke
full stroke for cooling
minimum stroke for cooling
Operands x and y are expressions, which values are float numbers. When value of operand is NA, the result of
function is always NA.
Operand var in the extra function is the name of the on-line variable. The results of those functions are same as
in the fermentor at the current time.
Additionally exist two functions, which checks stability of the on-line measured variable:
stab (var, time, diff)
- stability of variable
stab_value (var, value, time, dev) - stability of variable by value
Operands time, value, diff and dev are expressions, which values are float numbers. When value of
operand is NA, the result of function is always NA. Operand var must be name of the on-line measured
variable.
Function stab returns 1 then the difference of maximum and minimum value of the variable var is not
larger as enabled difference diff during last time minutes, otherwise returned 0.
Function stab_value returns 1 then the value of the variable var is not larger as value+dev and not
smaller as value-dev during last time minutes, otherwise returned 0.
VARIABLES
Variables used in the expression are:
pre-defined variables - on-line and off-line variables, constants, formulas
internal variables (have only the last value; no history; the initially value is 0)
TIME - elapsed time from start of cultivation by minutes
INT - interval of the control algorithm by minutes
RINT - reading interval by minutes
TIME_AREAD - relative time after last measuring on-line data by minutes
TIME_BREAD - relative time before next measuring on-line data by minutes
To get value of variable at time, use square brackets:
variable
- last value of variable
variable [time] - value of variable at the beginning of the cultivation + time (minutes)
variable [-time] - value of variable at the last on-line interval - time (minutes)
where time is expression or time constant
When the control interval is not equal with on-line reading interval, the last value of on-line variables will be
read immediately from fermentor. The last value of all other variables (except internal variables) is value at the
last on-line reading interval.
CONSTANTS
Constants used in the expression are:
float number
NA (undefined value)
time (by format hour:min)
May 2009
ON-LINE SESSION
Before starting new cultivation you must:
open cultivation protocol (File | Open menu command)
edit cultivation protocol (Data editor menu commands)
install device for the first time (Install | Device menu command)
install on-line variables (Install | Variables menu command)
calibrate on-line variables (Calibrate button in the Setup Variables dialog)
set profiles to control the fermentor (Control laws | Profiles menu command)
set control algorithms to control the fermentor (Control laws | Statements menu command)
enter the organism name and cultivation comments (Run | New menu command)
enter the cultivation parameters (Run | New menu command, second dialog)
The Warning dialog at the time of open the protocol
If the protocol has on-line variables, which are not installed, then this warning dialog used.
Constant
Choose this button to change variable to constant (default mode). Enter the value of
constant to the edit control.
Off-line
Choose this button to change the variable to the off-line mode.
Link to
Choose this button to link the variable with the installed on-line variable (listed in
the list box).
Delete
Choose this button to delete the variable. The places of formulas in the protocol,
that includes deleted variable are replaced with '0' character.
Scale unit
Change the scale unit name of the variable.
Comments
Change the comment of the variable.
Ok
Press this button to close this dialog with changing current variable.
All
Press this button to close this dialog with changing current variable. All other online variables in the protocol, which are not installed, are changed in the same way:
to the constants, to the off-line variables or deleted.
Help
May 2009
The Cultivation Parameters dialog
Access interval
Enter the on-line access interval to measure (reading interval) and save to memory
the control set-points (values of profiles and values of control statements). Use
mini scroll bar to change this interval.
Start moment
Specify the start moment of cultivation. Use + button to increase and - button to
decrease the time moment. Use left mouse button to change hours and right mouse
button to change minutes.
Data name
Enter the data file name to the edit control. When name is entered without path, the
home directory is used.
Locate
Press this button to open a File Selection dialog to choose a file name.
Ok
Press this button to close this dialog. After that the On-line Session window is
created and on-line cultivation session is started (or pre-run status).
Cancel
Help
The On-line Session

After pressing Ok button in the Cultivation Parameters dialog, the On-line Session window is created and online cultivation session is started (or continued).
The on-line session has two modes:
PRE-RUN mode (before Starting is in the window caption). It is time before starting moment. Use this mode
to check connection and other settings.
CULTIVATION mode.
All on-line variables data is deleted when CULTIVATION mode is started. The set-points are sent to the fermentor
and run-time messages appear to the listbox only in the CULTIVATION mode. You can change the start moment
only in the PRE-RUN mode.
The new data are saved automatically every reading interval. The present values of fermentor parameters are
read every on-line reading interval.
Set-points could be calculated by algorithms or by profiles and values are sent to the fermentor every control
interval. The control intervals is equal with reading interval or custom interval (minimum is one second) .
After the set-point is calculated by algorithm, it is sent to the fermentor immediately. It is possible to send to the
same on-line variable different set-points during one control interval several times. When the set-point are not
May 2009
calculated by algorithm, it is calculated by profile. When there are no algorithms and profiles for output
variable, the variables are set to the manual mode (MAN mode).
When the Profiles dialog or Control Algorithms dialog is opened, the set-points are not calculated and not sent
to the fermentor.
In the PRE-RUN mode the start line is drawn with a red pen on the Chart window.
When the alarm control exists (use Alarm Control dialog) for a variable and this variable's value
is out of normal range, then the Alarm Warning dialog is opened during on-line session and alarm beeps are
emitted.
On-line Session window before starting (PRE-RUN mode):
On-line Session window after starting:
Start time
Change the start moment of cultivation. Use + button to increase and - button to
decrease the time moment. Use left mouse button to change hours and right mouse
button to change minutes. Use Start button to start at the current time moment.
Current time
Real time is displayed.
Elapsed time
Elapsed time from start of cultivation or start of pre-run.
Last reading
Last time (from start of cultivation) when the data were measured.
Last writing
Last time (from start of cultivation) when the data were controlled.
May 2009
Profiles int.
The control interval for profiles is displayed by format minutes:seconds mode,

where mode is R (equal with reading interval), C (custom interval) and C+ (custom
interval with synchronization with reading moment). Press Set button to open the
Control Interval for Profiles dialog to change the control interval for profiles.
Algorithm int.
The control interval for control statements is displayed by format minutes:seconds

mode, where mode is R (equal with reading interval), C (custom interval) and C+
(custom interval with synchronization with reading moment). Press Set button to
open the Control Interval for Algorithms dialog to change the control interval for
control statements.
Reading interval
Change the on-line reading interval for measuring on-line data. Use micro scroll bar
to change this interval.
Input variables
List of on-line measured variables with measured data. The first number is physical
channel number. Select the variable to set alarm control (also double click of left
mouse button opens the Alarm Control dialog for set or reset alarm limits). The
value of on-line measured variable is updated in the list box also, when the control
statement uses this value (the value of this variable measured from fermentor
immediately).
Output variables
List of on-line controlled variables with sent data. The first number is physical
channel number. The value of the data may be:
prerun
PRERUN mode, the data is not sent
disabled
the sending is disabled (Enable check box is unchecked), the data
is not sent.
NA
the set-points are not specified
value
the set-point has the value, this value is sent to the fermentor.
Use Disable all button to disable all on-line controlled variables (set-points will not
sent to the fermentor).
Use Enable all button to enable all on-line controlled variables.
Select the variable to set profile set-points and alarm control (also double click of
left mouse button opens the Profile dialog for set profiles).
Set Alarm
Press this button to open the Alarm Control dialog to set or reset alarm limits of
selected variable.
Profiles
Press this button to open the Profiles dialog to set the profiles of selected on-line
controlled variable.
Algorithm
Press this button to open the Control Algorithm dialog to edit the control
statements.
End
Press this button to end the on-line session. The On-line Session window is closed.
You can continue the on-line measuring (Run | Continue menu command) when
you ended during CULTIVATION mode.
Help
Run-time messages
List of run-time messages. Press Notes button to write yours messages. All this
messages are saved to file (filename is same as data file name and in the same
place, but file extension is FOM).
Standard message includes the time moment when message appeared and one of the following texts:
real time - for linking the real time and elapsed time
May 2009
Start of cultivation - the cultivation is started

User break - the on-line session is ended
User continue - the on-line session is continued
variable is out of alarm range - variable value is too small or too large
variable High Alarm is not accepted (range or precision is not correct, check installation) - the high alarm
limit sent to the fermentor is not accepted
variable Low Alarm is not accepted (range or precision is not correct, check installation) - the low alarm
limit sent to the fermentor is not accepted
variable setpoint is too large
variable setpoint is too small
variable setpoint value is not accepted (range or precision is not correct, check installation) - the set-point
sent to the fermentor is not accepted
Control Algorithm is not used, there are syntax errors - for using algorithm, correct this in the Control
algorithms dialog.
Additional messages exist for MARUBISHI fermentors:

AGIT and AIR are not controlled by DO (both AGIT and AIR have setpoints)
AGIT and AIR are controlled by DO (both AGIT and AIR have not setpoints)
Only AGIT is controlled by DO (AGIT has not setpoints)
The Alarm Warning dialog

When the alarm control exists (use Alarm Control dialog) for a variable and this variable's value is out of
normal range, then this dialog is opened during on-line session and alarm beeps are emited.
Variables
List of variables, which value is out of alarm ranges. Select one of them to reset or
change the alarm control.
Silence
Press this button to eliminate alarm beep sound.
Settings
Press this button to open an Alarm Control dialog to reset or change the alarm
control.
Cancel
Press this button to close this dialog.
Help
May 2009
The Alarm Control dialog
List of variables
List with all variables, possible set the alarm control. Select variable to set and reset
alarm control or change alarm ranges. The symbol '*' means, that the variable has
the alarm control.
Alarm Beep
Check the Alarm Beep check box to set the alam control.
Normal Range
Enter the normal range of the selected variable values to the edit controls.
Ok
Press this button to close this dialog with saving changes.
Cancel
Help
The On-line Measured Variables dialog

You can test the on-line measured variables. The values are measured after every 2 seconds.
List of on-line variables
List of on-line measured variables. One line includes the connection port (AD/DA
or COM), channel and name with scale unit.
Values
List of corresponding data measured after every 2 seconds.
Ok
Help
May 2009
INSTALL DEVICES AND CHANNELS

To start the on-line session the cultivation system has to be installed. The interface device installation is usually
carried out by an expert. After the fermentor is physically coupled with your computer, install the following
items:
coupled communication devices (AD/DA cards and COM ports). Use Install | Devices menu command.
connections between physical channels and on-line variables. Use Install | Variables menu command.
calibration coefficients for on-line variables connected to the AD/DA card. Use Calibrate button in the Onlines Variables Setup dialog.
The Devices dialog

The standard communication protocols for AnalogDigital/DigitalAnalog (AD/DA) cards, ethernet and serial
ports are available in BioXpert. You can install several AD/DA cards, ethernet and/or serial port protocols for
one Fermentor.
Devices
The list of installed devices. Choose one item from list to edit parameters or to
uninstall. One item includes name of device and I/O port address for AD/DA cards
IP address (ez-control and rocker), COM port number and device number (for
ADI1010, 1030 and Braun DCU) for serial port protocol.
Add
Press this button to open the Communication Interface between PC and Fermentor
dialog for installing a new device.
Edit
Press this button to open the Communication Interface between PC and Fermentor
dialog for edit the selected device parameters.
Delete
Press this button to uninstall the selected device.
Done
Press this button to close this dialog with saving changes. The FERMi.INI (i is
number of fermentor) file is updated with installation settings.
Help
May 2009
The Communication Interface between PC and Fermentor dialog

Install AnalogDigital/DigitalAnalog (AD/DA) card or serial port protocol.
Name
Choose an AD/DA card from combo box or none when you don't install a AD/DA
card (see APPENDIX to understand AD/DA cards exactly). Choose or enter the
I/O port main address in hexadecimal, physically installed to the selected AD/DA
card.
Protocol
Choose a serial port protocol from combo box or none when you don't have a serial
port interface. Choose serial port Com1, Com2, Com3 or Com4 through your
Fermentor is connected. Enter the Bio Controllers device number to the Device
Number edit control. It is possible to use same device (Bio Controller) for several
fermentors.
The ez-control and Appliflex rocker utilize ethernet communication by means of an
IP address (refer Installation and Configuration Manual).
Check
Press this button to open the AD/DA Card Test dialog for checking selected
AD/DA cards channels.
Settings
Press this button to open the COM Settings dialog for setting selected serial port
parameters.
Ok
Cancel
Help
May 2009
The AD/DA Card Test dialog

Check the incoming signals and the reaction of the external device.
Device
The device and I/O base address are displayed.
Channel
Select the channel number to get signal and send signals. Enter the number to the
edit control or change it by using micro scroll bars. The first channel number is 0.
Signal
Select the value by internal units for output channels and view incoming signal
values.
Get Signal
Press this button to get signal value (in the Signal edit control) of selected input
channel.
Send Signal
Press this button to send signal value (in the Signal edit control) to the selected
output channel.
Ok
Help
The COM Settings dialog
Baud Rate
Choose baud rate: 110, 300, 600, 1200, 2400, 4800, 9600 or 19200.
Data Bits
Choose data bits: 4, 5, 6, 7 or 8.
Parity
Choose parity: Even, Odd, None, Mark or Space.
Stop Bits
Choose stop bits: 1, 1.5 or 2.
May 2009
Ok
Press this button to close this dialog with saving changes. The [ports] segment in
the WIN.INI file in the MS-Windows directroy is updated with communication
settings.
Cancel
Help
IMPORTANT! For MARUBISHI fermentors the baud rate is 300 ... 9600, data bits is 7, parity is none, stop
bits is 1.
The On-line Variables Setup dialog
You must connect the on-line variables in the list of on-line measured parameters of the program with the
corresponding physical input and output channels.
Device
Choose the device to install the input and output variables on the measure and
control list. For AD/DA card channels the calibration part is opened.
Measure
List of input channel numbers connected to the on-line measured variables. Choose
one to edit.
Control
List of output channel numbers connected to the on-line controlled variables.

Choose one to edit.
Name
Enter the variable name to the edit control according to the selected channel.
Channel
Enter the physical channel number of the selected variable or change it by using
micro scroll bar. For Applikon Bio Controllers choose channel number and
amplifier number for input values and control setpoints. The numbering starts from
1 for AD/DA cards.
Mode
Choose the Measure or Control radio button to select measured or controlled

mode of the selected variable. For Applikon Bio Controllers choose a necessary
submode. Choose the Analog or Digital radio button to select analog or digital
channel (used for AD/DA cards).
Comments
Enter the variable comments to the edit control.
Scale Unit
Enter the variable scale unit to the edit control.
May 2009
Values Range
Enter the variables values range. The alarm limits and set-points can't exceeds this
range. The scale range for Y-axis on the Chart window will be same.
Precision
Choose the values precision. You can choose the precision from 0.0001 to 1.
Counter
Check the Counter check box to indicate, that the device connected to the selected
channel is the counter type. It mean that this device resets itself to zero when
counter is full. The current signal value is automatically added to that before the
reset. For example check the Counter check box for integrated inputs with autozero like alkali and acid consumption.
Calibration coefficients
Enter the calibration coefficients A and B to the edit controls or use Calibrate
button to calibrate the selected channel. In BioXpert is linear calibration used and
the value is calculated by the formula:
value = A * signal + B
Add
Press this button to add the new on-line variable with the name, comment, scale
unit, values range, precision, counter flag and calibration coefficients, or change
selected variable settings.
Change
Press this button to change the parameters of the selected variable. To change main
parameters (name, channel, mode, submode) you must also press this button. Other
parameters (comments, scale unit, values range, precision, gain, signal range,
calibration coefficients) will be saved automatically.
Delete
Press this button to delete selected variable.
Open
Opens a File Selection dialog where you can select the installation file (*.INI) to
load variables. You can delete currently used on-line variables before the selected
variables are loaded.
Save as
Opens a File Selection dialog where you can enter a name for the installed
variables. The installed variables are then saved to that file no further questions
asked.
Calibrate
Press this button to open a Linear Calibration dialog to calibrate the selected
channel.
Done
Press this button to close this dialog with saving changes. The FERMi.INI (i is
number of fermentor) file is updated with on-line variables settings.
Help
You have to remind that the last setup displayed in the Inputs and Outputs list is valid. Therefore it will be
reasonable always to keep to the same designations of on-line parameters. To work with standard procedures
developed by BioExpert use:
Gsum
O2
CO2
str
ALK
pO2
pH
pmp1
May 2009
for total air-flow through fermentor

for oxygen concentration in exhaust gas
for CO2 concentration in exhaust gas
for stirrer speed
for total amount of alkali fed into fermentor
for dissolved oxygen concentration
for pH
for feeding pump rate
The Linear Calibration dialog

You can calibrate the input and output signals.
Graph
Channel
Displayes the selected channel number, name, comment and INPUT for measured
channels and OUTPUT for controlled channels.
Mode
Choose the Level mode for static devices and Rate mode for pumps, which
measured the rate value (the scale unit is unit per minute).
Calibration Points
List of calibration points. The list includes signal and value pairs. Select a pair to
change and delete it.
Signal, Value
Enter the calibration point to the signal and value edit controls. Signal is done in
internal units or in the percents.
+, -, -All
Press these buttons to add new calibration point, delete a selected calibration point
or delete all calibration points.
Graph
Graph includes on-line measured signal or linear calibration curve, which are drawn
through the calibration points.
Start, Stop
Press these buttons to start and end measuring of one calibration point.
Unit
Press this button to open a Signal Unit dialog for changing the signal unit.
View
Press this button to view the calibration line in the graph. The straight line is drawn
through the calibration points.
May 2009
Ok
Press this button to close this dialog with placing the calibration coefficients A and
B to the edit controls in the On-line Variables Setup dialog (it is parent dialog of
this dialog).
Cancel
Help
For example, to calibrate the temperature sensor, choose the Level mode and and press Start button. The
temperature signal appears on the graph. After the signal reaches a constant level press Stop button, measure the
real value of temperature and type this into the Value edit control and press + button. The first pair of
calibration data will be displayed in the Calibration Points list box. To obtain the second pair of calibration data
change the temperature in the vessel and press Start button again. After the temperature has achieved a new
stable level press Stop button and type the current value of temperature into the Value edit control, press +
button. For more precise calibration repeat the procedure several times. Press View button to view the
calibration curve with calibration constants.
If you are content with the calibration curve press Ok button. Keep in mind that only the last calibration curve is
stored and used in further calculations.
All the rest of input and output signals could be calibrated as described above.
For feeding pump calibration use the Rate mode (the feeding pump is on-line controlled variable and connected
to the output channel). Type the signal value (% from maximum) into the Signal edit control and press Start
button. After the sufficient (for precise measurements) amount of liquid is pumped into the measuring device
press Stop button, measure the amount of liquid pumped in and type into the Value edit control the
corresponding value. Press + button and the calibration data pair will appear in the Calibration Points list box.
To enter the new calibration parameters press Ok button.
Usually most of the parameters need recalibration once per year. However, for precise measurements, the gas
analyser should be calibrated in the beginning of every cultivation.
The Signal Unit dialog
Signal is done in
% (percents) or Internal units (i.u.). For the 12-bits AD/DA cards 100 % is equal
to 4095 internal units.
Ok
Cancel
Help
May 2009
INSTALL Braun or Sartorius device

BioXpert V2 can be connected to a Braun or Sartorius device (in short: DCU) using DCU communication
protocol (e.g. DCU or Biostat). The DCU devices are equipped with a serial RS422/485 interface which allows
direct communications. The DCU device can be addressed individually, so that several systems can be
controlled by BioXpert via a single RS422 4-wire network. Communication with BioXpert is based on the
master-slave principle with a single asynchronous ASCII protocol.
Because of the master-slave principle the DCU system only transmits data to BioXpert on request. Depending
on the requirements individual records are transmitted to BioXpert. These records can be the process values
(measured or calibrated values). In remote control operation all process parameters controlled by recipes can be
specified by BioXpert (controller set point).
The general description of installing devices and channels are described in chapter INSTALL DEVICES AND
CHANNELS on page 57.
Installation
Use the original Braun or Sartorius cables, or:
Create cabling as follows; the DCU has a 9 pin D-SUB RS422/485 interface:
1=2 = GND
3 = TxD
4 = RxD
5 = RGND
6=7 = GND
8 = TxD +
9 = RxD +
In order to connect BioXpert the following electronic connections are needed:
May 2009
A 120 terminating resistor is needed at the beginning of the RS422 cable and a RS232/422
converter.
The Devices dialog

Instruction to install a DCU device:
Enable remote control REM located on the DCU device.

Go to Install menu and select Devices...
Select the Braun DCU serial port protocol.
Select the correct COM port (1 to 4).

Select the correct COM settings and Device number. The communication settings can be found in the
DCU device.
Press the OK button to save the dialog and the DCU device is added to the device list.
Passwords
The DCUs are protected with passwords. To view/ change communication settings, the password is 9 (Braun
DCU) or 19 (Biostat). To view/ change variable ranges the password is 9 (Braun DCU) or 753 (Biostat).
Note: 709 could also be a password.
May 2009
On-line variables setup dialog

To add the desired variables it is important to have similar channels and ranges in BioXpert as in the DCU
device. The order of the DCU channels is the same order as they are indicated on the DCU display. The DCU
can have one or two columns. For instance there are six process values when the DCU shows:
pH
pO2
Acid
Temperature
Redox
Base
Then the channels in BioXpert (measure) will be:

Channel 1 = pH pv
Channel 2 = Temperature pv
Channel 3 = p02 pv
Channel 4 = Redox pv
Channel 5 = Acid dose monitor
Channel 6 = Base dose monitor
For setpoints of control loops the counter goes from left to right, eg when DCU shows:
pH
Temperature
Stirrer
pO2
The channels in BioXpert (control) will be:

Channel 1 = pH sp
Channel 2 = Temperature sp
Channel 3 = Stirrer sp
Channel 4 = pO2 sp
Note:
When Stirrer is configured in the pO2 cascade of DCU, it does not respond to the setpoint sent by BioXpert!
The general installation of an on-line variable is described on page 60. When programming a variable, make
sure the range in BioXpert is similar to the variable range programmed in the DCU!
May 2009
Manual control set point

When set points are programmed in the On-line Variables setup it is possible to enter a manual set point.
Enter the menu Control laws in BioXpert
Enter the Manual setpoint menu.
Select the desired set point
Enable the checkbox for Manual and enter the new set point.
Press the OK button, now the new set point is activated and sent to the DCU.
May 2009
Communication check
To check if logging of process values is enabled:
Go to the Run menu.
Select Test...
When communication is not possible, check if the communication cables are connected properly and if all
settings are correct. When communication is still not possible restart the COM port by disable/ enable the COM
port in the Windows device manager (Windows Vista).
When different values are displayed by BioXpert and the DCU, make sure the ranges of the programmed
variables are the similar.
Limitations
There are some limitations when using BioXpert with a Braun DCU device.
BioXpert is not able to read digital sensor inputs, like level and foam
BioXpert is not able to switch control loops on and off
Rounding rules are not similar in BioXpert V2 and the DCU devices. This could lead to minor
rounding errors on first or second value behind the decimal point.
May 2009
GRAPHIC WINDOW
To visualise your cultivation system (process), use Graphic window. After Graphic window is opened (use
Window | Show graphic) you see the graphical representation of your fermentation process and values of
several kind of variables. Each user can make your own configuration. Graphic window includes picture (it is
windows bitmap file, that user can draw for example in Paintbrush) and set of variables, which user can put on
the right position with the mouse. All variables have same font and same updating interval.
Variable includes name, value (present value, percent or bar mode) and scale units (optional) on the one, two or
three lines, aligned to left, center or right.
When the alarm control exists (use Alarm Control dialog) for a variable and this variable's value is out of
normal range, then the value will draw by red color.
When the manual setpoint is active (use Manual Setpoint dialog) for a control variable, then the star character
* will draw after value.
Before using Graphic window install the picture, font, update interval and variables (use Install | Graphic menu
command or popup menus on the Graphic window, which appears clicking mouse right button on the picture or
variable).
Clicking mouse right button on the picture (non variables area) appears the Graphics setup menu.
Graphic setup Opens a Graphic Setup dialog where you can choose picture, variables, updating interval etc
for Graphic window. Graphic Setup dialog opens also after doubleclicking with mouse left
button on the picture.
Add variable
Opens a Variable for Graphic dialog to add new variable.
Font
Opens a Select font dialog to change the variables font.
Picture
Opens a Open graphic picture dialog to change the picture.
May 2009
Clicking mouse right button on the variables appears the Variables setup menu.
Edit
Opens a Variable for Graphic dialog to change parameters of pointed variable. Variable for
Graphic dialog opens also after doubleclicking with mouse left button on the variable.
Delete
Deletes the pointed variable from Graphic window.
Duplicate
Opens a Variable for Graphic dialog to add new variable with same parameters as pointed
variable. It is simple way to install more variables with same parameters.
Manual setp.
Opens the Manual Setpoint dialog to send the desired setpoint to fermentor.
Control profile Opens a Profiles dialog where you can specify the control variables set-points by curves.
Control stat.
Opens a Control Algorithms dialog where you can specify the on-line control variables setpoints by algorithm.
The Graphic Setup dialog
Variables
List of installed variables with name, mode and placement.
Add
Opens a Variable for Graphic dialog to add new variable.
Edit
Opens a Variable for Graphic dialog to change parameters of selected variable.
Delete
Deletes the selected variable from Graphic window.
Duplicate
Opens a Variable for Graphic dialog to add new variable with same parameters as
selected variable. It is simple way to install more variables with same parameters.
Picture
Opens a Open graphic picture dialog to change the picture.
Font
Opens a Select font dialog to change the variables font.
Interval
Change the updating interval for Graphic window. Use micro scroll bar to change
this interval.
May 2009
Done
Help
The Variable for Graphic dialog
Variable
List of all variables. Select one to Graphic window.
Text on Graphic
Enter the text for selected variable. By default it is variables name, but each user
can rename it.
Mode
Press Value for drawing present value, Percent for drawing percent (0% is Min
and 100% is Max) or Bar for drawing bar (Min is lower line, Max is upper line).
For bar mode enter the Bar width and Bar height by pixels.
Placement
Left and Top is placement of variables box left-top corner to left-top corner of
Graphic window by pixels. Choose auto from Width edit control to calculate
variables box width automatically or enter the fixed width by pixels.
Alignment
Choose left, enter or right to align the text to left, center or right. Choose 1 line to
draw name, value and unit to one line, 2 lines to draw name to first line and value
with unit to second line and 3 lines to draw all items to separate lines. Press Fixed
separator to draw separator to fixed place (entered number is by pixels).
Options
Check the Name is bold button to draw variables name with bold style. Check the
Without scale unit button to draw variable without scale unit.
Separator
Enter the character to separate name and value..
Setpoint
Opens the Manual Setpoint dialog to send the desired setpoint to fermentor.
Ok
Cancel
Help
May 2009
MULTI-FERMENTOR SYSTEM
To start and end your multi-fermentor system, use Run Manager. This dialog includes listbox, where each line
describes the starting parameters of the fermentor. Starting parameters are protocol name (not necessary, but
recommended), data filename, starting time and access interval.
Before using Run Manager install the connection and variables for each fermentor (use Install | Device and
Install | Variables menu commands).
The Run Manager dialog
User
User name is displayed. Each user has private list of starting parameters for running
on-line sessions.
Nr
Press this button to open the Fermentor Numbers dialog to renumerate the
fermentor numbers.
Protocol
Press this button to open the File Selection dialog where you can select the
cultivation protocol file (*.FRM) for all fermentors. When you used # character in
the protocol filename, the fermentor number are replaced instead of # for the each
line in the list.
Data
Press this button to open the Data Filename dialog where you must enter the data
filename (*.FRM) for all fermentors. The filename extension FRM is added
automatically. When you used # character in the data filename, the fermentor
number are replaced instead of # for the each line in the list. The file is saved
always in your home directory.
Starting time & Interval Press this button to open the Starting Time & Interval dialog to change the starting
times and intervals. By default the next full hour is selected to the starting time.
Add
Press this button to add new line (by next fermentor number) to the list.
Edit
Press this button to open the Edit Starting Parameters dialog to change selected
fermentors starting parameters.
Delete
Press this button to delete selected line from the list.
Comments
Enter the comments of current multi-fermentor system.
May 2009
Done
Press this button to close this dialog. Prompt appears when the changes are made in
the list.
Run All
Press this button to run on-line sessions for all fermentors in the list. Warnings
appears when the list includes same fermentor numbers, protocols are not exist,
data files exist previously or data filenames are not entered. New instance of the
BioXpert is created about the each line of the list.
For example fermentors 1, 2, 3, 4 and 5 are started:
End
Press this button to open the End On-line Sessions and Close BioXperts dialog to
end the on-line sessions and close BioXperts.
Save
Press this button to save starting parameters to the WIN.INI. Each user has private
set in the WIN.INI.
Help
The Fermentor Numbers dialog
First number
Enter the fermentor number of first line in the listbox. Use mini scroll bar to change
number. All other numbers will be sequential order by step one.
Update protocol ...
Check this check box to update protocol names for each line in the listbox. The
filename, which is selected in the File Selection dialog (by Protocol button in the
Run Manager dialog), are used.
May 2009
Update data ...
Check this check box to update data filenames for each line in the listbox. The
filename, which is selected in the Data Filename dialog (by Data button in the Run
Manager dialog), are used.
Update starting ...
Check this check box to update starting times and intervals for each line in the
listbox. The time and interval, which are selected in the Starting Time and Interval
dialog (by Starting time and Interval button in the Run Manager dialog), are used.
Ok
Cancel
Help
The Starting Time and Interval dialog
Start moment
Specify the start moment of cultivation of the first fermentor in the listbox. Use +
button to increase and - button to decrease the time moment. Use left mouse
button to change hours and right mouse button or shift key to change minutes. Start
moment of all other fermentors are different, then the delay between fermentors is
not zero. Each next fermentor is started after delay minutes.
On-line session interval
Enter the on-line access interval (in the minutes) to measure and control the
fermentor. Use mini scroll bar to change this interval.
Delay between ferment.
Enter the delay (in the minutes) between the fermentors. Use mini scroll bar to
change this delay.
Ok
Cancel
Help
May 2009
The Edit Starting Parameters dialog
Edit the parameters of selected line in the listbox in the Run Manager.
Fermentor number
Enter the fermentor number of the selected fermentor. Use mini scroll bar to change
this interval.
Protocol
Enter the protocol name with full pathname or use Locate button to open the File
Selection dialog where you can select the initial culivation protocol file (*.FRM).
Data
Enter the data filename without extension (it is always FRM).
Start moment
Specify the start moment of the selected fermentor in the listbox. Use + button to
increase and - button to decrease the time moment. Use left mouse button to
change hours and right mouse button or shift key to change minutes.
On-line session int.
Enter the on-line access interval (in the minutes) to measure and control the
selected fermentor. Use mini scroll bar to change this interval.
Ok
Cancel
Help
May 2009
The End On-line Sessions and Close BioXperts dialog
BioXperts
List of running BioXperts. The * character marks on-line sessions.
Actions
Choose End all on-line sessions only radio button to end all on-line sessions or
End all on-line sessions and close those BioXperts radio button to close
BioXperts, where on-line session is running or End all on-line sessions and close
all BioXperts radio button to close all BioXperts. Check the Including current
BioXpert check box to do chosen action to the current BioXpert also.
Ok
Press this button to close this dialog and end on-line sessions and close BioXperts
depending from chosen action.
Cancel
Help
May 2009
MESSAGES
BioXpert has error messages and warning messages. The message box includes caption, message text and
button(s). The BioXpert Error or BioXpert Warning and -fermentor number- are written in the caption.
Error messages
Insufficient disk space
Delete some files from disk.
Insufficient memory. Close some applications
Close some applications or add memory to your computer.
Out of local memory
Delete some variables or spline option.
Cannot create new directory
Operating system error.
name is not a valid user name
Enter the new name. User name can include letters, digits and underline symbol '_'.
Cannot create new file
Cannot open file
Unable to save
Cannot overwrite standard batch protocol
Cannot overwrite standard fedbatch protocol
Cannot overwrite standard continuous protocol
Choose another file name to save your data. You can't change the standard protocols.
Data filename is not specified. Cant run
Enter the data file name for on-line session.
Number of variables and number of data is not equal
For importing on-line data, the number of variables and number of data in the first data line must be equal.
name is not a valid name
Enter the new variable name. The variable name can include letters, digits and # or $ symbol last (letter is
first). The TIME, S# and P$ are reserved.
The variable name exists. Enter new name
You can't create many variables with the same name.
You must enter the name
The name cannot be empty.
ON-LINE mode is disabled during the cultivation. Install new variables
Use Install | Variables menu command for creating on-line variables in the CULTIVATION mode.
The last letter must be # character in the variable name
For substrates characteristics.
May 2009
The last letter must be $ character in the variable name

For products characteristics.
Variable name must not include # and $ characters
The # and $ characters are used only in the formulas and in the substrates and products characteristics.
Cannot replace the value. Choose variable first
Choose the variable from the list to replace the value.
The scale range for variable must be different
Enter the different scale limits.
The alarm range for variable must be different
Enter the different alarm limits.
The signal range for variable must be different
Enter the different signal limits.
The alarm range is out of fermentors installation range
The alarm limits will not exceed the maximum and minimum values defined in the On-line Variables Setup
dialog.
Wrong formula - formula
Correct the formula.
You must enter the percentage (90% is recommended)
Enter the value for calculating 'clear auto-zero' operation.
Cannot make more variables
You can't exceed the maximum variables limits. It is 150.
Cannot setup this printer. Use Control Panel
Use Program Manager Control Panel Printers bitmap to choose and setup the printer.
Cannot print. Insufficient memory or an invalid port specification
Close some applications or choose a valid port.
Not enough disk space for spooling. Free disk space
Free disk space. Delete some files.
Not enough memory for spooling
Close some applications.
General error during printing
System error. Reboot your computer.
Serial port not initialized
Check your communication settings and try again.
Could not establish link with Fermentor
Check power and connection or communication settings.
COM port not available
Use another COM port.
Too many fermentors are connected to the COM
Increase the on-line intervals in the running BioXpert's.
May 2009
Warning messages
Hardware key is not exist
Put the hardware key to the printer port (LPT1: or LPT2:) or to the serial port (COM1:) in the NEC version
and press Ok button. For running BioXpert in the DEMO mode press Cancel button.
Only 60 minutes are supported in DEMO version
You can run the on-line session for 60 minutes in the Demo version.
This action is not possible in the DEMO version
Press Ok to accept this message.
Evaluation time (until date) is over. Only DEMO version is running
Press Ok to accept this message. You must order a new version of BioXpert.
End the on-line session
Press Yes to end the on-line session.
Free disk space in drive is nr KB. Are you sure you want to save data to this disk
Press Yes to save the data to selected disk. This warning appears when the disk space is smaller then
KBytes.
500
Save changes to current file

Press Yes to save data to current file. Press Cancel to cancel the current command.
Replace existing file
Press Yes to save data to the existing file.
Are you sure you want to delete the off-line values in the specified time
Press Yes to delete all off-line variables data points in the specified time.
Are you sure you want to delete variable
Press Yes to delete the variable.
This variable is used in formulas. Delete this variable (depending formulas are reset to 0)
Press Yes to delete the variable and change the depending formulas.
Inputs/Outputs have same channel numbers. Do you want change it
Each channel which used, will be connected to the one on-line variable. Press Yes button to change
channel numbers.
Are you sure you want to delete all data
Press Yes to delete all data excluding the constants first values.
Do you want delete all currently used formulas
Press Yes to delete all currently used formulas before loading new set of formulas.
Do you want delete all currently used on-line variables
Press Yes to delete all currently used on-line variables before loading new set of variables.
All currently used on-line data are deleted. Are you sure you want import selected on-line data
Press Yes to delete all currently used on-line data before importing new data.
All data of variable of selected time range are deleted. Do you want this
Press Yes to delete data. The result is NA then the value is NA (not depended from operation) or data are
deleted by 0. The result is 0 then data are multiplayed with 0.
May 2009
Relation exists. Delete old relation

Press Yes to delete previous relation between ASCII file variable and on-line variable in the BioXpert.
Replace existing picture
Press Yes to save the Chart window picture under the same name.
Are you sure you want to delete the picture
Press Yes to delete the selected Chart window picture.
The picture is out of page. Do you want to print it
Press Yes to print the Chart window picture. Some parts may not be printed.
Are you sure you want to delete all control statements
Press Yes to delete all control statements.
Are you sure you want to quit from BioXpert
Press Yes to quit from BioXpert.
May 2009
Index
A
About, 8
Access interval, 51, 52
AD/DA, 4
AD/DA card, 57
AD/DA Card Test, 58
Alarm Beep, 56
ASCII format, 39
A-stat, 3
Grid, 36
I/O port main address, 58

icon, 7
input and output signal, 62
Installation protocol, 10
integrate, 30
interface, 5
internal units, 62
irregular time, 26
Batch, 14
Baud Rate, 59
bitmap, 14
Buttons window, 16
C
Calibration Coefficients, 22, 61
calibration point, 62
Channel, 62
chart, 5
Chart Pictures, 39
Chart Values window, 11
Chart window, 11
Clear 'Auto Zero', 27
Close, 13
C-molar, 32
COM Settings, 58
communication protocols, 57
constant form, 28
Continuous, 14
Convergence criterion, 32
Counter, 61
cultivation comments, 22
cultivation data, 10, 22
CULTIVATION mode, 52
cultivation protocol, 9
D
Data Bits, 59
data curves, 34
data editor, 5
Data name, 51, 52
Decimal time, 36
default printer, 14
Device, 60
directory, 21
drive, 20
E
end date and time, 22
end the on-line session, 54
error messages, 77
Exit, 14, 15
F
Fed-batch, 14
FERM1.INI, 5
fermentor number, 19
file name, 21
FORMULAS, 9, 29
May 2009
H
Header, 36
Help window, 18
Home directory, 19
I
K
keyboard topics, 18
L
Level mode, 63
Line Width, 39
Linear Calibration, 61
ln, 30
Load cultivation protocol and
data, 20
M
Manually scale range, 35
margins, 39
Marks, 36
Master formula, 30
Maximize, 13
menu bar, 13
Minimize, 13
multi-fermentor, 6
multi-fermentor system, 69, 72
Printer Setup, 40
Products, 9
Program Manager, 7
program mode, 19
R
rate, 30
Rate mode, 63
Ready, 11
ready-to-publish, 14
Relative weight, 32
Run-time messages, 54
S
S#, 30
Scale Unit, 60
selected printer, 40
serial port, 57, 58
Set Alarm, 54
Set Control, 54
Signal, 59
Silence, 55
Simple formula, 30
Size, 13
start date and time, 22
Start moment, 51, 52
Status bar, 11
Stop Bits, 59
Substrates, 9, 31
Switch To, 13
SYLK format, 14, 39
system menu, 13
System Variables, 41
T
TIME, 35
total, 30
U
user name, 19
NA, 27, 29, 54

new time point, 26
new user, 19
Values Range, 60
Values window, 18
Variables, 9
Variables window, 11
O
OFF-LINE variables, 9
off-line points interval, 26
off-line time, 26
ON-LINE variables, 9
on-line interval, 43
On-line Session window, 11
organism name, 22
P
P$, 30
Parity, 59
peripherals, 4
Precision, 44, 45, 54, 61
PRE-RUN mode, 52
W
Wait, 11
warning messages, 77
X
X-axis, 34
Y
Y-axis, 34, 36
Z
Zero-lines, 36

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Available Formats

BioXpert V2

BioXpert V2 user manual page 1

DATA PRINT, EXPORT AND IMPORT............................................................................................................................... 39

BioXpert V2 user manual page 2

What you should know

BioXpert V2 user manual page 3

Hardware and software requirements

BioXpert V2 user manual page 4

THE LOGICAL STRUCTURES

The logical structure of one BioXpert V2

Cultivation protocol and data

Data and protocol

Control laws only

BioXpert V2 user manual page 5

The logical structure of multi-fermentor system

Fermentors with BioControllers

BioXpert V2 user manual page 6

INSTALLATION OF BIOXPERT V2 TO HARD DISK

BioXpert's command line options

Starting the BioXpert V2

BioXpert V2 user manual page 7

Starting the BioXpert V2 the very first time

BioXpert V2 user manual page 8

BioXpert V2 user manual page 9

BioXpert V2 user manual page 10

Desktop of the BioXpert V2

On-line Session window

Chart Values window

BioXpert V2 user manual page 11

WHAT YOU CAN DO

Recalculate DEMO.FRM file

Run new cultivation using standard batch protocol

BioXpert V2 user manual page 12

The menu bar

The system menu commands

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The file menu commands

Open Standard Open standard Batch (BATCH.FRM), Fed-batch (FEDBATCH.FRM) or Continuous

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Terminates the BioXpert program.

The data editor menu commands

Opens a Formulas dialog to add, delete and set formulas.

BioXpert V2 user manual page 15

The chart menu commands

Refreshes the Chart window.

Opens a Scaling dialog to change scale representation.

The run menu commands

Starts some actions before measurement is actually started:

BioXpert V2 user manual page 16

Ends or breaks the on-line session.

Opens an Alarm dialog to add and remove variables alarm control.

The control laws menu commands

The install menu commands

BioXpert V2 user manual page 17

The window menu commands

Brings a Chart window to front on the desktop of BioXpert.

Show on. sess.

Brings a On-line Session window to front on the desktop of BioXpert.

Creates and hides a Graphic window.

The help menu commands

BioXpert V2 user manual page 18

HOW TO START BIOXPERT V2

The New Cultivation or Recalculation dialog

mini scroll bar