User Manual
Contents
1. IMPORTANT Genie Il uses a proprietary tube strip that maximises optical and thermal efficiencies Other tubes and strips will not fit IMPORTANT Forcing non supported consumables will cause damage to the instrument and invalidate the warranty IMPORTANT The shape of the tubes is such that they will only fit in one way round The locating pins on the block have corresponding holes in the strips Version 1 00 BOX CONTENTS The following is a list of contents in the box for Genie II Genie Il instrument Power supply Power lead USB connection lead Stylus USB memory stick containing Genie Explorer and this manual as a PDF file Version 1 00 SITE PREPARATION HOW TO SET UP GENIE I The laboratory bench should be level and stable The instrument should be placed centrally on the lab bench and the surfaces surrounding the instrument must be clear of obstructions at all times Care must be taken not to unduly restrict the air at the front of the instrument and the outlet vents at the rear Restricting airflow may impede operation and could affect performance Electrical points should be close to the instrument to avoid injury from trailing wires It is recommended that the instrument is kept away from sinks and other wet areas Genie II is an electrical instrument and care should be taken not to operate if there is a risk of water damage Version 1 00 CONNECTIONS Genie Il is ready to us2. Genie User Manual OptiGene Unit 5 Blatchford Road Horsham West Sussex RH13 5QR United Kingdom Tel 44 0 1403 274980 Fax 44 0 1403 271017 www optigene co uk info optigene co uk Information in this document is subject to change without notice OptiGene Ltd assumes no responsibility for any errors that may appear in this document This document is believed to be complete and accurate at the time of publication In no event shall OptiGene Ltd be liable for incidental multiple or consequential damages in connection with or arising from use of this document Genie Il and its design is a registered trademark of OptiGene Ltd or its subsidiaries in the UK and other countries Table of Contents To load a saved profile 18 SAFETY NOTICES ceceecceceecerees 3 PROVING EA EE 20 SPPON Profile eee ee ee 20 EEE EEE EIS Temperature 20 How to obtain sup DOF teeseescscsesssssssssee 5 Amplification cccccceesseceeeeeeees 21 ANNE al aer 21 Supported consumables a 5 RESUS seecae 22 VIEN er 22 BOX CONTENTS 6 CONNECTING TO A COMPUTER 25 SITE PREPARATION 2ccecceceecees 7 Genie II Software updates 27 How to set up Genie Ile 7 CONNECTIONS errereen 8 GENIE EXPLORER eeeeeseeeeeeeees 29 Opening amp Closing the Lids g Main Menu cccccccscecsceeseeeseeeseeees 29 Inserting TUDES ccccccccccccccccccceccccec
3. e e e W O a a n m GEN3 1035_26 06 2014_09 23 13 gen 26 06 2014 09 35 26 06 2014 09 23 a GEN2 1225_19 06 2014_15 30 54 gen 19 06 2014 15 32 19 06 2014 15 31 TMZ EEan EANG SMES ADEA be displayed in the same way as E GEN2 1225 19 06 2014 15 28 32 gen 19 06 2014 15 29 19 06 2014 15 28 LogView Feb Duncan Gen i GEN2 1225 19 06 2014 15 28 51 gen 19 06 2014 15 29 19 06 2014 15 29 e i GEN2 1225 19 06 2014 15 14 10 gen 19 06 201415 15 19 06 2014 15 14 e ana ct ive run i GEN3 1035 19 06 2014 15 07 09 gen 19 06 201415 08 19 06 2014 15 07 e B GEN3 1035 19 06 2014 14 53 43 gen 19 06 201415 07 19 06 2014 14 53 a GEN3 1035 19 06 2014 15 02 58 gen 19 06 2014 15 06 19 06 2014 15 03 m GEN3 1035 19 06 2014 14 53 43 Copy gen 19 06 2014 15 01 19 06 2014 15 01 ex GEN3 1035 Eg gE Computer amp Local Disk C Version 1 00 42 SERVICE Clicking the Service button on the main menu will produce the following screen From here it is possible to change the date and time of the instrument s clock and update firmware or FPGA code on the instrument instead of using the drag amp drop method described in the instrument user manual OPTIONS The Options button allows the default locations of files to be set Profile Default location for saving profiles Data Default location for saving run files Default Profile File Select DefauitProfileFile n n onoo
4. o ll Default Profile File Sets a default profile to be used when a new run is started To reset back to the program defaults click Reset Default Profile Click Save to save changes to the default locations Version 1 00 43 GENIE II TECHNICAL SPECIFICATION Sample Number Touchscreen Cooling method Temperature control type Temperature accuracy Temperature gradient Detection optics Approvals Dimensions 16 wells 2x8 strips High brightness TFT LCD module 800x480 Forced convection Multi zone independent digital PID Programmable up to 8 C Photodiode with high quality interference filter 510 nm long pass 20cm H X 21cm D X 30cm W Version 1 00 OpotiGene Unit 5 Blatchford Road Horsham West Sussex RH13 5QR United Kingdom Tel 44 0 1403 274980 Fax 44 0 1403 271017 www optigene co uk info optigene co uk Information in this document is subject to change without notice OptiGene Ltd assumes no responsibility for any errors that may appear in this document This document is believed to be complete and accurate at the time of publication In no event shall OptiGene Ltd be liable for incidental multiple or consequential damages in connection with or arising from use of this document Genie Il and its design is a registered trademark of OptiGene Ltd or its subsidiaries in the UK and other countries Version 1 00 45
5. occurs remove power from the instrument Do not touch the instrument or any fluid flowing from it while it is connected to the mains supply Always follow local health and safety guidelines Normal safe local operating standards should be applied at all times The warnings above are for guidance only Please consult the instrument supplier if there is any doubt Disconnection Method Genie Il is disconnected by removal of incoming mains power source to the unit Following disconnection the unit should be left for a period of at least 5 minutes before any internal assemblies are removed or examined When in use the heating blocks and heated lids are hot so allow to cool before touching the surfaces Safe removal of fluids from Genie II will depend on the chemistry used This will also require knowledge of the fluids used in the system to adhere with local health and safety and COSHH regulations If in doubt consult the person responsible for the equipment in the laboratory Version 1 00 SUPPORT HOW TO OBTAIN SUPPORT For the latest services and support information go to http www optigene co uk support htm IMPORTANT When directed to do so contact OptiGene Ltd to schedule maintenance or calibration of a Genie II instrument IMPORTANT If a Genie Il instrument is kept in a very cold environment the battery will not begin charging until the internal temperature has reached 15 C SUPPORTED CONSUMABLES
6. press Test Any point pressed on the screen will then be marked Calibrate the touchscreen by touching the target points shown on the screen the stylus should be used for this It is also possible to run the touchscreen calibration when the instrument first starts Press and hold down on the welcome screen for 5 seconds to initiate DATE AND TIME 10 07 2014 16 31 03 Set Date click in the white box for date and enter in the format DD MM YY Time click in the white box for time and enter in the format HH MM SS Press Set to save or click the cross to cancel Version 1 00 RUN On Genie II there are two ways to start a run either quick start by touching one of the predefined profiles saved on the instrument or by creating a new profile Predefined profiles can only be selected for quick start if they are saved anywhere on the instrument file system QUICK START LAMP amp Anneal Anneal Other POR I PR CIVIS pugs isense ci uk bug ill gt O FF a b idle 11 Jul 2014 15 47 AMD amp Anneal Amplification Anneal 98 C 9 05 C 80 C Edit OESE 11 Jul 2014 15 49 PROFILE SCREEN LAMP amp Anneal prof 11 07 2014 15 44 Anneal prof 11 07 2014 15 44 Amplification Anneal 98 G CO Y as idle 16 Up to six saved profiles can be shown on the main screen to allow quick starting of an assay The six profiles are selected from the Buttons p
7. the Utilities tab and press Update Genie II will prompt for a file to use for the update Touch on the file and touch Open Genie II will then install the updated software Please wait for it to finish before trying to do anything else If the update was a firmware update Genie II will restart when completed If an FPGA software update was performed Genie II will require a manual restart by turning the instrument off and on from the switch on the rear of the unit Genie II will automatically delete the files when the update has completed 28 Version 1 00 GENIE EXPLORER In addition to standalone operation Genie instruments can be run and completely controlled by a computer and the results data then stored and analysed The software that supports remote operation is called Genie Explorer and is included on the OptiGene USB memory stick that is included with the Genie instrument installation instruments are in chapter 6 To run Genie Explorer double click on the icon on the desktop or run from the Start Menu MAIN MENU When the program has loaded the first screen that will be displayed is the main menu where there are several options New Profile Active File Service and Options EM Genie Explorer No Instruments connected Version 1 00 29 GENIE EXPLORER DISCOVERY PANEL EA Genie Explorer Opticene A
8. Amplification screen displays the fluorescence measurements for each well made during the Amplification phase plotted against time OREDO bee TOO 00 200 OOOO Sw 01 0200 Time AMPLIFICATION RATE Isothermal Ratio shows the amplification take off time during the Amplification phase Isothermal Ratio peak time is similar to the C or C values in qPCR assays a020 MINN MISA 002009 MFO WO 023502 MAM s0 MLM MEM lime Genie Explorer can detect the trace peaks and report them automatically To access the graph options click Settings on the graph and a side panel will appear Version 1 00 37 Select the Peak detection option None Simple or Full and check the default peak criteria The peak threshold minimum value of peak can be adjusted to ensure that all valid peaks are identified while others are not The Anneal tab shows the plot of the fluorescence measurements for each well made during the Anneal phase plotted against temperature Version 1 00 38 ANNEAL DERIVATIVE ae CAU or Sese SLID GHop Duncan Gen Mes Thame OptiGene Enayeres RTLAMP_O01 gen The Anneal Derivative tab shows the plot of the derivative of fluorescence for each well Floorescence dev vaise made during the Anneal phase plotted against temperature Select the Peak detection option None Simple or Full and
9. OW GAIN This option is mainly for use if the user is running experiments with Calcein The range of values is between 0 and 7 Some guidelines on values are 0 Normal use Default 4 Low gain for use with Calcein 7 Lowest gain BLOCK GRADIENT The Block Gradient facility enables a gradient to be set across the blocks This is especially useful when setting up assays for optimisation of the amplification temperature Version 1 00 32 Example of setting up a gradient Set temperature of the midpoint of the block as the temperature of the Isothermal stage on the Temperature Profile screen SBS Digs Tens C Then set the temperature range for the Block Gradient 0 block by adjusting the Block Gradient parameter For example if the midpoint temperature is set to 63 5C and the gradient is set to 7 C that will set well 1 to 60 C well 2 to 61 C etc through to 67 Cin well 8 SAVE Profiles can be saved in order to repeat experiments Clicking the Save button will store the profile on the computer The default location is set within Genie Explorer and can be changed if desired Any saved profiles from Genie Explorer can also be copied to a Genie instrument s internal memory and run directly from the instrument Copy the saved profile to the Profile folder on the Genie instrument and then access it on the instrument as normal OPEN Any saved profiles from either G
10. age in the Toolbox Pressing one of buttons on the main menu will pop up a preview of the profile and allows the user to start edit or cancel the run To create a new profile press the Other button on the main screen This allows access to any predefined profiles or creation of a new one Cancel to return to the main menu Press the tick to select a file or to create a new profile If there are many profiles scroll down by dragging on the window Version 1 00 TO CREATE A NEW PROFILE Profile New Press the New button on the profile screen Click the graph to adjust the profile by touching the appropriate temperature or time box 20 Time mins Once the required changes have been Profile New x e e e made pressing the tick button will Preheat Amplification Anneal g C ge tome B __ ajx accept the changes Clicking the cross zz ED in the top corner will cancel any wat at 0 05 ec changes Amplification Pressing the play icon will accept the changes and prompt the user to start Temperature C D the run To set a thermal gradient across a block enter a range of temperatures in Amplification the Amplification temperature box at 60 67 ec The range of temperatures should be entered separated by a hyphen as for 30 00 mics shown below Profile Isothermal 65 C Anneal prof Anneal 98 C 80 C prof go Save pr
11. aph to a jpg file Report will display all of the results of the experiment in an organised report form which can be printed or saved These buttons allow the data to be saved in different formats Version 1 00 40 ANALYSIS amp GRAPH OPTIONS Click the Settings button on a graph and Genie Explorer will display the graph options for that graph From this window several aspects of the graphical information can be modified SMOOTHING Smoothing Smoothing can be applied to all of the graphs A 0 Drag the slider or change the Points value to Points set the number of readings that are averaged to create a data point on the graph NORMALISATION Normalisation allows all the fluorescent signals to have their background level a HE removed calculated over a specified period l_ Normalisation l of time From 60 sec To 180 Sec ms D Select by ticking the Normalisation o Noo l o bn checkbox and setting the start and end times for calculating the background level e g 60 seconds to 180 seconds Amplification 100 000 00 a A A O IDE This screenshot shows data that has not vc been normalised the initial signal levels are Fluorescence different for each well 20 000 00 0 00 T T T T T T T tT T T 50 00 15 00 00 25 00 00 35 00 00 45 00 00 55 00 09 10 00 00 20 00 00 30 00 00 40 00 09 50 00 Time Armplificabon s 20 000 00 z zu With nor
12. ccce 9 NEW ae eer et eee ener 30 Thermal Profile cccceceeceees 31 DALGCEY sedrasi 9 Graph Options ceeeeeeeeeeeeeeeees 34 Channels sence scvessccesceescsatenczenseecanes 35 Battery MONITOT sssssssssssrrrrreeeeeseeees 10 NOTOS iena a ee re 35 Screen Brightness Control 11 ACUVE corratier 36 Profile eee 36 USER INTERFACE O E S 12 Temperature eT re 37 np Amplification cccccceeeseeeeeeeeees 37 RSE E OE EEEa aa Amplification Rate s es 37 Main Menu cccccccccccccc 13 7a 0s eee a eee ene 38 Anneal Derivative 0 ceceee 39 TOOIDOX ccccccccccccecsccccecseceecsseceesssseees 13 GSU i E 39 BUTTO eronata a 13 l l POW CY oss sercccen ee yeeeucctoeecacecesnceeetees 14 Analysis amp Graph Options ot CONUS eer cee aceceereene naa 1a FIC vonir 42 UtilitieS asensesenenssensessesserenrssnes 14 Touchscreen calibration 15 Te en eee een ee eee 43 Date and Time ccceceeceeeeeess 15 OT OMSesarensdencttereocterinctmaninsatmaton 43 PU PEASE EE EEE EEN ANE EE 16 K oE eorsmscceectacventsamantecenenans 16 GENIE II TECHNICAL SPECIFICATION Profile SCFECN ccceceeceececceceeees 16 44 To create a new profile 17 SAFETY NOTICES Please read the following notices carefully before using Genie Il The equipment supplied has been designed to be completely safe to use However to avoid any risk to the safety of t
13. check the default peak criteria The peak threshold minimum value of peak can be adjusted to ensure that all valid peaks are identified while others are not Tismo OptiGene Enzymes_RTLAMP_O01 gen Annes Denvanve This page shows the results in a tabular format and displays the Amplification Rate peak times and Anneal Derivative peak temperatures Version 1 00 39 ADDITIONAL TOOLS From left to right the buttons are Save The results will be saved to a gen file for subsequent access from either the instrument or software Save Profile The profile currently being run will be saved Stop This will stop the run in progress Oa Oz Skip To advance to the next phase press the Skip button Extend If more time is required on the current phase press the Extend button and the run will extend by 10 minutes A confirmation box will pop up every time Extend is pressed and the run profile will be updated to show the new time The buttons below the graphs can be used to OQ Q oo zoom in and out of the graph in different 5 VA directions The Reset button will return the graph to its original state From left to right the buttons are Save to Text will save the raw data toa comma separated txt file for import into a spreadsheet application such as Microsoft Excel Save to Image will save the current gr
14. e settings only apply when battery Power g Powered Display dim time 5 min Display dim time how long the Display dim level 4 instrument waits without input before stancby time 23 nin dimming the display Display dim level the brightness level the instrument will use after the specified idle time These settings only apply when battery powered Standby time how long the instrument waits before turning off the display COLOURS The background colour and the default colours of the lines on graphs can be changed here Click the background button or a graph 80000080 g grap number and then drag the cursor on the colour chart to select a colour The two small coloured boxes on the right show the colour that is currently set Cur and the default Def colour Pressing on either will set the colour UTILITIES Utilities Touchscreen This will start the Touchscreen touchscreen calibration see below Date amp Time Set the time and date within the instrument Update Update Allows updating of the instrument software See Chapter 6 14 Jul 2014 10 49 30 C 30 C Version 1 00 14 TOUCHSCREEN CALIBRATION Touchscreen calibration Touch screen to start Touchscreen calibration Touch the target points Touching anywhere on the screen with the exception of Test or Skip will invoke the touchscreen calibration To check the sensitivity of the screen
15. e straight out of the box without any external connections It can be operated standalone taking power from its internal battery In order to charge the battery or to use Genie II with a computer some connections must be made Connect the power supply plug into the back of the instrument and then attach the power cable to the supply Located at the rear of the instrument is an on off power switch When in the on position Genie II will power up and progress through its checks POWER INLET POWER SWITCH USB TO PC OPENING amp CLOSING THE LIDS Gently lift the lids upwards Close the lids by lowering gently Care must be taken to ensure that objects are not obstructing the lids when trying to close it and under no circumstances should the lids be forced open or closed Version 1 00 INSERTING TUBES IMPORTANT Genie Il uses a proprietary tube strip that maximises optical and thermal efficiencies Other tubes and strips will not fit IMPORTANT The shape of the tubes is such that they will only fit in one way round The locating pins on the block have corresponding holes in the strips BATTERY Genie II has an internal rechargeable battery When Genie II is delivered the battery should be fully charged and ready for use The battery monitor is on the status bar next to the block temperature reading cy C9 AB Idle 10 Jul 2014 16 07 40 C 41 C g To see more details on the battery press the batte
16. emperature and time Time 3 gt Minutes sothermal Check that the Isothermal checkbox is ticked Temperature 65 00 C and then alter the temperature and time to Duration 30 n suit the assay conditions 7 Anneal If the assay requires an anneal check the Start Temperature 95 00 C Annea box and alter the start temperature End Temperature 80 00 2C end temperature and cooling ramp rate This dialogue box shows how to set an annealing Rate 0 05 c Sec Ramp C Sec curve from high to low temperatures Version 1 00 31 ADVANCED BOX The Advanced button shows a pop up screen showing several options which allows changes to be made to the instrument control parameters Preheat Isothermal Ramp rate 1 00 C Sec Ramp rate 1 00 K ClSec Mid Point Temperature pE Measure period 15 Sec Block Gradient 0 C Anneal Low Gain Initial rate 1 00 C Sec Settling time 60 Sec Measure period 0 gt Sec RAMP RATE The Ramp rate specifies how fast the heating will occur It can be set for the three different phases independently MEASURE PERIOD The Measure period is the interval between measurements of fluorescence and is measured in seconds It can be set for both the isothermal and anneal phases SETTLING TIME The Settling time is the time that the instrument will wait once it has reached the desired annealing temperature before it starts to take readings L
17. en will zoom out to the full extent of the graphs Version 1 00 24 CONNECTING TO A COMPUTER Genie II is a standalone instrument however for software updates data upload and analysis it will need to be connected to a PC running Microsoft Windows XP Vista 7 IMPORTANT Do not plug any Genie instrument into the computer before installing Genie Explorer Genie Explorer can be installed from the USB drive included with any Genie Instrument So NT ieee Welcome to the Genie Explorer Setup Wizard P a The installer will guide you through the steps required to install Genie Explorer on your computer WARNING This computer program is protected by copyright law and international treaties Unauthorized duplication or distribution of this program or any portion of it may result in severe civil or criminal penalties and will be prosecuted to the maximum extent possible under the law fg Genie Explorer a Select Installation Folder The installer will install Genie Explorer to the following folder To install in this folder click Next To install to a different folder enter it below or click Browse Folder c Program Files x86 0 ptigene Genie Explorers Install Genie Explorer for yourself or for anyone who uses this computer Everyone Just me Open the USB drive in My Computer Run the file Genielnstall msi Follow the onscreen instructions A pr
18. enie Explorer or a Genie instrument can be run from Genie Explorer Navigate to the profile file select it and all the parameters will be loaded in RUN Pressing Run will start the experiment On clicking Run this box will appear This allows selection of which block is being r aJ Select Block used and also options for saving of the run file The default location for saving the files is set within Genie Explorer and can be changed in Options If the Genie instrument only has one block then only block A will be selectable Version 1 00 33 GRAPH OPTIONS Clicking on Graph Options will display the following screen WATT TTF PEEVE Choose either 8 Wells one block or 16 Wells two blocks Genie Il only supports 8 wells It is also possible to enter well names change plot colours set line styles and to select which wells are visible on the results display The tabs allow the parameters for all graphs to be adjusted Click on the tabs for each graph and alter settings as required For more information see section Analysis and Graph Options Version 1 00 34 CHANNELS If the Genie instrument supports multiple channels such as the Genie III the Channels button will be available Select which channels are to be used in the profile by checking the correspond
19. he equipment operator or anybody in the vicinity of the equipment please read this chapter before unpacking and using the instrument If there is any doubt as to the correct use of the equipment contact the vendor Notices Using the instrument in a manner not specified by OptiGene may result in personal injury or damage to the instrument Always ensure that the surface on which the instrument is placed is level and stable and will not cause the instrument to topple over Ensure that the surface is suitable for the weight and size of the instrument If the instrument is dropped it may be damaged The instrument should never be lifted by its covers Always ensure that the base or sides are used as the lifting point The instrument is electrically powered Please ensure that the correct voltage settings have been applied before applying power to the instrument If in doubt consult a qualified electrician The instrument has a rating label affixed to the rear Please consult this if needed Version 1 00 Always disconnect the equipment before moving or removing any guards or covers Switch off at the mains remove the mains plug from the wall socket and remove the cable from the inlet socket on the rear While every effort has been made to protect the inside of the instrument against splashes the instrument carries no IP rating If fluids are spilt on the instrument they may cause damage and cause an electrical hazard If a spill
20. her screens can be accessed using the tabs LOG 2014 07 11 GEN2 2007_0019 gen A PROFILE Notes This shows the temperature profile that is running Amplification At the top of this screen there is a text box to edit the run description a button to add notes about the run and a button to save the Temperature C Time mee p rofi e 11 Jul 2014 15 53 AB TEMPERATURE Active Block A B This shows the current temperature of the block as the experiment is progressing Extend Temperature C Advance Stop C3 P A B Amplification LOG 2014 07 11 GEN2 2007_0019 gen A Temperature EXTEND Active Block A B This adds 10 minutes to the current phase of the run 4 Extend Temperature C Advance Stop 20 Time mins C3 P A B Amplification Version 1 00 20 LOG 2014 07 11 GEN2 2007_0019 gen Temperature __ Toe ADVANCE Active Block A B Advances to the next phase of the run Preheat to Amplification or Amplification to Anneal Temperature C EJ STOP Active Block A B The Stop button will abort a run in progress A confirmation pop up box will prompt Yes or No Extend Temperature C Advance lt 06_03_14 wainwright dog meat_O01 gen Profile Temperature AMPLIFICATION This shows the fluorescence data that is being acquired duri
21. ing tick box Clicking on the Notes button allows experimental notes to be entered and saved as part of the profile Version 1 00 35 ACTIVE On starting a run Genie Explorer will display the Active window The status icon of the Genie instrument which is running will change showing red labels for the blocks that are active The taskbar at the bottom allows selection of the different running profiles If multiple channels are being used each channel will show as a different tab Genie Explorer OptiGene 1 connected A a Run Profile WA GEN3 1035 T 2 v E f pd o a E o E 00 20 00 Time hh mm ss Hal There are several tabs available to display the thermal profile and measured readings from the run i e Profile Temperature Amplification Amplification Rate Anneal Anneal Derivative and Result all GEN2 1045 Block A B Profile Temperature Amplification Amplification Rate Anneal PROFILE Run Profile The Profile screen shows the run profile settings Version 1 00 36 TEMPERATURE The Temperature screen displays the measured temperatures of the blocks and the heated lids plotted against time Temperature C 00 02 00 Time hhc a CAUners OptiSente Si Desctoc Duncan Gen filer Tams OptiGene Enzymes RTLAMP DL gen The
22. layed in the bottom left hand corner of the main menu screen LAMP amp Anneal Anneal Other 11 Jul 2014 15 47 e To download the latest firmware visit the OptiGene website http www optigene co uk Click on Support and click on the appropriate link on the right hand side of the page and download the zip file e Open the zip file and extract the contents to a new folder The contents of the folder will include the latest firmware FPGA software and this manual e f Genie II already has the latest FPGA software only the firmware will need to be updated e f both firmware and FPGA software updates are required update the FPGA software first followed by the firmware e 6 f itis a firmware update the file will be a mot file whereas if it is an FPGA software update it will be a rbf file Version 1 00 27 eD Organize v Share with v Burn New folder PROFILE Genie N_N_01_r c3_23Jull3 mot Buttons Power Colours Touchscreen Date amp Time Update 14 Jul 2014 10 49 30 C 30 C FF y LOG PROFILE O Ta TA A B Idle 14 Jul 2014 10 51 30 C 31 C To install the updates connect Genie II to a computer Navigate to My Computer and open the Genie II drive The drive is named with the instrument serial number e g GEN2 2001 Copy and paste or drag the firmware or FPGA software files onto the Genie II drive Now on Genie II select the Toolbox touch
23. malisation the levels come Fluorescence together and allow for easier analysis Version 1 00 41 PEAK DETECTION Simple The software looks at the plot and assigns the peak to the highest plotted point that is above the Threshold value Multiple peaks can be detected Full The software performs more complicated analysis of peaks above the Threshold value Multiple peaks can be detected Invert inverts the graph FILE To view previously run data go to the main menu and click the File button Then click on either a Genie instrument or PC to browse for a run file Files are saved as gen files by default in the folders specified in Genie Explorer Options or in the Log folder on a Genie instrument The run file is encrypted N Genie Explorer ad as eel hy pe The requested file will be loaded Ji DropboxPersi Name Date modified Date a E GEN3 1035_10 07 2014_14 22 34 gen 10 07 2014 14 24 10 07 2014 14 22 5 a n d a n a lys S of t h e d a t a C a n b e B h m GEN2 2004_04 07 2014_13 46 03 gen 04 07 2014 13 49 04 07 2014 13 46 Website m GEN3 1035_04 07 2014_13 29 15 gen 04 07 2014 13 34 04 07 2014 13 29 el e e e a GEN2 2004_04 07 2014_12 05 28 gen 04 07 2014 12 12 04 07 2014 12 05 le f d T h f d d J Results z l y Profiles a GEN2 1225_19 06 2014_15 31 09 gen 03 07 2014 12 18 19 06 2014 15 31 le p e r O r
24. ng the amplification phase of the experiment Fluorescence F 15 Time mins 06_03_14 wainwright dog meat _001 gen ANNEAL This shows the fluorescence derivative data that is being acquired during the anneal phase of the experiment FC Derivative 88 Temperature C C3 ass idle 11 Jul 2014 16 05 Version 1 00 21 06_03_14 wainwright dog meat_001 gen SELECTION OF GRAPHS Pressing the well name on either the Amplification or the Anneal page cycles a Z3 u rs the state of the related curve on the graph Derivative th between normal highlighted and off 5 C3 ass idle 06_03_14 wainwright dog meat_001 gen File Oe suse as This shows the results of the experiment ai A2 Each sample name is shown along with Byes o d S amplification time and anneal temperature Po o o o g o as as J T Tooo as CO ass Idle 11 Jul 2014 16 07 RESULTS VIEW To view previous runs press the folder icon on the status bar cy C9 A B Idle 10 Jul 2014 16 07 40 C 41 C S Open file m E This will display a file browser sais window t All Genie Il runs are saved in the LOG folder To open click on LOG and then tick icon or double press on the folder name 11 Jul 2014 15 59 Version 1 00 22 a Open file 40G File 2014 Each run is stored in a folder by date order Year Mon
25. ny Genie instruments that are connected to the computer will be shown in the panel on the left side of the screen Multiple Genie instruments can GEN3 1035 be connected at the same time If any instrument is connected and not displayed click the scan for instruments button in the bottom left corner and the program will attempt to connect to them NEW Clicking the New button will display the following window which will allow a new experiment to be set up and run on an instrument Multiple profiles can be set up at the same time and selected via the taskbar at the bottom of the window opticene i 1 connected a Profile 1 Ther ma A Experiment Name Profile Name ca Run Profile GEN3 1035 Temperature C 00 15 00 00 20 00 Time hh mm ss Estimated run time ES Minutes M Seconds Advanced 7 Anneal Preheat Activation Isothermal Start Temperature 98 00 C Temperature 4500 C Temperature 65 00 E Cc End Temperature 80 00 C Minutes Duration 30 Minutes Ramp Rate 0 05 i oc Sec ila Version 1 00 30 THERMAL PROFILE The Thermal Profile tab allows setting of the thermal profile that is to be used and calculates an estimated run time for the desired profile Preheat Activation If activation is required for the enzyme then 1 tick the Preheat Activation checkbox and set GC l l the required t
26. ofile Pressing the save icon will save the profile Name the profile press the tick button and it will be saved within the PROFILE directory in the on board memory allowing it to be loaded for future runs Version 1 00 17 O CO P A idle Isothermal 65 C Anneal prof Anneal 98 C 80 C prof O CO P A idle u o L o 3 E al o a E T H ai co Temperature C pS LAMP amp Anneal Amplification 11 Jul 2014 15 49 24 09 2012 12 50 24 09 2012 12 51 10 Jul 2014 17 01 4 Time mins 4 Time mins TO LOAD A SAVED PROFILE Pressing one of the quick start buttons on the main menu will pop up a preview of the profile and give the user the choice to start edit or cancel the run Alternatively press the Other button and a file browser will be displayed Choose the profile to be loaded and press the Open button A preview graph will appear and allow the user to start edit or cancel the run Pressing Edit will open the main profile screen Changes can be made as required To begin the run press the play icon A prompt will be displayed Select A B or Both to run or Cancel to abort Version 1 00 WELL NAMES Profile Anneal 98 C 80 C prof To assign names to the block wells click on the well names area Temperature C 4 Time mins To change a well name press on the ila at Firs
27. ompt may appear requesting installation of LNET Framework 4 0 This must be installed prior to installation Follow the link to the Microsoft download page http www microsoft com en gb download details aspx id 17718 Choose a location for the installed program Version 1 00 Confirm Installation The installer is ready to install Genie Explorer on your computer Click Next to start the installation Confirm to start the installation Installing Genie Explorer Genie Explorer is being installed Please wait The installer will copy all necessary files to the computer Installation Complete Genie Explorer has been successfully installed Click Close to exit Once the installation is complete exit by clicking Close Please use Windows Update to check for any critical updates to the NET Framework Cancel Back Close A Genie instrument can now be connected to the computer When connected via USB and switched on the Genie instrument will appear as a USB drive and will be accessible from Genie Explorer Version 1 00 26 GENIE Il SOFTWARE UPDATES It is recommended to keep the software on Genie Il up to date Upgrading may improve performance and add new features to Genie Il There are two types of software on Genie II the firmware and the FPGA software The current versions of firmware and FPGA software that are installed on Genie II are disp
28. p Anneal Anneal Other Here the pop up shows that the instrument is discharging Battery Status Discharging 5500 mAh 16 8V 0 44 3h 34min active time gt C3 P ass Idle 11 Jul 2014 15 46 Version 1 00 10 SCREEN BRIGHTNESS CONTROL Next to the battery icon is the brightness control 5 P 4 Idle 10 Jul 2014 16 07 40 C 41 C g Touch the icon and a slider will appear on the right hand side of the screen Move the slider to the desired position Press the icon again to remove the slider Genie I Op tien Isothermal 65 C Anneal om Anneal 98 C 80 C It is not recommended to set the brightness at 100 for long periods of time as this will significantly decrease battery life Other USB NI VISA varon 2 zar beta 1 PRELIMINARY VERSION S N GEN2 2003 REPORT PROBLEMS ON bugs optisense co uk bugzilla 86 10 Jul 2014 17 10 33 C 34 C Version 1 00 11 USER INTERFACE Genie II uses a touchscreen for viewing and inputting data Touch the screen gently and press the appropriate keys when required The touch screen can be operated while wearing protective gloves or by using the stylus included with the instrument IMPORTANT Do not use a pen or any other sharp implements to touch the screen GENIE Il WELCOME SCREEN When switching on the LED above the screen will be amber in colour Wait for the light to change to green then touch the screen to access the main men
29. ry icon and the monitor will appear as a pop up in the bottom right hand corner of the screen To remove the pop up press on the status bar indicator again Battery Status Charging 5589 mAh 16 9V 0 3A 3h 38min active time Battery monitor pop up IMPORTANT Genie Il s internal battery will only charge when the instrument is plugged into mains electricity and the instrument is switched on Genie II can be placed into standby using the power button in the bottom left corner The LED above the display will glow brightly until the battery is fully charged At this point Genie Il can be switched off using the switch on the rear cy C9 AB Idle 10 Jul 2014 16 07 40 C 41 C g t Note If this button is pressed during a run Genie II will not enter standby When in standby normal operation can be resumed by pressing anywhere on the screen Version 1 00 BATTERY MONITOR LAMP amp Anneal Anneal Other The battery status can be seen but there is no pop up 5 C3 P ass Idle 11 Jul 2014 15 47 LAMP amp Anneal Anneal Other Here the pop up shows that the battery is currently charging Battery Status Charging 5499 mAh 16 9V 0 44 3h 34min active time 11 Jul 2014 15 47 LAMP amp Anneal Anneal Other Here the pop up shows that the battery is fully charged Battery Status Battery Full 5541 mAh 16 9V 0 04 3h 36min active time 11 Jul 2014 16 05 LAMP am
30. t Block well names amp abbreviations text box an d ty pe a name an d Well Name Abbreviation Well Name Abbreviation Z a b b rev j a t j on if d es j re d cc po D oo ao vy Da pa T vy The AB button will switch to the oc tar ny second block Pressing the cross returns back to the run screen with no changes made to that well Pressing the tick button returns to the run screen with changes saved If the profile is saved at this point the well names and abbreviations will also be saved as part of the profile The well names screen can be accessed at any time the instrument is running by clicking on the Results tab and clicking anywhere on the well names column When a run is started the main screen Genie II will display a preview of the run that is LAMP amp Anneal active As the run progresses the grey line showing the profile will turn red OptiGene Other Block A will appear on the left and Block B on the right If both are started then the preview will appear LOG 2014 07 11 GEN2 2007_0020 gen in the middle of the page USB NI VISA Mell beta 1 PRELIMINARY VERSION S N GEN2 2007 REPORT PROBLEMS ON bugs optisense co uk bugzilla 4 A Amplification B Idle 11 Jul 2014 16 13 65 C 37 C Q Touching the graph will take you to the active screens Version 1 00 19 ACTIVE Once a run is started the software will go to the Temperature screen initially The ot
31. th Day Oe 11 Jul 2014 15 59 42 C 43 C Open file LOG 2014 File 07 T 06 Each run is stored in a folder by date order Year Month Day 11 Jul 2014 15 59 41 C 42 C Q o Open file LOG 2014 07 File 11 08 07 Each run is stored in a folder by date order Year Month Day CO ass idle Sets The default filename for the each run fLOG 2014 07 11 File GEN2 2007_0019 gen GEN2 2007_0018 gen followed by a sequential number GEN2 2007_0017 gen is the instrument serial number Touch on a file a preview will appear in the right hand pane then touch the tick icon to load it To delete a file touch the trash can 5 C3 FP ass Idle 11 Jul 2014 15 59 419 C 42 c g Q icon l When the file has opened Genie II will display the profile that was run the temperature log amplification data anneal data and the results table Version 1 00 23 ZOOMING FUNCTION Zooming is available on temperature fluorescence and anneal graphs 06_03_14 wainwright dog meat_001 gen s File Block A Chicken To zoom in on the area of interest F C touch the plot area and drag to the Derivative N right and or down 11 Jul 2014 16 07 37 06_03_14 wainwright dog meat_001 gen File Block A FC To zoom out touch on the plot area Derivative M ae and drag to the left and or up Turkey C3 A Idle A double press on the scre
32. u Version 1 00 12 MAIN MENU To start a predefined run touch the name of Genie Il __ opiceneft LAMP amp Anneal the assay and it will begin Alternatively touch Other to create a new profile or Anneal open a saved profile Other To view profiles or data from previous runs touch the folder icon J on the status bar USB NI VISA i Vason 225 eta 1 PRELIMINARY VERSION To access the toolbox touch the spanner icon S N GEN2 2007 REPORT PROBLEMS ON bugs optisense co uk bugzilla l A B Idle 11 Jul 2014 15 47 37 C 37 C z i OO c on the status bar IMPORTANT When running for the first time check that the date and time on the status bar are correct These can be changed by clicking on the date and time v cy C9 YP A B Idle 10 Jul 2014 16 07 40 C 4icc S TOOLBOX Pressing the spanner icon in the taskbar will load the toolbox cy C9 A B Idle 10 Jul 2014 16 07 40 C 41 C g BUTTONS Set up the quick start buttons on the main screen Buttons s v fPRcriLe isathermal 65 C Anneal prof JE Touching will allow the user to browse the saved profiles on the a B instrument and assign that profile to the je corresponding quick start button on the Ce Sei SETGeH Other button To remove the buttons untick the box Q a o A B Idle 10 Jul 2014 16 28 36 C 36 C Z next to the p rofi e na m e Version 1 00 13 Thes
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