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Related Manuals for Optigene Genie II
Summary of Contents for Optigene Genie II
- Page 1 ® Genie II USER MANUAL (Instrument Software Version v1.18)
- Page 2 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® II and its design is a registered trademark of OptiGene Ltd. or its subsidiaries in the UK and other countries.
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Page 3: Table Of Contents
Table of Contents TABLE OF CONTENTS ......I Run ........... 16 Profile Screen ....... 16 SAFETY NOTICES ........ 3 To create a new profile ....16 To load a saved profile ....17 SUPPORT ..........5 ACTIVE ..........20 Profile .......... 20 How to obtain support....... - Page 4 Observing a run ........ 42 Profile ........... 42 Isothermal ........42 Isothermal Ratio ......42 Anneal .......... 43 Anneal Derivative......43 Peaks ..........44 Results .......... 44 Analysis and Graph Options ..... 45 Genie® II Graph Options ....45 Opening previous run files ....47 Additional features ......
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Page 5: Safety Notices
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. - Page 6 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.
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Page 7: 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® II instrument is kept in a very cold environment, the battery will not begin charging until the internal temperature has reached 15°C. -
Page 8: Box Contents
Chapter Chapter BOX CONTENTS The following is a list of contents in the box for Genie® II: Genie® II instrument • Power supply • Power lead • USB connection lead • USB memory stick containing Genie® II software and this manual as a ‘.PDF’ file •... -
Page 9: Site Preparation
Chapter Chapter SITE PREPARATION HOW TO SET UP GENIE® II 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. -
Page 10: Connections
CONNECTIONS Genie® II is ready to use straight out of the box without any connections as it can be used as a standalone instrument and has an internal battery. However 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. -
Page 11: Inserting Tubes
INSERTING TUBES Each of the heating blocks has locating pins. Genie® II strips have holes that locate on these pins. The strips will only fit in one orientation. IMPORTANT! Genie® II uses a proprietary tube strip that maximises optical and thermal efficiencies. -
Page 12: Battery Monitor
BATTERY MONITOR The battery status can be seen but there is no pop-up. Here the pop-up shows that the battery is currently charging and is at 97%. Here the pop-up shows that the battery is fully charged. The pop-up shows that the instrument is in use and the battery is at 99%. -
Page 13: Screen Brightness Control
SCREEN BRIGHTNESS CONTROL Next to the battery icon is the brightness control. To utilise, 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. Version 1.13... -
Page 14: Embedded Software
Chapter Chapter EMBEDDED SOFTWARE 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. IMPORTANT! Do not use a pen or any other sharp implements on the screen otherwise damage could occur. -
Page 15: Main Menu
MAIN MENU To begin a new run touch ‘Run’. To view profiles or data from previous runs touch ‘View’. To access the utilities touch ‘Utilities’. INITIAL SET UP IMPORTANT! When running for the first time check the time and date on the status bar. -
Page 16: Utilities
UTILITIES TOUCHSCREEN CALIBRATION Touching anywhere on the screen with the exception of Test or Skip will invoke the touchscreen calibration Here the user is required to touch the target points shown on the screen, this will calibrate the touchscreen To check the sensitivity of the screen press ‘Test’. -
Page 17: Set Time And Date
SET TIME AND DATE Click in the white box for date and enter the date. The date should be in the format DD/MM/YY. Click in the white box to enter the time. The format should be HH:MM:SS TURN OFF Pressing ‘Turn Off’ will place Genie® II into standby. Genie® II can be placed into standby mode by pressing and holding the power symbol on the status bar. -
Page 18: Run
PROFILE SCREEN Pressing ‘Run’ will take the user to the profile screen. Here the user can choose to create a new profile, load an existing profile or cancel and return to the main menu. TO CREATE A NEW PROFILE Press the ‘New’ button on the profile screen. -
Page 19: To Load A Saved Profile
Pressing ‘Save’ will save the profile. Name the profile, press ‘Okay’ and it will be saved within the ‘Profiles’ directory in the on-board memory allowing it to be loaded for future runs. To set a gradient across a block, enter a range of temperatures in the ‘Amplification’ temperature box. - Page 20 Changes can be made if desired. To begin the run press ‘Start’. A prompt will ask whether the experiment is to be run on block A, block B, or both. Only the block or blocks that are available (i.e. not already running) will be offered.
- Page 21 WELL NAMES To assign names to the wells, click on the ‘Wells’ button. To change a well name, press on the well and type a name. ‘More’ switches to the second block ‘Okay’ returns back to the run screen with changes made. ‘Cancel’...
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Page 22: Active
ACTIVE Once the run has started the ‘Active’ screens (which are no longer greyed out) will be accessible. The software will automatically go to the ‘Temperature’ screen initially. The other screens can be accessed using the tabs below ‘Active’. PROFILE This shows the profile that is running. -
Page 23: Amplification
ADVANCE Advances to the next phase of the run. STOP The ‘Stop’ button will stop a run in progress. A confirmation pop up box will prompt ‘Yes’ or ‘No’. AMPLIFICATION This shows the fluorescence data that is being acquired during the amplification phase of the experiment. -
Page 24: Results
RESULTS This shows the results of the experiment. The sample name and its respective amplification time and anneal temperature are displayed. Whilst Genie® II is running, the display can switch the views for ‘Temperature’, ‘Amplification’, ‘Anneal’ and ‘Results’ between block A and block B by pressing the ‘A/B’... -
Page 25: Notes
NOTES On the ‘Notes’ screen, notes about the experiment that is being performed can be added and will be stored as part of the log file. VIEW To view previous runs press the ‘View’ button on the top menu. This will display a folder browser window. - Page 26 All Genie® II runs are saved in the ‘LOG’ folder. Click on ‘LOG’ then ‘Open’. (Alternatively double clicking on the folder name will open the folder) Each run is stored in a folder by date order: Year/Month/Day. Each run is stored in a folder by date order: Year/Month/Day.
- Page 27 Each run is then stored numerically in sequential order. Touch on a file, then ‘Open’ and wait for the file to load. 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. ZOOMING FUNCTION Zooming is available on temperature, fluorescence and anneal graphs.
- Page 28 To zoom out, touch on the plot area and drag to the left and/or up. A double press on the screen will zoom out to the full extent of the graphs. Version 1.13...
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Page 29: Connecting To A Computer
Chapter Chapter CONNECTING TO A COMPUTER Genie® II is a standalone instrument; however, for software updates and other applications, it will need to be connected to a computer. IMPORTANT! Do not plug Genie® II into the computer before installing software. The PC software can be installed from the USB drive included with Genie®... - Page 30 Accept the License Agreement. The installer will display the processes being performed. The installer will copy all necessary files to the computer. Version 1.13...
- Page 31 Windows 7 and Vista, manual installation of the Genie® II driver may be required. This is performed by locating the file. It can be found by clicking Start > All Programs > OptiGene > “Win 7 GenieII driver”. Right click on the file and click ‘Install’. Version 1.13...
- Page 32 Genie® II is now visible as a USB drive in ‘My Computer’ and the name appears as the instrument’s serial number. Log files and profiles can be copied from Genie® II to the computer and vice versa. Genie® II is now ready to be used and controlled from the computer. Version 1.13...
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Page 33: Genie® Ii Software Updates
For Versions 0.99 or earlier please contact OptiGene directly for the correct upgrade files. It is highly recommended to upgrade. For Versions 1.00 and later go to the OptiGene website and check on the ‘Support’... -
Page 34: Via Pc
To download the latest firmware, click on the link and download and save the ‘.zip’ file. • 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. If Genie®... - Page 35 A pop-up will be displayed. If the instrument is detected, the name of the instrument will be shown. (If it is not shown, check the instrument is turned on and properly connected, and click ‘Find’ to try again). Click ‘OK’ Navigate to the extracted ‘.zip’...
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Page 36: Via Instrument (V1.17 & Later)
VIA INSTRUMENT (V1.17 & LATER) To install the updates, connect Genie® II to a computer. Navigate to ‘My Computer’ and open the Genie® II drive. The drive is named after the instruments serial number, e.g. GEN2-1105. Copy and paste (or drag) the firmware or FPGA software files onto Genie®... - Page 37 The selected file will be uploaded to Genie® II. 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 with the switch on the rear of the unit. Genie®...
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Page 38: Pc Software
Chapter PC SOFTWARE WELCOME SCREEN From this screen there is the ability to choose to start a new experiment, or review data saved from previous runs. To carry out an experiment make sure that Genie® II is connected to the computer and switched on. To start a new isothermal run, click the ‘Isothermal’... -
Page 39: Setting Up A Run
SETTING UP A RUN PROFILE SCREEN Opening a profile allows modification of all of the experiment parameters: Notes • Assays • Wells • Profile details • Graphs • Peaks Classification • Genotypes • Click upon the desired tab to view or modify settings. It is recommended that users work through the tabs in order, i.e. -
Page 40: Assays
ASSAYS This is a list of assay types that may be used in the experiment. They are used to define assay-specific peak classification. WELLS Choose if the experiment is using 8 or 16 wells (default is 8). There is the ability to enter well names, change plot colours, line styles and choose to make the sample visible on the results display or not. - Page 41 If activation is required for the enzyme then tick the ‘Preheat/Activation’ checkbox and set the required temperature and time. Check the ‘Isothermal’ checkbox is ticked and then alter the temperature and time to suit the assay conditions. If the assay requires performing an anneal, check the ‘Anneal’...
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Page 42: Graphs
The ‘Options’ button shows a pop-up screen showing several options, which allows changes to be made to the protocol parameters. GRAPHS The ‘Graphs’ tab allows the parameters for different graphs to be adjusted. Click on the tabs for each graph and alter settings as required. -
Page 43: Genotype
GENOTYPE The ‘Genotype’ tab allows the user to define peaks, which can be used for automated genotyping by the software. RUN DIALOGUE BOX On clicking ‘Run’ this box will appear. This allows selection of which block is being used and also options for saving of the run file. -
Page 44: Observing A Run
OBSERVING A RUN PROFILE The ‘Profile’ screen allows observation of the temperatures of the blocks and the heated lids plotted against time. It acts as a thermal record of the run. ISOTHERMAL The ‘Isothermal’ screen allows observation of the fluorescence of each well plotted against time. -
Page 45: Anneal
The Genie® II software can detect the peaks and report them automatically. To access the graph options, click ‘Settings’ and select the ‘Graphs’ tab, and select the corresponding graph. Select the ‘Peak detect’ option (‘None’, ‘Simple’ or ‘Full’), check the default Peak criteria and click ‘Okay’. -
Page 46: Peaks
If the Peak detect box is set on ‘Simple’ or ‘Full’ then the peaks will be displayed in the results table. Check that the peak criteria are correctly set. PEAKS This page shows the results in a tabular format and displays the peaks for the different profiles used within the experiment, the position of peaks, the peak width... -
Page 47: Analysis And Graph Options
ANALYSIS AND GRAPH OPTIONS GENIE® II GRAPH OPTIONS Click the ‘Settings’ button and it displays the ‘Graph Options’ window. From this window several aspects of the graphical information can be modified. There are four tabs on this page and each tab allows the user to check and modify settings appropriate for that tab i.e. - Page 48 PEAK DETECT None: no peaks are detected. Simple: The software looks at the peak and assigns the peak to the highest plotted point. Multiple peaks can be detected. Full: The software curve fits and assigns the centre of a peak and can report multiple peaks.
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Page 49: Opening Previous Run Files
OPENING PREVIOUS RUN FILES To view previously run data go to the main menu and click ‘File’ > ‘Log’ and navigate to the file required. Files are saved by default in a Genie® II folder in ‘My Documents’. The run file is encrypted. The requested file will be loaded back into the software and analysis of the data can be performed as... - Page 50 EXPORT FUNCTION The Export function allows that data from each graph can be individually exported as a tab- delimited ‘.txt’ file that can be imported into a spread sheet for additional end-user manipulation. The example below shows if the Isothermal graph is exported, it will export time versus fluorescence for each well.
- Page 51 Export temperature versus fluorescence for each well. Anneal graph Anneal Derivative Export temperature versus fluorescence derivative for each well. graph Export the Well, Name, Peak Position, Value, Width, Weight, Peaks graph d²Y/dX², Relative and Class for each well. Results graph Export Well, Name, Genotype, Abbreviation, and Peaks for each well.
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Page 52: Technical Specification
Chapter TECHNICAL SPECIFICATION Sample Number 16 wells (2x8 strips) Sample Volume 10 µl to 150 µl Touchscreen High-brightness TFT / LCD module (800x480) Heater technology Ceramic substrate with resistive coating Cooling method Forced convection Temperature sensor High-precision thermistor Temperature control type Multi-zone independent digital PID Temperature control range ambient - 100°... - Page 53 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® II and its design is a registered trademark of OptiGene Ltd. or its subsidiaries in the UK and other countries.