Manual
Contents
1. RO IC Name Type FAM HE ROK IC C5 pC Amplification pos pos A NCA Amplification on E DNA extraction neg neg 7 me l Saves selected control Deletes selected control Adds new control Software Operation Manual How to adda test 13 Save the test Press Save or OK buttons Name C trachomatis Ureaplasma Tests Infections List Influenza A B BM hominis G vaginalis N gonorrhoeae Ctrach T vaginalis N gonorrho T vaginalis C trachomatis G vaginalis Influenza A Influenza B M genitalium M hominis N gonorrhoeae Ureaplasmaspp Test System Status Completed Save your time oe THI Create Test Protocol Channel gt FAM Mt HEX x ROX O cts Threshold and Internal Control FAM T a9 T IC Controls interpretation settings Type Amplification ONA en S eooo Deen O ALA 1 4 Fluorometer C trachomatis Ureaplasma Step 1 Sepi Step2 Protocol C trachomatis Ureaplasma Fluoroscence End Point Analysis Test Id Colo Name Test Type FAM HEX ROX Cy 5 g d 1 E ckground C trachomatis Ureapla Background C trachomatis Ureaplasma2. 5 Check the Fluorometer status in the left lower part of the program window the status must be Connected If status is Not Connected there are some problems in communication between PC and external unit see Software Installation page 1 Before measuring Software Operation Manual End point analysis of PCR products FEP 1 Turn on the ALA 1 4 check the connection between the computer and the ALA 1 4 and launch FEP program 2 The Step 1 window Setting Measurements parameters will appear ALA 1 4 Fluorometer FEP 02 05 12 15 06 Step 1 x Step1 step 2 ALA 1 4 Fluorometer Select a program p Anaiyue Z Kinetic Ff er PCR product End point analysis PA Fluorescence End Point Analysis Previous Protocol of PCR Amplification Products Select rotor type Rotor type 36x0 5 ml tubes 48 x 0 2 ml tubes x Number of a Measurements e z s 5 vo Select a User v Add nag Preferences Help Next PREV 7 Previous Protocol Select rotor type Rotor type 4 Then select the rotor type 360 5 ml tubes 48x 0 2 ml tubes Select rotor type Rotor type 36x05 mitubes cjg Y x 0 2 ml tubes y Software Operation Manual End point analysis of PCR products FEP 7 8 5 Optionally you can set number of measurements we advise to put at least 2 Number of R Measurements a 2 gt y 6 After all the parame
3. Medical Biological Research amp Technologies Multi ALA 1 4 escen Multi Channel Automatic Lumin piosan ALA 1 4 Multi Channel Fluorometer Software Manual Author Pavel Bankovsky Riga Latvia 2012 All right reserved Biosan Ltd Version 2 Table of Contents Getting Started e Software Installation 2 00 eee ee ee eee eee ee eee e Connection settings between PC and ALA 1 4 2 022 002 e Software Operation Manual End point analysis of PCR products FEP e Software Operation Manual How to addatest 00008 Software Installation 1 Turn on ALA 1 4 and connect it to your computer 2 Open SetupFEP exe 3 Chose the setup language Select Setup Language x Select the language to use during the installation ig Setup Fluorometer g O x Welcome to the Fluorometer Setup Wizard This will install Fluorometer v1 5 on your computer It is recommended that you close all other applications before continuing Click Next bo continue or Cancel to exit Setup Cancel 5 Read and accept the License Agreement i Setup Fluorometer lOl x License Agreement Please read the Following important information before continuing Please read the Following License Agreement You musk accept the terms of this agreement before continuing with the installation END USER LICENSE AGREEMENT FOR FLUQROMETER SOFTWARE IMPORTANT PLEASE RESO THE TERMS A
4. ee Channel Internal Control Testing for Information about test reagents etc Threshold and Internal Control Controls interpretation settings Name lt Enter New Control gt Test System Status Not pleted HINT Enable channels Internal Control and Testing for 1 Type in Test s name 2 Press Add Button Save Delete faii Create Test Protocol Name C trachomatis Ureaplasma Select the channels Channel Internal Control Testing for Information about test reagents etc 2 Select which channel is 3 Select the testing for 4 Type in any information for Internal Control Information about test reagents etch Testing for C trachomatis 12 Software Operation Manual How to add a test Set the positive and negative threshold levels Threshold and Internal Control FAM HEX ROX T T T T T T IC IC Ic 1 Set the Positive T and Negative T 2 Set the value for Internal Control IC Threshold values threshold Threshold agd Internal Control FAM HEX ROX T 35 T 35 T4 T 3 0 T 35 IC IC IC 3 0 Set the controls optional Controls interpretation settings Mame Enter new Control 1 Type in the control name mm I pos 2 Type in the control type neg nd neg 3 Select the result for control ad eq Controls interpretation ettings a eq rL
5. lt Back Cancel 8 Actual window offers to create a desktop icon It is possible to refuse creating by removing tick Create a desktop icon i Setup Fluorometer 5 x Select Additional Tasks Which additional tasks should be performed Select the additional tasks you would like Setup to perform while installing Fluorometer then click Next Additional icans lt Back Cancel 2 Software Installation 9 Please check settings and click Install If it is necessary to change some previous settings click Back ig Setup Fluorometer Ioj x Ready to Install Setup is now ready to begin installing Fluoromeber on your computer 4 Click Install to continue with the installation or click Back iF you want to review or change any settings User information OC machine Biosan Lid Destination location C Program Files Fluorometer Additional tasks Additional icons Create a desktop icon F F Cancel 10 After device is connected to the PC and switched on Found New Hardware Wizard window will appear Chose Yes this time only and press Next to proceed Found New Hardware Wizard Welcome to the Found New Hardware Wizard Windows will search for current and updated software by looking on Your computer on the hardware installation CD or on the Windows Update Web site with your permission Can Windows connect to Windows Update to search for sothware
6. EE EE _ e e A a a neg eg pos 0 pos 1 pos 2 pos 3 pos 4 pos 45 pos G pos 7 and more FAM Er ES i ii OE U HEX ROX CY5 IC samples s 5 5 s 5 s 5 s FAM A ee eee HEX ROX CY5 IC _ _ Samples s s 5 5 5 5 5 5 FAM A re ee HEX ROX CY5 IC Samples s s FAM a HEX ROX CY5 IC lt lt lt Samples s s FAM O HEX ROX CY5 IC Samples s s 10 Software Operation Manual End point analysis of PCR products FEP 10 4 As Excel file press Excel button in the Results table control panel or choose Excel report in the toolbar and click Save Reports 2 m Sample Sample Sample Sample Sample Sample Sample 1 2 a 4 5 B Fi a Sample Test For T vaginalis T vaginalis T vaginalis T vaginalis T vaginalis T vaginalis T vaginalis T vaginalis Sample Sample Sample Sample Sample Sample Sample Sample Note you must have Microsoft Excel to save the results 10 5 As a JPG image press Picture button in Relative fluorescence units window for the required channel and click Save Picture 11 After finishing using ALA 1 4 fluorometer clo se the software Software Operation Manual End point analysis of PCR products FEP 11 Software Operation Manual How to add a test ALA 1 4T Fluorometer Name l Save Delete j Create Test Protocol Tests Infecti List
7. FResultInterpretation Test for Value HE IC T mara a fee R 2 I I I I Same Tvenas Sempe Tweoimaistpo wae SS O asame Tvenas Same Tvasrasoe O SSC a 7 6 Sample Tvegnais Same Tvaorasme O o o sence Togas Snes oos 120 OO ee Leme Tegra Songe agiats p0n dt 38am Teona Samme vai fe View Advanced T E Show RFU Export ta fi Excel F Report Software Operation Manual End point analysis of PCR products FEP Saving the results 10 1 In the program press Save button in the toolbar 10 2 Save as a PDF report press Report button in the Results Table control panel or choose PDF report in the toolbar The report can also be printed When the button is clicked the report is automatically saved in FEP Protocols folder Reports Es iy Ga Results Table Advanced View FEP 02 05 12 15 06 1 Sample Tvaginais Sampe Tavaginalis pos 8 1 20 0 2 Sampe Tvaginais Sample vaginalis pos 124 aj o o y o 4 Sampe Tvaginais Sample vagna oe saj o y o 5 Sampe Tvaginais Sampe vaginalis pos zae tf 6 Sample Tvaginais Sample Mvagnaismeo o osje saj oe y oo 8 Sample Tvaginalis Sampe Mvaginaisiposi te eaj o oo 2 Sample T vaginalis Sampe Mvagmatisiposi 126 zaj oe oo 10 Sampe Tvaginais Background Background Background 10 3 Electrophoresis image Scroll down the report to the last page Electrophoresis interpretation FEP 17 08 12 14 45 Interpretation results
8. List Influenza A B M hominis G aginalis N gonorrhoeae C trach a M hominis G vaginalis T waginalis Influenza A Influenza B Ctrachomatis M genitalium N gonorrhoeae Software Operation Manual How to add atest 17 3 4 4 f Threshold and Internal Control Parameters Description User sets the coefficients provided in reagents manual for specific channels If the channel is used for Internal Control then ji 1 threshold level is available If the channel is used for infections 2 threshold levels are available Not set Threshold and Internal Control Set Threshold and Internal Control FAM HEX ROX CI D ESED Ts 3 4 4 1 f Internal Control Threshold level IC Description Internal Control Threshold level 3 4 4 2 f Positive Threshold value Description Positive Threshold level for Two Threshold levels tests 3 4 4 3 f Negative Threshold value Description Negative Threshold level for Two Threshold levels tests 18 Software Operation Manual How to add a test 3 4 5 f Controls settings table Description Adds controls supplied with parameters taken from reagent s manual Empty Control s table H Enter new Control Filled Control s table Name Type FAM HE Ads IC Cy 5 H C Amplification pos pos n eee PIMA npicain Pd nd GDN estraction meme Default controls type Default controls list Entering a control Type DMA isolation 3 4 5
9. h Hum of channels 4 Channels FAM HEA ROX CYS 4 Press Set Port if FEP device detected will show on the bottom of the window your ALA 1 4 is successfully connected to the PC if not then try any other available ports ALA 1 4 settings FEP device port Virtual COM from 3 to7 ue Number of channels 4 FAM HEX ROX CY5 Mum of channels 4 Channels FAM HEX ROS CYS COM4 FEP device detected 5 After parameters have been set click OK to close Serial Port Setup window and press OK button A Note Software will not work if NASBA DRV m is closed Connection settings between PC and ALA 1 4 5 6 Before measuring 1 After successful installation of software and driver setting of connection of unit with computer check connection with computer through USB cable 2 Switch on the unit on the rear side of the unit After switching on the display readouts are following ALA_1 V 4 0 Note Before detection the unit must be warmed for 15 min after switching on Note If the unit was not used for more than 7 days it must be warmed for 8 hours 3 Test measurement must be performed for reliable connection evaluation between unit and computer It can be performed with prearranged test measurement tubes empty tubes or even with the empty rotor It 4 Before the measurement read carefully point User s manual then set the measurement and sample parameters according to the given instructions
10. res now and every time connect a device O No not this time Click Hest to continue If you do not have internet connection choose to install from PTEE EE ee E A specific location Choose the folder USE lt gt Serial Cable where you have installed the software IF pour hardware came with an installation CD lt or floppy disk insert it now What do you want the wizard to do O Install from a list or specific location Advanced Click Next to continue Software Installation 3 12 Then choose Yes connect and search for software on the Internet and click Next to start installation Found New Hardware Wizard The wizard could not find the software on your computer for y USB lt gt Seral Cable Ih is recommended that you connect to the Internet so that the wizard can search online and look for the appropriate software No do not connect to the Internet now IF you know another place where the software might be located click Back and select the Advanced option Cera Chea 13 Upon finishing driver installation press Finish Found New Hardware Wizard Completing the Found New Hardware Wizard The wizard has finished installing the software for USE Serial Converter Click Finish to close the wizard 14 Run the program for the first time If Windows firewall blocks Fluorometer and NASBA DRV programs click unblock l Fluorometer Windows Security Al
11. spp Internal Control 2 HB Unknown C trachomati Ureapla Sample C trachomatis Ureaplasma spp Internal Control 3 Unknown C trachomati lreaplal Sample C trachomatis Ureaplasma spp lintemal Control M Unknown C trachomatis Ureapla Sample C trachomatis Ureaplasma spp Internal Control 5 Unknown C trachomatis Ureapla Sample IC trachomatis Ureaplasma spp lintemal Control EI Unknown C trachomatis Ureapla Sample C trachomatis Ureaplasma spp Internal Control a i nknown C trachomatis lreaplal Sample C trachomatis Ureaplasma spp intemal Control 8 E Unknown C trachomatis Ureapla Sample C trachomatis Ureaplasma spp Internal Control 9 Unknown C trachomatis Ureaplal Sample IC trachomatis Ureaplasma spp Internal Control 10 a Unknown Jreapla Sample C trachomatis Ureaplasma spp Internal Control 11 J Unknown trachomatis Ureapla Sample C trachomatis Ureaplasma spp Internal Control 12 C Unknown C trachomatis Ureapla Sample C trachomatis Ureaplasma spp intemal Control ii Unknown C trachomatis Ureapla S ample C trachomatis Ureaplasma spp Internal Control 1 M Unknown C trachomatis Ureaplal Sample C trachomatis Ureaplasma spp intemal Control 15 known C trachomatis Ureapla Sample C trachomatis Ureaplasma spp Internal Control 1 gl a Unknown C trachomatis U reaplal Sample C trachomatis Ureaplasma spp Internal Control ri aS Unknown C trachomatis Ureapla Sample C trachomatis Ureaplasma spp Internal Control 19 Unknown C trachomati
12. 1 f Control s name field 3 4 5 2 f Control s type field Description Description Enter the type of the standards via keyboard User sets the name of the standards Default table Entering standard FAM 3 4 5 3 f Threshold value for controls for each channel Description User sets the value for thresholds values for 3 4 4 1 f Internal Control Threshold level IC page 18 FAM in example above oos neg eq nd values for 3 4 4 2 f Positive Threshold value page 18 CY 5 in example above Controls with value means that value is not set or channel is not used Entering threshold value FAM IC Software Operation Manual How to adda test 19
13. 4 1 2 f Add new test button Description Button adds a new test with name entered in 3 4 1 1 f Test name field New Test was added Channel Inte Tests Infections List E FAM fai Create Test Protocol 3 4 1 4 f Create Test Protocol Description Button creates a template in Step 2 for a test selected in Tests infections List Tests Infections List Influenza A B M hominis G vaginalis N gonorrhoeae C trach T vaginalis N gonorrho T vaginalis C trachomatis G vaginalis Software Operation Manual How to adda test 15 3 4 f Tests Editor Window Description Edit Test Dis In this windows user Adds Edits Deletes Tests pa era Tests Database is empty vee Tests Infections List Internal Control Testing for Information about test reagents etc HEX ROX Cy 5 Threshold and Internal Control FAM Controls interpretation settings lt Enter New Contral gt Test System Status Not Completed HINT Enable channels Internal Control and Testing for ox Tests database is filled with 6 tests Name C trachomatis Ureaplasma Se Channel Internal Control Testing for Information about test reagents etc ai Influenza A B x M hominis G vaginalis X HEX oO Ureaplasma spp X N gonorrhoeae C trach ROX T vaginalis N gonorrho E cy 5 T vaginalis C trachomatis Threshold and Internal Control G vaginalis FAM Influenza A I
14. F Lo 3 Reports E m Experiment Analytic _ Kinetic Channels FAM HEX V ROX CY 5 FAM Relative Flourescence Units JOE HEX R6G Relative Flourescence Units 3 1 100 1 000 a 800 800 700 ee 2 ew s B i 500 pn 400 200 200 200 200 100 100 0 0 Graph Fluor Sample v Auto Scale Adjust Scale Zoomin Zoom Out Exportto Excel Picture Graph Fluor Sample v Standard Auto Scale Adjust Scale Zoom n Zoom Out Export to Excel Picture Result Interpretation c Name for Type FAM Value HEX IC Value b 1 Sample galis Sample 8 1 20 0 Completed 100 2 Sample vaginalis Sample 12 4 3 3 Ta ay E me left 0 00 00 epee Uiii aeia i LL k L Measurements completed 1 B ime elapsed 0 01 00 4 Sample T vaginalis Sample 0 1 16 2 5 Sample T vaginalis Sample 7 4 21 0 Status FINISHED 6 Sample T vaginalis Sample 0 8 4 4 7 Sample T vaginalis Sample 12 0 6 8 Add 5 measurements a Sample T vaginalis Sample 11 0 6 1 9 Sample T vaginalis Sample 12 6 22 1 10 Background T vaginalis Background Background 2 0 Background 2 0 View Advanced w gt ShowRFU Export to G Excel Ej Report A Fluorescence Signal on channels FAM and HEX B Progress window C Results window FEP Results Table 38
15. ND CONDITIONS OF THIS LICENSE AGREEMENT CAREFULLY BEFORE CONTINUING WITH THIS PROGRAM INSTALL Biosan End User License Agreement EULA is a legal agreement between you Ceither an individual or a single entity and Biosan for the Biosan software product s identified above which may include associated software components media printed materials and online or electronic documentation SOFTWARE By installing copying or otherwise using the SOFTWARE you agree to be bound by the terms of this EULA This license agreement represents the entire agreement concerning the program between you and Biosan referred to as licenser and it supersedes any prior proposal representation or understanding between the do not accept the agreement lt Back Cancel Software Installation 1 6 Enter the Username and Organization name ig Setup Fluorometer i 0 x User Information Please enter your information User Mame OC machine Organization Biosan Ltd lt Back Cancel 7 Itis recommended to use default destination folder and click Next to see next window 15 x ie Setup Fluorometer Select Destination Location Where should Fluorameter be installed iJ Setup will install Fluorometer into the Following Folder To continue click Wexk IF you would like to select a different Folder click Browse Browse t least 60 7 MB of Free disk space is required
16. ce End Point Analysis Name Sample Test T vaginalis v Type v Add Delete ld Colo Name Test Type FAM HEX ROX Ges 1 7 Sample T vaginalis Sample T vaginalis Internal Control 2 BE Sample T vaginalis Sample T vaginalis Internal Control 3 BE Sample T vaginalis Sample T vaginalis Internal Control 4 9 Sample T vaginalis Sample T vaginalis Internal Control 5 BE Sample T vaginalis Sample T vaginalis Internal Control E 6 BE Sample T vaginalis Sample T vaginalis Internal Control 7 BE Sample T vaginalis Sample T vaginalis Internal Control 8 GP Sample T vaginalis Sample T vaginalis Internal Control 9 Sample T vaginalis Sample T vaginalis Internal Control a I 10 Background T vaginalis Background T vaginalis Internal Control SERI LEER Note In order to proceed to measurement step at least one background sample must be set Enter Preset Name To save the protocol for future use press be Protacoi enter the name and press OK T vaginalis 04 Apr 12 Software Operation Manual End point analysis of PCR products FEP 8 Place samples in the rotor 9 Close ALA 1 4 lid Results will be ready in a couple of minutes from 30 sec to 2 min Results can be viewed only after measurements 10 Press Run to start measurement ALA 1 4 Fluorometer Last Run FEP 02 05 12 15 06 Step 3 _ _ _ File Run Calibration Window Help O G W l i Steps 1 2 Results Z
17. ert To help protect your computer Windows Firewall has blocked To help protect your computer Windows Firewall has blocked some features of this program some features of this program Do you want to keep blocking this program Do you want to keep blocking this program Name Fluorometer Publisher BioSan Keep Blocking Kreck gt Ask Me Later Windows Firewall has blocked this program from accepting connections from the Internet or a network If you recognize the program or trust the publisher you can unblock it When should unblock a program Name NasbaDrvy Publisher RRR Keep Blocking Csa gt Ask Me Later Windows Firewall has blocked this program from accepting connections from the Internet or a network If pou recognize the program or trust the publisher you can unblock it When should unblock a program 15 If there are any problems during installation then contact your system administrator 4 Software Installation Connection settings between PC and ALA 1 4 1 Before running the program it is recommended to check connection settings 1 1 Connect unit to the PC with a USB cable 1 2 Connect unit to the power supply 1 3 Switch on the Power switch on the rear of the unit 2 Open the program NASBA DRV by double clicking mouse on the program icon in the task bar 3 Options window for the ALA 1 4 unit FEP device port Choose port Set pork no port selected
18. nfluenza B M genitalium v M hominis N gonorrhoeae Ureaplasmaspp Controls interpretation settings Name Type FAM HEX ROX IC CY 5 b C Amplification INCA Amplicon od e DNAetacfon Test System Status Completed 16 Software Operation Manual How to add a test 3 4 3 f Channel Options Description Setting the measurement channels Ifa channel is going to be used as Internal Control if needed What illness is going to be tested on a channel Not completed Completed Channel Internal Control Testing for Channel Internal Control Testing for E FAM sai R FAM C trachomatis 7 O HEX hi X HEX O Ureaplasma spp v T Cy 5 T T CY 5 3 4 3 1 f Channel Selection 3 4 3 2 f Internal Control Channel ce a Not set Set Description Channel Channel Description Not set Set User sets the channels on User sets the internal O FAM X FAM Internal Control Internal Control which measurements are control channel if needed going to be performed C HEX E HEX O Rox R ROX O cy 5 O cy s 3 4 3 3 f Test Selection Not set Set Testing for Tarenti 3 4 4 f Information Window C trachomatis T Information about test reagents etc Description User can type in any information about tests reagents used etc TF Description User selects which test from 3 4 2 f Tests Infections list to be performed on a specific channel Tests Infections
19. s Ureaplal Sample C trachomatis Ureaplasma spp intemal Control 190 Unknown C trachomatis Ureapla Sample C trachomatis Ureaplasma spp Internal Control 20 Unknown C trachomatis Ureapla S ample IC trachomatis Ureaplasma spp Internal Control 210 Unknown C trachomatis Ureaplal Sample C trachomatis Ureaplasma spp internal Control a PA IN Tei Ss fea z PEE a Edit Test Discard All Settings Help Back Save Protocaiii ru 14 Software Operation Manual How to add a test Press this button to make to save this template protocol for future use 3 4 1 f Adding Saving Deleting a test Description Commands for Adding Saving Deleting a test Name C trachomatis Ureaplasma Add Empty Name Filled Name C trachomatis Ureaplasma 3 4 1 1 f Test name field Description Text field for naming tests or infections 3 4 1 3 f Delete test button Description Button deletes selected test 3 4 1 4 f Save test changes button Description Button saves changes made to an existing test 3 4 2 f Tests Infections list Description List of Tests Infections available for testing Completed tests are indicated with Bold font T vaginalis N gonorrho Not completed tests are indicated with regular font Not completed tests can be used as a test names for a MultiPlex test C trachomatis G vaginalis Fi caste Tetra 3
20. ters are set click Next button to go to Step 2 Setting Samples Nent 7 Inthe Step 2 Samples window fill in samples name test and type Not Filled ALA 1 4 Fluorometer FEP 02 05 12 15 06 Step 2 step1 Step 2 Protocol FEP 02 05 12 15 06 Fluoroscence End Point Analysis Name Test v Type x Add Delete ld Colo Name Test Type FAM HEX ROX Cy 5 a gt 1 Unknown 2 HB Unknown 3 Unknown 4 n nknown 5 BB Unknown E E Unknown 7 Unknown ld Colo Name Te Adding multiple samples te Type in the Name or select Test field press Add FREE an t o a button b 4 gt Name sample Test Influenza A B a Test Test Test Click lcii k N gonorrhoeae C tra N gononrhoeae C trar fit M hominis G vaginal M hominis G vaginal Influenza 4 B Influenza 4 B Adding a single sample By selecting and typing in sample s name selecting the needed test and giving type of the sample by default type is Sample 1 By holding down left mouse button and moving it across the fields you want to select then pressing Delete button Deleting sample multiple samples 2 Pressing Discard All Setting button Note this command will delete all added samples information Filled ALA 1 4 Fluorometer FEP 02 05 12 15 06 Step 2 3S step1 step2 Protocol FEP 02 05 12 15 06 Fluoroscen
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