Jurica Bioreactor - BiocomSoftware.com
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1. now write out each decimal place by shifting digits one by into the ones place and writing the truncated value for i 0 i places i tempfloat 10 0 digit int tempfloat itoa digit amp outstr c 10 once written subtract off that digit tempfloat tempfloat float digit if extra gt 8 and not rightjustify for int i 0 i lt extra i outstr c outstr c 0 return outstr EXAMPLE APPLICATION include floatToString h set to whatever is the location of floatToStrig void setup Serial begin 9600 char buffer 25 just give it plenty to write out any values you want to test now run a series on the floatToString function looking at the precision of the float Serial println floatToString buffer 1000000 321 5 Serial println floatToString buffer 1000000 321 5 Serial println Serial println floatToString buffer 100000 321 5 Serial println floatToString buffer 100000 321 5 Serial println Serial println floatToString buffer 10000 321 5 Serial println floatToString buffer 10000 321 5 Serial println Serial println floatToString buffer 1000 321 5 Serial println floatToString buffer 1000 321 5 Serial println Serial println floatToString buffer 100 321 5 Serial println floatToString buffer 100 321 5 Serial println ll2. PHE 5431 10 T T handle high tem perature pH electrode PHE 5431 10 T T handle high tem perature pH electrode with ATC High temperature insertion type pH electrode High temperature insertion type ORP electrode PHE 5431 10 shown ORE 5431 10 T T handie high temperature ORP electrode smaller than actual size t Specify ATC sensor PT100 for 1002 Pt RTD or PTIK for 1000 Q Pt RTD for additional cost Note PHEH 51 2 MNPT installation fitting is required for first time installation see omega com for installation fitting Comes complete with operator s manual NT M il a Ordering Examples PHE 5431 10 high temperature pH electrode U S A and Canada PHE 5431 10 T T handie high temperature pH electrode and PHEH 51 D 45 Our Industrial pH Instrumentation and Electrodes product line continues to expand visit omega com for new details sii Y PESCE e e 4 x CM 4 i y ir op eer s 4 v A Ex z f et 20 gt 1 5 ne ir i TI i IN PA ec 2 Cable unsealed Disassembled Cable secured assembled et The 1058_0 PhidgetPhSensor transducer NaOH addition line eristaltic pump NaOH resevoir r 4 inch A Male Luer to medical tubing 6 4MM tubing adapter Part MTLL360 0 22uM Female leur lok to male luer slip Syringe fie NS Fem to Male Luer Checkvalve Part VPS5401068N Female Luer to 10 32 t
3. 2 looking at effect of changing precision Serial println floatToString buffer 100000 321 6 Serial println floatToString buffer 100000 321 6 Serial println Serial println floatToString buffer 100000 321 7 Serial println floatToString buffer 100000 321 7 Serial println Serial println floatToString buffer 100000 321 8 Serial println floatToString buffer 100000 321 8 Serial println Serial println floatToString buffer 100000 321 9 Serial println floatToString buffer 100000 321 9 Serial println check negatives and rounding and some edge cases Serial println floatToString buffer 5004 321 5 Serial println floatToString buffer 5004 321 5 Serial println Serial println floatToString buffer 99 999 3 Serial println floatToString buffer 99 999 3 Serial println Serial println floatToString buffer 100 1 Serial println floatToString buffer 100 1 Serial println Serial println floatToString buffer 100 999 1 Serial println floatToString buffer 100 999 1 Serial println Serial println floatToString buffer 54 321 8 Serial println floatToString buffer 54 321 0 Serial println Serial println floatToString buffer 8 321 5 Serial println floatToString buffer 0 321 5 Serial println Serial println floatToString buffer 1 0001 5 Serial pr
4. L eV 1 6 NV 5 689SESIN rawway dura c ui qsna 09 TILA ung imdepe Burqat EPIN NW t9 o 13n 2 amp ui2 4 Ion UN JP Y san apa 3 SHAG tHEJ su se LINEA SI N96 6 VEJ OLO WRISSY durg o 2400115 yoy jan jun pys yua uuig Filtration Overview Pressures were tested up to pump maximum generation with H O Expired Medium T Y MU Son 4 inch nedic f tubing DI Female luer to 1 4 6 4mm Fem to Male Luer Male Luer to tubing barb Checkvalve E 6 4MM tubing adapter Part FTLL 360 Part VPS540 068N Part MILL360 Female Luer to 1 4 18 NPI 1 8 NPT thrcad Sacket Weld Fitting Nickel plated brass to Male Luer 1 8 Pipe Part amp WU 31507 87 Part 18MTLL Tapped to 1 2 13 and NPTU4 18 Part 45005K 191 Stainless steel finishing washer k 2 Silicon Grommet Panel Hole 13 16 0 8125 ID 0 50 Part 1061T28 Stainless steel Flange Nut 1 27 13 Thread Size Silicone O Ring ASS68A 014 Part 9396K 19 SSS r1 22222220j N i 72 BZ DR e si LL 12 se te Aluminum Tubing 1 2 OD 37 ID External thread 1 2 13 Part 89965K 54 ooo oom I Se am m m w o 4 m ooo t i I U Spinner paddle Overview This impeller design is a proof of concept It was hand shaped from teflon and is to be replaced with a stainles
5. Serial LED s FTDI USB Controller Digital Pins Qi L gt we OP 7 NEM Power LED iunmi ti sun c9 9 meos Reset Button S ham E22 225575 ICSP Header Power Jack i 4 POUER ATmega 328 ao MSV Gnd Vin gt gt 16 MHz Crystal Oscillator Power Pins Analog Pins LCD GND to LCD pin 16 Backlight LCD 45v to LCD pin 15 Backlight LCD 10K potentiometer LCD pin 3 to potentiometer wiper middle spad LCD pin 2 to 5v Power LCD pin 1 to GND Power L AGLI NI 304 e fe bad T artit OALLLELELELL e Wed TT 4 2 Pt Po 2 m em MANIT Pin13 pH LED status Pin12 LCD DB7 to LCD pin 14 Pin11 LCD DB6 to LCD pin 13 Pin10 LCD DBS to LCD pin 12 Pin9 LCD DB4 to LCD pin 11 Pin8 LCD EN to LCD pin 6 Pin7 LCD RS to LCD pin 4 wm m twang PAY 2 yep dep ead Pin5 LCD RW to GROUND Pin4 NaOH pump trigger Pin3 pH Buzzer wo Outn 4 i ATMEGA 328 t SAQUE eeu ind B d Pint PH TEMP ADC Pino PH ADC WOD 10 u2 upsnoun 6007 2 NDT2955 eo UIN 1C4 MC332690 5 0 T 5U GND 6ND GND GND Arduino 2009 NIIT END RESET SCIOPBS 11 5084 moshpesz 55082 061081 XTALI Chee AREF POLSECS RUCC FOCDEC4 AGND POLDECI POLZPCZ ucc eoc LCI GND RDCOoPC 0 NOD RINDEDE XTAL
6. w High Temperature High Pressure Steam Sterilization Easy Installation Applications High Temperature Environment Continuous Processing Applications Harsh Conditions Steam Sterilization The high temperature insertion type electrode is designed for periodic exposure to steam sterilization or continuous high temperature This pH electrode is housed in a durable thermoplastic PAS body and is rated for temperatures up to 135 C 27 5 F The use of the double Porous PTFE liquid junctions with matched viscosity electrolytes provides a reference cell which permits extended periods of pH measurements in the presence of sulfides or other silver com plexing agents This electrode also incorporates pressure com pensating devices to protect the electrode from extreme tem perature induced pressure deviations Ten foot cable length and BNC connector are standard Specifications pH Range 0 to 14 pH Temperature Range 5 to 135 C 25 to 275 F 25 psig La Pressure Range 500 psig 25 C si Accuracy 0 1 over full range PHE 5431 10 T shown Impedance 125 Q standard version smaller than actual size Reference Cell Double junction KCVAgCI KNO3 Reference Junction Porous PTF Wetted Materials PTFE glass membrane polymer outer body i EPR O Rings E Response Time 10 seconds to 95 of reading Drift Less than 2 mV per week To Order visit omega com phe543110 for Pricing and Detalls PHE 5431 10
7. partial pressure Similar to CO dissolved O influences cell activity and division Again the inherent design of a closed and vented spinner flask is not adequate for the dissolved O needs of larger volumes of spinner culture Although less significant than dissolved CO concentrations controlled addition of dissolved O often allows for peak activity to be maintained throughout density and volume curves Finally the issue of contamination has been of significant concern The need to open the flask almost daily to perform cell counts and add medium has led to significant losses due from contamination even within class Il environments The Jurica bioreactor design is intended to alleviate this by allowing sampling and medium addition via sterile off the shelf medical valves Testing to date has allowed both the introduction and removal of medium in even the most hostile of environments without contamination issues Programmable logic controller PLC Overview The Arduino Duemilanove was chosen as the highest performing board in its price range With analog and ADC pinouts sensitive to the mV mA ranges it can communicate directly with pH O and temperature sensors with minimal noise and amplification It is also capable of running full Java and Shell scripts The USB port and Buildroot linux support wireless giving the option to interface with the Bioreactor wirelessly Additional memory was added using external USB flash RAM Pin 13 LED
8. 1 2 13 on one side and NPT 14 18 on the other Silicon Grommet Pane Hole 13 16 0 3125 ID 050 Parte LOG T28 Silicone O Ring ASSSRA 9014 AQ Poni9 396k 19 Stainless steci Flange Nut L 2 13 Thread Sire AAO SIS MAAN CLL Lp E we m r b AE c omo e NS i e GP D E R sie cenere 4 medical tubing vi i Female luor to 1 4 6 3mm ruhing harh Pari FTLL360 Fen io Male Luer Checkvalve Part VPSS4N 068N 0 22uM Female leur joh to male luer slip Syringe finer Fem to Male Luer Chock valve Part VPS5401068N u 1 8 NPT thread Past JAMTLL Custom adapter Tapped to 12 13 on ome side 10 32 thread to iil NPT 14 18 on the other malo luer Parte KFTL E Biack UOxide O Suc Swivel Silicone O Rings n g Flange Nut ASS6BA 9014 8 1 4 20 Parrvo 196K 19 1 2 Width WR Height Part 90477 4029 Push in High Temperature Flexible Grommet M535489 35 AN 911 A4 7 Silicon Grommet Panel Hole 13 16 40 8125 ID 7 0 50 1 4 ID S OD s Part 1061T28 Pari 1061T25 Silicone poo Driginat Cap Drilled nut ASS68A 1129 1 4 inch stuinles steel 13 16 th hole and 7 16th hole Pans 9306K 140 o D d finishing washer t Silicone D Rings 4 2 ASS6HA 4010 1 2 Inch i Part 9396K 15 stainless sieel M i Finishing washer Stainless e e Nut
9. CL MAX PARAM CHAR NUM rest of the line parsed out int cmd n parms populated size of cmd parm up to max params char cmd parm CL MAX PARAMS NUM CL MAX PARAM LEN up to six parameters of twelve characters each separated by commas or spaces unsigned int cl i cl j cl k cl char cl in ch char process command line if Serial available Serial println Receiving delay 500 cl_i 0 cl_j 0 cl_k 0 cl 1 0 cmd_line 0 0 cmd_parm_str 0 0 clear param string cmd_n_parms 0 for int x x lt CL_MAX_PARAMS_NUM x cmd_parm x 0 0 clear out previous parameters get a command line boolean first_word true while Serial available cl_in_ch upper Serial read cl in ch Serial read cmd linelcl i cl in ch if first word 88 cl in ch first_word false cmd_str cl_i 0 add null terminator cl_i continue if first word cmd str cl i cl_ in ch else build cmd parm str cmd_parm_str cl_j cl_in_ch if cl an che er in enes cmd_parm cl_k cl_1 0 cl_k cl_1 0 else cmd_parm cl_k cl_1 cl_in_ch cmd_n_parms cl_i end while if first_word we had parameters so cmd_parm_str cl_j 0 null terminate param string cmd_parm cl_k cl_1 0 and the last param cmd_n_parms cl kri remember number of parameters k doesn t get a chance to increment for last parm
10. at google Version 0 4 20120525 5 25 2012 Author Mike Rightmire Jurica Labs Center for the Study of RNA University of California Santa Cruz mrightmi ucsc edu SI include WProgram h include lt LiquidCrystal h gt include pHduino h include float2string h include commandline h include string h include stdlib h include lt avr eeprom h gt include freemem h Creates the LCD instance LiquidCrystal lcd PH LCD RS PIN PH_LCD_RW_PIN PH LCD E PIN PH LCD D4 PIN PH LCD D5 PIN PH LCD D6 PIN PH LCD D7 PIN ordinary variables char myStr 16 int val E int val R int val T float E float R float T float pH int i float f f2 unsigned long int my timero unsigned long int my timer boolean pH alarm status true struct of parameters struct myRec T boolean start flag unsigned int time between acquisitions ms boolean temperature sensor flag float temperature constant celcius boolean pH alarm flag float pH inf float pH sup float pH_add_Na0H float pH add HCl myRec void parameters reset void myRec start flag true myRec time between acquisitions ms PH INITIAL TIME BETWEEN ACQUISITIONS MS myRec temperature sensor flag false myRec temperature constant celcius PH TEMPERATURE VALUE INITIAL CELCIUS myRec pH alarm flag true The following sets pH ALARM boundaries myRec pH_inf 7 0 myRec pH_sup 8 0 The follo
11. 2 RESETH 0861 RULC NE osto GPIDI QuT 1 903 GPI0D UNTO POZ T lt DFO1 PXDIPOD GNDI GHD2 UCC31 HE GNDS TEST GPI03 amp THEBRE DM Gj ow N AGIDO SLEEPN MBRXD RB 1t ik narxo P9 PLC Code Overview The Arduino uses a variation of the C programming language These are a series of customized sketches derived from an opensource model written originally by Carlos Neves et al pH system input parameters and the control logic for pumps and displays were added Mr Neves is appropriately credited in the comments of the script and should not be removed pH_subsystem_Bioreactor1_v1_0 5 25 2010 pde pHduino pde pHduino firmware for Arduino Copyright c 2089 Carlos A Neves http code google com p phduino This program is free software you can redistribute it and or modify it under the terms of the GNU General Public License as published by the Free Software Foundation either version 3 of the License or at your option any later version This program is distributed in the hope that it will be useful but WITHOUT ANY WARRANTY without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE See the GNU General Public License for more details You should have received a copy of the GNU General Public License along with this program If not see lt http www gnu org licenses gt Version 0 4 20090920 Author Carlos A Neves caneves
12. 5 key to decrease the differential to the desired setting minimum 1F maximum 30F 4 Press the SET key again to access the heating mode The LCD will display the current mode C1 for chiller mode and H1 is for heater mode Press the SET key once more and programming is complete Controller MUST in the C1 mode for correct operation Controller will automatically drop out of program mode and return to operating mode 30 seconds after last key press Troubleshooting Controller Error Messages Display Messages e E1 Appears when the up or down Okey is pressed when not in the programming mode To correct if the E1 message appears even when no keys are being pressed replace the control e E2 Appears if the control settings are not properly stored in memory To correct Check all settings and correct if necessary EP Appears when the probe and or flow switch is open shorted or sensing a temperature that is out of range To correct Check to see if the sensed temperature is out of range If not check for probe damage by comparing it to a known ambient temperature between 30F and 220F Replace the probe is necessary Also check for proper water flow through heater If water flow is correct flow switch EE Appears if the EEPROM data has been corrupted To correct This condition cannot be field repaired Replace the control e CL Appears if calibration mode has been entered To correct Remove power to the control for least
13. Cursor 11 1 lcd print ALARM digitalWrite PH BUZZER PIN HIGH else pH_alarm_status false lcd setCursor 11 1 lcd print B lcd print digitalWrite PH BUZZER PIN LOW else pH_alarm_status false digitalWrite PH_BUZZER_PIN LOW void process_cmd void placeholder for serial line input University of California Santa Cruz mrightmi ucsc edu Bioreactor1 pH Subsystem based on pHduino by Carlos A Neves v 1 0 Author Mike P Rightmire University of California Santa Cruz June 2010 MRightmi UCSC Edu Jurica Biology UCSC Edu S 11 firmware version define PH PHDUINO VERSION 0 4 20090920 define PH PHDUINO CODENAME acetic acid define PH BIOREACTOR1 VERSION 1 0 20100610 define PH BIOREACTOR1 CODENAME BIOREACTOR1 button pin define PH BUTTON CTRL PIN 2 buzzer pin define PH BUZZER PIN 3 LCD pins define PH LCD RS PIN 7 define PH LCD RW PIN 7 unused define PH LCD E PIN 8 define PH_LCD_D4 PIN 9 define PH_LCD_D5_PIN 10 define PH_LCD_D6_PIN 11 define PH LCD D7 PIN 12 Status led pin define PH LED PIN 13 Sensor pins Previously ADC pins define PH PH ADC PIN define PH_REF_ADC_PIN 1 define PH_TEMP_ADC_PIN 1 Add NaOH trigger pin define NAOH_TRIGGER_PIN 4 Sketch parameters define PH_PH_LOWER_LIMIT 0 0 define PH PH UPPER LIMIT 14 0 define PH PH VOLTAGE ADC LONER LIMIT 0 0 define PH PH VOLTAGE ADC UPPE
14. Jurica Bioreactor Design notes and schematics Engineering reference only Not intended to replace the user s manual Mike Rightmire June 24 2011 Contents Genera V N Lost MINER MEME MEM EE EI EMI IE 2 Programmable logic controller PLC nnnm nnne nnne 4 OV EV WCW PTT T m 4 PLC COOC RR EE E I 6 OVERVIEW een 6 pH_subsystem_Bioreactor1_v1_0 5 25 2010 pde ana anha rea e nera enen reper nenen rene pene 6 91910 VI 00 RR RO O RT 7 es 8 float2string h ieri 8 COMINCI 10 FUMIO COME OW elite aa 11 Sad MT M 11 VISSE CE ARR EE 12 OVVIO antiorario 12 PIDINE ian 14 So E DO PUR DEIMNS ODORE 14 SECC ARR RO ERE 16 Collapsed for insertion ei 16 ICE RI 17 SER E 18 IMEGIUM AANO Nrct 19 SAID NE ee ee een ee een 20 VET NENNT 20 ON ren ee CA EEE I 21 SO I 21 i 1 a MN RI 22 VET RA 22 Tg EAU EEE 23 VET RR 23 NAO Fa CITI Na NING pantera phase tentate TALIA TANA TAN 25 Perstaltic RO 26 OCS MM Tu 26 misi MR I E 28 VEN 28 General Overview The Jurica bioreactor project was implemented to improve and maximize the growth rate cell density and general cellular activity of suspension HeLa cells at low 3 liter volumes A secondary motivation was to create a growth environment w
15. R LIMIT 5 0 How many CONSECUTIVE pH senses ABOVE setpoint will trigger a single addition of NaOH Each sense happens at APPROXIMATELY one second define PH ADD NAOH NUM READINGS 15 Time between NaOH additions REGARDLESS of pH sensings define PH TIME BETWEEN ADD NAOH MILLISECONDS 00000 60 seconds define NAOH LENGTH TRIGGER MILLIS 1000 constants currently unused define PH R constant J K 1 mol 1 currently unused define PH F 96485 Faraday constant C mol 1 8 31451 general gases Gain of the non inverter amplifier stagel of the schematic circuit considering a nernstiane glass electrode delta E 59 2mV pH and no influence from offset voltage divider Gains currently usued thanks to Phidgets 1130 pH interface freemem h this function will return the number of bytes currently free in RAM written by David A Mellis based on code by Rob Faludi http www faludi com int availableMemory int size 1024 Use 2048 with ATmega328 byte buf while buf byte malloc size NULL free buf return size j float2string h floatToString h Tim Hirzel tim growdown com March 2008 float to string If you don t save this as a h you will want to remove the default arguments ki uncomment this first line and swap it for the next I don t think keyword arguments compile in pde files char floatToString char outstr fl
16. R PURPOSE See the GNU General Public License for more details You should have received a copy of the GNU General Public License along with this program If not see http www gnu org licenses Version 0 4 20090920 Author Carlos A Neves caneves at google Version 0 4 20120525 5 25 2012 Author Mike Rightmire Jurica Labs Center for the Study of RNA print ADC value and voltage of electrochemical potential val E readADC PH PH ADC PIN PH TIME ADC READINGS MICROSECONS E 1 val E 5 0 1024 R PH GAIN STAGE1 PH val E analogRead 1 E val E 5 0 1024 Serial print info val E pH sensor pin Serial println val E Serial print info E mili volts Serial print E Serial println V pH 7 2 5 val E 200 00 8 257179 0 000941468 T Calc takes into account temp T pH 0 0178 val_E 1 889 Most basic calc no adjust for temp pH 0 0178 E 200 1 889 Basic calc using voltage not ADC input floatToString myStr pH 2 lcd setCursor 0 1 lcd print pH lcd print myStr lcd print Serial print info pH Serial println myStr print alarm signal if myRec pH alarm flag true if pH lt myRec pH inf pH gt myRec pH_sup Serial println alert pH ALARM ACTIVE pH alarm status true lcd setCursor 11 1 lcd print digitalWrite PH BUZZER PIN LOW delay 200 lcd set
17. Stainless Steel Flange Nut 12 13 Thread Sire ovt utt Custom Stainless steele Tubing 1 4 OD 194 ID 1 4 28 0 2280 external thread 10 32 Internal thread Custom stainless steel 12 OD 37 1D External thread 1 2 13 WIDEMOUTH Medium supply Bottle Sampling Overview A significant issue has been contamination whilst adding medium or sampling for cell density The medical grade luer one way check valves to withdraw active medium without potential backwash from the exterior This has been successfully tested in extremely contaminated environments active bacterial incubators J sampling system uses off the shelf a I I i Lj I I I U l i i I LI L U 4 r peany euImUI TE OI pra PEUIDIXS 08CC 0 OC tl qI 96170 wnunxew qO tl Tuign Jag sso urg s Woisny nn s nce mu nu opis pousrum jo uonrsod 30N aauxux Sursum DI jams ssajurejs des 10 Suvo Joy MOL L uos oj ujs pym pajud o des 12uujds Wet T9 Mi 87 b 1 IN Hu Fs ssapums TILNX amd 1n ajeur o PRAM TE 01 d v3 i ar a MITT PACI T KI ONNNNNNNNNNNNNN UNNNNNNNNNNNNNN N89010F Sd A H d 3A EA3221 dan SUN or wag 09 T1L4 Wed ra 9 gio E s STLIGOL nung o dO 8 6 CI t l Fwqm x amp e PER y 8I t 1 A WINT9 Me 4 INN Buja p 12215 sxojureis
18. U adewj F od q j CI xew p610 qo QUI p 6 5 inches tip to center of bend E Y Gg e puaa bed SY xddy j Supeonp jeuuojxo I Z I J peor jeurojxa JO SOYSU Q E i 07 4 130 lt SOYOU P E97 euoruiodoud Jou a eos 0 JOU 93ewI odid GO yaur 7 1 6 5 inches tip to center of bend Mns o 4 N EX Y FU jejoj SOYOUI spud gjoq uo Surpeslq pes y jeulojxa J IVNAALNI C 70T oz pnjo N JO qour SUO jeuoniodold 10u SOUIUI p C97 oleos 0 ou oSeu odiq HOYS CI xeu 7610 dO UU p T Pipe assembly Collapsed for insertion Inserted un Sealing Finishing washers Note that the finished convex side is facing the lid where the seal will be made The flat washer here represents the lid against which the finishing washers will seal This is here for demontration only and is not a part of the final assembly O Rings are pressed against the surface of the lid as well as against the pipe itself by the sloping surface of the convex side of the finishing washer washer Teflon flat Medium addition m nel Male Luer to fn 4MM tubong adapter Part MFLLI60 0 22uM Female leur lok to male 8070 lucr slip Syringe filter Fem to Male Luer heckvalio Pate V PSS401068N Female Lauer 10 1 4 18 NPT Nickel plate brass Part WU 31 507 87 Custom adapter Tapped to
19. WG24 D224V 1aV for tre SL type GND Blazk Zirzuit protection This motor is not equipped with a zirzuit for protection against overvoltage and zonnestion to terminale at the inzorrest polarity Be careful not to apply surge voltages that exceed the rated voltage and not to connect to the inzorre gt t polarity MWP1000 mWP1100 Zutting hole dimensione Sutting hole dimensions 55 35 2 5 30 d w ra 1 X 683 bored hole 85 0401 A _ 4 04 San A Waen using front Screw 7 T a S2W v mounting mounting 10 amp A j s 705 gt m 3 M3TAP Panel thizkness 1 0 to 1 2mm WP10 CM 7 7 L Panel tnirkness 1 0 to 1 2mm 18 5 i weignt 230g WP11 CL Weigat 230g Using an optional panel Taizknes5 1 2 Material properties 3U3304 Heating Overview The heating system uses an external wrap around spinner flask heating element Heating control is provided by an external Auqualogic thermostat containing its own high temperature probe and control circuitry The PLC is not needed for temperature control Aqualogic TR115SN Part 7909 23115 aquaagic TR115SN TR230SN EC115R and EC230R Controller Operation and programming Step Enunciator Description Display 1 Forc Fahrenheit or Celsius Fl 2 S1 Blinking Setpoint Temperature E24 3 DIF Blinking Differential Temperature GI 4 C1 or H1 Cooling or Heating Mod
20. ake sure we round properly this could use pow from lt math h gt but doesn t seem worth the import if this rounding step isn t here the value 54 321 prints as 54 3209 calculate rounding term d float d 0 5 if value lt d 1 0 divide by ten for each decimal place for i 0 i places i d 10 0 0 5 pow 10 places this small addition combined with truncation will round our values properly tempfloat d first get value tens to be the large power of ten less than value one if value lt tempfloat 1 0 while tens 10 0 lt tempfloat tens 10 0 tenscount 1 if tenscount gt 0 charcount tenscount else charcount 1 if value lt charcount 1 charcount 1 places minwidth 1 both count the null final character if minwidth gt charcount extra minwidth charcount charcount minwidth if extra gt and rightjustify for int i 0 i lt extra i outstr c write out the negative if needed if value lt outstr c if tenscount outstr c 0 for i20 i lt tenscount i digit int tempfloat tens itoa digit amp outstr c 10 tempfloat tempfloat float digit tens tens 10 0 if no places after decimal stop now and return otherwise write the point and continue on if places gt 60 outstr c
21. e t Liquid Crystal Display LCD The LCD display provides a constant readout of the sensor temperature and indicates if the output relay is energized When the S1 enunciator is constantly Illuminated during operation the relay is energized the display is also used in conjunction with the keypad to allow the user to adjust the set point temperature differential and heating cooling modes Programming Steps and Display The control can be programmed in four simple steps using the LCD display and the three keys on the face of the control See photo for display and keys 1 To start programming press the SET key once to access the Fahrenheit Celsius mode The display will show the current status either F for degrees Fahrenheit or C for degrees Celsius Then press either the up arrow or down 1 arrow key to toggle between the F or C designation 2 Press the SET key again to access the set point temperature The LCD will display the current set point temperature and the set point enunciator will be blinking on and off to indicate that the control is in the set point mode Then press either the up key to increase or down key to decrease the set point to the desired temperature 3 Press the SET key again to access the differential The LCD will display the current differential and the DIF enunciator will be blinking on and off to indicate that the control is in the differential mode Then press either up T key to increase or the down
22. er attachments were chosen for disposability sterility and so flow direction was non dedicated and pipes could be allocated for different uses based on circumstance The lower sidearms are dedicated for probe housing Shown is the Omega PHE 5431 10 high temperature pressure pH electrode The probe housings are high temperature pressure marine hull cable run anc 765000 Silicon o rings provide the sealing Liquid Tight Wire Seal Provides low cost watertight cable entries into panels and junction boxes UL and CSA approved to work with round and flat cable Resistantto saltwater gasoline alcohol ketones and mineral oil Safe underwater to 300 ft 150 PSIG Vendor Ancor Marine Grade Products SKU ANC 765000 Weight 060 NPT Size 1 2 Min Max 5 47 ANG Range 20 4 Description Round Cost 15 29 Quantity 1 Click to Enlarge Add to Cart Product Pictures anc 765000 autoclavable marine hull cable run 13 0 inches total height iping Schematics P Burpeolyj TVNAALNI C 01 Jo your suo tm sur a 6 5 inches tip to center of bend _ ir 6 5 inches tip to center of bend gt Fre A en VIDA ur pusg pusg beg SP v xddw ssuour GET seyout G euriaeQqueo edrd Huote qabuen sog eutT1823zuao edtd Huote uabueT 13 0 inches total height your Ty pueg Bea SH xddy Surpeoly TVNYALNI ZE 01 jo Your SUQ jeuonsodoid 10u ajeos oj JO
23. five seconds Reapply power If the CL message still appears replace the control Aqua Logic Inc 8268 Clairemont Mesa Blvd Suite 302 San Diego CA 92111 Tel 858 292 4773 Fax 858 279 0537 Email info aqualogicinc com www aqualogicinc com
24. here sterility could be maintained outside of a class Il cabinet or incubator even during sampling and media addition The primary design requirement is to create an easily reproducible bioreactor that could be built for less than 5000 from existing off the shelf components so additional vessels could be assembled quickly as required The Jurica Lab cultures HeLa cells for the harvest of active macromolecular spliceosome We have conceptually designed the Jurica Bioreactor with three primary concerns towards maximization of this harvest The first is the collection of a very active and healthy spliceosome The spliceosome is most active when the cells are rapidly dividing and our goal is to culture cells which are doubling less than every 24 hours The second concern is the volume of spliceosome harvested Since more active cells create more of the macromolecule a larger number of these highly active cells will increase the overall harvest In a standard spinner flask the cells are able to reach a maximum of 4x10 cells per mL based on a number of constraints Our reactor is intended to alleviate these constraints and thus increase the maximum cell density Some of the more recognized constraints are Surface contact As cells have greater cell to cell contact rate they become less active There are a number of chemotactic factors both positive and negative which are affected by the direct adhesion of cells to one another There is an idea
25. hread Stainless Steel Stainless steel Fanes Nut 1 4 inch finishing washer Flange Nut a 1 4 28 Push in High Temp Grommet M835489 35 AN 93 A4 7 1 4 ID 5 8 OD Part 1061 T25 Silicone O Ring ASS68A 010 Part 9396K 15 gt gt gt gt gt ANANNNAANANANNI LE ZIA i o wi e ee nn Ars ADAMA M vum 1 T Stainless Steel 1 4 OD External thread 1 4 28 pr Internal thread 10 32 M i NOTE End must remain T above medium surface omo o SS mc m m o Sar Peristaltic pumps Overview Two Welco WP1000 peristaltic pumps DC motor 8 24V 20 150RPM WP10 P1 4M2 W4 CP reside on the control box and are mounted in with the optional mounting panel inch sterilized medical tubing is threaded through the pumps and attached to vessel pipes with medical grade luer locks zip tie secure ties on the tubing luer connection is recommended to add additional slip resistance for high pressure applications including the medium addition and NaOH systems In this configuration pressure has been field tested to the maximum capability of the pump The pumps are driven by outside power directed by the Pump control circuit see above The pump can be triggered by either the PLC or a manual button on the control case M Dimensions WP1000 amp WP1100 WELCO DC Brushless Motor amp Gear WMotor wiring terminal dimensione diagrame 240210 Red A
26. intln floatToString buffer 1 0001 5 Serial println Serial println floatToString buffer 0 000001 5 Serial println floatToString buffer 0 000001 5 Serial println Serial println floatToString buffer 0 000001 5 Serial println floatToString buffer 0 000001 5 Serial println Serial println floatToString buffer 0 00001 5 Serial println floatToString buffer 0 00001 5 Serial println Serial println floatToString buffer 0 000099 5 Serial println floatToString buffer 0 000099 5 Serial println alternative technique that depends on stdio h Serial println Serial println dtostrf 1 0001 2 5 s 5 char s 32 Serial println dtostrf 1 0001 2 5 s delay 1000 Serial println void loop commandline h commandline h http www arduino cc cgi bin yabb2 YaBB p1 num 1250265171 1 1 With some modifications define CL_MAX_CMD_CHAR_NUM string define CL_MAX_PARAMS_NUM define CL_MAX_PARAM_ LEN parameters define CL_MAX_PARAM_CHAR_NUM 63 max length of the parameters string define CL_MAX_CMD_LINE cmd spacers parameters 18 max length of the command 3 max number of parameters 20 max length of the 80 max length of the string char cmd line CL MAX CMD LINE entire input command line char cmd_str CL_MAX_CMD_CHAR_NUM first word of command line char cmd parm str
27. l contact rate which is difficult to attain without a highly controlled and monitored environment A balance must be preserved between breaking up the cells through agitation and the damage to cells from shearing Chemical signaling down regulation A more significant factor affecting the density of HeLa are the chemotactic agents which trigger down regulation of mitosis It is understood that cells almost immediately begin to secret down regulators in response to both mitosis and cell adhesion Even when adhesion is controlled a buildup this signaling chemistry in the closed spinner environment can significantly down regulate cell division Adding medium traditionally reduces this effect but its effectiveness is limited as volumes and cell density increases CO Partial pressure Some research implies the single greatest impact on cell density and division rates may be the concentration of dissolved CO During initial incubation cells need to additional environmental CO traditionally through an incubator s 5 atmospheric partial pressure However as the cells begin producing waste CO not only does the addition of CO become unnecessary but the waste CO can reach toxic levels In our previous cultures we have seen a significant drop off in cell division rates once the culture reaches 1 5 liters at 4x10 cells mL This corresponds with the research s estimates of when waste CO exceeds a spinner flask s ability to aerate it O
28. oat value int places int minwidth bool rightjustify char floatToString char outstr float value int places int minwidth bool rightjustify false this is used to write a float value to string outstr oustr is also the return value int digit float tens 0 1 int tenscount 0 currently unused define PH GAIN STAGE1 PH 4 8262 gain 4000mV 14 59 2mV 828 8mV Stage2 gain applyed to VREF currently unused define PH GAIN STAGE2 REF 2 0 One 60Hz cycle cycle has 16 66ms or 16666us limit up to 1 000 000us One 5 Hz cycle cycle has 20 00ms or 20000us limit up to 1 000 000us uncomment the right line define PH_TIME_ADC_READINGS_MICROSECONS define PH_TIME_ADC_READINGS_MICROSECONS 16666 60Hz 20000 50Hz Initial temperature for non temperature sensor mode define PH TEMPERATURE VALUE INITIAL CELCIUS 37 0 Initial interval between acquisition define PH INITIAL TIME BETWEEN ACQUISITIONS MS 1000 Initial pH range to the pH alarm define PH ALARM INF 7 0 define PH ALARM SUP 8 0 functions readADC function unused unsigned int readADC unsigned char channel unsigned int reading time double d int i long t0 us d 0 0 i to us micros while micros t8_us lt reading_time i d analogRead channel d i return unsigned int d int i float tempfloat value int c 0 int charcount 1 int extra 0 m
29. ocess data Check for input from serial line process_cmd End loop METHODS void process _data void char tempType digitalWrite PH LED PIN HIGH if myRec temperature sensor flag true val T readADC PH TEMP ADC PIN PH TIME ADC READINGS MICROSECONS T 100 valT 5 0 1024 tempType Actual else T myRec temperature constant celcius celcius temperature to operates without a temperature sensor tempType Assume endif Send temp data to readouts floatToString myStr T 1 lcd setCursor 8 0 lcd print tempType lcd print myStr lcd print char 223 degree symbol lcd print C Serial print info Serial print tempType Serial print myStr Serial print Degrees Serial println C val_R readADC PH_REF_ADC_PIN PH TIME ADC READINGS MICROSECONS R PH GAIN STAGE2 REF val R 5 0 1024 pHduino h pHduino h pHduino library for Arduino amp Wiring Copyright c 2009 Carlos A Neves http code google com p phduino This program is free software you can redistribute it and or modify it under the terms of the GNU General Public License as published by the Free Software Foundation either version 3 of the License or at your option any later version This program is distributed in the hope that it will be useful but WITHOUT ANY WARRANTY without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULA
30. s steel version after flow patterns can be verified The goal is not only dis aggregation of cells but a continuous up draft of medium along the shaft and down draft returning along the vessel sides This constantly brings CO saturated medium to the surface where forced ventillation can dissipate the CO and allows for additional O absorption This may or may not be sufficient to avoid O sparging Should this design be insufficient for CO removal a full screw type impeller reaching all the way to the surface my be employed However this is non optimal as it removes room for additional pipes and sensors pH subsystem Overview pH balance is of course critical for cell culture This system uses a high temperature pressure pH electrode which communicates directly with the PLC Based on readings the PLC will trigger drop wise addition of NaOH solution every 30 60 seconds HCl addition can be used in conjunction however is not recommended In a healthy vessel pH creep is always to the acidic and allowing for both base and acid additions creates the possibility of chasing one s tail in a constant oscillation This probe was chosen for its and its cable s ability to withstand autoclaving and thus avoid the need for assembly in a class II hood after sterilization The 1058_0 PhidgetPhSensor transducer is used to interface the BNC probe with the PLC board High Temperature Insertion Type Electrode PHE 5431 10 Series
31. so add 1 we have a command line return 1 else i cmd_str cl_i 0 terminate command str which normally happens when we start parsing parameters we don t have a command line return Pump control circuit Overview This is a simple pump trigger circuit to allow pump activation from either the PLC 5 volt output pin or a manual button mounted on the control case The pumps require a 12v power source 5v is used simply to trigger the circuit and not run the device The TIP 120 is a NPN transistor C TIP120 x L E Arduino 5 Digital Output Pin pra 1k BCE Common ground for 144005 external power and the arduino board Diode External power source 12v Peristaltic Pump 12v DC Motor Arduino 5v Supply Pin Base to microcontroller Emitter to ground Collector to device Diode from E to C when connected to inductive load like a DC motor Vessel schematics Overview The vessel was designed using an off the shelf 3 liter spinner flask The flask has four inch and four inch steel pipes through the cap and one inch steel pipe at the upper sidearm used exclusively for sampling The second upper sidearm houses a large gauge filtered port for ventilation This will ultimately be replaced with a forced air system to sweep the headspace The pipes are threaded to allow medical grade luer lock fittings for medical tubing attachment and one way flow check valves Removable lu
32. wing sets target pH boundaries myRec pH add NaOH 7 3 myRec pH add HCl 7 9 eeprom write block amp myRec void 0 sizeof myRec Start setup void setup void parameters reset Init serial port Serial begin 9600 setup LED button and buzzer pinMode PH LED PIN OUTPUT pinMode PH BUTTON CTRL PIN INPUT pinMode PH BUZZER PIN OUTPUT initialize LED and buzzer digitalWrite PH LED PIN LOW digitalWrite PH BUZZER PIN LOW begin LCD lcd begin 16 2 lcd clear lcd noCursor lcd home lcd display Buzzer test digitalWrite PH_BUZZER_PIN HIGH delay 500 digitalWrite PH_BUZZER_PIN LOW LCD write tests digitalWrite PH_LED_PIN HIGH lcd setCursor 8 0 lcd print Jurica lcd setCursor 8 1 lcd print Labs delay 5000 lcd setCursor 0 0 lcd print Bioreactor1 lcd setCursor 0 1 lcd print pH subsys v1 0 delay 5000 digitalWrite PH LED PIN LOW lcd clear Serial write tests Serial println Jurica Labs Serial println Bioreactor1 Serial println pH subsys v1 0 read parameters from EEPROM eeprom read block amp myRec void 0 sizeof myRec Free memory check Serial println availableMemory End Setup Start Loop void loop void my_timer millis if my_timer my_timer gt myRec time between_acquisitions_ms reset the timer my timerO my timer if myRec start flag true pr
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