AgileReader™ Software Manual
Contents
1. Basic parameters Well mapping Quantitative Cut off Ratio Inhibition Q C Print options Parameters Measurement type End Point bi H Filter wavelength nm Incubation ai M Quantitative Use incubator Mam x Cutoff Temperature Ser RatioMnhibition ps jc mac Reference filter Gi Shaker Use shaker Starting method f Immediate D f Delay Plate motion f Measurement unit e Continuous t Stepping Unit None 2 Data To show the result of an experiment File Experiment Setup Help a x Results Calibration C A B D E F G H J K M N 0 Q R T U Vv Wo 1 Protocol E 2 Experiment file path Sample exp 3 3 Measuremen t type End point g 4 Measuremen tmode Continuous 5 5 Main 1 filter nm 450 6 starting method Immediat 7 Need shake N 8 Need incubate N 9 Need quantitative Yes 10 Quant method 0 plat 11 Quant standards number 5 12 Quant replicates number 5 13 curve fit method Cubic polynomial O 14 cutoff method Double threshold 15 Upper threshold label for lt 0 16 Lower threshold label for gt 0 17 Meed ratio inhibition Inhibition 18 Bo well C10 19 Need quality control Yes 20 oc1 1 000 PC 1 000 NC 1 500 gt 0 21 9c3 0 500 gt 0 000 PC 1 000 6 0 000 gt 1 000 22 Pass condition OC 061 3 E 22 AT re MA d Setup menu functions The setup menu is used for COM por2. Using the built in Incubator The incubator will set the temperature of the plate at ambient temperature Users can enable the Incubator by 1 Click the use incubator tab 2 Enter the desired temperature Using the built in Shaker The built in Shaker in ACT AMPR 750 can let user define 3 settings low 8Hz Medium 11Hz and High 14Hz Users can also define how long the shaker needs to be active by seconds To enable the Shaker 1 Click the Use shaker tab 2 Define the speed Low Medium High 3 Define the time in seconds Measurement unit Users can define the Measurement unit to suit their experiments needs To define the Measurement unit 1 Click on the unit tab and select the desired Measurement unit Define Calculation User can define Quantitative Cutoff Ratio Inhibition and QC calculation method To define calculation method 1 Click on the tab in respect to Quantitative Cutoff Ratio Inhibition and QC calculation 2 The AgileReader lets users define each calculation method criteria 13 AT e Well Mapping Users can define 5 types of different wells Blank Standard Sample Positive and Negative To define Well Mapping 1 Click on the Well mapping tap on the main working acres 2 Users can define Blank Standard Sample Positive and Negative for each well File Experiment Setup Help LIN 8 1 5 ur Basic parameters Well mapping Quantitative Cut off Ratio Inhibition C
3. Use the current protocol to re process data results Section C Message During operation the message will show on the right side of the tool bar 1 IINIT Message text Section D Temperature monitor When incubator is active the temperature will show on the right side of the tool bar Section E Status monitor After initialize the tool bar will show the plate state and the connection status The plate in out is defined as green red The connection on off is defined as blue grey la x au ap Plate state F Plate state Connection 63 Connection a Temperature monitor 48 4 wert Bee At Section F Working area The AgileReader allows you to define protocols and acquiring microplate data an exp experiment file will contain 2 information the Protocol and the Data The Protocol is to define parameters the data is to show experiment data i File Experiment Setup Help A Basic parameters Well mapping Quantitative Cut off Ratio Inhibition Q C Print options Parameters Measurement type End Point D Filter wavelength nm Previous Current Maint 405 kal J Reference filter Bei fo fso 7 Starting method C Immediate Delay bh sec Plate motion C Continuous Stepping fo ms Incubation Use incubator Temperature b Ze Shaker jv Use shaker Speed Ge Low 8Hz C Medium 11Hz C High 14Hz Tim
4. Print options hap layout G KM Select type first then assign location to fill F 1 1 eal 3 1 LC 1 1 POSO1 STOOL STDO2 STDOS 5T004 5 F 1 7 1 2 2 T 3 7 4 7 5 7 POSOL STOOL STOO2 STDOS STDOO4 STOUSS 1 Z 1 L 2 3 E EE L 1 5 3 BLEOL STOOL STO02 STOOS STOO4 5 M 1 CU 1 4 T 4 CC 3 4 L 4 4 C 5 4 MEGOL STOOL amp STO02 STOOS STOO4 STOOS 1 2 1 5 5 T 3 5 4 5 Le So MEGOL STOOL STOO STOOS STOO4 5 Fill direction Ce Row C Column Type Sample Mame SAM 3 Replicate direction ea DO Fill number fi Column Replicate number fi 14 Quantitative The AgileReader allows user to define quantitative analysis to determine the absolute or relative abundance There are 4 different types of curve fitting on the AgileReader Users can use Curve on plate Stored curve Standard line and Concentration factor To define Quantitative analysis 1 Make sure the check mark is clicked on the Quantitative in Basis Parameter 2 Click the Quantitative tap in Basic Parameter 3 Define the desired parameter Si Fie Experiment Setup Help gt S 7 8 1 8 settings Curve on plate Data curve fit scale scale Li CH Cubic polynomial Linear Linear C Logio C Lon f Stored cure 1 Standard line f Concentration factor 15 Cutoffs Cutoffs are used to class
5. 0 500 gt 0 000 PC 1 000 NC 0 000 gt 1 000 ed Pass condition QC 061 AND QC3 23 24 Plate layout GH 1 2 3 1 5 6 7 8 9 10 11 12 26 A SAM01 1 SAM02 1 SAM03 1 SAM04 1 SAM05 1 SAM06 1 SAM07 1 SAM08 1 SAM09 1 SAM10 1 SAM11 1 1 1 7 8 SAM01 2 SAM02 2 SAM03 2 SAM04 2 SAM05 2 SAM06 2 SAM07 2 SAM08 2 SAM09 2 SAM10 2 52 111 2 2 28 Cc SAM01 3 SAM02 3 SAM03 3 SAM04 3 SAM05 3 SAM06 3 SAM07 3 SAM08 3 SAM09 3 SAM10 3 SAM11 3 SAM12 3 29 D POS01 1 STDO1 1 STD02 1 57003 1 570041 1 E POS01 2 57001 2 STDO2 2 57003 2 57004 2 2 S0 _4 Calibration When Quantitative is checked in the protocol calibration curve will be displayed according to the setting parameter Results Calibration 2 RE REGER BEIS AE ER Es 23 Calibrators 24 Name 25 co1 31 72 STD02 Si c03 STD03 43 C04 STD04 49 res STDO5 Meas 0 159 0 095 0 118 0 120 0 165 0 144 0 105 0 139 0 120 0 204 1 102 1 051 1 123 1 057 1 119 1 090 1 119 1 071 1 085 1 062 1 183 1 262 1 229 1 252 1 332 120 000 145 000 1000 000 1200 000 Calib curve Fit type cubic polynomial Meas scale linear Conc scale linear 0 0 1575 Formula Conc ABS a0 31 6 a2 C C aS CTCTC a0 2 954E 1 al 3 712E 3 a2 3 476E 6 a3 1 137E 9 Layout Shows the well mapping layout of the plate Different types of well uses a different
6. AgileReader setup menu Bi Welcome to the AgileCon installation program Pr setup cannot install system files or update shared files if they are in use Before proceeding we recommend that you close any applications you may be minning Exit etup EEN 7 Click on the icon to install 8 Select Program group then click continue the AgileReader software will start installation 9 Click OK when the AgileReader finishes installation To start AgileReader 1 From Start menu 3 Programs ACTGene AgileReaderTM 2 Select the correct COM port for connection then click OK E File e Basic parameters well mapping Quantitative Cut off Ratio Inhibition C Print options Parameters Measurement type End Point Filter wavelength nm Previous Current maint IIe Reference filter Starting method Ze Immediate C Delay Flate motion f Continuous f Stepping Incubation M Use incubator Temperature is 4c Shaker Use shaker Measurement unit Unit Nang Quantitative Cutott Ratio lnhibition COM port sethng Select COM port At sde Reg AgileReader Menu Software Structure Main Window Overview i File Experiment Setup Help A B ALONE Basic parameters Well mapping Quantitative Cut off Ratio Inhibition Q C Print options Parameters M
7. Cutoff report 10 Ratio Inhibition matrix Ratio Inhibition report 11 Q C validation QC report 12 Data list Show the data list Matrix show as well mapping configuration 40 AF sone Interpreting the results The AgileReader will generate the results after every experiment in the data tab on the right Users can use to result Calibration Data Cutoff Ratio Inhibition Q C Kinetic to view their experiment results Result Click on the result tab to see the parameter setup plate layout Raw OD and Con Matrix of the experiment If check Quantitative cutoff Ratio Inhibition QC calculation method the criteria of the calculation method will also show on this page Results Calibration Data Cut off Ratio Inhibition ES Kinetic Report A B E D E E G H I J K L M N 1 Protocol parameters AN Experiment file path Sample exp EA Measurement type End point 4 Measurement mode Continuous 5 Main 1 filter nm 450 Starting method Immediate SE Need shake No 8 Need incubate No 9 Need quantitative Yes 10 Quant method Curve on plate aug Quant standards number 5 SA Quant replicates number 5 Pa Curve fit method Cubic polynomial 14 Cutoff method Double threshold 15 Upper threshold label for lt 0 16 Lower threshold label for gt 0 17 Need ratio inhibition Inhibition 18 e well C10 19 Need quality control Yes 20 qc 1 1 000 PC 1 000 NC 1 500 gt 1 200 ally QC3
8. EQ4 EQ4 6 a a 2 a ce a 4 Ratio Inhibition Calculation Method Select a 20 as a standard value to calculate the rest of the well plate Bn Basic parameters Well mapping Cuantitative Cutoff Ratio inhibition 5 Ratio J Inhibition C Ratio BIBO Definition of BO 1 Ratio Inhibition operating procedure a N b C N d QD definition Ratio Bn B0 Inhibition 100 Bn BO Must have sample on BO position or the AgileReader will show error Please check BO is a replicate of the sample if there are many replicate of the sample the BO will be the average of the replicates of the sample BO value is O then the AgileReader will show error ratio is over 200 then the AgileReader will show HI lower then 200 then the AgileReader will show LO Ratio is represent as blue Inhibition represent as red 38 AT ne Se Q C Calculation Method The criteria of the QC calculation can used to determines on the reliability if this experiment 1 PU QUOT BY NO Can use a maximum of 4 equation for calculation all of the calculation result are considered to determine pass or fail of the QC calculation method The value of a can be 1000 000 0 The value of b can be 1000 000 0 The value of 6 can be 1000 000 1000 000 The value of H can be 9999999 999 9999999 999 The value of L can be 9999999 999
9. 9999999 999 To determine pass or fail the queation uses a OR AND XOR to determine Basic parameters well mapping Quantitative Cut Off Ratio Inhibition GC Print options DU General equation L gt aP 40 H L a i C H act Mi si fi 1 5 gt JIE M ace fo sl SEA fi fo um acs 05 z el 4 fi fo ali Pass condition if C true then PASS LL OC Jor IER AND 39 Printing options Users can set Name User and Note to differentiate different experiment reports Users can also check the boxes next to the sections for printing Colum to determine which data users will need to show on the report PO AI es IN en 9 Basic parameters Well mapping Quantitative Cut of Ratio Inhibition Q c Print options Print options Title setting Mame User Mote A Sections for printing fe Title Delta abs matrix DC validation kd Parameters W Calibration fe Data list lt Layout Kinetics fe Cutoff matrix lt Blanked abs matrix lt Ratiolnhibition matrix Title The title of the experiment Parameters Shows the protocol parameters of the experiment Layout The well plate layout of the experiment Raw abs matrix The OD value from the ACT AMPR 750 Blanked abs matrix The OD value minus the blank Delta abs matrix The delta OD curve Calibration The calibration value Kinetics Kinetics value for the experiment Cutoff matrix
10. AR ne LAA A AgileReader SOFTWARE USER MANUAL Version 1 1 ACTGene Inc provides this publication as is without warranty of any kind either express or implied including but not limited to the implied warranties of merchantability or fitness for a particular purpose Information in this publication is subject to change without notice and does not represent a commitment on the part of the vender Any errors or omissions which may have occurred in this publication despite the utmost care taken in its production will be corrected as soon as possible but not necessarily immediately upon detection AF re ON Weg Contents cantiectae ct ceatcacedactaaseiacteacheashene 1 SOME Al INAANO KAKANAN EE AA AA AA 2 lege H Te AA 3 AgileReader Menu Software Gtructure a 4 Mam Window eee eee eee 4 SE BAYAN 5 B TOOD AA ee ee eee 8 Sili fe GD AA nes 8 EC ee IMO MMO Mc E 8 Section E Status monitor NEEENE NENNEN ENNEN 8 F WOKING AA EEEE EAE EEEE E EESE 9 Section G Desktop Bar 10 M ul e te 11 Eileen E 11 Define Primary and Reference wavelengths a 12 Starting method to read plates a 12 Pde MOON waaa AA AA AA AA 13 USING Te DUNIA ul ele e 13 Usmo the DUN EE 13 Measurement unt 13 Bye la 28 e EU den E 13 WE MAPPING ME 14 SE EEN 15 N i e E
11. Device Manager figure A 1 In Device Manager double click USB Serial Port figure A 2 to enter port setting figure A 3 Please remember the com port number for further use in appendix B Fill in 57600 8 None 1 None in those blanks Press button Advanced to enter advanced COM seiting figure A 4 USB transfer size is to be selected as max number 4096 Latency timer is to be smallest number 1 Upon finishing above procedure please go to appendix B for further operation system Properties System Restore Automatic Updates Remote General Computer Name Hardware Advanced Device Manager e The Device Manager lists all the hardware devices installed 2 on pour computer Use the Device Manager to change the properties of any device Device Manager Drivers Driver Signing lets you make sure that installed drivers are compatible with Windows Windows Update lets you set up how Windows connects to Windows Update for drivers Hardware Profiles Go Hardware profiles provide a way for you to set up and store pa different hardware configurations Hardware Profiles Figure A 1 AT AF one Device Manager File Action View Help e FS A gt SL USER d Computer De Disk drives Display adapters 24 DYDICD ROM drives Floppy disk controllers L Floppy disk drives 2 IDE ATAJATAPI controllers Keyboards H t 4 Mice and other pointing devices ER 1 Monitors S Network adapters HY
12. ENNA NAGAGANAP AA 16 E 16 AA RP 17 POPU O ING E 18 AgileReader connection setup a 19 Start AgileReader under PC mode 19 Setup Connection between AgileReader and the 6 19 Setting up USB connection Between ACT AMPR 750 and AgileReader 20 Main Menu Configuration Aa 21 lgl elle AA 21 EES BN le AA PA PAA 21 TUNGONG aaa NA AABANGAN ANA AE 22 SEH Menu TCT AA 23 TOO Bar Menu CONAN Aa pakana pap GANGBANG GA AA 24 AT ne ABRA Defining Parameters for Experiment E E E E E Well Mapping Quantitative measuring ae AP Cutoff measuring method Ratio Inhibition Calculation Method Q C Calculation Method ME Printing options Interpreting the Appendix A results SEN Ol RE EE EH PO GE AT ne ABRA System Requirements 128MB of RAM above for Windows XP Windows XP Professional SP2 Windows Vista 32bit Windows 7 Microsoft Office 2003 or Microsoft Office 2007 20MB of available hard drive for the program files CD ROM drive 16bit color display 800 x 600 Keyboard mouse and RS232 serial port or USB AF sone Software Installation To install AgileReader Mr Software 1 Start Windows Close all unnecessary Windows programs Place CD in the CDROM drive Double click the AgileReader folder within the CD ROM Double click install bat program o QE Se Y Click OK on the
13. Ports COM LPT Ei Communications Port COM1 Ei Communications Port COM ECP Printer Port LPT1 pi USB Serial Port COM 1 g s Processors GR Sound video and game controllers Hd System devices ag Universal Serial Bus controllers Figure A 2 USB Serial Port COM3 Properties General Port Settings Driver Details Bits per second GRX Data bits Parity Stop bits Flow control None Advanced Restore Defaults Figure A 3 48 Figure A 4 49
14. SD A i 4 1 5 E eler w DCH 0 5 gt E SC A 1 SEA 0 gt ai 4 Pass condition if C true then PASS 0 1 AND 3 17 Print options Users can define the Name User and Printing selections for the experiments on the AgileReader To define print options 1 Click the Print options on the Basic parameters 2 Enter the desired field for print options File Experiment Setup Help 5 Basic parameters Well mapping Quantitative Cutoff Ratio Inhibition oC Print options Print options Title setting Mame User Mote Sections for printing w Title w Parameters iw Layout w Raw abs matrix w Blanked abs matrix E M OC validation Calibration v Data list iw Cutoff matrix if Ratiolnhibition matrix 18 AT ne ABRA AgileReader connection setup To control the AC T AMPR 750 through the AgileReader users must set and test the COM port connection on the PC User can connect the AgileReader with ACT AMPR 750 through USB or 35232 interface Start AgileReader under PC mode 1 2 5 Attach the appropriate cable to an available 45232 serial port or USB port Plug the other end of the cable into the RS232 serial port or USB port on the reader Plug all power cords into electrical outlets Power ACT AMPR 750 ACT AMPR 750 is in standalone mode power off while pressing Option button to switch to PC mo
15. ald fo U Positive Cutofflahep fu y papeteng C Double Calculation 2 Double cutoff method Users can define the high and low threshold The high and low value can be from 0 0000 4 0000 The AgileReader can determine the positive negative results and between Basic parameters Wel mapping Guantitatve Lut off Ratio Inhibition AN r cutoff setings Cutoff method Single KILL High threshold 2 If result threshold then C Positive Low threshold 1 2 Di Ge 4 Cutof label CC Calculation 36 3 Calculation cutoff method Users can create a maximum of 4 formulas as the threshold calculation and make the result as 5 groups Every formula can be calculated from the positive or negative control results with the equation a tb C The value for a b and c can be 1000 000 1000 000 Example With four threshold the threshold higher then EQ1 as default Between EQ1 and EQ2 Between EQ2 and EQ3 is Between ECO and EQ4 is Below EO 4 is Basic parameters well mapping Quantitative Cut off Ratio Inhibition Q C Print options Cutoffsetings Cutoff method C Single f Double Ce Calculation Calculate number E E Reverse Label of all limits EQi a PC b NC e a bl ch 1 at EQI1 EQ2 EQ2 a PC BNC H aa ian SN cen b e a a b a ES a EQJ
16. ate direction Name TETO GG Row G Row Fill number fi C Column Conc 32 000 al C Column Replicate number fi 2 Well mapping method a Select the type well users would like to define Blank Positive Negative Sample Standard Users can also enter the concentration value for the standard b Determine where on the well the well type needs to be and left click on the position on the well c Right click on the mouse to select the fill option 3 Fill and replicate direction rule Row is to fill or replicate the well vertically column is to fill or replicate the well horizontally 30 AF sone 4 Fill and replicate well rules a Fill number Is to replicate the number of different samples b Replicate number Is to replicate the sample how many times on the well plate Example of filling and replicate the well plate 5 Blank POS and NEG can only have 1 set within AgileReader 6 STD can configure 1 15 set a maximum of 96 7 Sample max of 96 8 Types of well a BLK User can define BLK for the blank well and are defined as a light green on the well plate b POS Uses can define positive control on the well plate and are defined as a light red on the well plate c NEG Users can define negative control on the well plate and are defined as 3 AF one a light blue on the well plate d Sample Users can define the sample on the well plate and are defined as an light orange on the well plate
17. ature hd Ratio lnhibition if Ele DC shaker fe Use shaker Two point interval E SEC Speed Ge C Medium 1 C Highii 2 Time fi SEC Measurement unit hd Quantitative h Cutoff Starting method Ce Immediate C Delay Plate motion Continuous Stepping 26 AT re sei Weg a End Point Parameters Measurement type End Point Filter wavelength nm Previous Current Incubation Use incubator lm Quantitative W Cutoff Wain faso uns Temperature fe Ratio lnhibition fis re Geng QC jf Reference filter Her fo Jago shaker M Use shaker Speed Ge LowiSHzi C Mediumi1H C Highe1 3 Time if SEC Starting method C Immediate f Delay 4 Sec Plate motion Measurement unit Continuous Stepping K Unit None b Two Points Parameters Measurement type Two Points Filter wavelength mm Previous Current Maint 450 Main ken Jans fe Reference filter ei faso Jago Ret faso eng Starting method Incubation Use incubator Temperature fe Patio lnhibition iE C W aC Shaker Two point interval 7 SEC fe Quantitative Pe Cutoff fe Use shaker Speed Ge Lowi8Hz C Medium 1Hz C Hight Aa Time VU re SEC C Immediate Ce De
18. ave the experiment parameters Save As Save the results under a new ID Generate Preview report Generate experiment report in data Export Print report Export report to excel file and select to print report Exit Close the AgileReader software AF sone e Experiment Menu Experiment Menu contains function to set the experiment and view the data mi Fie ERT setup Help r Protocol Gi Ei Parameters Measurement type Eng Point Filter wavelength nm Incubation ES Iw Quantitative Previous Current M Use incubator CG Culot Maint aso Temperature ECH 0 l Ze Ratiofnhibition ac M Reference fitter Shaker Use shaker Starting method Ze Immediate Delay Plate motion Stepping rut rnga Protocol Set the environment Data View data for the experiment The Protocol and Data function can also function on the right tab of the main menu EF Pila Experiment Help 1 sl oe e Basic parameters Wall mapping Guanttatve Cut off Raba inhibition oC Print options Parameters Me acurement ippo End Point D E r i i Her eraebaregin rir Incubabon re Ceurgerg T Line E Cut Maint 450 F Ze E Rabadahibikan z GG Referee fiter Shakar Lape trike Saring mamod mimi C Delay Plate maton E Continuous Measurem n vr C giper Leg Lpigt 6 Setup Menu The set
19. color to represent source data Shows the source data for the quantitative measurement 6 In end point measurement if there is no reference filter then the main filter M1 data is the source data If there is reference filter then M1 R1 is the source data 6 In Two points measurement if there is no reference filter the source data will be M1 e In Two points measurement if there is reference filter then the source data will be D1 M1 R41 e During Kinetic measurement user cannot use reference filter the M1 data will be the source data Calibrators Will use CO1 C15 to represent every STD s name and OD value and will show the average measurement and the standard Conc value Calib Curve When using standard curve Curve on plate or stored curve will use curve fitting to create a standard curve Residuals table Will use C01 C15 to show standard OD value C set Average Abs and Concentration and Residual Ccal Cset 42 AT ore Curve Viewer User can double click on the curve to enable the curve viewer User can also store the curve in the save curve tab on the bottom The default stored curve are in AgileReader StdCurve Curve Yiewer EN log Abs 0 30 2 00 2 00 3 20 log Conc ABS 80 81 6 a2 C C 83 0 0 al 2 954E 1 al 3 712E 3 Save Curve a2 3 476E 6 a3 1 137E 9 Data sheet According to the well plate mapping the AgileReader will display all the result The data she
20. de Configure the communication COM port between ACT AMPR 750 and the PC Setup Connection between AgileReader and the PC 1 2 Ensure AgileReader is connected to the computer Ensure on the AgileReader LCD shows is in PC mode Ensure the COM port setting is Baud rate 57600 Data bits 8 bits Parity check no Stop bits 1 Flow control no Go to start gt program files3 ACTGene gt AgileReader to execute the AgileReader software After executing ACT AMPR 750 the PC will show the startup screen with the software version of the AgileReader In the initial setup the AgileReader will scan all available ports if there is no response from the AgileReader the AgileReader will show off line 19 7 Select the desired COM port for the communication between the PC and ACT AMPR 750 Currently the AgileReader supports COM 1 COM16 gt Select COM port 8 Press OK on the AgileReader to start communication between ACT AMPR 750 and AgileReader 9 Press Init on the tool bar of AgileReader The AgileReader will use the desired COM port and send a signal to the AgileReader If the ACT AMPR 750 responds to the LCD the AgileReader will show ON LINE Setting up USB connection Between ACT AMPR 750 and AgileReader 1 On ACT AMPR 750 standalone mode go to SETUP COMPUTER 2 Change the RS232 to USB 3 Power on the ACT AMPR 750 again while pressing option button on the instrum
21. e h f sec Measurement unit bil e MV Quantitative ly Cutoff vv Ratio Inhibition V Q C 0303014 A Menu B Tool bar C Message D Temperature monitor E Status monitor F Working area G Desktop bar AF sone Section G Desktop Bar The desktop bar is to select between the Protocol and the Data this function can also be accessed under experiment E File Egemen Swap Heip 0 ze Basic parameters Wall mapping Guantlanve Cut zg Rabo inhibibon o Print opsone Paramelert Neapureznert type End Point Filler amargi nm Prous Curent pe incubator i 7 kaini jaso e D Tamparatura e fis t on Ba 6 Reference fier Shakar Ape Slorling method ferris Dali Plate motion Continuous Medsurtmen urd C Slapping mpa 10 AgileReader Function Basic Parameters e Measurement types The AgileReader provide 3 types of measurement types end point two point and Kinetics File Experiment Setup F x 1 a Plate state l Connection Basic parameters well mapping Quantitative Cut off Ratio Inhibition Q C Print options Parameters Measurement type End Paint AM o End Point n Incubation ULE o Two Foints Quantitative Kinetic Use incubator Kinetics x Cutof 0 Temperature i nAg Ratio nhibition 5 H GG Reference
22. e Standard Users can define the standard on the well plate and are defined as a light purple on the well plate Users can fill in the value of 0 001 999999 999 Si File Experiment Setup Help PO ER Map layout Select type first then assign location to fill 1 1 2 1 4 Z 1 5 BLEOL BLEOL BLEOL 1 pes Fa 1 1 Kia 1 2 KA l 3 A 1 3 zs 1 5 Fa WE KA Kira Ea NM 1 1 1 2 1 3 M 1 4 NM 1 5 NEGOL NEGO NEGO PESO NEGOL 1 1 CI CU 1 5 STOOL STOOL ST T ae STOOL Type Standard Mame Cone 1 000 al Fill direction C Row Column Replicate direction Pow Fill number fi H C Column Replicate number E lt I Quantitative measuring method ACT AMPR 750 supports 4 types of Quantitative method Curve on plate Stored curve Standard line and Concentration factor 1 Curve on plate Uses the standard on the well plate for the calibration curve There are 7 types of curve fitting on the AgileReader a Linear regression b Quadratic polynomial c Cubic polynomial d gt Point to point e Cubic spline f 2 parameters logit log g 4 parameters logistic Basic parameters Well mapping Quantitative Cut off Ratio Inhibition Q C Print options LiUantitative settings scale Linear C scale Ge Linear C 0 Ce Curve on plate Data curve fit cubic polynomial Linear regression Stored curve Quadratic po
23. easurement type End Point D Filter wavelength nm Incubation Previous Current Use incubat Use incubator Cutoff Wain 405 bi Temperature z NM Ratio Inhibition is Hoc 6 jv Reference filter Her 490 2 lv Use shaker Speed Low 8H2 r Starting method C Mediumf11H2 C Immediate High 14H2 A Menu Time B Tool bar Delay sec r sec C Message l D Temperature monitor m Plate motion E Status monitor Measurement um Continuous F Working area Stepping fo ms None G Desktop bar 0303014 J Quantitative Section A Menu Section B Tool bar Section C Message section D Temperature monitor section E Status monitor Section F Working area Section G Desktop bar Section A Menu The File Menu contains function for processing data from the AgileReader Experiment Setup Mew EC Load Lave Save As Generate Preview report Export Print report cubation ia Use incubator Temperature Reference filter Shaker Use shaker Starting method f Immediate f Delay Plate motion f Continuous C Stepping Unit tive Cut off Ratio Inhibition Q C Print options Measurement unit Quantitative iw Cutoff Ratiolnhibition iw OC New open new file window Default file name is new exp Load Load an existing results record Save S
24. ent to switch to the PC mode Appedix A for USB setting 20 Main Menu Configuration Graphic User Interface The graphic user interface will have the function menu tool bar message status Temp connection status and working area Protocol and data New Load Save Save As Generate Preview report Export Print report Exit File Experiment sep w Protocol Data File Experiment Setup COM port setting Filter tune File menu functions Under the main menu of the AgileReader there are four options Files Experiment Setup and Version 1 Load Load experiment file When loading exp file AgileReader M SW will check Save Save experiment file Save As Save experiment file using different file name Close Close experiment file Generate Preview report Generate report after experiment is done must generate report first before saving to Excel 6 Export Print report To export to excel or to Print report using the printer connected to the PC 7 Exit Exit the AgileReader SE ZS Ss 7 e AF re Experiment menu functions There are 2 functions under the experiment menu Protocol and Data Protocol is to setup the parameters of a experiment and data is to show the results of an experiment 1 Protocol To setup the Parameters Well mapping Quantitative Cutoff Ratio Inhibition Q C and print options of a experiment File Experiment Setup SIGE gt S F7 tl Seck
25. et will show Name Well ID Replicate numbers Abs SD CV Conc Measuring unit Cuttoff and Inhibition Yo The average of every value will display a avg next to the well ID Results Data Rationnnibiton oc Knete Repon Name Well Replicate Abs 8D cv Conc Unit cutor bs POS01 D4 1 0 022 POS01 E4 2 0 039 D ini ein ae ay ican DR NEG01 G4 1 0032 e an NEG01 H4 2 0115 SAMO1 A 1 0 036 SAMD1 B1 2 0 112 SAMD1 C1 3 0 100 SAMO2 A2 1 0 029 i SAMO2 B2 2 0 071 e B SAMO2 C2 3 0 014 8 SAMO A3 1 0006 _ SAMO3 B3 2 0 003 IT SAMO C3 3 0010 s SAMO4 Ad 1 0120 Sa _ SAMO4 B4 2 0048 m am o SAMO4 C4 3 0 041 He SEN SAMOS AS 1 0280 m e _ SAMOS B5 2 0167 SAMOS C5 3 0158 _ SAMOG AB 1 0 292 ma a SAMOG B6 2 0 222 Ss la SAMOG C6 3 0 159 2 2 ice Cutoff results When clicking the cutoff box and finished the configuration ACT AMPR 750 will show the cutoff results according to the well mapping Depends on the conditions there will be max 5 symbols to interoperate the cutoff results gt C gt 7 gt 0 Ratio Inhibition results When clicking the Ratio Inhibition tab and finished configuring The AgileReader will show the sample OD value and standard OD value BO using Inhib
26. filter shaker Use shaker Starting method CJ Ce Immediate ang Di f Delay 6 Two points read During the two points read the ACT AMPR 750 reads at 2 wavelength with 2 reference reads as optional File Experiment Setup Help Basic parameters yell mapping Quantitative Cut off Ratio Inhibition a c Print options Parameters Measurement type Two Points Filter wavelength farm Incubation Previous Current Use incubator i Cutoff Main Aen 450 Temperature Iw Ratiolnhibition Main i eee wae Reference filter Quantitative Shaker Ret 1 o o gt Use shaker Two point interval 70 SEC Ber lo 450 Staring method Ze Immediate f Delay Flate mation Measurement unit Ze Continuous C Stepping Unit mai 1 e Kinetics read During a kinetics read users can define the kinetic method by select the Kinetic method tap User can define average rate Maximum rate Maximum Abs Total delta Abs Time to max rate and Time to max Abs User can also define the number of times the plate been read and intervals File Experiment Setup Help lei F FIN 5 Basic parameters wei mapping Quantitative Cut off Ratio Inhibition CG Print options Parameters Measurement type Kinetics d Filter wavelength hm Incubation anon mw Quantitative Previous Current Use incubator utott hain 450 asp Temperatu
27. ify results Users can define 3 different Cutoff methods Single Double Calculation 1 Make sure the check mark is clicked on the Cutoff in Basis Parameter 2 Click the Cutoff tap in Basic Parameter 3 Define the desired parameter i File Experiment Setup Help S 1 E Basic parameters Wel mapping Quantitative Lut off Ratio Inhibition OC Print options Cutoff settings Cutot method e Single result threshold then Threshold 0 f Positive t f Double Calculation Ratio Inhibition The AgileReader will take a standard BO and other samples to calculate the Ratio Inhibition factor 1 Make sure the check mark is clicked on the Ratio Inhibition in Basis Parameter 2 Click the Cutoff tap in Ratio Inhibition 3 Define the desired parameter 5i File Experiment Setup Help gt S 7 18114 e Ratio Inhibition e Ratio BIBO Inhibition 100 B BO Definition of HO 16 AT ere Se Q C The AgileReader can make Q C rules for experiment to determine the results 1 Make sure the check mark is clicked on the QC in Basis Parameter 2 Click the Cutoff tap in QC 3 Define the desired parameter Si File Experiment Setup Help 1 T 4 5 D Basic parameters well mapping Quantitative ut off Fatio Inhibition QC Print options QC General equation L gt aPC 6 H L a a 0 H w OC NIA si
28. ime to max rate j Time to max Abs PA Measurement unit e Stepping Unit ih a Kinetic method Uses can select Average rate Maximum rate Maximum OD Total delta OD Time to max slope Time to max OD 29 b Measure number User can enter the measuring numbers of the plate from 3 30 times 6 Measure interval User can select the measure interval When plate motion is in Continuous from 4500s in Stepping 5500s Well Mapping 1 Save and load map layout Users can load their map layout by pressing the folder under map layout or the disk icon to save under map layout Man layout Select type first then assign location to fill 10 11 12 preter BE fap ies ap ete gr etal qe aa Sp sie op eet age SAMOS SAMOG SAMO Samos samos SAMI10 SAM11 2 Tae Iro ANI tendare samos samog SAM10 SAM11 SAM12 Clear All an Mame 5T001 1 Toa EE Se ar 7 samos samog samio SAM11 SAM12 SE C 1 1 2 1 6 3 1 c4 1 c51 Posoi STD01 sTooz sToo3 sTOO4 STOOS 2 1 2 c 2 2 3 2 c4 2 C5 2 POS01 STOOL STD02 sToos stood STDOS 00 21 1 c2 3 c3 3 4 3 cs5 3 601 STOOL 2 ST003 sToo4 STDOS 5 age 1 ea AG Ge NEGoL STD01 STD02 sToo3 STDOd STDOS Negative Standard NEGOL STOOL STOO Seefe T005 Type Standard Fill direction Replic
29. ition Ratio is represented in Blue Inhibition is represented in Red Over 200 the data will show Hi lower than 200 will show LO 1 1041396 101 50 997556 96 52 SH agar To 0 00 0 00 9 60 1041396 101 950 99 75 96 52 34 27 To 0 00 UU DU 104 13 101 50 99 75 96 52 347 UU UU So DU 100 43 96 35 39 96 100 43 96 35 39 96 100 00 96 35 39 96 35 39 96 33 35 39 96 33 44 Q C results After clicking the QC calculation method and finished configuration the AccuMate will show the QC criteria Pass condition Result on the data sheet Results Calibration Ratioflnhibition OC F H A E 2 E E I J E L M 1 Quality controls A Controls 3 control abs conc 4 PC 0 009 82 512 5 NG 0 073 110 217 D criteria H QC1 1000 PC 1 000 NC 4500 lt 41 200 S 903 0 500 lt 0000 pc L000 NC 0000 lt 41 000 H Pass condition 10 vor TRUE then PASS 1 OC QC1 AND 3 12 Result 13 OCH FAIL 14 65 PASS 15 OC FAIL l Kinetic results When using the kinetic measuring method AccuMate will display the kinetic curve of every reading User can check the reaction rate easily on this screen 45 View Report To view report users will have to go into file and click the Generate Preview report tab for the AgileReader to generate report After reports being generated users can use the Export pri
30. lay be SEC Flate motion C Continuous Measurement unit f Stepping fo SP e maid 207 C N reference filter Parameters Measurement type kinetics Filter wavelength mm Previous Current Maint IER 405 Starting method C Immediate f Delay SEC Flate motion Continuous f Stepping Incubation Use incubator Temperature fs He shaker fe Lise shaker Speed Ce LowfSHz Medium 1Hz C Hight Aa Time ioe SEC Measurement unit ke mod Kinetics Kinetics measuring method can only select main filter and no WwW Quantitative fe Cutoff lt Ratio lnhibition lt DC Average rate haximum rate Maximum Abs Total delta Abs Time to max rate Time to max Abs kinetics method Average rate Measure numbers 3 E CU SEL Measure interwal Filter wavelength Users will need to select the filter wavelength for the desired experiment In addition users can also select a reference wavelength ACT AMPR 750 will automatically calculate the Delta OD as for difference between the main and reference filters Starting method Define when to start the defined experiment parameters a Immediate Start right after pressing the execute tab b Delay Users can define from 0 999s delay to start Plate motion To define how the plate motion when measuring a Continuous When measuring the plate is in continuous motion and
31. lynomial Point to point Cubic spline C Standard line 2 parameters logitlog 4 parameters logistic Concentration factor 33 AT re sei Weg 2 Stored curve Users can load their existing stored curve for quantatitive the stored curve are under AgileReader StdCurve file name is cuv Basic parameters Well mapping Quantitative Cut off Ratio f Inhibition Q C Print options Jyantitative settings Curve on plate Stored curve Uy C Standard line C Concentration factor 3 Standard line User can use the Abs A Conc B equation and enter the value of A and B to calculate a standard line The Value of A can be 999999 999 999999 999 The value of B can be 999999 999 999999 999 Basic parameters Well mapping Quantitative Cut off Ratio Inhibition Q C Print options LUantitative settings Curve on plate Stored curve C Concentration factor 34 AT ne 4 Concentration factor User can enter a factor for calculate the concentration The value of F can be 999999 999 9 35 Cutoff measuring method ACT AMPR 750 supports 3 types of Cutoff measuring methods 1 Single cutoff method User can enter a threshold of 0 0000 4 0000 and define the result is positive or negative Basic parameters Wel mapping Guantitative Cut off Ratio J Inhibition OC Cutoff settings cutoff method gt Single If result threshold then Thresh
32. not stopping b Stepping User can define the stop time when measuring from 0 999 ms In kinetic mode there is no stepping time Incubation Users can define the incubator temperature by clicking the incubation tab ACT AMPR 750 incubator can save the temperature from 3 50 C 28 6 Shaker The shaker onACT AMPR 750 can select 3 types of speed and the shaking time can range from 0999s Measurement unit Users can select 15 types of measurement unit None G dL U L l G L ug dL l ABS l mg dL I OD l mABS i U mL ug mL mEq L mmol L umol L ng mL When select to None user can enter the desired measurement unit Two point interval Users can select the 2 point interval from 5 999s Kinetic method numbers and interval When user select kinetic measurement user can select the method numbers and interval Di Fie Experiment Setup Help P 9 7 1 e Basic parameters well mapping Quantitative Cut off Ratio Inhibition c Print options Parameters Measurement type Kinetics Filter wavelength mm Incubation Go Previous Current Use incubator winger ee kd Cutoff SE E Gb nang Ww Ratioflnhibition IE lt LL Shaker Use shaker Speed e Low SEN Medium IH kinetic method Average rate Immediate E Average rate Delay Time Weasure numbers MIO i sap Maximum Abs NEA ene Total delta Abs Plate mation T
33. nt option to save to Excel or print The report will be saved in Program Files ACT Gene AgileReader Data under excel file CO NOT Lu PJ ltz 25 E 3 5 C gt Experiment tte gt Mame User Mote Date 06 10 08 gt Protocol parameters Experiment file path Measurement type Measurement mode Main 1 filber nm Staring method Heed shake Need incubate Need quantitative Quant method Quant standards number Quant replicates number Curve fit method Cutoff method Upper threshold label Lower threshold label Need ratio inhibition BO well Need quality control OC OC Pass condition Calibration Time 17 06 44 Sample exp End point Continuous 450 Immediate Curve on plate 5 5 Cubic polynomial Double threshold for gt 2 000 for 1 200 Inhibition C10 Tes 1 000 PC 1 000 NC 1 500 gt 1 200 0 500 lt 0 000 PC 1 000 NC 0 000 lt 1 000 OC QC1 AND OCH 46 M N Atin Se Appendix A Setting of USB Serial Port your Windows XP 98SE PC has USB ports only please install the attached USB to RS232 driver on PC Connecting the USB cable between PC and ACT AMPR 750 then power it up Please set up your Windows XP computer as follow Under Systems Tasks of My Computer screen press View system information In System Properties select icon Hardware and press button
34. re j Ratiolnhibition 16 e nG lt OC Shaker Use shaker Starting method 9 Kinetic method Average rate e Immediate ae Measure numbers NA PAG Delay Maximum abs Measure interval Total delta Abs Plate motion Time to max rate j Time to max Abs PARU Measurement unit C Stepping Unit maid To select a measurement type Click the tap under measurement type and select the desired method of End point Two points Kinetics Define Primary and Reference wavelengths a Primary wavelength is defined alone the ACT AMPR 750 reads the plate only once at a single wavelength If a Reference wavelength is defined the plate will be read twice and automatically to calculate the delta Abs between the two readings To select the Primary and Reference wavelengths 1 Select the Measurements type of End Point and Two Points 2 Enter the Primary wavelength in Main1 or Main2 and the reference Ref1 or Ref2 Starting method to read plates Users can define the starting method of plates reading Immediately the ACT AMPR 750 starts reading the plate right after executing tap is pressed Users 12 AT ne ABRA can also define how long the plate reading delays To define the starting method 1 Click on the Immediate tap or define how many seconds needed to be delayed Plate motion Users can define the plate motion while reading the plate to be Stepping in milliseconds or Continuous
35. t configuration and filter setting The AgileReader can setup up to 8 filters 1 COM port setting User can change the desire COM port to communicate between ACT AMPR 750 and AgileReader ACT AMPR 750 will automatically detect all available COM port on the PC COM port setting 2 Filter tune The AgileReader has one 8 slot filter wheel for the users to install filters After installing new filters on the ACT AMPR 750 it is important to set the correct filter wavelength on the AgileReader Check the check box on the left to enter desired wavelength for the filter and press the Tune key after the desired wavelength is entered Filter amp lamp tune x Fiter wavelength settings Tune Filter MoU fo Filter Mod Jane Filter No 2 fo Filter No 3 fo Fiter No A 49n ca 1 1 4 Fiter No 5 II PE on Tool Bar Menu Configuration There are Init Execute Stop COM port setting Plate In Out Shaker Incubator and post processing tabs on the tool bar menu 1 Init tab After connecting ACT AMPR 750 and AgileReader users must initialize first before any changes can be made gt Gielen 2 Exec tab To execute the desired parameters for the experiment OSO 8 4 5 3 Stop tab To stop the current action for the ACT AMPR 750 i 4 COM port setting To setup the COM port connection between the PC and the AgileReader 5 Plate in out To open close the plate
36. the plate status will show on the status bar 6 Shaker The shaker tap is used to configure the shaker The shaker has 3 speeds low 8Hz Medium 11Hz High 14Hz 7 Incubator To initialize the incubator users can configure the incubator from ambient 3 50 C 8 Post Processing Use the parameters on the main manual and refresh the data SOl F 3 S Aa 9 Message Shows the status and messages from ACT AMPR 750 1 INIT 10 Temperature monitor To monitor the incubator temperature within ACT AMPR 750 Plate state 3 31 NG 0 Connection EJ Status monitor To monitor the status of ACT AMPR 750 After initialization there will be two lights showing on the status monitor Red Green represent plate is Out In Blue Grey represent connection status between ACT AMPR 750 and AgileReader 25 AT ere Se Defining Parameters for Experiment Defining Parameters When starting experiment users must first define the parameters such as wavelength reading method incubator and shaking In addition users can also define the calculation such as Quantitative Cutoff Ration Inhibition and QC 1 Measurement Type Users can define 3 types of measuring types End point two point and Kinetic Basic parameters Well mapping Quantitative Cutoff Ratio Inhibition oC Print options Parameters Measurement type Two Points End Point Incubation IT Use incubator Temper
37. up menu contains the AgileReader M system configuration File Experiment COM port setting E Filter tune Basic parameters wei mapping Quantitative Cuto Parameters ff Ratio Inhibition OC Print options Measurement type Eng Point M Filter wavelength nm Incubation KIA Quantitative Main Use incubator Cutofi Temperature 3 es e Ratio nhibition Reference filter Ri Shaker Useshaker Starting method f Immediate f Delay Plate motion z F uni E Coalinuous Measurement unit f Stepping Unit None COM port setting To set the communication COM port between the AgileReader and PC Filter tune The AgileReader can setup to 8 different filter wavelength Config the filter wavelength AF sone Section B Tool bar gt S E 4 el 1 Post processing Incubator Shaker Plate infout COM port setting stop Execute Initialize Initialize Any commands issued from the AgileReader to the ACT AMPR 750 must initialize first Execute To start the defined protocol Stop To stop executing the defined protocol COM port setting To set the COM port to communicate between the ACT AMPR 750 and the PC Plate in out To open or close the plate compartment Shake start the shaking function on the AgileReader Incubator To manually start the incubator when incubator is initialized the temp will show on section D temp monitor Post processing
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