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Programming

This section gives instructions for the two methods of programming the Alpha Cycler systems. The first
method uses the

Program Wizard

to automatically generate a program based on a few user defined

parameters. The second method is accessed through the

New program

button from the Home Screen

and allows the user to control every element of the program.

Note:

When programming an Alpha Cycler protocols are built with a

steps and stages

structure.

Individual steps can be created and a collection of those steps make up a stage. Stages have a number of
cycles applied to them and all steps in a stage will cycle the specified number of times before progressing
to the next stage. Protocols can have multiple stages comprising multiple temperature steps.

USING THE PROGRAM WIZARD

The Program wizard allows users to automatically generate a protocol based upon the following
criteria:

•  Primer Sequence or Tm’s
•  Length of amplicon
•  Template source (bacterial, eukaryote or plasmid)
•  Special considerations

Special considerations has a series of options which accommodate for the use of hot start Taq polymerases,
adjusts the temperatures based upon the amplicons A/T and G/C bias and will allow for the user to add
a touchdown PCR stage as a means of improving specificity.

• From the Home Screen select

Program wizard

.

The Program wizard consists of four steps which require user input in order to generate a suitable
protocol. The first step is to specify the melting temperature either from the primer sequences of from
the Tm values.

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Содержание PCRmax Alpha Cycler 1

Страница 1: ...PCRmax Alpha Cycler 1 2 and 4 Operation Manual PCRmax rev 10 ...

Страница 2: ...mplate programs 25 Gradient 26 Creating user Profiles 27 Creating a new user account 27 To log in as an existing user 27 Logging out 27 Changing a user password 27 Creating USB Login 28 Programming 29 Using the Program Wizard 29 Manual program entry 33 Adding a stage 33 Editing step parameters 35 Adding a gradient step 35 Adding a temperature or time increment or decrement 36 Deleting a step or st...

Страница 3: ...ransferring a program from a USB memory stick to the Alpha Cycler 53 Instrument settings and defaults 54 Preferences 54 Instrument settings 55 Temperature log 55 Auto restart 55 Date and time 56 Program defaults 56 Updating the Alpha Cycler software 59 Procedure 59 Technical support and servicing 60 Replacing blocks 60 Additional information 61 User maintenance 61 Fault Finding 61 Fuses 61 Insulat...

Страница 4: ...unit and block include a gradient feature manually adjustable heated lid and programming features such as touchdown active sample cooling advanced reporting and health check options as standard to allow for most applications to be performed easily ALPHA CYCLER CONFIGURATIONS The Alpha Cycler systems can be configured with any combination of 96 or 384 well format blocks in the AC 1 AC 2 and AC 4 ch...

Страница 5: ...E FIRST TIME REPLACE THE FUSES FOR AC4 REPLACE 8A FUSES WITH 15A ANTI SURGE FUSES FOR AC2 REPLACE 5A FUSES WITH 12 5A ANTI SURGE FUSES THE FUSE HOLDERS ARE LOCATED BESIDE THE POWER SWITCH OF THE UNIT IF THE AC 4 IS INTENDED TO BE USED IN AUSTRALIA THE UNIT MUST BE A FIXED INSTALLATION AND CONNECTED DIRECTLY TO THE MAINS FUSE REMOVAL AND REPLACE The anti surge fuses are located on the right side of...

Страница 6: ... A AC 4 LES FUSIBLES DOIVENT ÊTRE REMPLACÉS AVANT LE BRANCHEMENT DE L APPAREIL À L ALIMENTATION SECTEUR ET SA MISE SOUS TENSION WICHTIGER HINWEIS WENNSIEDENAC 2 AC 4BEI120VVERWENDEN TAUSCHENSIEDIESICHERUNGEN AUS BEVOR DAS GERÄT AN DIE STROMVERSORGUNG ANGESCHLOSSEN UND DAS ERSTE MAL ANGESCHALTEN WIRD BEIM AC4 ERSETZEN SIE DIE 8 A SICHERUNGEN MIT TRÄGEN 15 A SICHERUNGEN BEIM AC2 ERSETZEN SIE DIE 5 A...

Страница 7: ...E COMPLETATA PRIMA DI COLLEGARE IL SISTEMA ALLA RETE E DI ACCENDERE L UNITÀ NOTA IMPORTANTE SI UTILIZA EL AC 2 AC 4 A 120 V ANTES DE CONECTAR LA UNIDAD A LA RED Y ENCENDERLA POR PRIMERA VEZ SUSTITUYA LOS FUSIBLES PARA EL AC4 SUSTITUYA LOS FUSIBLES DE 8 A POR FUSIBLES PROTECTORES DE SOBRETENSIÓN DE 15 A PARA EL AC4 SUSTITUYA LOS FUSIBLES DE 5A POR FUSIBLES PROTECTORES DE SOBRETENSIÓN DE 12 5A LOS S...

Страница 8: ...are fitted with an over temperature cut out If a safety problem should be encountered switch off the unit at the mains socket and remove the plug from the electricity supply INSTALLATION The instrument should be carried using both hands Never move or carry the instrument when in use or connected to the mains electricity supply The AC 2 AC 4 have a weight of 30kgs 47kgs respectively it is advised t...

Страница 9: ...arranty does not apply if damage is caused by fire accident misuse neglect incorrect adjustment or repair damage by incorrect installation adaption modification fitting of non approved parts or repair by unauthorised personnel Cole Parmer Ltd liability is limited to the cost of repair or replacement of the product and excludes in particular indirect and consequential loss damage costs or expenses ...

Страница 10: ...ordon de l alimentation secteur INSTALLATION Transportez l appareil à l aide des deux mains Ne déplacez et ne transportez jamais l appareil en cours d utilisation ou lorsqu il est relié à l alimentation électrique secteur Les modèles AC 2 et AC 4 pèsent respectivement 30 kg et 47 kg Il est recommandé de faire appel à deux personnes pour soulever et transporter l AC 2 et de faire appel à trois pers...

Страница 11: ...ique pas en cas de dommages provoqués par un incendie un accident une utilisation inappropriée une négligence un réglage incorrect une réparation inadéquate une installation une adaptation ou une modification inappropriée l installation de pièces non approuvées ou la réalisation de réparations par un personnel non autorisé La responsabilité de Cole Parmer Ltd France se limite au coût de réparation...

Страница 12: ...en Alle Cole Parmer Ltd Geräte erfüllen internationale Sicherheitsanforderungen und sind mit einem Übertemperatur Ausschalter ausgestattet Sollte ein Sicherheitsproblem auftreten schalten Sie das Gerät an der Netzsteckdose aus und entfernen Sie den Stecker aus der Stromversorgung INSTALLATION Das Gerät sollte mit beiden Händen getragen werden Transportieren Sie das Gerät unter keinen Umständen wen...

Страница 13: ...erechtigten Anspruchs wird Cole Parmer Ltd das fehlerhafte Teil oder das gesamte Gerät kostenlos austauschen Diese Garantie gilt jedoch nicht wenn der Schaden durch Feuer Unfall unsachgemäße Verwendung Nachlässigkeit falsche Einstellung oder Reparatur falsche Installation Anpassung oder Modifikation sowie durch das Anbringen von nicht genehmigten Teilen oder durch eine Reparatur von dazu nicht aut...

Страница 14: ...ruzione anti surriscaldamento Se si dovesse verificare qualche problema di sicurezza disconnettere la presa di corrente e rimuovere la spina INSTALLAZIONE Questo strumento deve essere trasportato usando entrambe le mani Non spostare né trasportare lo strumento quando è in funzione o collegato all alimentazione di rete L AC 2 e l AC 4 hanno un peso rispettivamente di 30 kg e 47 kg si consiglia di f...

Страница 15: ...danni provocati da incendi incidenti uso non conforme negligenza errori di regolazione o di riparazione danni dovuti a installazioni adattamenti e modifiche non corretti montaggio di componenti non approvati o riparazioni effettuate da personale non autorizzato La responsabilità di Cole Parmer Ltd è limitata al costo della riparazione o della sostituzione del prodotto ed esclude in particolare qua...

Страница 16: ...os para ajustarse a los requisitos de seguridad internacionales y están equipados con un cortacircuitos por sobretemperatura Si se produce un problema de seguridad desconecte la unidad de la toma de red y desenchúfela del suministro eléctrico INSTALACIÓN El instrumento debería transportarse con las dos manos No mueva ni transporte nunca el instrumento cuando esté en funcionamiento o conectado al s...

Страница 17: ...boratorio durante un plazo de dos 2 años Si la reclamación es justificada Cole Parmer Ltd sustituirá cualquier componente defectuoso o cambiará la unidad gratuitamente Esta garantía no se aplicará si el daño ha sido causado por un incendio accidente mal uso negligencia ajuste o reparación incorrecta daños por una instalación incorrecta adaptación modificación montaje de piezas no aprobadas o repar...

Страница 18: ...your local PCRmax distributor or Cole Parmer Ltd directly at Cole Parmer Ltd Beacon Road Stone Staffordshire ST15 0SA UK Tel 44 0 1785 812121 Fax 44 0 1785 810405 Technical Support email CPtechsupport coleparmer com Sales email cpenquiries coleparmer com Web www coleparmer com ...

Страница 19: ...id Selectable heated lid temperature 35 to 115 C or off Lid uniformity 5 C Pre heat lid Yes Warm up time from ambient 2 min Over temperature cut out Yes Regulated heated lid pressure Manually adjustable The heated lid is only operational if the block temperature is set above 35 C Above figures are quoted at an ambient temperature of 20 C 2 C Programming Program interface 10 and 7 HD touch screen O...

Страница 20: ...r com Communication ports USB port on the front of the AC 1 Connection for USB memory stick USB port on side of the AC 2 AC 4 Connection for USB memory stick Type B USB port on rear of unit For Internal use only Dimensions AC 1 AC 2 AC 4 Height mm 330 330 330 Width mm 260 535 535 Length mm 430 470 700 Weight kg 10 30 47 Power AC 1 AC 2 AC 4 Voltage 100 230V 50 60Hz 100 230V 50 60Hz 100 230V 50 60H...

Страница 21: ...nt for AC 1 2 Note that block removal can only be performed by a qualified service engineer 3 Plug the mains cable into the mains cable inlet of the unit 4 Connect to the mains electricity supply with the plug provided or one wired correctly for the supply Switch the power ON using the switch located on the rear AC 1 or side AC 2 AC 4 of the unit The front display will then light up NOTE A 250mm a...

Страница 22: ... adjust the lid pressure on the samples allowing for a variety of consumables to be used To adjust the pressure a Rotate the knob anti clockwise to raise the lid to the highest position b Place the samples in the block and close the lid c Rotate the knob clockwise until resistance is felt then give a further quarter of a turn this will give the correct pressure Do not over tighten 4 Once the press...

Страница 23: ...plates or programs saved on the unit New program allows the user to manually build a custom thermal cycling program Program wizard allows the user to automatically generate a protocol based on primer sequences Tm s and template size Edit program gives access to the File Manager and allows the user to search for programs and reports stored on the unit and to edit existing programs Block status allo...

Страница 24: ...llow you to toggle between recent pages you have open End users can also close open pages by swiping the windows left or right as you would normally with Android interfaces Note If you have opened multiple pages for example you been in settings started writing a protocol and had a protocol running selecting the recent button allows you to easily toggle between these open pages When users are requi...

Страница 25: ...C 05m00s 95 C 05m00s 95 C 05m00s Final extension 72 C 05m00s 72 C 05m00s 72 C 07m00s Final store 10 C for infinite time 10 C for infinite time 10 C for infinite time Thermal cycling conditions Parameter Gradient 50 to 60 deg 3 Step Template RT PCR Template Stage 1 Number of cycles 35 35 1 Step 1 95 C 00m30s 95 C 00m30s 45 C 40m00s Step 2 50 to 60 C 00m30s 56 C 00m30s 95 C 05m00s Step 3 72 C 00m30s...

Страница 26: ...mum temperatures see diagram below The maximum temperature gradient range which can be set is 29 C depending on block type and the minimum is 1 C within the temperature range of 10 C and 100 C Examples are given in the table below Gradient Set temperature Lowest temperature Highest temperature C C Column 1 C Column 12 C 10 55 50 60 15 55 47 5 62 5 29 55 40 5 69 5 To program a gradient step see sec...

Страница 27: ...share these programs with everyone see the programming section TO LOG IN AS AN EXISTING USER Select LOGIN from the top of the Home Screen Select Log in from the login screen Log in with your user specific name and password Tap on Log in Note Each Alpha Cycler has a administration level user accessed by logging in with the following Username admin Password admin LOGGING OUT To log out simply tap th...

Страница 28: ...d click Authorize USB drive Note Any USB drive can be authorised as the users login device When logging in via USB all specified user defaults will be carried forward and applied Removing the USB drive will logout the user To log in with the authorised USB drive simply insert the authorised USB into the Alpha Cycler When a program is started from a logged in user and the user then logs out the run...

Страница 29: ...ing to the next stage Protocols can have multiple stages comprising multiple temperature steps USING THE PROGRAM WIZARD The Program wizard allows users to automatically generate a protocol based upon the following criteria Primer Sequence or Tm s Length of amplicon Template source bacterial eukaryote or plasmid Special considerations Special considerations has a series of options which accommodate...

Страница 30: ...imer then tap on Done Primer sequences can be uploaded direct from the root of a USB drive To input your own primer Tm values tap I d like to provide the melting temperatures myself Tap on the line Primer 1 C a keyboard will appear on the screen Type in the melting temperature of the first primer then tap on Done Type in the melting temperature of the second primer then tap on Done After completin...

Страница 31: ... below 0 5kb will be given an extension time of 30 seconds Tap NEXT PAGE at the top right of the screen to progress to the next step To go back tap on PREVIOUS PAGE The next step is to select the source of the DNA Select one of the three options Tap NEXT PAGE at the top right of the screen to progress to the next step To go back tap on PREVIOUS PAGE Finally use the check boxes to take into account...

Страница 32: ...ameters of a Program wizard generated program can be adjusted either before or after it is saved Ensure that heated lid is set how you wish it to be and add any special stages such as a final extension or a store step at this point To save the program tap SAVE at the top right of the screen Select whether the program will be available to Everyone or Just me current logged in user and assign a name...

Страница 33: ...s as set by the user in the Settings see section on Settings A Toggle on and off the Heated Lid B Toggle on off Preheat Lid C Toggle on off Sample Cooling before the run begins D Add a new stage adds a stage with one temperature step plus the option to add further temperature steps within the same stage The stage can be cycled up to 99 times E Add a special step including Touchdown Final Extension...

Страница 34: ...a window will open scroll the temperature in that window and select Change to update to the new hold temperature To change step hold time the same applies but to the duration not temperature Note Alpha Cycler Temperature steps carry an inherent hold time of 30 sec and temperature of 95 C 56 C and 72 C for a three step stage Tap Add stage to complete adding the first stage and step 34 ...

Страница 35: ...o edit the parameters of a step e g the temperature hold time ramp rate etc tap on the grey shaded area of the step The Change step parameters window see below will open Make any changes to the parameters then tap on Change to accept Note The ramp rate heating cooling rate from the previous step to the current step can be defined between 0 1 ºC sec up to 3 ºC sec or MAX ADDING A GRADIENT STEP Sele...

Страница 36: ...ature ADDING A TEMPERATURE OR TIME INCREMENT OR DECREMENT Select the step on which you wish to add the increment or decrement and tap on the grey shaded area The Change step parameters window will open Toggle ON the parameter Temperature change per cycle or Time change per cycle as desired Next define the increment or decrement temperature or time Tap on Change to accept the changes Note The maxim...

Страница 37: ...lete stage all steps within the stage must be deleted this can be done by highlighting the temperature steps press the screen underneath the temperature step box to highlight and then press DELETE Note At the top of the screen there is an UNDO button to undo the last series of commands if a mistake such as unintentionally deleting a step stage is made SAVING THE PROGRAM To complete writing a progr...

Страница 38: ...ed Click on the box marked Protect the program from further changes and assign a password To alter the program the password must be known Programs with password protection can not be interrupted stopped mid cycle without applying the password Note The RUN AND SAVE button allows you to start the protocol from the programing screen without the need to first save and then go into the File Manager to ...

Страница 39: ...ctivate the polymerase this step will not cycle Touchdown stage allows users to generate a touchdown protocol which will change the temperature uniformly across the entire block each cycle between two set temperatures high to low over a defined number of cycles Define the starting maximum annealing temperature and the end minimum annealing temperature The temperature change per cycle will be equal...

Страница 40: ... is increased by for example 15 to 20s per cycle during the final stages of the reaction Final extension allows users to add a final temperature step at the end of normal cycling Final store allows users to store the PCR reactions in the system at a set temperature until they are ready to be taken out for further analysis The default temperature is 10 C as this is suitable for storing DNA for prol...

Страница 41: ...ms from this list The Pre run screen will be displayed The Pre run Screen shows a graphical representation of the program allowing for a rapid check of the temperature parameters Any of the parameters can be edited at this point Touch any stage or step to edit the program Touch RUN AND SAVE to start the program Note that this will over write the existing program if any edits have been made Touch B...

Страница 42: ...will begin automatically Note This route of selecting a program does not allow you to view the thermal profile before it is run An alternative way of accessing the File Manager is to go through Edit program Using this route you will be able to view the program in the Pre run screen and make any changes before sending it to the thermal cycler Once you are satisfied the program is correct tap RUN AN...

Страница 43: ...e writing a program and selecting favourite as images below In Edit programs check the Star icon to Favourite a Program In New Program press the three stacked boxes icon and check Favourite to assign it as such NOTE Favourite programs can then be visualised together on the home screen see instrument setting section for how to display Favourites on the home screen 43 ...

Страница 44: ...e in the AC 1 and is accessed by clicking on the four arrow icon in the status bar With the AC 2 AC 4 status of each block is shown separately across the bottom of the screen To view the running program in more detail from the Home Screen tap on Block status Note With the AC 2 AC 4 the status of all blocks will be displayed 44 ...

Страница 45: ... be downloaded free from the App store Android and iOS When viewing an individual program there is the option to toggle between viewing the real time temperature of the block and the program display To view the block temperature tap on DISPLAY REAL TIME TEMPERATURE at the top right of the screen Note see settings too toggle between displaying the average temperature across the block or the actual ...

Страница 46: ...ed block for the AC 2 AC 4 Health report on the system Upon first using the App you will be asked to provide an email address so you can be contacted by your local service centre if the they find an error in the systems health report How to Use the Alpha Track App To scan the QR code start a program on the Alpha Cycler ask it to display the QR code see Pg42 launch the Alpha Track App click the QR ...

Страница 47: ... information and generate an instrument report which is visible on the Alpha Track home screen the end user can select to send this report to the Bibby Technical Team for review Should the system require a visit repair further diagnostics to be carried out the end user will be contacted using the details provided in the App NOTE For the multiblock AC 2 AC 4 systems one QR code can be scanned which...

Страница 48: ...C 4 all active blocks can be stopped together from the block status screen To stop an individual program first select the full screen display by tapping on the block area close to program name to open up the full screen Alternatively programs can be stopped from the Home Screen by tapping on the status bar This will open up the run screen 48 ...

Страница 49: ... of the software while the unit is running a program Simply use the Return button or Home button at the bottom of the screen to access other areas of the software Program finished When a program has completed a Summary Report will be displayed on the screen Click on OK to close the report Note With the AC 2 AC 4 a report will be presented for each individual block as each program finishes 49 ...

Страница 50: ...person at the top right of the screen Select whether to view the files available to Everyone or just the currently logged in user Note If a USB memory stick has been inserted into the USB port A USB icon will also be visible at the top right of the screen To view files stored on the USB memory stick tap on the USB icon SEARCH FOR A FILE Tap on the magnifying glass icon to enable a search for a par...

Страница 51: ...splayed in chronological order Tap on a report from the list and the individual Summary Report will be displayed Tap OK to exit Note It is not possible to view the temperature log contained within the report on the Alpha Cycler itself it must first be copied to a USB memory stick then viewed on a PC using Excel The file will be saved as a csv file See the directions given in the next section for c...

Страница 52: ...le s you wish to delete selected files will be highlighted blue Tap again to deselect Touch the delete icon large X at the top right of the screen A prompt will appear to confirm the delete once confirmed the selected files will be deleted from the system s memory If you choose not to delete a file touch Cancel Touch the tick icon next to Done to return to the File Manager 52 ...

Страница 53: ...tap on the USB icon to select the destination then tap the Paste icon clip board TRANSFERRING A PROGRAM FROM A USB MEMORY STICK TO THE ALPHA CYCLER Transferring programs from one Alpha Cycler to another avoids the user having to re write new programs for each additional instrument and is an easy way to share optimised protocols with other Alpha Cycler users From the Home Screen select Edit program...

Страница 54: ...The system must be restarted for the system settings and defaults to be applied If the settings are changed always restart the system Touch any of the headings on the left hand side to view and edit those settings Once all the settings and defaults have been set as required touch the Back button at the bottom of the screen to return to the Home Screen PREFERENCES This allows you to select the pref...

Страница 55: ...spective of the length of the power failure Selecting Never will mean the system will not auto restart after a power outage In addition the user can select a time in which if the power comes back on in that window then the system will resume The options are shown below Note the time periods in the auto restart allow the end user to select windows of power loss which they deem acceptable for the po...

Страница 56: ...ls created on the system Note Defaults are merely a starting point and are not fixed if the default value is not appropriate for your reaction simply edit that value here or during programing Use the heated lid Use this to set the heated lid temperature to approximately 10 C higher than the hottest block temperature in the program Touch ON OFF to toggle between settings Touch the temperature butto...

Страница 57: ...nd activation time may need to be altered for different reagents This can be changed by editing an individual program Add a pause after polymerase activation This will cause the unit to pause at the same temperature as the polymerase activation step The program will only continue when the user manually touches the resume button This step can be useful when additions need to be made to the samples ...

Страница 58: ...l The Alpha Cycler software has an administrator level which allows the administrator to reset passwords for users and delete accounts which are no longer required Default Admin Login Details User admin Password admin 58 ...

Страница 59: ...be given the option to carry out the update or not If Yes is selected the installer will describe the process on screen The user will be asked to confirm the installation of the new Alpha Cycler App and a confirmation note will assure end users that existing files and data will not be over written Android will ask the user to confirm the install and show the access the Alpha Cycler App has Select ...

Страница 60: ... mail cpservice coleparmer com Phone 44 0 1785 810475 We are continually striving to improve our products and software If you have any comments or suggestions on how we can do things better please send them to us at sales coleparmer com REPLACING BLOCKS Please note that thermal blocks in Alpha Cycler thermal cyclers are not interchangeable Thermal blocks can be replaced under warranty in case of p...

Страница 61: ...ng Cole Parmer Ltd accepts no responsibility for damage to units which are not properly packed for shipping If in doubt contact your supplier providing the serial number of the unit FUSES If the display on the front panel is not lit one of the two fuses may have blown Check that there is no external cause such as a faulty plug or lead Check both fuses and replace the faulty fuse with a new one of ...

Страница 62: ...Notes 62 ...

Страница 63: ...Notes 63 ...

Страница 64: ...are and remain the property of such third parties CP EMEA PM 0001 0520 PCRmax_Manual Contact Us UK T 44 0 1480 272279 E info coleparmer co uk W coleparmer co uk Germany T 49 0 9377 92030 E sales coleparmer de W coleparmer de France T 33 0 1486 37800 E cpcontact coleparmer com W coleparmer fr Italy T 39 0 1313 89513 E itsales coleparmer com W coleparmer it USA T 1 847 549 7600 E sales coleparmer co...

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