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1. 34 tus ae 35 Saving Collected Data to file svcicsuscssnciccascseenscivenssseasnesesisecanncavscenscaurtacncdeieunscivvensssaveonnnouveanens 35 Dr FINES EEE AATE E TETE 36 Further informatiONn ssssssissicssssesssosssssvessssssseosssosisoss tresors skoss vsnsesvous cxenssenseanasdnansesoanseanacesenes 36 EE b EPPA EEEE SN NNN 37 Rule Matrix Sheet csssssicsissssstessssesocvosssesessussesess soss PUDE OR ITE EVE NI SOR GUIDE EN sKK EE 37 Profile Editor file layout 38 Fuzzy logic control file layout 4 oeseecteeres eu tonio tht v nin uel YIU MER EREERRE C CRVx ERES KU REN UR VERRE CR NERVOS 38 WS UMS GUNNS riy Mc Ge 38 acid psi 39 nis nisi 40 NS UMP EU Bir 41 sane 42 MMOD IM e 42 VUA MT 43 SUDAN eee p 43 SEES UD MUA dies 44 pln e 44 fao m DIE fT 45 Software Sensor control file layout scscccssccceccsscecccesnesesswscsesnonecoswcsensesecouncesvocstcnstsseanssessvnes 46
2. Start dete fIGMfU Start tima 2701 AR TCAP Cerver Closec 0010 01 22 01 43 Fuzzwy Comrcller 09 O01 22 03 05 Started Sotware Sansor 097 001 22 03 13 Started You have the possibility to synchronize your fermentations to a certain time point for example at inoculation or when induction of recombinant protein is induced Press the synchronize button and the Batch Age counter in the Batch information window with reset and count from that moment You are only allowed to set the synchronization time once during a batch By clicking the View Process Data button you can see the batch specific process data in table format as shown in the figure below Both collected derived and offline data can be edited for the current and finished batches FoxyLogic PhD MSc Mikkel Holmen Andersen Aarhus Denmark Email info 9 FoxyLogic com Program homepage www FoxyLogic com 13 Pune Data Foel ima com TW 1 User und Buleh Inbermuliun Run IN f1 nar Nania 2 Isar Engli fox4 4 q P l Off lina Nara v A VUL 4E HH U FSE 1007 30 HFE jon cer Na rat VET LYLE Lid C9 9 22103 INT GTA cocer zz t x f fa D SUME Sax tE xx po oT a C X 1d X 21 c gw SLT Mm CI EX bil ie I C9 cer SCC STA SPY SLT Lil tC x Icx po le a COM cer KER rat rey Vis Pelt Nel ns n Pal bee Nel tee tst 4 OT ET ed ba be ee ee NE ET De
3. Select User KIKI User OEI Greate New User ID fi jeer User Name Default User Surname Default Log In As User Login Default User Last Login 031 0 01 FoxyLogic PhD MSc Mikkel Holmen Andersen Aarhus Denmark Email info 9 FoxyLogic com Program homepage www FoxyLogic com 12 Fermentor Control Program manual version released 15 February 2005 Once a user is logged in to the database the menus Batch Start Stop and View Batch Data becomes available To start a batch select the Batch Start Stop submenu Start Batch Run Likewise stopping of a batch is done by selecting End Batch Run In the View Batch Data menu you can choose to display the currently running batch data as well as old batch data You are only allowed to see and edit data for which you are logged in The window shown below allows you to display and edit batch information such as stain media and product information Only the specific Batch Owner can stop and edit the batch data In this window the Run log is also shown Ratch Informalinn Fazyl agic cam 2001 c User Information Iser ID f Ilser Name Defaut liser Surname Default liser I ngin D fault Baich Information Run ID H gt pi Date Slaited fos 10 31 2 Date Ended View Process Data BIARIEH CLL URE Master Strain Wurki ig Elrain Colony Morphology Mecium Composit on Numb2rS ze of Tubes Pet i To Use
4. If you see incorrect data being sampled try to set your international settings to English You can do this by going into Control Panel and then click on International In the first panel select English then restart the computer Fermentor settings BioStat Fermentor Before you start the Fermentor Control host program the fermentor has to be set up for host connection To do this go into the MAINTENANCE menu on the fermentor FoxyLogic PhD MSc Mikkel Holmen Andersen Aarhus Denmark Email info 9 FoxyLogic com Program homepage www FoxyLogic com Fermentor Control Program manual version released 15 February 2005 and step down to the HOST setup To alter the settings enter the 2 digit password to access the interface parameters Then set these as indicated below ADR 1 SPEED 9600 DATA 7 STOP 1 PARTY EVEN Finally press the remote button to ON The fermentor is now ready to communicate with the host computer During the fermentation run you can manually manipulate the settings on the fermentor by setting the remote button to OFF While doing this you are unable to use the computer as controller and the host program will prompt you to set it to ON again However data collection will continue and the Fermentor Control Program will update its controls to match the manually entered changes Pump setting The current version of the Fermentor Control Program only supports anti foam for substrate pump 1 and substrate addit
5. The rules are read as follows i If pO2 is A and dPO2 is B then dSub is C ck Cc CK 0k CK CK 0C 0C CC ck CC Sk S A e x A kx AG KG X xo X p02 dPO2 dSub TA B C VL VL NL L VL NL OK VL NM H VL NS VH VL NS VL L NL L L NM OK L NS H L ZE VH L PS VL OK NM L OK NS OK OK ZE H OK PS VH OK PM VL H NS L H ZE OK H PS H H PM VH H PL Vi VH PS L VH PS OK VH PM H VH PL VH VH PL FoxyLogic PhD MSc Mikkel Holmen Andersen Aarhus Denmark Email info FoxyLogic com Program homepage www FoxyLogic com 39 Fermentor Control Program manual version released 15 February 2005 RuleSoftSub fuz KRRKKRKRKK RRR RR KE KR KKK KKK KR KEK RRR RK KEK KER KR KKK KKK Rulebase Function This function defines the rules by which the Fe Logic Controller x decides how to change the output new Sub i SetPoint The rules are read as follows i If SubConc is A and Sub is B then dSub is C ck Ck 0k CC 0C CCS C S S E Sk A x M KG kx A ko SubConc Sub dSub A C B VL L PM L L PM OK L PS H L ZE VH L NS VL OK PM L OK PS OK OK PS H OK ZE VH OK NS VL H PM L H PS OK H ZE H H NS VH H NM FoxyLogic PhD MSc Mikkel Holmen Andersen Aarhus Denmark Email info FoxyLogic com Program homepage www FoxyLogic com 40 Fermentor Control Program manual version released 15 February 2005 RulepH fuz KKKKKKKK KKK KKK KKK KKK KKK KKK KKK KKK KKK KKK KKK KK Ax kx
6. Yes No No Value dpOs Yes No No Value OffLine1 OffLine2 OffLine3 No Yes No Value FoxyLogic PhD MSc Mikkel Holmen Andersen Aarhus Denmark Email info FoxyLogic com Program homepage www FoxyLogic com 30 Fermentor Control Program manual version released 15 February 2005 Script Editor FoxyLogic com 2004 c Do not delete Private TEMP OnOff STIR_OnOff pH_OnOff pO2_OnOff SUB2_OnOff FOAM_OnOff Private TEMP sp STIR sp pH sp pO2_sp SUB2 sp Private EFT pv TEMP pv STIR pv pH pv pO2 pv SUB2 pv ACID p BASE pv F AM pv Private SOFTSUB pv dp02 pv Private OffLine 1 OffLine 2 DffLine 3 Private RetumValf1 3 Do Not Delete or change Above lines Do Not Delete or change below lines Function Return alues returning values to fermentor program Return al 0 TEMP OnOff Retumval 1 STIR_OnOff Return al 2 pH OnOff Return al 3 p02 OnOff BP ahi all A EO Abd One Error Check Script The scripting language is Visual Basic for Applications VBA and is used in all Microsoft products For further information on the scripting language look at the vast amount of tutorial on the internet To run a script you need to load it first and then enable scripting in the Main window There is a button for error checking the script before you enable it Any error in the script will be highlighted in red Only one error at a time can be detected thus if you have an error i
7. manual version released 15 February 2005 ct CT CT CT CT 7 10 1 a a a a a a 6 input neurons hidden neurons output neurons normalizi normalizi normalizi normalizi normalizi normalizi normalizi normalizi for for for for for for for for ng ng ng ng ng ng ng ng 690852724783 55511445324077 33279807975446 76790615316649 62716938875695 70851685138183 81530304552233 5995947894898 07018053152791 83893895019787 64046452277924 7156447001138 1447226361594 55428566971051 37339583572718 53391862540241 76129192600924 20420568026137 76739950388887 46606857496196 24797688068116 775868607126456 Sensor nnf 1 7 0 lt Layer 1 2 0 7 lt Layer 2 3 10 Layer 3 6 75 6 15 0 Da 500 500 0 lt Da 561 1561 1000 lt Da 2 49 3 4 6 Da 14 sel 04 lt Da Tebe Xil 206 Da IEL 111 0 lt Da ILI 111 0 lt Da n 3 75971694937615 4 07726719544041 2 00296094186734 2 61862385034799 311159557450939 4 76992159623709 4 47678086519426 4 50154060592303 4 89244243765186 2 2039747074752 9E 03 5 61447788129139 4 74065055034103 4 20382532575943 5 44396819603226 320312337113613 4 88720637047502 5 62109124202305 5 01611692828678 5 16288281421997 252562096981901 5 85182486128104 5 78181110953004 5 48794084622698 5 39671696089882 1 31704114401821 6 58589330859152 6 0067
8. 02 0 01 L 0 02 0 01 0 01 0 OK 0 01 0 0 0 01 H 0 0 01 0 01 0 02 VH 0 01 0 02 0 02 0 03 FoxyLogic PhD MSc Mikkel Holmen Andersen Aarhus Denmark Email info 9 FoxyLogic com Program homepage www FoxyLogic com 45 Fermentor Control Program manual version released 15 February 2005 Software Sensor control file layout input neurons 0 above hidden neurons 3 above Example nnf ll 3 0 lt Layer 1 3 2 3 3 lt Layer 2 3 3 1 3 lt Layer 3 1 Range 1l maxfl minfl lt Data Range 2 max 2 min 2 lt Data Range 3 max 3 min 3 lt Data Range 1 maxfl minfl Data a lt Marker below neuron weighs and Layer 2Neuron 1Weight 1 Layer 2Neuron Layerf2NeuronflTreshold Layer 2Neuron 2Weight 1 Layer 2Neuron Layer 2Neuron 2Treshold Layer 2Neuron 3Weight 1 Layer 2Neuron Layer 2Neuron 3Treshold Layer 3Neuron lWeight 1 Layer 3Neuron Layer 3Neuron 1Treshold output neurons 3 above for normalizing inpu for normalizing inpu for normalizing inpu thresholds are given lWeight 2 Layer 2Neu 2Weight 2 Layer 2Neu 3Weight 2 Layer 2Neu t 1 t 2 t 3 for normalizing output ron ron ron lWeight 2 Layer 3Neu ron 1 1Weight43 2Weight 3 3Weight 3 1Weight43 FoxyLogic PhD MSc Mikkel Holmen Andersen Aarhus Denmark Email info GFoxyLogic com Program homepage www FoxyLogic com 46 Fermentor Control Program
9. 2 2 VH 2 4 4 HF ox ON RNO pH mf pH pH Member Function Ck CK CK Ck Ck Kk Ck CI CK CC CC CK C I C x M KK x KK KG Ko ko ko ko KKK Values in this function are the offset from the pH SetPoint For example bs with Setpoint to 6 8 the function looks like this i VL 6 3 6 55 6 55 6 7 K i L 6 55 57 6 7 6 8 X OK 6 7 6 8 6 8 6 9 7 H 6 8 6 9 6 9 7 05 i VH 6 9 7 05 7 05 7 3 VL pH Very Below SetPoint L pH Low Below SetPoint OK pH Close to SetPoint H pH High Above SetPoint VH pH Very High Below SetPoint KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKK KKK VL 0 5 0 25 0 25 0 1 L 0 25 0 1 0 1 0 OK 071 0 0 O H 0 Ql 0 1 0 25 VH 0 1 0 25 0 25 0 5 FoxyLogic PhD MSc Mikkel Holmen Andersen Aarhus Denmark Email info FoxyLogic com Program homepage www FoxyLogic com Fermentor Control Program manual version released 15 February 2005 dpH mf dpH Change in pH Member Function cc ck c ck ck ck ck ck ck ck c ck ck ck kk KKK ck ck ck ck ck ck KK KK ck ko ck Sk ko kk ko ko ko ko oko Values in this function are the change in pH over the last 5 min 10 data points Change in pH Low Change in pH Zero Change in pH High H Change in pH Very High Ck Ck ck ck ck ck ck ck ck ck ck ck ck ck ckckckockockckck ckck ck ck ckck ck k ck ck k kc k kk kk morus TEL VL Change in pH Very Low VL 0 03 0 02 0
10. 3 wire cable with the following specified connections It is a standard serial cable RS 232C to RS 232C Female at PC end DB 25 at fermentor end DB 25 DB 89 Pin Pin Receive 3 2 lt gt 2 Transmit Transmit 2 3 lt gt 3 Receive Ground 7 5 lt gt 7 Ground NOT CONNECTED 21 must not be connected NOTE Make sure that pin 21 on the fermentor is not connected with a wire to the PC this can switch the serial mode from RS 232 to RS 422 B1 For BioFlo Ill 3000 and 4000 open the back of your fermentor and change the settings of the micro switch S1 as follows Consult you instrument manual to locate the switch Settings of switch 1 S1 on the fermentor control board 1 81 1 and S1 2 are used for setting the baud rate Baud Rate S1 1 S1 2 9600 OFF OFF 2 S1 3 is used for setting the parity check Parity 1 3 Even ON 3 S1 4 is used for setting mode Mode S1 4 non multidrop OFF 4 S1 5 S1 6 S1 7 51 8 are used for setting unit number Unit 51 5 S1 6 81 7 S1 8 0 ON ON ON ON B2 For BioFlo 110 set the base address to zero and select the AFS mode Then set the unit number to 1 micro switches on the back of each module C Install the program and you are done Use at own risk FoxyLogic PhD MSc Mikkel Holmen Andersen Aarhus Denmark Email info FoxyLogic com Program homepage www FoxyLogic com 52 Fermentor Control Program manual version released 15 Feb
11. KG ok Rulebase Function This function defines the rules by which the Fuzzy Logic Controller decides how to change the output new Sub SetPoint The rules are read as follows If pH is A and dpH is B then dSub is C KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKK pH dpH dSub A B Q VL VL NL L VL NL OK VL NM H VL NS VH VL NS VL L NL L NM OK L NS H I ZE VH L PS VL OK NM L OK NS OK OK ZE H OK PS VH OK PM VL H NS L H ZE OK H PS H H PM VH H PL VL VH PS L VH PS OK VH PM H VH VH VH L FoxyLogic PhD MSc Mikkel Holmen Andersen Aarhus Denmark Email info GFoxyLogic com Program homepage www FoxyLogic com 41 m Fermentor Control Program manual version released 15 February 2005 p ant Oxygen Member Function d uM cU ees x Values in this function are the offset from the substrate SetPoint For example with Setpoint to 20 the function loo like this a VL 14 16 6 18 m x L 16 18 18 20 m a OK 18 20 20 22 e a H 20 22 22 24 X VH 22 24 24 26 m X VL pOxygen Very Below SetPoint d ns pOxygen Low Below SetPoint m OK pOxygen Close to SetPoint r JB pOxygen High Above SetPoint x MHZ pOxygen Very High Below SetPoint KKK KKK KKK KK KKK KEK KKK KKK KKK EKER ck ck ck ck ck ck ck ck ck kckkkk k VL 6 4 4 2 L 4 2 2 0 OK 2 0 0 2 H 0 2 2 4 VH 2 4 4 6 dpO2 mf d
12. STIR_sp ReturnVal 8 pH_sp ReturnVal 9 pO2_sp ReturnVal 10 SUB2_sp ReturnVal 11 OffLine_1 ReturnVal 12 OffLine_2 ReturnVal 13 OffLine_3 ReturnValues ReturnVal End Function Do Not Delete or change Above lines Do Not Delete or change below lines Sub Main a b c d e f g h i j k m n O p q r S t U V Values Coming from fermentor program ON OFF TEMP OnOff a 1 if on 0 if off STIR_OnOff b pH_OnOff c pO2 OnOff d SUB2 OnOff e FOAM_OnOff f SetPoints TEMP_sp g 10 42 STIR sp h 0 1200 pH sp i 2 12 pO2 sp j 0 100 SUB2_sp k 0 100 Process Values EFT pv2l minuttes TEMP pv2m STIR pv n FoxyLogic PhD MSc Mikkel Holmen Andersen Aarhus Denmark Email info 9 FoxyLogic com Program homepage www FoxyLogic com Fermentor Control Program manual version released 15 February 2005 pH_pv o pO2_pv p SUB2 pv q ACID pv r BASE pv s FOAM pv t SOFTSUB pv u dpO2 pv v End Sub Do Not Delete or change Above lines Function YourScript Put your code here End Function FoxyLogic PhD MSc Mikkel Holmen Andersen Aarhus Denmark Email info 9 FoxyLogic com Program homepage www FoxyLogic com 50 Fermentor Control Program manual version released 15 February 2005 Wiring between RS 422 converter and BioStat fermentor Warning Do NOT connect the BioStat fermentor and computer directly you most insert a RS 232
13. is little to decide however since the only thing you have direct control over is addition of substrate The other parameters are in the hands of the hardware embedded PID control which does a good job of it But the collected data can be used as input for the controller that is pO dpO and substrate set point In the future other parameters may be added as they are demanded Thus to setup the fuzzy logic control a rule database made of if X is A and Y is B then Z is C rules is needed A pO B dpO gt or substrate setpoint C substrate setpoint output To gather and organise knowledge about the relationship between these FoxyLogic PhD MSc Mikkel Holmen Andersen Aarhus Denmark Email info 9 FoxyLogic com Program homepage www FoxyLogic com Fermentor Control Program manual version released 15 February 2005 inputs and corresponding output linguistic values a rule matrix is usually used By filling in control words like Positive Large PL Negative Medium NM and Zero ZE the controller knows what to do when a rule is applicable A rule matrix is organised as follows If X is A and Y is B then Z is C ae ONU NENNEN Xx B A ZC Substrate Feed Rate M Low Low Ok EE Very Low NM NM PO Nese High PM PM PS ZE NM Very High PL PL PM NS NL Very Low VL Low L Ok High H Very High VH and Negative Large NL Negative Medium NM Zero ZE Positive Small PS Positive Medium PM Positive L
14. overflow metabolism can inhibit cell growth and thus product production The output from the software sensor can be used as input for the fuzzy logic control module such that the optimum substrate concentration in the fermentation tank is maintained One of the initial steps towards a successfully working neural network software sensor is to decide on the network layout On the basis of information from many different sources a two layered fully connected backpropagation network was chosen besides input units one hidden layer and an output layer are forming the sensor network A sigmoid activation function is used and a threshold term is added to the neuron output function preventing the network to be trapped in a local minimum Input data are rescaled to values within a range of 1 to 1 and output data between 0 1 and 0 9 Currently 7 inputs are being used as input for the software sensor as these parameters can be derived from data collected by the main fermentor control program The single output from the net is giving the estimated substrate concentration FoxyLogic PhD MSc Mikkel Holmen Andersen Aarhus Denmark Email info 9 FoxyLogic com Program homepage www FoxyLogic com 24 Fermentor Control Program manual version released 15 February 2005 Sampling Training Data To successfully implement the neural network software substrate sensor several things will have to be done Firstly before a neural network can be used in process
15. research laboratory Finally intelligent control over set points seemed an obvious thing to implement Together these goals merged to the development of the current program To make the program as simple and logical as possible the amount of choices and possibilities are kept at a minimum Tool tip texts tell you how to manipulate controls etc when the mouse pointer is over a given control for more than a second The final goal is of course to make the present manual useless Computer system requirements Windows 95 98 NT 2000 XP min Pentium processor 333 MHz more processor power needed for fuzzy logic and neural network modules min 64 Mb ram min 200 Mb hard disk space standard PC serial port RS 232C converter for BioStat fermentors RS 232C to RS 422 Serial cable On Windows 95 98 DCOM95 98 needs to be installed free from Microsoft Access Database Version Microsoft Access database program Access 2000 or newer is needed to manipulate the process database if you want to generate batch reports or print data The database that ships with the Fermentor Control Program is in Access 2000 format If you want to migrate to Access 2000 or higher open the BioStatDB mdb file in Access 2000 and you will be prompted to save in the new database format Answer Yes to upgrade database The Fermentor Control Program will recognise both types of format However you cannot make a replica of the database with Access 2000 as this is not
16. sr mg nm cse cst Three offline data sets are currently available named OFF LINE DATA1 OFF LINE DATA2 OFF LINE DATA3 In the Options menu you can change these names by names that reflect better the data type you are entering See Option Menu below To enter or edit offline data click on the Edit Off line Data button This will disable the updating of the process data table to give time to edit the data points Once you are done click on the same button and the data will be updated to the database and data collected meanwhile will be displayed At any time you can export processes data to a file in XML file format This format is widely accepted by other software Database Tools In the File menu several database tools are found The other 3 are all for maintaining the database These functions are only available when the program has just been started and for users with Administrator access rights Extract Training Data will be discussed below in the software sensor section Compact Database will clean up the database and results in a small and faster database file You should perform this operation every five fermentation runs Backup Database simply takes a hard copy of the BioStatDB mdb file and stores it at the place you select New Database is the most time consuming tasks and is only recommended when the database is getting very large The Access database has
17. 2917026126 6 14373079522539 6 72524523699054 862045554242181 6 05080369541756 6 83353179971728 6 68183040672656 5 89377109576784 881741732913483 6 79689200943925 6 48903361213386 5 71646575314079 5 76345170922498 1 05396959398222 6 6408101149373 6 77572340921539 6 4611797591754 6 51309051786101 9676087450954 6 63938795227694 6 26645007661729 6 28712647986319 6 9047299117058 893013309514196 3 46269380877619 1 289020065767987 772507148584088 142435148016983 116109640507782 294935149743334 714685982976691 0 above 7 above 10 above input 1 input input input input input input output 1 1 80911790847808 5 14461334762 47022078826548 9332829367535 20751871486971 51055109425313 69934179131986 49377125642577 18318606970833 6 77483369274218 846169386530807 1 59577601775878 FoxyLogic PhD MSc Mikkel Holmen Andersen Aarhus Denmark Email info FoxyLogic com Program homepage www FoxyLogic com E 02 47 Fermentor Control Program manual version released 15 February 2005 Training data is file Training data output file lt 17 data points e rol kHOOKHOKk1000k000k k ypu e substrate concentration t mmol L or any other 17 1 output ulture Vol conc t 1 Feed Rate 1 o action Vol Sub mL Total C u
18. 5 3 8 j Process poz ON OFF buttons above z 3 19 55522 them does this For z I Process Subs2 example to set agitation 2 z 5 1 455337 to ON click the OFF I suem E button which then shifts E Z E Doa is dSubs2 edere A tool E text E i2 0 08069 E also tells you how to change i The slider 3 E Ta 200 below is enabled and with the mouse or keyboard page up page down arrows you can set the new set point Below the slider there is a numerical display that indicates the current set point When you change to the given set point the number turns red Once accepted by the fermentor it turns green again Be aware that this can take up to 30 seconds The value is set immediately but the program only checks all actual set points every 30 seconds A special case is when the pO level is set The host program uses agitation to control FoxyLogic PhD MSc Mikkel Holmen Andersen Aarhus Denmark Email info FoxyLogic com Program homepage www FoxyLogic com 10 Fermentor Control Program manual version released 15 February 2005 the level of dissolved oxygen in the fermentation tank When you click the pO2 button the stirr slider is disabled and the stirr button displays the text pO2 Casc meaning that oxygen cascade controls the agitation When you turn off the pO2 again the stirr control is enabled and left at the last setpoint given by the pO2 cascade control Th
19. C to RS 422 converter between For long distances the converter should be as the computer and may require additional power supply Cable between the RS 232C to RS 422 converter and the computer This is a standard serial cable PIN out on 9 and 25 RS 232C serial ports on computer DB 9 Corresponding Pin DB 25 Pin Signal Function RD Received data TD Transmitted data RTS Request to send Clear to send DSR Data set ready SG Signal ground DCD Data carrier detect 0 DTR Data terminal ready ROUO 0 01 Nm Oo Oo ANO O 4 e Cable between the RS 232C to RS 422 converter and the fermentor This is a non standard serial cable which you have to provide yourself RS 422 on fermentor HOST PIN SIGNAL CONNECT TO ON CONVERTER 422 485 2 GND GND 3 DOB TxD Rx 4 RIB RxD Tx 5 RGND 6 7 GND GND 8 DOA TxD Rx 9 RIA RxD Tx No PIN numbers have been assigned to the converter 422 side as these vary between different vendors Use at own risk Mikkel H Andersen August 2000 FoxyLogic PhD MSc Mikkel Holmen Andersen Aarhus Denmark Email info FoxyLogic com Program homepage www FoxyLogic com 51 Fermentor Control Program manual version released 15 February 2005 Wiring between PC and BioFlo fermentors If you want to use the Fermentor Control Program with your BioFlo 110 BioFlo III or BioFlo 3000 fermentor you do NOT need a RS 232 to RS 422 converter All you need to do are a few things A Get a
20. Dh cinpnjhBii e 46 FoxyLogic PhD MSc Mikkel Holmen Andersen Aarhus Denmark Email info 9 FoxyLogic com Program homepage www FoxyLogic com Fermentor Control Program manual version released 15 February 2005 SEM SON MIE Versene kenriannuiseisvdnpni 47 Training data input file ie D I HRRITAE EUER ER M ORARE MUR ERINRR RE COUR RN EUR AR CUN IS MIN RE 48 Training data output file 48 Standard Script sie 49 Wiring between RS 422 converter and BioStat fermentor e eere 51 Wiring between PC and BioFlo fermentor ecce eese eerte ee ee eee eere eese seen aae 52 FoxyLogic PhD MSc Mikkel Holmen Andersen Aarhus Denmark Email info 9 FoxyLogic com Program homepage www FoxyLogic com Fermentor Control Program manual version released 15 February 2005 Introduction The control and collection software for the research bench top fermentors was made to facilitate and automate some general and time consuming tasks Initially the program was made to collect the process data during fermentation and save these for further evaluation in other programs Soon however there was also a need for a more user friendly program compared to the on board fermentor control and the possibility of a TCP IP client connection that significantly reduced the on site time a factor not to be overlooked in a
21. Fermentor Control Program manual version released 15 February 2005 FoxyLogic Fermentor Control Program BioStat A B C D CT MD DCU and Micro DCU 200 300 Systems BioFlo IIT 2000 3000 4000 and 110 Systems See www foxylogic com for other systems Version 4 3 February 2005 FoxyLogic PhD MSc Mikkel Holmen Andersen Aarhus Denmark Email info FoxyLogic com Program homepage www FoxyLogic com Fermentor Control Program manual version released 15 February 2005 Table of contents Introd ctiOn m Y 5 System FEQUIPEMEIIS m 5 Access Database Version sess sess vese sees PY EP NEC ES PP UST PESE EY NEAR FEN EIN ER ERR NY vvt te ESTEE PRESE VR ROSE 5 Installing the Fermentor Control Program e ecce esee ee eee eee eene etae to seta seta aae 5 Un installing the Fermentor Control Program eese eee ee eee eee eee ee eee te eese seta sae 6 About time and time resolution in windows systems eee ee eee eee eee ee eerte eene etna 6 DIVER 0 4 PF IP 6 About decimal symbol in windows systems eee e ecce eee eee ee eren eee ee eese seen ee setae seen a 6 Fermentor Setngs ia oisi ciree ittis Deko niae bip EoevVEE KE AkV bio dd U E eR CUdPds e EHE RE AK fR RE REPE RR EN CUR AV ERG 6 P
22. Fermentor Control Program folder and run the program with the fermentor First the tool looks for available and free serial ports on FoxyLogic PhD MSc Mikkel Holmen Andersen Aarhus Denmark Email info 9FoxyLogic com Program homepage www FoxyLogic com Fermentor Control Program manual version released 15 February 2005 your computer Then you select the port which the converter is attached to and press the Test Connection button Every 2 seconds the program sends a telegram to the fermentor and checks the returned telegram If the fermentor is correctly setup a text message will tell you so If no connection is detected then check you cabling and converter As a last resort you can contact me by Email support foxylogic com but only if you attach the Run log and Error log generated by the TestComm tool BioFlo Fermentors To setup the communication between a computer and the fermentor a protocol has to be used BioFlo III 2000 and 3000 fermentors To enable the right type of protocol you need to open the back of your fermentor and change the settings of the micro switch S1 as follows Consult you instrument manual to locate the switch Settings of switch 1 S1 on the fermentor control board 1 S1 1 and S1 2 are used for setting the baud rate Baud Rate SI 1 S1 2 9600 OFF OFF factory setting 2 S1 3 is used for setting the parity check Parity S1 3 Even ON 3 S1 4 is used for setting mode Mode S1 4 non mul
23. PO2 Change in pO2 Member Function kkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkk x Values in this function are the change in pO2 over the last 5 min 10 data i points VL Change in pO2 Very Low d cae ee Change in p02 Low a OK Change in pO2 Zero Ea 7 HE Change in pO2 High m x MH hange in p02 Very High d KKK KKK KKK KKK KEKE KKK KKK KKK KKK KKK ck ck ck ck ck ck KKK KKK VL 3 2 2 1 L 2 1 1 0 OK cr 1 H 0 1 1 2 VH 1 2 2 3 FoxyLogic PhD MSc Mikkel Holmen Andersen Aarhus Denmark Email info FoxyLogic com Program homepage www FoxyLogic com Fermentor Control Program manual version released 15 February 2005 Sub mf Sub Substrate Member Function KEK KKKKK KKK KKK KKK KKK KK ck kokokockck ck ck ko ck okockock ck k ck ck ckockck Values in this function are the offset from the substrate SetPoint For example with Setpoint to 2 pump action the function look like this Leo LS 2 s OK 1 5 2 2 245 H 2 245 ROS 3 L Substrate Below SetPoint P OK Substrate Close to SetPoint H Substrate Above SetPoint KKK KKK KKK KK KKK KKK KKK KKK KKK KKK ck ck ck ck ck ck ck ck KKK KKK L 1 0 5 7045 0 O 0 5 0 0 Vio H 0 0 5 0 5 1 dSub mf dSub Change in Substrate output Member Function dock KK KKK KK RR KKK KKK kck kokckckokckockck kokckckock kockok EK KEK This member function gives the change in SetPo
24. ace the control you want to change and finally you set the set point When this is done click the Add Entry button and the new entry will appear on the list In the file menu you can both save profiles and load old once If a wrong action is in the list you simply click on the entry in the list and then press the Delete Entry button Entries that have been executed are shown in green pending once are red If you load a profile during a run actions with time points less that the current elapsed fermentation time will be ignored and shown in green All actions made by the profile control are logged in the batch database and the RUN Iog file FoxyLogic PhD MSc Mikkel Holmen Andersen Aarhus Denmark Email info 9 FoxyLogic com Program homepage www FoxyLogic com Fermentor Control Program manual version released 15 February 2005 Fuzzy logic control module Fuzzy logic control is equivalent to have computers reason like humans do just much faster Normally when we think of computers making decisions the output would be true or false However fuzzy logic is a way of letting the computer say little big bigger not so big and so forth and have an output decided upon from these vague inputs Fuzzy logic has some strength over conventional control algorithms like for example Proportional Integral Derivative PID control Often biological systems are non linear difficult or impossible to model mathematically However fuzzy
25. an upper size limit of 2Gb Therefore you need to export process data out of the database and store this in another FoxyLogic PhD MSc Mikkel Holmen Andersen Aarhus Denmark Email info 9 FoxyLogic com Program homepage www FoxyLogic com 14 Fermentor Control Program manual version released 15 February 2005 database The New Database performs this task It accumulates new user batch and process data in the BioStatDBBackup mdb files and deletes process data from the BioStatDB mdb file This process is time consuming and could be left to run during the night For example it takes 20 minutes to move data from four 5 day fermentations In the Main Control Window a progress bar will show you how much data have been moved 0 100 When the BioStatDBBackup mdb gets near the 2 Gb size limit this in turn is backed up automatically and given a date extension to the file name ddmmyy e g BioStatDBBackup010102 mdb A new accumulative BioStatDBBackup mdb file is then created A copy of the old User and Batch information is kept in the BioStatDB mdb file to provide data consistency unique User and Run ID s This means that you can later combine all BioStatDBBackupddmmyy mdb database files into one big historian database if you have access to MS SQL Server MySQL or similar programs that can handle very big databases Administrator Tool Like the database tools this function is only available when the program has just been
26. and the decimal separator is a This format is readable for most spreadsheet programs Below is an example of a data file User MHA Start date and time 26 09 98 14 54 06 Total Fermentation time 000 01 10 TIME TEMP pH pO2 STIRR SUBSTRATE ACID BASE FOAM Predicted Subs Conc C RPM mL mL mL mL any 30 6 5 20 765 2 4 5 0 111 30 6 4 20 745 4 5 5 0 109 30 2 6 6 21 650 6 5 6 1 109 You can only save data in an ASCII formatted file after stopping data collection after which the Save menu is enabled If you need a data file to process before that make a copy of the BackupData log file found in the Fermentor Control Program folder At any time you can export processes data to a file in XML file format This format is widely accepted by other software FoxyLogic PhD MSc Mikkel Holmen Andersen Aarhus Denmark Email info FoxyLogic com Program homepage www FoxyLogic com 35 Fermentor Control Program manual version released 15 February 2005 Log files A set of log files is generated in the directory where you chose to install the Fermentor Control Program There are four different log files User log file contains data about each user s fermentation runs with accompanying date and time entries When you start a fermentation run you will be prompted to enter your user name Your user log file will then be appended with data about the new run If you are new to the program a new log file will be made autom
27. arge PL Take RULE 3 from the figure found on next page If pO is Low and Substrate Feed Rate is High then ASubstrate Feed Rate is Negative Small Or in short If pO is L and Substrate is H then ASubstrate Feed Rate is NS As you can see it is easy to use the rule matrix to make the rulebase file for the controller program The above matrix will yield 25 rules which should be entered into the RuleSub fuz file Likewise the rules for the RuledpO2 Fuz and RuleSoftSub Fuz files can be created by filling in a rule matrix for each case The change in Substrate Feed Rate is determined by the values given in the dSub MF file Some work must be put into adjusting the values given in controller files however only the rule files need essential editing to fit your expression system Sub MF Substrate Member Function converts substrate setpoint to fuzzy value pO2 MF pO Member Function converts pOxygen setpoint to fuzzy value dpO2 MF dpO2 Member Function converts dpOxygen setpoint to fuzzy FoxyLogic PhD MSc Mikkel Holmen Andersen Aarhus Denmark Email info FoxyLogic com Program homepage www FoxyLogic com 21 Fermentor Control Program manual version released 15 February 2005 pH MF dpH MF SoftSub MF dSub MF RuleSub FUZ RuledpO2 FUZ RulepH FUZ RuleSoftSub FUZ value pH Member Function converts pH setpoint to fuzzy value dpH Member Function converts dpH setpoint to fuzzy value Member Fun
28. ark Email info FoxyLogic com Program homepage www FoxyLogic com 29 Fermentor Control Program manual version released 15 February 2005 Australia 2000 escherichia coli cultivations In IEEE Conference on Decision and Control Sydney M Akesson P Hagander and J P Axelsson An improved probing controller for substrate feeding in fedbatch cultures of e coli simulations and experiments In Computer Applications in Biotechnology Quebec Canada 2001 Scripting Module Adding a scripting feature to the Fermentor Control Program greatly increases your possibilities when adapting the program to your needs You have full control over all setpoints and you can make calculations that are then passed back to the Fermentor Control Program as a new setpoint or an off line value The below table shows you which values you can use in the script and which you can return to the Fermentor Control Program Variable oe p buts Control Variable Type Time EFT Yes No No Value minutes Temperature Yes No On Off Setpoint Value 0 or 1 0 150C Agitation Yes No On Off Setpoint Value 0 or 1 0 1500 rpm pH Yes No On Off Setpoint Value 0 or 1 2 12 PO Yes No On Off Setpoint Value 0 or 1 0 100 Substrate Yes No On Off Setpoint Value 0 or 1 0 100 Foam Yes No On Off Value 0 or 1 Acid Yes No No Value 0 10000 mL Base Yes No No Value 0 10000 mL Predicted Sub
29. atically RUN log file contains all information about executed profiles TCP IP activity user runtime etc A new Run log file is generated each time the program is started erasing the old one A Run log is also created by the Client software but only communication errors etc are logged Fuzzy log file contains all data and outputs from the fuzzy logic control module This file can be used as information if you wish to modify the control files E g look for situations where your logic in the rule files is not complying with the sampled data to reach the intended state BackupData log file contains all sampled data from a fermentation run and the file is continuously updated This file can be used in the event of a power out or hardware breakdown and the file layout is identical to the file format of the data file you save from the Save menu The old BackupData log is deleted whenever you start a new fermentation run Further information If you have any suggestions for improvements or identified bugs in the Fermentor Control Program please contact me by Email info FoxyLogic com For information about upgrades FAQ and for updated fuzzy logic information please consult the Fermentor Control Program home page at www FoxyLogic com FoxyLogic PhD MSc Mikkel Holmen Andersen Aarhus Denmark Email info FoxyLogic com Program homepage www FoxyLogic com Fermentor Control Program manual version released 15 February 2005 App
30. compatible with the Fermentor Control Program This is due to a Microsoft backward compatibility policy Installing the Fermentor Control Program The program is delivered with an Installation and Setup Wizard To start the wizard run the file called SETUP exe After you have downloaded the program unzip the file in a temporary directory before running the SETUP exe file If you use a NT 2000 or XP system be sure to login as administrator before running the SETUP exe The installation wizard prompts for an installation directory and it is recommended that you use the default setting When the installation is finished you can be asked to restart your computer Although annoying this is normal Windows behaviour In FoxyLogic PhD MSc Mikkel Holmen Andersen Aarhus Denmark Email info 9 FoxyLogic com Program homepage www FoxyLogic com Fermentor Control Program manual version released 15 February 2005 some cases if you have an old Windows 95 98 version the wizard needs to update your system and restart your computer to continue the installation This will not affect anything else A file called St6unst is left in the Fermentor Control Program folder Do not delete this since the un installer program uses this file if you wish to remove the program Un installing the Fermentor Control Program To un install the program use the Add Remove option found in the windows control panel Press the Add Remove button and browse to the Fe
31. control the network needs to be trained with historical process data obtained from previous fermentation runs Thus data from previous fermentation or new data has to be prepared in files to be used for neural network training From the Fermentor Control Program it is possible to collect the training data automatically Firstly under the Software Sensor menu there is an entry called Sample Training Data Using this function you are prompted to enter the off line measured substrate concentration corresponding to the time point the sample was taken Off line measurements could easily been made with on of the many kits available for determine e g glucose concentration This information is together with seven other parameters added to two training data files See appendix and to the process database After the collection of enough data has been completed see below you can extract and save the training data sets automatically In the File menu under Database Tools there is a menu called Extract Training Data A window will be shown with all extracted data Select Save Training Data and you will be prompted twice to give file names for the two training files Input and Output data These two files are then ready for the Sensor Training tool Furthermore a representative data set can be removed from the sampled data from above which will be put into two validation files See below Every 10 sampled datapoint is
32. ction converts predicted substrate concentration to fuzzy value dSub Member Function converts fuzzy value to substrate setpoint Rules for pO and dSub substrate control DO stat Rules for pO and dpO substrate control DO stat Rules for pH and dpH substrate control pH stat Rules for Sub and Sub substrate control FoxyLogic PhD MSc Mikkel Holmen Andersen Aarhus Denmark Email info 9 FoxyLogic com Program homepage www FoxyLogic com 22 Rule 1 IfpO2 is low and dpO2 is high then output is Zero Veg lov Lov Ok Bigb Veg Bigb 1 0 mte ter ak Bigh Ver igh Rule 2 IfpO2 is Ok and dp O2 is high then output is positive small Rule 3 IfpO2 is low and substarte feed rate is high then outp ut is negative small Fermentor Control Program manual version released 15 February 2005 8 a 4 Negalite Lz Nega r a Posit reld e 0 5 p02 Level deltap02 Megatite Large Positive dd ediua fosilire Large p02 Level deltap02 Negalite Large Hegar id dia Positive ediua Positive Large Hegalit Small p02 Level Substrate Feed Rate Negative Large Negativ ld diua Negatr Small Posi re mall Positive ld edium Positite Large Zero Centerof Mass Qutputto Fermentor A schematic drawing of how the controller is working is shown above The file layout is tabulated and every line starting with an asterisk is ignored More information about values and file layout i
33. d from the fermentor and stored in the database In Vessel and Supply Tank Settings you can enter the volumes of your default fermentor and supply tanks Furthermore you can set your default batch start up volume which will then be the default value in the input box that is shown when you begin a fermentation run Setting these values accurately will give you a better synoptic window where the live process values are shown as calculations are based on these values In Off line Data Types you can change the names of the three off line data fields which are supported by the database By doing so you can have a better description of the data and its format that has to be entered Please note that the underlying database fields are not changed and should like all field names be left like they are if you use Access to manipulate your process data License Key is not in use at the moment but may become a future feature if false Email registrations become a problem The program is freeware to the benefit of all I use addresses to send update information but also ask for support information Email addresses are not given to third parties FoxyLogic PhD MSc Mikkel Holmen Andersen Aarhus Denmark Email info FoxyLogic com Program homepage www FoxyLogic com 33 Fermentor Control Program manual version released 15 February 2005 TCP IP client control This control is the major force of the Fermentor Contr
34. d fuzzy logic module since as stated above no liable model exists by which the predicted substrate concentration can be used to reach the desired concentration Alternatively you can use the software sensor to help identifying different phases of the fermentation process Instead of collecting substrate concentration data point you can enter an unique integer for each phase and train the neural network with that The network will predict the current phase the fermentation is in FoxyLogic PhD MSc Mikkel Holmen Andersen Aarhus Denmark Email info 9 FoxyLogic com Program homepage www FoxyLogic com 27 Fermentor Control Program manual version released 15 February 2005 Current Input Parameters The currently supported inputs for the software substrate sensor are Feed Rate pump action time t Volume Substrate feed mL e Total culture volume mL e Offset pO pO setpoint 7 pO current ApO last 5 min Offset pH PHsetpoint PHeurrent Previous substrate concentration t 1 For training the measured substrate concentration at time t is needed The file layout of the training data files is tabulated and lines starting with an asterisk are ignored These files can be generated automatically by the Fermentor Control Program More information about values and file layout is given in the legend of the above files see manual Appendix pH Stat The pH Stat is a powerful tool to control a simple fed batch feedi
35. e control with the new settings by selecting the menu Reset Reload The software substrate sensor Biological systems are difficult to model largely due to the inherent non linearity of such systems However neural networks can help users to describe and model phenomena that are too complex for analytical methods or empirical rules Neural networks can efficiently be used to forecast process values in fermentation processes since they are able to map describe non linear functions In the case of fermentation processes neural networks are for instance able to forecast the substrate concentration on the basis of inputs such as culture volume pH pO and current substrate feed rate Neural networks are used in large scale fermentation systems to aid the supervisor in keeping the batch in good shape thus maximising the product output Since this is also the main goal in the research laboratories a neural network software sensor module has been incorporated into the Fermentor Control Program The idea behind this addition is to enable researcher to predict the available substrate concentration and also to have a tool to validate off line substrate concentration measurements As many expression systems are using the fed substrate to either induce or control the expression of recombinant protein or product it is of importance to know the free concentration of the substrate Too low a substrate concentration leads to low expression and when high
36. e current version of the Fermentor Control Program only supports addition of anti foam by the substrate pump 1 Therefore no slider control is available for this pump It has to be setup manually on the fermentor prior to a run The actions of the pump are being logged during the run and are stored in the collection data file Time panel This is an information only panel When the program is started only the current date and time are shown Once you initiate the fermentation run the start date and time is registered These are saved in the log files and the collection data file together with the user name At the top a timer is started displaying the elapsed fermentation time The profile module as reference timer uses this counter Status bar Elapsed Fermentation Time hh mm ss 002 43 19 Start date ard tine 20 05 01 07 14 40 Curren datz anz time 20 05 01 09 57 59 EP Closed ES i26 aae EG on KE etsutt Default The status bar gives you an up to date view of the state of several interfaces First it tells you whether the TCP IP is open closed or listening See TCP IP client control It also tells you what IP number the host computer has And it shows you if the connection to the fermentor is on or off and finally you can see the current user logged in and the name of the batch owner Holding the mouse pointer over each box in the status bar a tool tip texts will be displayed to tell you
37. e mm DO Setpoint D QU NODE ROC et tie ME Sh ce EEE NE a Nf ee E Response O Threshold Time As shown in the above figure the feed rate is increased at timed intervals and the effect on the dissolved oxygen DO is followed If the culture can utilise the additional substrate aerobically a drop in the DO is seen On the other hand if the respiratory system is saturated the addition of more substrate will not result in a decrease in the DO but instead by product metabolites are formed that can inhibited product formation and cell growth During the feeding pulse the probing controller turns off the dissolved oxygen controller so that the stirrer speed is kept constant This will allow the detection of the DO drop Once the pulse interval has ended the DO is again controlled using the agitation speed This guarantees aerobic conditions and ensures that the oxygen level has the same value at every pulse start For a further detailed look for the work of Mats kesson et al M kesson et al On Line Detection of Acetate Formation in Escherichia coli Cultures Using Dissolved Oxygen Responses to Feed Transients Biotechnology and Bioengineering vol 64 September 5 1999 M kesson Probing Control of Glucose Feeding in Escherichia coli Cultivations PhD thesis 1999 M Akesson and P Hagander A simplified probing controller for glucose feeding in FoxyLogic PhD MSc Mikkel Holmen Andersen Aarhus Denm
38. endix Rule Matrix Sheet FoxyLogic PhD MSc Mikkel Holmen Andersen Aarhus Denmark Email info FoxyLogic com Program homepage www FoxyLogic com 37 Fermentor Control Program manual version released 15 February 2005 Profile Editor file layout 0 Temp 30 False 0 Subs2 7 False 1000 pH 5 False 3000 Temp 37 False 23000 Temp 42 False 24000 Temp 37 False 24000 Subs2 2 False Fuzzy logic control file layout RuleSub2 fuz KKK KKK KKK KKK KKK KKK KKK KKK KKK KKK KKK KKK ko ko ko ko ko ko ko ko ko ko ko ko Rulebase Function This function defines the rules by which the mcd Logic Controller decides how to change the output new Sub SetPoint The rules are read as follows ox If pO2 is A and Sub is B then dSub is C CK CC CK Ck CC CCS CK CC CC CC CK Sk S S E x E E MG KG KG A ko o p02 Sub dSub A B C VL L NM L L NS OK L PS H L PM VH L PL VL OK NM L OK NS OK OK PS H OK PM VH OK PL VL H NL L H NM OK H NS H H NS VH H NM FoxyLogic PhD MSc Mikkel Holmen Andersen Aarhus Denmark Email info FoxyLogic com Program homepage www FoxyLogic com 38 y rd Control Program manual version released 15 February 2005 RuledpO2fuz i LkkkkxkXXRXAAXREXXAREXTAREIEXEAKXEE Rulebase Function This function defines the rules by which the a Logic Controller decides how to change the output new Sub a i SetPoint
39. int for the substrate pumpe NL Negativ Large NM Negativ Medium NS Negativ Smal ZH Zero Change PS Positiv Small PM Positiv Medium PL Positiv Large psi de db di dir dir di dir dio di dir di div dir dir dio dir dir div dir dir di di die dir dir dir dir dir dir dio dir div dir dir dir di div div div dir dir d NL 0 3 3 0 225 0 225 Q15 NM 0 225 0 15 0 15 0 075 NS 0 15 0 075 0 075 0 ZE 0 075 0 0 0 2075 PS 0 0 075 0 075 0 15 PM 0 075 0 15 0 15 0 225 PL 07 65 0 225 0 225 03 FoxyLogic PhD MSc Mikkel Holmen Andersen Aarhus Denmark Email info FoxyLogic com Program homepage www FoxyLogic com 43 Fermentor Control Program manual version released 15 February 2005 SoftSub mf SoftSub Soft Substrate Member Function p dir di dir di dir di dir div di dir div di div dir dir div di dir div dir div div div di dir di div div di div di div div div div div dir div div div div dir di div div dir d Values in this function are the offset from Lhe desired substrate concentration Setpoint VL Substrate Conc Very Below SetPoint L Substrate Conc Below SetPoint OK Substrate Conc Close to SetPoint H Substrate Conc Above SetPoint VH Substrate Conc Very Above SetPoint CK CK Koo Kock ck ck Koo Ko Kok ck Kk Kk Ko KK Kk ko Ko KK S SK ko Kk Ko Kk KK Kk Kk Kk Kk Ko Kk Kk Kk ko ck kk VL 6 4 4 2 L 4 2 2 OK 2 0 0 H 0
40. ion for substrate pump 2 Therefore pumps have to be set to apply with this before the control program is started Please consult with the operating manual for the fermentor Communication port setting The connection between the BioStat fermentor and the host computer goes trough the standard PC serial port and an RS 232C to RS 422 signal converter The converter can be bought in most PC or electronic stores for approximately 100 Please refer to fermentor hardware user manual and the Fermentor Control Program homepage for instructions on wiring or see appendix When the control program is started it looks for the serial communication port to which the fermentor is attached The default port number is 2 as Comm port 1 is usually used for the mouse If Comm port 2 is not available you will be prompted for another port number 1 to 8 If the given port is free then program continues to search for the fermentor and you can see in the status bar when the host program found it See also Status bar If the status bar continues to display the fermentor is OFF then check that the remote button is ON the cable is plugged to the right Comm port and that the converter is working Restart the program to alter the Comm port number if necessary Communication test tool If you are experiencing problems in connecting the fermentor to the PC then you can use the TestComm test tool to check the connection Download the tool from FoxyLogic com place it in the
41. k Email info FoxyLogic com Program homepage www FoxyLogic com 16 Fermentor Control Program manual version released 15 February 2005 The graph window In this window the collected data are shown in a simple XY scatter plot Checking the corresponding check box beside the graph display chooses the different graphs of process data All graphs are shown as default On the other side the graph scale is shown For simplicity it is divided into two different scales and you can change between them by clicking on the scale A tool tip text also tells you how to change it Below the graph selection box there is a window which shows the position of the mouse pointer when this over the graph area If the pointer is over a data point the value of that point is shown together with the time of it T Graphic Control FoxyLogic com 2001 c Graph Layout Print Graph CO CICS a SS PI I NINI PINS NINI NINI GI 3 o O NULAN C PNI Gad OC sd 0000 Ot NI 65 10 NOK Vg rann 35 512 Desired substrate concentration 2 36 Time min 116 zl In the menu of the graph control you can change the layout of the graph window The scaling of the volume and the time axis can be changed Furthermore you set how many of the obtained data point you wish to see Finally you can chose to print the displayed graph at any point during the fermentation run Only the curves shown in the graph will be pri
42. logic is empirically based and model free thus opens doors for control systems that would normally be deemed unfeasible for automation Furthermore fuzzy logic is very robust and does not need precise and noise free inputs to generate usable outputs Finally fuzzy logic is not conceptionaly difficult to understand and it can easily be modified and fine tuned during operation Essentially fuzzy logic revolves around a rule base made of simple plain language if X is A and Y is B then Z is C rules The rules describes the response to a number of inputs X and Y which could be pO pH etc and A and B are linguistic variables representing the input values Although words like large negative small and hot are imprecise they are descriptive of what must actually happen So instead of making ridged control algorithm a small number of rules offer a much more flexible control without any mathematical model of the system This is what experts do when they assist in controlling ill described systems by reasoning from prior experience and act accordingly to it There are several very good tutorials and bibliographies on the Internet if you are interested in learning more about fuzzy logic See the program homepage for more information www FoxyLogic com Fuzzy logic rule matrix So what to do to get the fuzzy logic controller running First of all it has to be decided which parameters can be used for control For the lab bench fermentors there
43. many in ignit luper Number ot neurone in hiddan leger 10 Number ot neurons in oulput kwer sen wi mind Pir funna aco E Zn x H EIE M Vnkdalice nf Tintin hE TaK j i D nin ree nm e nu iu ra m un an wo P Neues Newtwareh Tarinine Curt inl x Tuiimim Dun reon pak Harhar ab anning Manni adi owl ama f m Cycles TU ULL ULI a m Lownie D 10 ud vi vui rae Laming mamanu Te181 LL ih l VA ass Shap mhen emo ys lees than uu VIK Dt 4H5 Fed Prine anne EF linea A n Nuput ere H fu Lez fna FEE TER VALA zi Kae sn KR x m M 5 pee N 7bz The window that pops up is the Neural Network Training Control and in this window you can set the various training parameters as well as test the network performance with data you enter Once you click the Start Training button a graph FoxyLogic PhD MSc Mikkel Holmen Andersen Aarhus Denmark Email info 9 FoxyLogic com Program homepage www FoxyLogic com 26 Fermentor Control Program manual version released 15 February 2005 plotting the error of the training network in predicting the output of the training data and the validation data is depicted It is important to follow these curves as they tell you when to stop training Validation is done by following the root mean square RMS error on the substrate co
44. n your script the correct it and do error checking again before you enable the script Alarm module The alarm module can be used to control the way you log messages and to raise alarms during a fermentation run If you need to know when the maximum agitation speed is reached you can set a maximum speed and get the exact time logged in the Batch Log for you Or if oxygen is dropping below a certain setpoint due to over feeding or foaming you can get an Email send to your normal Email account or to your mobile phone if you have an Email server that will send SMS messages Alarm Settings FoxyLogic com 2004 c Alarm Limit Settings r Email Server Settings Low Alarm Limit High Alarm Limit Email Address foxylogic stofanet dk Agitation Foo 1 Mail Server Address mail stofanet dk Temperature 10 User Name pH Password I p02 Test Email Communication Alarm Handling Settings iv Send Alarm to Run Log Send Alarm to Beep Send Alarm via Email Fermentor Control Program manual version released 15 February 2005 You can change the default alarm limits by entering new limits in the text boxes for low and high alarms These values are stored in a file and will be loaded when you restart the Fermentor Control Program again For the Alarm module to work as an Email server you need to enter your Email address and also the Email server name that you use for your normal Email on your network You can find the server name b
45. ncentration predictions Subpredicted SUbreal Thus the trained network tries to predict the substrate concentration from new data in the validation data set and the output value is compared to the real value in the same data set Once the sum of RMS errors on the validation data set starts to increase during training the network is sufficiently trained and the program will save that network for later evaluation In the sensor training tool that follows the fermentor program a graph shows the RMS errors of the training data and the validation data set On the graph F1 Fn shows the points during training where the network has been saved Stop training when the RMS error on the validation data set increases slowly Using the substrate sensor The trained neural network file sensor nnf will have to be placed in the Fermentor Control Program folder Once a fermentation run has been started you can turn on the sensor and watch the displayed results in the fermentation tank and the graph windows Possible uses of the predicted substrate concentration are to validate other sensor readings such as off line substrate measurements 35 512 Desired substrate concentration 2 224585 JE Time min 115 135 If you decide that the performance of the software sensor is good you can use the fuzzy logic control module to adjust the substrate feed rate to optimise product formation The neural network output must be integrated with the rule base
46. nesssnnesnnsnesnsnnssnssessnenesenene 23 The software substrate Sensor e esscocscocesscessccesccesocesoocesocessecssocesoosecosesscessccesocesocessosssseessese 24 FoxyLogic PhD MSc Mikkel Holmen Andersen Aarhus Denmark Email info FoxyLogic com Program homepage www FoxyLogic com Fermentor Control Program manual version released 15 February 2005 Sampling Training Data sisscesccseiscsesscacssessedsavesssesssvaveceseensecdsvnsssesnnesscecsvesvevevsnsntecosvssusceeovees 25 How much data are needed Psicccissasssinccsccaticancsinscencenticasskincsascechaladccinacanceskecasacaioatsecnatnane 25 The sensor training TOG Me 26 Using the substrate SeISOr ise eisestas ocakeesU EE presa oE VF e REPE ANLE yo eR VU Io 22 PE dE PER o VE eU 2 P PEE dvd ca Pbdd nb bre 27 Current Input Parameters eso eeeecss eessessse sese os tear es Pa seonosssvnnsssssensnsess sontessousseenseeestesssensess 28 PE SUA c 28 Probing Feeding Control P 29 S ripting NTA er c HN 30 PAR Mu 31 Option Settings au esie noi rore sri d op ve qk EXE EFC Ev D Fuel QUA PI EEDIEEHE METER SEVA Mo VH DF V D iooi Tp EN so 33 data sampling PAG ossi ie de 33 TCP IP chent COMMUN m sss troei 34 Host Setup e 34 Firewall BSS UGS T
47. ng generator of the data the FoxyLogic PhD MSc Mikkel Holmen Andersen Aarhus Denmark Email info 9 FoxyLogic com Program homepage www FoxyLogic com Fermentor Control Program manual version released 15 February 2005 fermentation process A problem with neural nets is that they will fit almost any data set giving enough training Therefore noise and errors in the data set are fitted as well if training is prolonged To avoid overfitting the validation set is used to check whether the network is overtrained or needs more training cycles The sensor training tool The training tool is installed together with the Fermentor Control Program and is found in the program folder To begin with you chose to create a new neural network by selecting the New Network in the File menu In the Initialise Neural Network window you chose the number of hidden neurons and press Initialise Network You can now see the network by selecting the View Network in the View menu After this enter the Training menu and select the Load Training Data menu to tell the program where to find the four training file created above input training data output training data input validation data output validation data Finally select the Train Neural Network to begin training be Maar Natamb GaRvara 5 avse Trairar Cro nye 2000 e l r heme es es r iakee Noural Kotwork x Neural Network Layout Nuls of
48. ng strategy When cells are consuming a substrate by products are produced and these will affect the pH in the fermentation tank which normally will decrease By adding new substrate mixed with e g NH4OH pH will change pH Stat Settings pH trigger value Substrate pulse interval 2 min Substrate setpoint C Add substrate below pH setting To start the pH Stat tick the ON field in the low part of the window If you the pH Trigger Value to the pH you want in the culture and turn of the normal pH control the substrate pump will run for a certain time pulse interval with a certain speed Substrate Setpoint Select whether you need substrate added when the pH is below or above the trigger value this depends on the acid or base in the substrate mixture You can control the growth rate of the culture by correctly setting the setpoints FoxyLogic PhD MSc Mikkel Holmen Andersen Aarhus Denmark Email info FoxyLogic com Program homepage www FoxyLogic com 28 Fermentor Control Program manual version released 15 February 2005 Probing Feeding Control Module The probing feeding controller is an extreme controller It will try to push the maximum out of the fermentor by maximising the feeding rate The rationale behind the probing feeding controller is to take advantage of the characteristic saturation in the respiratory system which occurs when overflow metabolism is present Feed Rate Time ee EE EE
49. nted on the default Windows printer The resolution is not terrific and the option is only intended for preliminary analyses and simple data inspection whereas the saved data file can be used in any spreadsheet program most of which have excellent graph options From version 3 0 of the program an extra graph has been added This graph shows the predicted substrate concentration By using the software substrate sensor module current process values are used to predict the substrate concentration in the fermentor broth See Software Substrate Sensor If the module is in use you can enable the graph The data are shown in an insert graph with a time window of 60 minutes The FoxyLogic PhD MSc Mikkel Holmen Andersen Aarhus Denmark Email info FoxyLogic com Program homepage www FoxyLogic com m Visible Graphs 4 v Temp M pH jv p02 Mos JV Substrate Iv Acid v Base I Sub Conc pen Ran 000 08 Curve Point No Point 17 Fermentor Control Program manual version released 15 February 2005 graph is self scaling Use this graph to inspect the correctness of the software substrate sensor If you see large differences sample more training data for this fermentation phase Synoptic process data window A window showing all recent process data in a synoptic display as shown below has been added The latter window is for information only The status of the pumps and volume levels are shown The predicted substrate c
50. ol Program package It gives you the ability to sit at you favourite spot on the planet and perform small or big changes in fermentation conditions without the irking trip to the laboratory The client program only differs from the host program in a few points You cannot control the profile fuzzy logic module or software substrate sensor and you cannot start or stop data acquisition Else it has the same layout as the main control program Host setup You need to enable the server built into the main Fermentor Control Program to allow client computers to access the fermentor Go into the Remote Setup menu and chose whether you want a free of secure connection with the client In secure server mode you specify the IP number by which the client uses to connect to the Internet T Remote Connection x To setup a remote control computer you need to provide the name and ip address Enter these below in the given format V Enable remote connection LEU Protein au dk Local computer NAME Local computer IP Proc ro 20 200 Remote computer IP Be aware though that this will not work if your Internet service provider gives the IP address dynamically to you as it is in most cases In this case use the free connection instead it is not insecure as only the client program can communicate with the host program When you setup the host computer to enable client control the IP address of the host is given Local IP number Remember to
51. oncentration is only shown when the software sensor is turned ON The levels of liquid in the fermentor tank and supply tanks are changing to reflect the process data sampled For this to work best you have to enter data for your specific fermentor setup This only has to be done once in the Vessel and Supply Tank settings found in the Set Options menu fe Current Process Data PoxyLogic cam 2001 c FoxyLogic PhD MSc Mikkel Holmen Andersen Aarhus Denmark Email info FoxyLogic com Program homepage www FoxyLogic com 18 Fermentor Control Program manual version released 15 February 2005 Profiles module The profile module is a significant improvement of the Fermentor Control Program With this control you can design timed programs by which the fermentor should follow Since you are not around 24 hours a day this control will let you change setting points at any time during a fermentation run The elapsed fermentation time is used as reference time Profiles are turned on by selecting the profile enabled entry point in the Profiles menu A Profile Manager FoxyLogic com 2001 c x File Elapsed Fermentation Time 000 02 34 Delete Entry Selected Point Time Control Setpoint pH Profile editor Profiles can be created when the fermentor is running By selecting the Edit Profile menu point a window as seen below is opened Here you select the time when you want the change to take pl
52. ost HPT dip get D 6 Pump Setting TR 7 Communication port setting sssossssesssecssecesocesoosssocessecssocesoossoosssoesssecesocesoosssosssseessocssooseo 7 Communication test t0o0l eessoosscesssesssecssoccesocesoosssoecsscesocessosssocsesscsssecesocesoossscessecesocessosseo 7 BioFlo Fermento qr 8 Loop and pump settings for BioFlo eessssvessssvensvvvensvseenssnesnnnnesnssnesnennssnnsssnnnssssnnnssnnnessnnseee 9 The main control window Ae 10 Control Seri Ws vvs 10 Time PLATA Me tiveness 11 Siatus DAL septimo NE NN PPKS reaS PN EREE sSSvOSE 11 The database Sy SUC MB PR I 12 DTE MNT DER TIT 14 Administrator M P 15 Historian Database Layout T 16 The egraph Wet OW e Tr P 17 Synoptic process data window sescsssasesscesssesccsssonssscsevessseessesnssvosnssossesseonosevesesssovocsevseersessssoanees 18 Jasutl wupnll Gr 19 Profile editor EE a vss esssS besss vSro S ssori 19 Fuzzy logic control Mm du Ul ssssssssesssesissssso ssssscosssssssesscsisses osssso ssssssssssassnssssosssesiesssss sesssss sse 20 Fuzzy een makk 20 Running the fuzzy logic module esesevessssvessesvessesesssnnesnsnnesnsnnesnsn
53. rmentor Control Program entry Finally click remove You may be asked if you want to remove shared files If so answer NO when prompted These files are Visual Basic runtime files which may be used by other Visual Basic encoded programs About time and time resolution in windows systems Available timer interfaces in Windows have very poor time resolution This means that the time points are not precisely spaced with the given sample rate 30 sec and is partly an effect of event based programming Nevertheless to communicate with the fermentor a millisecond resolution is necessary and therefore a special function is used to give this resolution IMPORTANT One drawback is that you have to restart your computer every 23 days to reset the function counter The best thing to do is to restart the computer before every new fermentation run but that will probably be the normal case anyway About decimal symbol in windows systems Due to a bug in Microsoft Visual Studio the handling of the decimal symbol is not easily accomplished The Fermentor Control Program will try to follow the international setting on your computer To know which decimal symbol to use in files used by the program have a look at the output files generated by the program and use the same in your own input files MF fuzzy logic profile and neural network training files Also have a look at the text in input boxes the correct decimal symbols for your system is given there
54. ruary 2005 Mikkel H Andersen March 2002 FoxyLogic PhD MSc Mikkel Holmen Andersen Aarhus Denmark Email info FoxyLogic com Program homepage www FoxyLogic com 53
55. s menu FoxyLogic PhD MSc Mikkel Holmen Andersen Aarhus Denmark Email info 9 FoxyLogic com Program homepage www FoxyLogic com Fermentor Control Program manual version released 15 February 2005 The main control window The main control window allows you to control and set up the fermentor before and during a run The menu bar contains the functions and setup programs needed to start stop save data enable TCP IP remote connection to the client program edit profiles and to control the fuzzy logic and software sensor modules Some of these menus are only available during time when a batch is running All batch and process data is stored in a Access database also kx Main Control FoxyLogic com 2001 c xj File User Batch Profiles Fuzzy Logic Software Sensor view Fiemote Setup About Temp Stirr pH po2 Foam Subs2 AUTO pO2CASC AUTO CASC AUTO AUTO Elapsed Fermentation E 5 E fase ake jl Time hh mm ss Subs2 Setpoint 000 02 58 6 i 000 02 58 Process p02 i 19 41 i Process Subsz n E Start date and time 09 10 01 22 01 46 ae sa E E E 0 00492 Zee Closed 172 16 4 161 ae On ns Default Default Control window The control panel is Temp Stirr pH pO2 Foam Subs2 where you can AUTO pO2CASC AUTO RC AUTO AUTO manipulate set points on E ele eas E the fermentor As shown 21 4 in the figure using the 5 S E graphical sliders and
56. s given in the legend of the above files see Appendix Running the fuzzy logic module When you turn on the fuzzy logic control a green ON will show in the EOE Fuzzy Control window between the pO and substrate slider controls ON You can follow the input data pO current feed rate and dpO 2 and Subs2 Setpoint the output change in feed rate All input and output data and actions M nos made by the control is logged in the fuzzy log file see log files 13 55622 Process ubsz In the submenu of the under the Fuzzy Logic menu you can decide 1 455337 how often the controller should run Furthermore you can turn on and FER 3 off the different types of fuzzy logic control to run your fermentor in dSubs DO stat mode or in pH stat mode 0 09069 FoxyLogic PhD MSc Mikkel Holmen Andersen Aarhus Denmark Email info FoxyLogic com Program homepage www FoxyLogic com 23 Fermentor Control Program manual version released 15 February 2005 Under the Fuzzy Logic menu you can select which functions should be running and how often You can also start a test run where the fuzzy logic controller just saves data in the fuzzy log file Turning on the test run no changes to the substrate feed rate is done so you can see and adjust the performance for the controller without losing your fermentation If you make changes to the control files dpO2 mf dSub mf etc or the rule files you can reset and reload th
57. selected for validation during neural network training You can also use the backup files called TrainingDataln log and TrainingDataOut log You need to edit these files in a text editor and add a line to the top This line is telling the training tool how many data points and input output data there are in the file See appendix for file layout The file layout of these files should be identical to the training data files saved by the Extract Training Data program discussed above How much data is needed There is no easy way to answer this question But to train a neural network for use in process value forecasting as a rule of thumb you need at least 5 times the number of weights in the net Number of inputs number of hidden units number of hidden units number of outputs To calculate the number of hidden units use a general rule of Number of inputs outputs 2 3 This should give 7 inputs 6 hidden units and 1 output unit Therefore for training you need at least 250 data points containing process values and measured substrate concentration It is advisable to try different numbers of hidden units to obtain the best results Besides the training data set you need to have a smaller validation data set which represents the training data set This set is not used for training but to check the network during training A central goal during network training is not to memorise the training data but rather to model the underlyi
58. started After the first log in access is disabled The tool is used to control user access rights to the program There are 3 levels of user rights each with different access rights associated with them Program Functions Batch Observer Batch Owner Administrator Start Stop Batch View Batch Process Data Edit Batch Process Data Changes Process Setpoints Profile Editor Settings Fuzzy Logic Settings Substrate Sensor Settings Internet server Settings Change Options Database Tools Edit User Rights Selecting the Administrator Tool menu will result in a prompt for a password This password can only be obtained from me by sending a request by Email Passwords will only be given to persons who have registered with a valid Email address when downloading the Fermentor Control Program KX KKK KKK AK Mom SOR US SN AN x After entering the password you will be shown a window in which all users in the database are listed A selection panel with Batch Observer Batch Owner and Administrator options are shown to the right Select the user then the access rights FoxyLogic PhD MSc Mikkel Holmen Andersen Aarhus Denmark Email info FoxyLogic com Program homepage www FoxyLogic com 15 Fermentor Control Program manual version released 15 February 2005 and click Set User Rights Historian Database Layout FoxyLogic PhD MSc Mikkel Holmen Andersen Aarhus Denmar
59. tidrop OFF 4 S1 5 S1 6 S1 7 S1 8 are used for setting unit number Unit S1 5 S1 6 S1 7 S1 8 0 ON ON ON ON factory setting Settings of the micro switch S2 as follows Consult you instrument manual to locate the switch l S2 1 S22 S2 3 S24 ON ON ON ON factory setting BioFlo 110 Fermentor For the BioFlo 110 fermentor you need a cable like shown below DB9 PC DB25 BioFlo 110 2 2 3 3 5 7 On the BioFlo 110 box set the Base Address to Zero on the fermentor see Manual page 70 5 3 3 and select AFS mode as protocol Set the subunit addresses to unit 1 FoxyLogic PhD MSc Mikkel Holmen Andersen Aarhus Denmark Email info 9 FoxyLogic com Program homepage www FoxyLogic com Fermentor Control Program manual version released 15 February 2005 Loop and pump settings for BioFlo 2000 3000 4000 and Before you start the Fermentor Control Program you may need to manually setup the use of pumps on the BioFlo fermentor in the right order Thus Acid Base Antifoam and Substrate needs to use the indicated pumps as shown below If not the values and setpoint on the fermentor are not recognised properly by the Fermentor Control Program Feed 1 for Acid Feed 3 for Antifoam Feed 2 for Base Feed 4 for Substrate Finally when you start the Fermentor Control Program for the first time you need to change the fermentor type from the default BioStat fermentor to a BioFlo fermentor type This is done in the Option
60. u offset pum po2 5 min Offset pH Substrate any 17 7 lt 17 data poenty 7 inputs 0 0 1100 1 3 1 1 111 0 0 100 0 1 0 004 1 0 11 0 6 2 1112 0 2 0 012 0 32 11 0 6 6 1116 O 0 008 0 37 O 0 9 11 1122 0 2 0 004 0 18 O 1 7 23 1134 0 9 0 052 0 04 O 1 8 110 1214 0 1 0 018 0 04 10 1 8 121 224 0 1 0 006 0 06 O 1 8 239 360 0 1 0 01 0 05 O 0 0 1000 O 0 p d 75 2 34 1044 4 6 0 07 0 05 75 2 48 1060 O 0 01 0 05 11 2 5 74 1088 O 0 01 0 04 O 2 5 82 1097 0 1 0 04 0 05 1 2 5 191 1216 O 0 1 0 06 O 2 5 338 1378 0 O 0 05 O 2 5 500 1561 0 1 0 04 0 04 1 FoxyLogic PhD MSc Mikkel Holmen Andersen Aarhus Denmark Email info FoxyLogic com Program homepage www FoxyLogic com 48 Fermentor Control Program manual version released 15 February 2005 Standard Script txt Do not delete Private TEMP OnOff STIR_OnOff pH OnOff pO2 OnOff SUB2 OnOff FOAM_OnOff Private TEMP sp STIR sp pH sp pO2 sp SUB2 sp Private EFT pv TEMP pv STIR pv pH pv pO2 pv SUB2 pv ACID pv BASE pv FOAM pv Private SOFTSUB pv dpO2 pv Private OffLine 1 OffLine 2 OffLine 3 Private ReturnVal 13 Do Not Delete or change Above lines Do Not Delete or change below lines Function ReturnValues returning values to fermentor program ReturnVal 0 TEMP OnOff Return Val 1 2 STIR OnOff ReturnVal 2 pH OnOff ReturnVal 3 pO2_OnOff ReturnVal 4 FOAM OnOff ReturnVal 5 SUB2_OnOff ReturnVal 6 TEMP_sp ReturnVal 7
61. u entry under File to download sampled data from the fermentor host computer The response time is dependent on the traffic on the Internet and speed of you Internet connection After a 74 hour fermentation run getting data from the host computer can take over one minute over a modem connection During the data download a progress bar is shown in the status bar that is running from 0 to 100 completed Furthermore the mouse pointer icon is showing a time glass When all data are received the controls and graphs are updated in the main control window Graphing is working like on the host computer and downloaded data can be saved at anytime Importantly when you use the controls to adjust set points these they will not change on the fermentor before you select the Send Data menu entry Thus you can make all changes and then send them to the fermentor It is a good idea to check the settings you made by getting all data again Be aware that you cannot make changes to agitation while the pO cascade is running If you want to set the agitation to a constant speed then turn off the pO cascade send this instruction to the fermentor before setting the stirring set point and sending this to the fermentor Saving Collected Data to file After finishing a fermentation run the user is prompted to save the collected data A file dialogue box is used to select the target where to store the data file The file format is a tabulated ASCII text
62. which is what FoxyLogic PhD MSc Mikkel Holmen Andersen Aarhus Denmark Email info FoxyLogic com Program homepage www FoxyLogic com 11 Fermentor Control Program manual version released 15 February 2005 The database system Starting from version 4 0 a new database system has been introduced The program utilises the widely used Microsoft Access database for the storage of user batch and process data This data is then available for historical investigation using up to date database technology Furthermore all data are easily available for the software substrate sensor during training a future automatic feature PROCESS USERID RUNID DATE START DATE END BATCH INFO RUN LOG The database is built up of three sub databases a user batch and a process database These are linked together by unique UserIDs and RunIDs to form what is called a relational database system TEMP SETPOINT pH SETPOINT When the program is started you will have to login to PO2 SETPOINT the database This is done by selecting the 3983 SETPOINT User Batch menu and selecting User LogOn A DO window as below will be shown You can create a samplen SUB new user profile by clicking Create New User or OFFLINE DATA1 simply log in as default user Password 111 New OFFLINE DATA2 users are by default set to have Batch Owner access CFFLINE DATAS rights 1 Current User FoxyLogic com 2001 c
63. write this number down and take it with you since you will need it to hook up to the host program Once a fermentation run is started the first field in the status bar should display the text Listening If this is the case you can now connect via a client to the host control program Firewall issues The server has not been tested for use when it is situated behind a firewall so I m keen to know of success or type of problems from users You will need to get the firewall administrator to setup a static TCP IP port mapping for the Fermentor Control Program embedded server The port that the server is listening on has number 345 If you are using a personal firewall like ZoneAlarm you have to enable the Fermentor Control Program as safe for Internet communication Contact me for further information if needed info FoxyLogic com FoxyLogic PhD MSc Mikkel Holmen Andersen Aarhus Denmark Email info FoxyLogic com Program homepage www FoxyLogic com Fermentor Control Program manual version released 15 February 2005 Client setup Once the client program has been installed on the remote computer and it is connected to the Internet the first thing to do is to enter the host computer IP number Do this by selecting the Remote Host menu entry When you have entered the host computer IP address a network ping is sent to the host computer If there is a connection all you have to do is to select the Get Data men
64. y looking under Email accounts in your favourite Email client Use the Test Email Communication button to check that it is working The Email address and server name are stored in a file and will be loaded when you restart the Fermentor Control Program again FoxyLogic PhD MSc Mikkel Holmen Andersen Aarhus Denmark Email info FoxyLogic com Program homepage www FoxyLogic com 32 Fermentor Control Program manual version released 15 February 2005 Option settings In this window you can enter your fermentor specific data to fit your setup All these settings are saved in the Windows registry and thus should only need to be set once or when ever you change you setup m Set Options FoxyLogic_com 2001 fc Fermentor Type Vessel Type Offline Data Types License Key Vessel and Supply Tank Settings 3 Vessel Volume 2000 mL Start Volume 1100 mL Substrate Volume 1000 mL Acid Volume 40 m Base Volume 3 mL Anti Foam Volume 8 mL pms In Fermentor Type you can select your default fermentor type and the default serial communication port NOTE Currently only B Braun BioStat and New Brunswick BioFlo fermentors are supported but as others become available these will be included See www foxylogic com for more information In Fermentor Type you can also select the data sampling rate which defines how often process values are collecte

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