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Chapter 3

User’s Guide

Document 609909-AA

Biomek 2000

3-9

Then, on the worksurface, click on the labware where the Mix at Location action
should take place.. In this example, the 96-well flat plate in location B2 is selected.

The following Mix at Location dialog will appear.

Once you have defined all actions and tip handling options in the screen, click OK
when done.

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Summary of Contents for Biomek 2000

Page 1: ...Beckman Part No 609909 AA April 1998 Beckman Instruments Inc 2500 N Harbor Blvd Fullerton CA 92834 3100 Copyright 1998 Beckman Instruments Inc Printed in U S A Biomek 2000 User s Guide ...

Page 2: ...he written permission of Beckman Instruments Inc The product warranty does not apply to software which is warranted on an as is basis without fitness for any specific purpose with the exception of the media which is warranted against defects in materials and workmanship for a period of one year The software is copyrighted and may not be altered or given to a third party without the written authori...

Page 3: ... Safety ix Side Loader SL x SL Incubator x High Density Replicating System xi Plate Reader xi Wash System xii Heater Cooler Block xii Biomek 2000 Safety Features xii Summary of Warning Information xii Introduction Introduction 1 1 Intended Use 1 1 Theory of Operation 1 1 Workstation Components 1 1 Automation Features 1 2 Modular Platform for Easy Upgrades 1 3 Pipette and Wash Tools 1 3 Accessories...

Page 4: ...les of Operation General Information 3 1 The Edit Module 3 1 Creating a Method 3 4 Setup Initial Configuration and Default Configuration 3 5 Setup 3 5 Initial Configuration 3 6 Default Configuration 3 7 Placing Labware on the Worksurface 3 8 Specifying a Method Step Action 3 8 Error Messages During Labware Placement 3 10 Pipette Transfers 3 10 Source 3 12 Destination 3 14 Tool Options 3 15 Tip Han...

Page 5: ...ance Characteristics and Specifications 3 27 Basic Operating Procedures Basic Operating Procedures 4 1 Editing the BioWorks Demo Method 4 1 Changing the Initial Configuration 4 7 Viewing and Editing a Transfer Function 4 8 Adding a Transfer Function 4 11 Inserting Messages and Pauses 4 13 Saving a Method 4 16 Running a Method 4 17 Recommended Maintenance Procedures Maintenance Procedures 5 1 Gener...

Page 6: ...able of Contents User s Guide Document 609909 AA Biomek 2000 iv Parts Supplies and Accessories Diagnostics Overview 6 1 General Information 6 1 United States Sales Telephone Number 6 1 World Wide Web 6 1 ...

Page 7: ...communications Operation of this equipment in a residential area is likely to cause harmful interference in which case the used will be required to correct the interference at his own expense This manual is copyrighted and all rights are reserved This document may not in whole or in part be copies photocopied reproduced translated or reduced to any electronic medium or machine readable form withou...

Page 8: ...Notice vi Biomek 2000 ...

Page 9: ...re needed to lift the Biomek grasping the front rail and the back support Do not connect the Biomek to an electrical outlet until it is positioned properly on the bench Electrical Safety To reduce the risks of electrical shock this equipment employs a three wire electrical cord and plug to connect the equipment to earth ground To preserve this safety feature Make sure the matching wall outlet rece...

Page 10: ...ult in splashing of liquids therefore take appropriate safety precautions such as the use of safety glasses when working with potentially hazardous liquids Use an appropriate containment environment when using hazardous materials Observe the appropriate cautionary procedures as defined by your safety officer when using flammable solvents in or near a powered up instrument Make sure that the vacuum...

Page 11: ...nance Turn the POWER off and UNPLUG the Biomek before changing fuses or performing any maintenance Do NOT autoclave Pipetting or Wash tools autoclaving may cause damage to the internal parts Perform only the maintenance described in this manual and in the Biomek 2000 Maintenance and Troubleshooting Guide Mainte nance other than specified in these manuals should be performed only by Beckman trained...

Page 12: ...ced to quit the run in progress if you press the SL Stop switch Use of the SL stop switch may result in spill age or splattering of liquids in transit Click on the Stop button on the BioWorks Run window to stop the instrument if it is not an emer gency SL Incubator Operating the incubator at 4 C for longer than twenty four hours may result in ice formation within the chamber adversely affecting te...

Page 13: ...the tools described to perform the steps defined in the Plate Reader user s manual Do not touch or loosen any screws or parts other than those specifically designated in the instructions of the Plate Reader user s manual Doing so could cause misalignment and possibly void warranty Never perform any operation on the Plate Reader in an environment where damaging liquids or potentially damaging gases...

Page 14: ... cooling sequence Include a shut down command in all Biomek routines Provided water cooling is maintained extended cooling operations do not adversely affect block life span The TEMP command may not permanently turn off the block if a programmed event list is executing Biomek 2000 Safety Features The Biomek 2000 workstation is equipped with several safety features A Stop switch is located on the f...

Page 15: ...gh density transfers photometric measurement and high capacity operation The entire system is controlled by powerful and user friendly BioWorks software with an intuitive graphical interface Theory of Operation BioWorks software quickly guides the operator step by step through simple graphic menus and prompts by using the following features Workstation methods are easily configured to follow labor...

Page 16: ...ns Provides liquid level sensing when an appropriate tool is used to detect when the pipette tip is just touching the liquid during an aspiration Allows you to develop labware definitions for custom labware Allows you to edit the characteristics of the tool definitions to optimize for different types of liquids Figure 1 Biomek 2000 Laboratory Automation Workstation 1 Head Assembly 5 Worksurface 2 ...

Page 17: ... Biomek 2000 workstation uses individual tools to aspirate and dispense fluids to labware Pipette tools transfer from 1 µL to 1 mL with high precision Multichannel tools increase throughput by transferring eight high precision samples simultaneously Disposable pipette tips are used to eliminate the risk of contamination between samples without intermediate wash steps Liquid Level Sensing tools pro...

Page 18: ...m P1000L Single Tip Tool 50 1000µL 100 mm MP20 Eight Tip Tool 1 20µL 50 mm MP200 Eight Tip Tool 5 200µL 50 mm Wash Tools Volume Range Max Reach Wash 1 Single Channel Tool 1 x 50µL to 1 x 150 mL 40 mm Wash 8 Eight Channel Tool 8 x 50µL to 8 x 18 75 mL 40 mm HDR Tools Pin Diameter Nominal Sample Density 96 Pin HDRT 0 015 or 0 045 in 3 456 small pin or 1 536 large pin 384 Pin HDRT 0 015 or 0 045 in 3...

Page 19: ...munication ports and software communication links are provided for attachment and automated control of additional third party devices The functionality of the Biomek can be further customized for specific applications through the BioScript Pro scripting language BioWorks The Biomek Workstation is controlled through BioWorks software which runs on the PC controller BioWorks provides a graphical use...

Page 20: ...User s Guide Chapter 1 Document 609909 AA 1 6 Biomek 2000 Figure 2 Connecting the Biomek Workstation to the Computer ...

Page 21: ...Chapter 1 User s Guide Document 609909 AA Biomek 2000 1 7 Figure 3 Connecting the Biomek Workstation to the Side Loader Controller ...

Page 22: ...n emergency STOP switch is located on the front of the worksurface Use the Stop switch at the base of the workstation if an emergency stop is required Pressing this switch will freeze the workstation but not the Side Loader Click on the Stop button on the BioWorks Run window to stop the instrument if the stop is not an emergency Plate Reader Wash Unit HCB Controller ...

Page 23: ...empt to physically restrict the movement of the head and bridge assembly or to exchange labware reagents or tools while the instrument is operating as indicated by the amber safety light at the end of the bridge Use the Stop switch at the base of the workstation if an emergency stop is required Stop Button ...

Page 24: ...User s Guide Chapter 1 Document 609909 AA 1 10 Biomek 2000 ...

Page 25: ...earth grounded Never use a three to two wire plug adapter Never use a two wire extension cord or a non grounding type multiple outlet receptacle strip Any servicing of this equipment which requires removal of any covers or panels can expose parts which involve the risk of electric shock or personal injury Refer such servicing to Beckman trained qualified personnel Do not use any power supply other...

Page 26: ...rials Observe the appropriate cautionary procedures as defined by your safety officer when using flammable solvents in or near a powered up instrument Make sure that the vacuum is attached prior to any method that contains any wash or aspirate functions Moving Parts The bridge and head assembly may suddenly move To avoid injury due to moving parts you must observe the following Never attempt to ex...

Page 27: ...ce Do NOT autoclave Pipetting or Wash tools autoclaving may cause damage to the internal parts Perform only the maintenance described in this manual and in the Biomek 2000 Maintenance and Troubleshooting Guide Maintenance other than specified in these manuals should be performed only by Beckman trained qualified personnel It is your responsibility to decontaminate components of the Biomek before r...

Page 28: ...e data and be forced to quit the run in progress if you press the SL Stop button Click on the Stop button on the Run win dow to stop the instrument if it is not an emergency Use of the SL stop button may result in spillage or splattering of liquids in transit SL Incubator Operating the incubator at 4 C for longer than twenty four hours may result in ice formation within the chamber adversely affec...

Page 29: ...instructions of the Plate Reader user s manual Doing so could cause misalignment and possibly void warranty Never perform any operation on the Plate Reader in an environment where damaging liquids or potentially damaging gases are present Never touch the surfaces of the interference filters or optical lenses DO NOT install the Plate Reader in a stack location that could inhibit access to the Stop ...

Page 30: ...gerous heating of the assembly DO NOT operate the assembly without adequate water flow 1 to 2 liters minute Full power time out faults may be caused by loss of cooling water Should this occur the heater cooler unit assembly may be hot Always be sure to shut down the HCB as the last command of each heating cooling sequence Include a shut down command in all Biomek routines Provided water cooling is...

Page 31: ...are features refer to the BioWorks Software Reference Manual Note When running Biomek methods do not import or export meth ods or perform other CPU intensive operations as communication between the controller and Biomek workstation may be interrupted Note Beckman does not support the use of network drives to import and export Lab Books and methods when using BioWorks software Lab books should be d...

Page 32: ...ter 3 Document 609909 AA 3 2 Biomek 2000 When you click on the Edit icon the Edit window is displayed Refer to your BioWorks Software Reference Manual for a complete description of all of the features of the Edit window ...

Page 33: ...ethod from the menu bar then selecting Open The following screen will be displayed Select one of the methods such as the Demo method shown below from the list provided in the window by clicking on that method Click Open when done Once you have selected the Demo method you will be presented with the dialog shown on the following page ...

Page 34: ...operation or a labware move Then you usually click the labware the function will act upon In the case of pipetting functions you specify the labware where the sample is aspirated then you specify the labware where you want to dispense it In the case of labware moves you click on the item you want to move at its current location then you click on the location to which you want to move it Method Lis...

Page 35: ...ries components and options are available on the system for a given method Refer to the screen shown on page 3 4 the Setup button is shown located on the Biomek 2000 worksurface By clicking on the Setup button you will be prompted by the Setup screen which allows you to change the setup of the system You will use setup whenever you want to install or remove a wash unit six port valve Side Loader D...

Page 36: ...ticular run You can disable the Side Loader through Setup which will allow you more flexibility to place devices on the SL accessible locations of the worksurface Initial Configuration The Initial Configuration is the layout of the worksurface at the beginning of an assay The initial configuration does not include any transfers only the locations of the labware and devices The first line of any me...

Page 37: ...o the method Default Configuration If you are using the same initial layout for multiple methods you can edit the Default Configuration to reflect the common items This way when you create a new method much of the initial configuration layout will already be done for you To edit the Default Configuration select Options Default Configuration from the Edit module The worksurface is then displayed Pl...

Page 38: ... given the option of using Default Configuration as the starting point for the Initial Configuration Placing Labware on the Worksurface You place labware on the worksurface for use by a method as follows Select the piece of labware plate tube rack device etc from the Labware bar Use the buttons at the far right to select a labware category and use the scroll box to select a specific labware type w...

Page 39: ...ce click on the labware where the Mix at Location action should take place In this example the 96 well flat plate in location B2 is selected The following Mix at Location dialog will appear Once you have defined all actions and tip handling options in the screen click OK when done ...

Page 40: ...egarding the restrictions on placement of certain items These range from informational warnings about possible interference which you may choose to ignore based on your knowledge of the method to warnings which forbid you from placing labware at certain locations Pipette Transfers The most commonly used function of the Biomek is the pipette transfer Most pipette transfers define the transfer of a ...

Page 41: ...ced labware tools and tips on the worksurface you can then specify a pipette transfer to move liquid from one plate to another To do this click the Pipette Transfer button on the Function Palette click the Source plate on the worksurface then click the Destination plate The Pipette Transfer window shown below is used to define the transfer Pipette Transfer Icon ...

Page 42: ...sit to a well when a new tip is used and on the first visit to the well if the same tip is used Subsequent visits use tracking to calculate the proper depth When Sensing is selected the Tip Depth box becomes active Use this to set an aspirate depth below the depth calculated for the aspiration volume Enter the number of millimeters below the liquid level at which you wish to use the Biomek to aspi...

Page 43: ...ection of by Row by Column Box by Row or Box by Column Pattern is a non contiguous set of wells Patterns can be stored and recalled when needed End Action describes what the workstation should do when it has finished with the first piece of labware End Action is one of the following Stop stops the transfer after the source range has been completed Repeat Same Labware repeats the source range until...

Page 44: ...s not used in the Bioworks database To Deliver causes the tool to pick up the requested volume plus an additional overage amount which is programmed into the Tool Edit screen described later Only the requested volume is dispensed therefore liquid will remain in the tip and will be discarded with the tip To deliver cannot be used with blowout For many liquids the combination of To Contain and Blowo...

Page 45: ... used for the default By default there are two specified tool types for each of the pipetting tool deliver and repeat Make sure the tool type matches the delivery type selected at the destination Each tool type has been optimized for a specific delivery type Volume is the volume of liquid to be transferred Tip Handling Options Tip Change can be one of the following No tip change uses the same tips...

Page 46: ...lt To change this order label the tip rack when setting up the worksurface by double clicking on the tip rack then select the tip rack from the list in the Pipette Transfer window Advanced Options Note Validation of new labware is based upon the labware Type and corresponding dimensions To display the Advanced options click the Advanced button near the bottom center of the Pipette Transfer dialog ...

Page 47: ...o the capacity of the tool Internal Delay is for delivering liquid at exactly the same time interval from one destination to the next The internal delay will not take affect until the second transfer The system will wait above the destination and then deliver when the internal delay time is reached The clock starts at the delivery of the first sample This first transfer establishes the base time t...

Page 48: ...petting Functions These specialized pipetting functions are also available from the function palette These are described below Mix The Mix icon button is shown below A mix within a single well or at a single piece of labware can be programmed independently of a transfer using this function The following dialog appears when the Mix icon and a piece of labware are clicked ...

Page 49: ...e piece of labware The same volume is transferred between successive wells in the highlighted range If a mix is programmed on the serial transfer screen the mix occurs after the transfer of the liquid This means that when the system visits the first well in the range no mix takes place at that well A Serial Transfer is defined using the Serial Transfer dialog ...

Page 50: ... the system will automatically change tips between the two functions The logic behind this is that if the second function requires clean tips for each transfer within it then it should start with clean tips Reset Tip Rack The Reset Tip Rack icon button is shown below This is used to set the tip rack to a given tip You can select the first tip to be used anywhere in a rack This allows you to optimi...

Page 51: ...ent or buffer if the Six Port Valve is installed Wash Cycles controls the number of aspirate and dispense cycles per well visit Delay controls the time between wash cycles Wash at Sides is only available for flat bottom labware Internal Delay is the same as for pipetting It provides a consistent time between washes of consecutive wells Aspirate Duration controls the time the vacuum valve is opened...

Page 52: ... all of the liquid in the wells to the same height All of the other parameters for a bulk dispense operation are similar to those for wash and pipette functions Purge The Purge icon button is shown below Purge is used particularly in conjunction with the Six Port Valve when changing buffers In this situation it is necessary to remove the previous buffer from the lines before starting to use a new ...

Page 53: ...ou can move most labware items from one location on the worksurface to another location or to the Disposal unit In addition you can also use the Gripper Tool to remove lids from plates and tip racks and to stack labware on devices such as the Vacuum Manifold When a Side Loader is present you can move labware and tip racks between shelves on the Side Loader stack area and the worksurface You can al...

Page 54: ... Be aware however that changing the labware arrangement in the Initial Configuration of an existing method may cause transfer functions which occur later in the method to become invalid Saving Methods When you are ready to save your new method select the Method Save command from the menu bar in the Edit window You can enter a different name for the method if you wish or use the current one You wil...

Page 55: ... You can set the characteristics of the Run module using the Options menu from the menu bar in the Run module These options are as follows Alarms and Suppress All Alarms Various alarm levels can be set so that the system will warn the operator only during certain conditions When one of the following options is checked in the menu the alarm is enabled for that type of error condition System Fatal a...

Page 56: ... the button is clicked The method can be continued using the Continue button or stopped using the Quit button Trace is used to move the Biomek one motion at a time after Stop has been activated Go Up moves the pod directly up after Stop has been activated Cancel Loop cancels a loop after Stop has been activated The loop is cancelled once the current iteration completes Quit aborts the method immed...

Page 57: ...mance Characteristics and Specifications Performance characteristics for the pipette tools are shown below Tool Pipetting Precision P20 5 C V at 1µL MP20 5 C V at 1µL P200L 5 C V at 5µL MP200 5 C V at 5µL P1000L 2 C V at 50µL Wash1 15 C V at 50µL Wash8 15 C V at 50µL ...

Page 58: ...User s Guide Chapter 3 Document 609909 AA 3 28 Biomek 2000 ...

Page 59: ...es designed to illustrate the most important and commonly used features of the system For complete information on BioWorks features and functions refer to the BioWorks Software Reference Manual Editing the BioWorks Demo Method This section will guide you through the basics of editing by changing an initial configuration and a transfer function using the Demo method To begin double click on the Edi...

Page 60: ...e of the current lab book is shown in angle brackets at the top of the window If the BOOK1 lab book is currently the default skip to the next step in the middle of page 4 4 Otherwise change the lab book to BOOK1 by selecting Options Select Lab Book from the Menu bar ...

Page 61: ...Chapter 4 User s Guide Document 609909 AA Biomek 2000 4 3 Select Lab Book ...

Page 62: ... Book dialog Highlight the BOOK1 lab book then click on the Select button When the Edit window displays BOOK1 as the current lab book select Method Open from the Menu Bar of the Edit window This will display a list of available methods Select the Demo method from the list then click Open ...

Page 63: ...Chapter 4 User s Guide Document 609909 AA Biomek 2000 4 5 ...

Page 64: ...face The labware and locations set when the Initial Configuration line is highlighted will be used as the starting point BioWorks prompts you to verify that labware is arranged properly when you start a method To place labware on a worksurface location first you select the item from the Function Palette Labware Bar window Use the round buttons to select the type of labware then scroll to select a ...

Page 65: ...y If you add delete or move labware during a method you will notice that the labware displayed on the Worksurface window changes as you increment through the steps in the Method window This will allow you to verify labware positions as the method progresses Changing the Initial Configuration To change the Initial Configuration for this method first make sure that the Initial Configuration line of ...

Page 66: ...nd Editing a Transfer Function Familiarize yourself with a basic Pipette Transfer function by viewing the first transfer function in the Demo Method To do this double click on the second line in the Method window This displays the Pipette Transfer dialog for this step ...

Page 67: ...tion the Biomek pipettes 200µL from location A2 to B2 on the worksurface using the P200L tool When you have finished viewing the configuration click Cancel to exit the dialog without making any changes Next we will modify the configuration of the second transfer function ...

Page 68: ...ay the Pipette Transfer dialog To add a Mix function to this step click on the Mix option box for the source Then click on the Mix Values button to display the Mix Values dialog Edit the Mix Values dialog as follows Change the Mix Cycles to 3 Change the Aspirate and Dispense Rates to 5 Change the Aspirate and Dispense Heights to 50 ...

Page 69: ...nsfer window Note that the Edit Window will not reflect changes made to a transfer function when they involve parameters not included in the descriptor line Adding a Transfer Function Now you will add a new transfer function to the method Highlight the last transfer function in the Method window then click on the Pipette button on the Function Palette ...

Page 70: ...n the source plate Set the Destination Labware Action to Pattern and Direction to By Row Use the cursor to highlight at least 6 wells of the destination plate in any pattern you choose Note that if you select more than 6 wells only the first six will be used because there are only 6 source wells selected If you want to fill more than 6 wells on the destination plate you could either select more so...

Page 71: ...rt messages to the operator and system pauses in a method Using the same method now add a pause before the second pipette transfer to display a message to the operator We will display a message to inform the operator that the system will pause for one minute after the message is acknowledged From the Edit Window highlight the second pipette transfer in the Method Window then click on the Pause Sys...

Page 72: ...ms as follows Set System Activity to Message Set System Actions to Display message until canceled Type a message in the Message box Enable the Message Alarm and set the Interval if you wish The dialog should look like the one shown Click OK to add the Message step to the method Note that we have not yet added the pause itself ...

Page 73: ...at new method steps are always inserted before the highlighted line in a method Click on the Pause System button again This displays the System Pause Message dialog Specify a pause by selecting the dialog items as follows Set System Activity to Pause System Set System Actions to Pause system for then set the timer to 1 00 minute The dialog should look like the one shown Click OK when you are finis...

Page 74: ...ding you should save your edited method under a different file name To do so select Method Save As then enter a file name of your choice in the dialog Note that when you save a method it is automatically validated unless you request otherwise A method must be validated before it can be run ...

Page 75: ...structions If the Biomek has already been aligned and been in use you can run your new method now To run the method click on the Run icon in the icon bar of the BioWorks Edit window The Biomek 2000 Configuration screen will appear This screen will serve to remind you to set up labware tip racks and tools on the worksurface You will be prompted to accept the worksurface configuration When you have ...

Page 76: ...User s Guide Chapter 4 Document 609909 AA 4 18 Biomek 2000 The method will begin and the Method Run screen will be displayed showing a list of actions performed during the method run ...

Page 77: ...te Use the Align Position Calibrate command from the Edit module main window to perform a calibration on the system Perform Check Disk Use the MS DOS command chkdsk check disk with the f option to verify the file system and directory structure on the computer s hard disk and possibly free up some disk space Refer to the DOS and Windows manuals which were provided with your computer for more inform...

Page 78: ...ctioning properly The Warning light on the Head assembly The Warning buzzer on the Head assembly Emergency Stop switch on the workstation and on the Side Loader if applicable You can verify the first two by observing the workstation during a method and noting whether the light and buzzer come on at the appropriate times when a method is started To check the Emergency Stop switches run a method usi...

Page 79: ...lowing address and phone number for all inquiries in the U S Beckman Instruments Inc 4300 N Harbor Blvd P O Box 3100 Fullerton CA 92834 3100 Sales 1 800 742 2345 Service 1 800 551 1150 Fax 1 800 643 4366 World Wide Web You can also access additional information and find out more about new products for the Biomek 2000 from www beckmancoulter com The BioRobotics User Resources section contains infor...

Page 80: ...User s Guide Chapter 6 Document 609909 AA 6 2 Biomek 2000 ...

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