Operating instructions for. For visualization of your measurements

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1 Operating instructions for For visualization of your measurements

2 FermVis operating instructions Important message In the interest of preventing operator errors and incorrect measurement results, you must read these operating instructions completely through to the end. gas sensor GmbH Snirgelskamp Herten, Germany Phone / Fax / Rev050714

3 FermVis operating instructions Table of contents 1 General System requirements Installation Opening the software Reviewing recorded measurements again Printing graphics Saving the measurement data User information Basic settings - Options/Settings Options for measurements with shake flasks Options for measurements in the fermenters Starting the measurement Shake flasks Fermenter (flow through) Ending the measurement / saving the data Calibration - 1-point calibration Shake flasks Fermenter: Special trial conditions - get ambient air Display Display mode - Concentration, Rates, RQ User inputs during the measurement VVm Relative pressure Highlighting the measurement curve Zoom Error messages Interface occupied Missing sensors Incorrect sensor allocation Solving problems... 24

4 FermVis operating instructions 1 General 1.1 System requirements This software is suitable for recording data for sensors connected to a computer via a BACCom and possibly a BACCom EB multiplexer box. This should be run on a Windows 98 or higher operating system. The program itself needs only a slight amount of free memory. The hard drive s available storage capacity should be checked periodically to ensure the measurement data can be saved. The symbols below have the following meanings: Caution! Users can cause errors here Note! Advice on simplification or other help is given at this point 1.2 Installation Place the attached diskette/cd into the appropriate drive. Copy the file FermVis.exe into a directory of your choice (C:\...). After the first start, FermVis will create the directory C:\..\Data. The measurement data will be stored there. Likewise, the file FermVis.cfg is created. The various program settings are stored in this file. 1.3 Opening the software Click twice on the FermVis symbol in Windows Explorer or on the desktop after you have created a link there. The program starts. First, FermVis looks for the BACCom multiplexer box and the connected sensors. By default, FermVis expects the measurement system to be connected to the COM1 interface. If you are using a different interface, you can modify this setting under Options/Settings (see below). Page 1

5 FermVis operating instructions The program automatically searches the configured interface for all heads. The heads you have connected are indicated at this time. The following message appears, for example, in which the identification numbers of the connected BACCom and the corresponding sensors are displayed. A maximum of 16 sensors can be displayed. In case you have connected more heads than the program finds, go to Options/Settings, adjust the number of connected heads, and confirm with OK. The sensor heads will be searched for once again. However, if not all the heads you connected have been found, you need to press the SystemReset on the BACCom (see operating instructions for the corresponding sensors) with a sharp object. If this still does not bring about the desired result, please call your service department. 1.4 Reviewing recorded measurements again If you want to look at recorded measurement data again, you can call these up again in the File/Open menu. If the recorded file has been executed using a calculation, you can switch between the between the Concentration, Rates und RQ (see chapter 5) displays here, just as in the normal mode. 1.5 Printing graphics You can print the current graphics via the File/Print menu item. The printer settings are configured via File/Printer. 1.6 Saving the measurement data By default, the measurements are saved in the same directory in which the FermVis software has been saved, under the subdirectory C:\...\ Data. When starting the measurement, you can enter a Page 2

6 FermVis operating instructions file name. Otherwise, the file will be unambiguously stored with the current date including the precise time (e.g dat for a measurement started on 01-Mar-02 at 14:35:01 ( pm). Caution! When selecting individual file names please be aware: the danger of losing data exists through overwriting a file due to assigning the same name again! The files can be copied for processing at any time. The measurements do not need to be terminated for this. Page 3

7 FermVis operating instructions 2 User information 2.1 Basic settings - Options/Settings - When the menu item Options/Settings is selected, the following window appears Com-port Selection of the interface 2 Max. number of heads Number of connected sensors 3 Interval Default setting for the measurement interval 3 1. All available interfaces appear in the Com-Port box. Here, please select the interface to which the BACCom has been connected. 2. The number of connected sensors can be entered via the Max. number of heads input-field. Entering the number means that when the FermVis is opened, it looks only for the number of sensors preset here, which can minimize the software initialization time. 3. Entering the measurement interval (how often the sensors display and save a measurement) is established at this point as a standard for all measurements. They can also be individually selected during each measurement. Page 4

8 FermVis operating instructions 2.2 Options for measurements with shake flasks Various options can be set via the menu item Options/Fermenter. A new window opens in which you can select the following points. The data is saved with OK. The adjusted values can be modified any time before a measurement Fermenter: Name: Name of the shake flask 2 CO2 / O2 For selecting the number of connected sensors 3 Previous / Next Selects the next shake flask 4 More options / no options 5 Measuring interval 6 Calculation interval 7 Smoothing rate 8 Reactor type 9 Bottle volume Options for individual sensing points Specification of how often a measurement value is to be displayed Specification of how often OUR, CER, RQ are calculated and issued Integration interval for the measurement value (smoothing the sensor signal) Differentiation whether the measurement should be carried out in the flow or diffusion mode Volume of the flask as a reference value for the computations 10 Temperature Ambient temperature of the flask 11 Probe volume Fluid volume as the reference value for the computations 12 Pressure source Fixed setting: pressure measurement in BACCom 13 Diffusion constant Specific diffusion constant for the flask Page 5

9 FermVis operating instructions Caution! Take care filling-in the boxes! The set values are used to calculate the CTR, OTR and RQ. If the data is incorrect, the calculated values will likewise be incorrect! 1. Fermenter: The flasks can be designated using the Name box. By selecting the corresponding CO 2 - and O 2 sensors, these are allocated to the fermenter and saved as the standard setting in FermVis.cfg. 2. CO2 / O2 In the CO2 and O2 fields, you can select the connected sensors using the selection menu. The sensors can be identified by the ID (e.g ) Caution! Selected sensors must match those on the shake flasks! Be sure you compare the sensor ID s!! If other sensors are used on the shake flasks than previously allocated, the procedure get ambient air (see chap. 4) or 1-point calibration (see chap. 3) must be carried out 3. Previous / Next With this switch, you can select the respective previous or next shake flask and make the adjustments. 4. More options / no options Additional options can be displayed or hidden with this switch. 5. Measuring interval The measuring interval determines how often a measurement value is read out and saved. The smallest measurement interval is 20 seconds. How often the data is saved is determined by the file size. 6. Calculation interval Makes the settings on how often a value, e.g., the oxygen transfer rate (OUR), the carbondioxide formation rate (CER) or the respiration quotient (prevailing metabolism processes) (RQ) are calculated and saved. The minimal computation time is 5 minutes. Generally, a calculation is performed at the most every 15 measurements (see Measuring interval). 7. Smoothing rate Page 6

10 FermVis operating instructions This concerns the adjustability of the electronic averaging of the sensor signal. This can be used to smooth out the measurement values. An average is taken over a 15-second period per selected unit. 8. Reactor type With the help of the Reactor type switch, it can be differentiated via software if the subject is a gassed fermenter/flask, or a shaken/stirred fermenter/flask. To make measurements in shake flasks without a gas supply, the field Diffusion controlled must be activated and the specific diffusions constant, dependent on the flask used, must be entered. 9. Bottle volume Volume of the flask as a reference value for the diffusion computation. This enables the calculation of CTR, OTR und RQ. 10. Temperature This is the ambient temperature of the flask. With the aid of this input, the dilution of the gas through humidity (in flasks, 100% relative humidity) is compensated in the CO2 sensors (chap.3). 11. Pressure source This value is permanently set to Box for shake flasks. The pressure measurement and compensation of the ambient pressure is carried out via a pressure sensor in the BACCom. 12. Probe volume Volumes of fluid in the flask as a reference value for calculating the respiration quotients (RQ), the oxygen consumption rate (OTR) and the carbon-dioxide formation rate (CTR). 13. Diffusion constant Here, the specific diffusion constant of the flask being used needs to be entered to enable the calculation of the carbon-dioxide transfer rate (CTR) and the oxygen transfer rate (OTR). This calculation only works if a standardised sterile filter (see accessories) has been used for the air exchange. If a different stopper or filter is used, no guarantee can be given for the calculated value. Page 7

11 FermVis operating instructions 2.3 Options for measurements in the fermenters Various options can be set via the menu item Options/Fermenter. A new window opens in which you can select the following points. The data is saved with OK. The adjusted values can be modified any time before a measurement Fermenter: Designation of the fermenter 2 CO2 / O2 Allocation of the sensors via the ID numbers 3 Previous / Next Selects the next fermenter 4 No options / more options 5 Measuring interval 6 Calculation interval 7 Smoothing rate 8 Reactor type 9 Fermenter volume Displays or hides the options of the individual measurement points Specification of how often a measurement value is to be displayed Specification of how often OUR, CER, RQ are calculated and issued Integration interval for the measurement value (smoothing the sensor signal) Differentiation whether the measurement should be carried out in the flow or diffusion mode Fluid volume in the fermenter as the reference value for the computations 10 Dewpoint Cooler or gas temperature on the fermenter 11 Relative pressure 12 Pressure source 13 V/Vm [l / l min] Specifications for a known over/under pressure. See also chap Caution!!! Operator error is possible!! See below! Source of the pressure measurement, pressure of BACCom, pressure sensor integrated in sensor Volumemetric rate flow [l/min] through fermenter volumes [l], the flow in l/h is automatically computed. Page 8

12 Caution! Take care filling-in the boxes! The set values are used to calculate the CTR, OTR and RQ. If the data is incorrect, the calculated values will likewise be incorrect! 1. Fermenter: The fermenters can be designated using the Name box. By selecting the corresponding CO 2 - and O 2 sensors, these are allocated to the fermenter and saved as the standard setting in FermVis.cfg. 2. CO2 / O2 In the CO2 and O2 fields, you can select the connected sensors using the selection menu. The sensors can be identified by the ID (e.g ) Caution! Selected sensors must match those on the fermenters! Compare the ID s!! If other sensors are used on the fermenters than previously allocated, the procedure get ambient air (see chap. 4) or 1-point calibration (see chap. 3.2) must be carried out 3. Previous / Next With this switch, you can select the respective previous or next fermenter/shake flask and make the adjustments. 4. More options / no options Additional options can be displayed or hidden with this switch. 5. Measuring interval The measuring interval determines how often a measurement value is read out and saved. The smallest measurement interval is 20 seconds. How often the data is saved is determined by the file size. 6. Calculation interval Makes the settings on how often a value, e.g., the oxygen transfer rate (OUR), the carbondioxide formation rate (CER) or the respiration quotient (prevailing metabolism processes) (RQ) are calculated and saved. The minimal computation time is 5 minutes. Generally, a calculation is performed at the most every 15 measurements (see Measuring interval). Page 9

13 7. Smoothing rate This concerns the adjustability of the electronic averaging of the sensor signal. This can be used to smooth out the measurement values. An average is taken over a 15-second period per selected unit. 8. Reactor type With the help of the Reactor type switch, it can be differentiated via software if the subject is a gassed fermenter/flask, or a shaken/stirred fermenter/flask. In order to make measurements on the fermenter, the Flow through field must be activated and the corresponding V/Vm value in l / l min must be entered. The resulting flow in l / h is then automatically calculated. 9. Fermenter volume Volumes of fluid in the fermenter/flask as a reference value for calculating the respiration quotients, the oxygen consumption rate and the carbon-dioxide formation rate. 10. Dewpoint The temperature of the return flow or gas cooler is set at this point. If no cooler is available, the process temperature must be set. With this temperature, the dilution due to humidity in the gas is compensated in the CO2 sensor. The compensation of the dilution effect in the O2 sensor is carried out automatically through 1-point calibration. Page 10

14 11. Relative pressure Specifications of the relative pressure facilitate a reliable pressure compensation versus the ambient pressure, even if a certain amount of over or underpressure (measured against the ambient pressure) exists in the system. This value can be varied through a user input even during the measurement (see chap ), so that even pressure changes (e.g. through an increase in the volumetric flow rate) during a fermentation can be compensated. Caution! Continual pressure fluctuations in the fermenter cannot be compensated with this method!! For this, an additional pressure sensor must be connected, from which the measurement value is transferred to the gas sensors (service!). Caution! Modifications to the volumetric flow rate can cause pressure changes! Changes in pressure must be carried out manually in the active measurement window via the Control control-box. (see chap ) Caution! This relative pressure is also used during 1-point calibration! If the sensors are adjusted under other conditions, the attributes must first be changed under Options/Fermenter! 12. Pressure source With the Pressure Source you can select whether an ambient pressure measurement via a BACCom (Multiplexerbox) or a pressure sensor integrated in the sensor (if available) is used for pressure compensation 13. V/Vm The V/Vm value must be entered here in l / l min. V is the volumetric flowrate l/min and Vm is the liquid volume in the fermenter. This value is needed to carry out the computation of the carbon-dioxide transfer rate (CTR) and the oxygen transfer rate (OTR). Through a user input, this value can also be varied by the user during a measurement (see chap ) to ensure the calculated values are correct. Caution! Changes in the volumetric flowrate or liquid volume affect the calculation of the CTR, OTR and RQ! If the volumetric flow rate or liquid volume is modified during a measurement, the V/Vm can change also, and may have to be manually modified in the measurement's active window via the Control control-box. (see chap ) Page 11

15 2.4 Starting the measurement Shake flasks Use the menu item Window/New to start a new measurement. By activating the control box in front of the respective fermenter/flasks, you can choose the previously saved settings. This can still be changed at this point. Setting the options is carried out analogue to chap Activating the Calculation control-box switches on the CTR, OTR and RQ computations. To ensure these calculations can be carried out correctly, the concentrations of CO 2 and O 2 in the ambient air must amount to 0.04 vol.% and vol.%, which corresponds to the ambient conditions in the 1-point calibration (see chap. 3). If there are any other input concentrations (environment), these can be determined using the get ambient air menu item (see chap. 4) and used for the computations. The values are stored in the FermVis.cfg file and are available for all additional measurements. As soon as the ambient conditions (temperature, concentration of CO 2 and/or O 2 ) are changed between two measurements the starting conditions must be re-established using get ambient air or with the 1-point calibration. However, this is displayed starting only with creation/consumption rates of mol/ h l CO 2 or O 2 and is saved in the corresponding measurement file with the erg file extension. Page 12

16 In the Comments to Task box, you can name your measurement in the first line, which will appear in the upper left part of the window during the measurement. In the second line, you can enter additional information, which is subsequently written at the beginning of the file. After you have selected all options and confirmed with the OK box, the following window appears. Using Start, you can now start a new measurement, whereby you will be asked to confirm the file name or enter a new one. The measurement data is then saved in the C:\..\Data directory. (Format see chapter 2.5). You can start a new measurement with the rest of the sensors at any time. To do so, go back to the menu list and go to Window/New. Caution! Incorrect OTR, CTR and RQ calculations You need to be very careful when entering all option parameters. Please make sure that 1. a 1-point calibration (chap. 3) has been carried out during start-up operation. 2. modifications in the input concentrations are saved with get ambient air (chap. 4). Page 13

17 2.4.2 Fermenter (flow through) Use the menu item Window/New to start a new measurement. By activating the control box in front of the respective fermenter/flasks, you can choose the previously saved settings. This can still be changed at this point. Setting the options is carried out analogue to chap Activating the Calculation control-box switches-on the CTR, OTR and RQ computations. To ensure these calculations are carried out correctly, the initial concentrations of CO 2 and O 2 need to be established. In 1-point calibration (see chap. 3), the calibration conditions are applied as starting values. If there are any other input concentrations, e.g. other input concentrations, these can be determined using the get ambient air menu item (see chap. 4) and used for the computations. The values are stored in the FermVis.cfg file and are available for all additional measurements. As soon as the ambient conditions (temperature, input concentration of CO 2 and/or O 2 ) are changed between two measurements, the starting conditions must be re-established using get ambient air. However, the calculation is carried out starting only with changes in the concentrations of 0.06 vol % CO 2 or O 2 and is saved in the corresponding measurement file with the erg file extension. Page 14

18 In the Comments to Task box, you can name your measurement in the first line, which will appear in the upper left part of the window during the measurement. In the second line, you can enter additional information, which is subsequently saved at the beginning of the file. After you have selected all options and confirmed with the OK box, the following window appears. Using Start, you can now start a new measurement, whereby you will be asked to confirm the file name or enter a new one. The measurement data is then saved in the C:\..\Data directory. (Format see chapter 2.5). You can start a new measurement with the rest of the sensors at any time. To do so, go back to the menu list and go to Window/New. Caution! Incorrect OTR, CTR and RQ calculations You need to be very careful when entering all option parameters. Please make sure that 1. a 1-point calibration (chap. 3) has been carried out during the first startup operation. 2. modifications in the input concentrations are saved with get ambient air (chap 4). 2.5 Ending the measurement / saving the data To end the measurement, close the current measurement window (cross upper right). The data is located in the C:\..\Data directory and are saved in the following format: Measurement started at 12:00:01: Data format: dat or under the name you have entered. The files can be copied for processing at any time. The measurements do not need to be terminated for this. Caution! When selecting individual file names please be aware: the danger of losing data exists through overwriting a file due to assigning the same name again! Page 15

19 3 Calibration - 1-point calibration Shake flasks The 1-point calibration or 1-point adjustment is used to minimize the drift phenomena or, in the case of an optical sensor, for correction of mechanical shifts occurring when the sensor head and measurement adapter are unscrewed. Caution! The sensors no longer lie within specifications! Generally, adjustment should be carried out once monthly if the measurement adapter and sensor-head have been separated or in case of modified trial conditions (temperature). Place the sensors in a vessel with sterilized water and fresh ambient air (20.97 vol.% O 2, 0.04 vol.% CO 2 ). Wait until 100% rel. humidity has been reached in the vessel (e.g., the first drops of humidity condensate on the glass) and the signals are constant. Note! By setting the maximum humidity, the dilution effect of the oxygen sensor is directly compensated by the humidity. In the CO2 sensor, this is compensated via the temperature input box (chap. 2.3 no. 10 Dewpoint Carry out the 1-point calibration subsequently by clicking in the menu in Options/1-point calibration. You will now be requested to expose the sensors to fresh air, which you are already doing. Wait until the adjustment is finished. The sensors are once again ready to use. Page 16

20 3.2 Fermenter: The 1-point calibration or 1-point adjustment is used to minimize the drift phenomena or, in the case of an optical sensor, for correction of mechanical shifts occurring when the sensor head and measurement adapter are unscrewed. Caution! The sensors no longer lie within specifications! Generally, adjustment should be carried out once monthly if the measurement adapter and sensor-head have been separated or in case of modified trial conditions (temperature). Install the sensors in the exhaust gas line as explained in the sensor operating instructions. To perform the adjustment, conduct your process gas (0.04 vol.% CO 2 and Vol. O 2 ) for ca. 30 minutes through the non-inoculated (but filled with sterilized water) fermenter, which is temperature controlled according to the planned trial conditions. Note! By setting the maximum humidity, the dilution effect of the oxygen sensor is directly compensated by the humidity. In the CO2 sensor, this is compensated via the temperature input box (chap. 2.3 no. 10 Dewpoint Please make sure that CO 2 can still be expelled from the water initially. It is recommended to start a test measurement and to wait until the signals are constant. Carry out the 1-point calibration subsequently by clicking in the menu on Options/1-point calibration. The following window appears in which you can select the fermenter that has been set-up, respectively, the connected sensors. Confirm with OK. You will now be requested to expose the sensors to process gas, which you are already doing. Wait until the calibration is finished. The sensors are once again ready to use. Page 17

21 4 Special trial conditions - get ambient air - In order to correctly calculate the CTR, OTR and RQ parameters, input concentrations of vol.% O 2 and 0.04 vol.% CO 2 are used as a standard, which are determined during the initial calibration (see 1-point calibration). So that other input concentrations can also be used, they can be measured using the Options/get ambient air menu item and are then available for the subsequent measurements as they are stored in the FermVis.cfg file. If the input conditions change, these values must be re-determined again. Please make sure that CO 2 can still be expelled from the water initially. It is recommended to start a test measurement and to wait until the signals are constant. and RQ. By checking the check box in front of the fermenters, the corresponding boxes can be selected to assign the input concentrations to the sensors for calculating the CTR, OTR Caution! Incorrect values for CTR, OTR and RQ! Recheck the CO 2 and O 2 input concentrations. If necessary, carry out the 1-point calibration or get ambient air procedures once again. Page 18

22 5 Display 5.1 Display mode - Concentration, Rates, RQ - After a measurement has been started, a window with this measurement appears. The window is labelled with the name that was entered in the measurement text box. The concentration is displayed in vol.% on the right and left. The bottom axis is the time in hours. To view the calculated values such as CTR, OTR and RQ, you can change the display mode by clicking (left mouse button) on the left Y-axis. The various modes can be selected through clicking. However, the calculation is performed only starting with a change in the concentrations of 0.06 vol.% CO 2 or O 2, and in the case of shake flasks, at rates of mol / h l. You can see the control box (see chap. 5.2) in the left upper window. You can also activate it by clicking with the left mouse button. You can adapt the V/Vm value or the relative pressure with this later in case the gassing rate in the fermenter was modified during the measurement. Page 19

23 You can switch to the table view by clicking in the Table box. You can change back via the Chart box. However, values are stored in this mol / h l. table only when the CO 2 or O 2 concentrations reach more than 0.06 vol.% in the fermenters and, for shake flasks, the rate has changed by Note! If the field Table does not appear, you have forgotten to activate the Calculation box before making the measurement! End the measurement, start a new one, and click on the Calculation box! Page 20

24 5.2 User inputs during the measurement Process related modifications of, e.g., the gas rate in the fermenter or the process pressure would lead to calculation errors of OTR, CTR and RQ unless corrected. To avoid this, it is possible to activate VVm and Pressure Offset during the measurement by clicking with the mouse in the upper left corner on the Control box VVm If the gassing rate has been changed in the fermenter during a fermentation, you can manually change this value via the VVm input box. After changing the value confirm with RETURN Page 21

25 5.2.2 Relative pressure Process-related permanent pressure changes that would lead to deviations in the measurements can be modified in the pressure offset input box. After changing the value confirm with RETURN 5.3 Highlighting the measurement curve Each sensor head measurement is displayed through a coloured line, which can be highlighted for improved visualisation by clicking (left mouse button) on the line or by clicking the sensor head above the chart. To cancel the selection, just click somewhere else on the monitor with the left mouse button. In addition, the pressure is displayed if a sensor has been selected. 5.4 Zoom The display window is equipped with a zoom feature. You can magnify the desired portion of the measurement curve by holding the left mouse button and moving the mouse pointer to the desired position from the left to the right. To go back to the original mode, hold the left mouse button and move the mouse from right to left. Page 22

26 6 Error messages 6.1 Interface occupied If the interface is being used by another program, the following message appears. Choose a free interface via Options/Settings. 6.2 Missing sensors In case you have connected more heads than the program finds, go to Options/Settings, adjust the number of connected heads, and confirm with OK. The sensor heads will be searched for once again. However, if not all the heads you connected have been found, you need to press the SystemReset on the BACCom (see operating instructions for the sensors) with a sharp object. If this still does not bring about the desired result, please call your service department. 6.3 Incorrect sensor allocation In case a sensor already allocated to a fermenter is not connected or is defective, the following message appears. Check to make sure the sensor is connected or if it no longer functions. If you have any questions, please contact the service department. Page 23

27 7 Solving problems Error Possible cause Reference chap. Cannot find BACCom BACCom is not connected, or is connected to the wrong interface BCpreFerm operating instructions Supply voltage is interrupted BCpreFerm operating instructions BACCom crashed BCpreFerm operating instructions BACCom defective Service Cannot find sensors Sensors not properly connected BCpreFerm operating instructions Settings in FermVis are incorrect Chap. 2 Sensors crashed BCpreFerm operating instructions Sensors are defective Service Sensors are not within Incorrect adjustment Chap. 3 the specifications Adjustment is too long ago Chap. 3 Calibration is too long ago Service Sensors are defective Service Cannot start a All fermenters already being used Chap. 2.2, 2.3 measurement No sensors have been allocated to the Chap. 2.2, 2.3 fermenters Sensors are being used Chap. 3, chap. 4 Cannot switch over to the table Calculation not activated, no calculation Chap. 2.4 is performed Cannot switch over to Calculation not activated, no calculation Chap. 2.4 rates or RQ is performed No values in the table and no measurement curves in the rates and RQ display Concentration modification (0.06 vol.%) or creation rates (< mol/l h) are too small Incorrect or no determination of the input Chap. 3, chap. 4 concentration for calculating CTR, OTR and RQ 1-point calibration was not carried out Chap. 3 Calculated values are not plausible during start-up operation Error during input of the options Chap. 2.2, chap. 2.3 Incorrect input concentration Chap. 4 Page 24

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