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Biomek 3000 Quick-Start Guide.book

1. Head Assembly Front Rail Back Support Pe Deck Figure 1 1 Biomek 3000 Laboratory Automation Workstation 1 2 1 Bridge The bridge is the structure that moves in the X axis along the tower and front rail The bridge holds the head assembly and enables movement of the head assembly in the Y front to back and Z axes up and down Built into the bridge is an indicator light that displays the current operational status of Biomek 3000 workstation The Biomek 3000 workstation supports only one bridge Biomek 3000 Laboratory Automation Workstation Quick Start Guide Introducing the Biomek 3000 Laboratory Automat Beckman Coulter Inc 1 2 2 Head Assembly The head assembly is supported and positioned by the bridge and moves in the Y and Z axes The head assembly may hold various interchangeable tools such as the P200L Single Tip Tool or MP200 Multi Tip Pipette Tool that perform liquid handling and other operations The capabilities of the Biomek 3000 instrument change with the tool 1 2 3 Tools The Biomek 3000 uses interchangeable tools to perform various operations such as aspirating and dispensing washing or moving labware around the deck Tools are stored on the deck in a tool rack when not in use and can be installed or removed from the head assembly automatically as part of an automated method This allows
2. 6 Your tips are configured for your liquid transfer so click the up arrow next to Tip Handling to collapse Load Tool Step The Load Tool step is found on the Biomek 3000 Step Palette and is used to load a specific tool to the head assembly If a tool is already loaded to the head assembly that tool must first be removed using an Unload Tool step or a Change Tool step may be used to execute both actions Refer to the Biomek Software User s Manual Chapter 20 Using the Biomek 3000 Step Palette the configuration This allows more room for the step configuration Figure 2 8 The text displayed reflects your tip handling configuration Biomek Software Method1 New S Fie Edit Project Instrument Execution Options Help PEALE ELICE Start Use pod Poat x for transfer Instrurnent Setup A Load AP96_200uL tips change between sources and unload them when finished Q Transfer B Finish Click here to add a source Use this arrow to collapse and expand Tip Handling Stop when finished with Destinations x Replicate each well 1 time Advanced Dispense up to 1 time per draw Aspirate at most fo pL per transfer for repeated dispensing Transfer Details Method1 Biomek3000 Biomek3000 ETC 0 00 03 Figure 2 8 Transfer step with Tip Handling collapsed Beckman Coulter Inc Learni
3. To configure the labware named Dest as destination labware in the Transfer step Transfer Details Transfer details include a stop condition for 2 transfer operations a repeat pipetting configuration and a maximum tolerance in timing between transfer operations Refer to the Biomek Software User s Manual Chapter 15 3 4 3 Configuring Transfer Details Beckman Coulter Inc 1 Before you configure the destination labware click the down arrow in Transfer Details located just above the Current Deck Display to collapse that section You will not be making any changes to the options in this section Click on Dest sitting on P6 in the Current Deck Display This one operation accomplishes the same task as steps and 2 of Section 1 5 2 Configuring Source Labware Note Notice that the source labware configuration is now replaced with a brief sentence summary of the setup If you want to reopen this source configuration for any reason click anywhere in the collapsed configuration area The Volume field is highlighted which allows you to designate the amount of liquid to be dispensed For this tutorial you re transferring 100 uL so type 100 into the Volume field Note The volume is measured in microliters uL automatically and indicates the amount of liquid that will be dispensed 100 uL into each of the 96 wells so in this case you re dispensing a total of 9600 uL into the 96 well micr
4. the final step in a method provides to the Biomek Software options to clear the Biomek 3000 deck clear the User s Manual Chapter devices on the deck unload tips from the pod 13 Using Variables and and clear all global variables Refer to the Expressions in a Method Biomek Software User s Manual Chapter for more information 12 2 2 Configuring the Finish Step for information on configuring other options for the Finish step Finish Proceed to Section 2 3 Configuring the Instrument Setup Step to learn how to configure the Instrument Setup step you just inserted into the method view Biomek 3000 Laboratory Automation Workstation Quick Start Guide 2 4 2 3 Obstacle Avoidance When building a method you must ALWAYS use the Deck Editor and Instrument Setup step to tell the software what labware and ALPs are on the deck and the position each occupies If this is not done the pod could collide into these objects as it moves around the deck during a method run Learning to Create Methods for the Biomek 3000 Configuring the Instrument Setup Step A CAUTION An inaccurate Instrument Setup may result in pod and labware collisions or in inappropriate pipetting When creating Biomek methods it is important to use the Instrument Setup step along with the Deck Editor to tell the software what labware and devices are on the deck for obstacle avoidance see sidebar You l
5. COULTER Biomek 3000 Laboratory Automation Workstation Quick Start Guide Beckman Coulter PN 987837 Revision September 2004 B ule Coulter Inc 4300 N Harbor Boulevard Fulle rton CA Mea 3100 Copyright 2004 Bec n ea ulter Inc Printed in U S A Except as provided in writing signed by an officer to Beckman Coulter Inc this system and any related documentation are provided as is without warranty of any kind expressed or implied including that the system is error free This information is presented in good faith but Beckman Coulter Inc does not warrant guarantee or make any representations regarding the use or the results of the use of this system and related documentation in terms of correctness accuracy reliability currentness omissions or otherwise The entire risk as to the use results and performance of this system and related documentation is assumed by the user Except as expressly provided herein Beckman Coulter Inc makes no other warranty whether oral or written expressed or implied as to any matter whatsoever including but not limited to those concerning merchantability and fitness for a particular purpose nor is freedom from any patent owned by Beckman Coulter Inc or by others to be inferred LIMITATIONS OF LIABILITY Beckman Coulter Inc shall not be liable to any extent whatsoever for any damages resulting from or arising out of the use or performance of this system and related
6. Rename Pattern Figure 3 10 Rename Pattern Beckman Coulter Inc Using the Editors While Creating Methods 3 11 6 Enter LabwareQuickStart and choose OK Figure 3 11 appears Well Patterns D Re X EJE New Copy Delete Rename Save Cancel LL_quad_384 LR_quad_384 UL_quad_384 UR_quad_384 To create a new pattern select wells while holding down the Shift key To deselect wells use the Ctrl key to taggle wells from selected to unselected To invert the well selection drag the mouse across the pattern while holding down the Ctrl key Figure 3 11 New pattern renamed 7 Choose Save to save LabwareQuickStart in Well Patterns Note Refer to the Biomek Software User s Manual Chapter 11 Creating Well Patterns for more information on creating well patterns Biomek 3000 Laboratory Automation Workstation Quick Start Guide 3 12 3 5 Revisions Changes made to any item in a project file are saved but do not become revisions until checked in Once checked in a new revision is created for the project items Revisions can never be lost If a project item is later modified or deleted any revision of the project item may be restored Validated Methods When Accounts amp Permissions is enabled methods may be validated A validated method is a revision of a method that is checked in with a reason with or without an electronic signature and protected from further modification Re
7. refer to the Biomek Software User 5 Manual Chapter 15 2 Instrument Setup Step Biomek Software Method1 New File Edit Project Instrument Execution Options Help De eae BRS X Malo gt a gt vol Start Deck Den O O ba IV Pause to confirm setup Pause for bar code input ae Instrument Setup Labware Category lt Any gt Ba JV Verify Pod Setup Configure Sel H Finish P96 20uL_LLS BCDeep6Round BCDeep36Square Flat BCFullReservoir f F e i v mi ra e re Methodi Biomek3000 Biomek3000 ETC 0 00 02 Method Error Text Figure 2 6 Instrument Setup step with labware named Next you will configure a Transfer step using an MP200 tool If your instrument configuration does not include an MP200 tool any pipetting tool may be substituted Beckman Coulter Inc 2 4 Transfer Step A Transfer step loads tips aspirates and dispenses liquid and unloads tips This eliminates the need to insert four separate steps to complete a liquid transfer However there are steps in Biomek Software that allow these steps to be performed individually on the Intermediate Step Palette refer to the Biomek Software User s Manual Chapter 16 Using the Intermediate Step Palette Learning to Create Methods for the Biomek 3000 2 9 Configuring a Transfer Step The Transfer step transfers liquid from a single source to one or more destinations You are
8. Deck Layout Display double click the tool rack to display Labware Properties Figure 2 4 Labware Properties pl i Bl It peepee a i Drag the Gripper tool to the gripper position on the tool rack Gripper Figure 2 4 Labware Properties for tool rack Note Your Labware Properties for the tool rack may contain more tools on the right side depending on your instrument configuration 4 Drag the Gripper tool to the gripper tool position on the tool rack the larger position on the right 5 Drag the MP200 tool to either of the two remaining tool positions 6 Choose OK to close Labware Properties 7 From the Deck Layout Display double click the reservoir on P3 to display Labware Properties Figure 2 5 Labware Properties Labware Type Reservoir Maximum Volume 110000 pL Bar Code Po Labware contains a known z volume 100000 a uL of liquid type MAS Sense the liquid level the first time a well with Unknown or Nominal volume is accessed From the Liquid Sense the liquid level every time a well is accessed from the Liquid Y Show Labware Yolumes OK Cancel Figure 2 5 Labware Properties for Reservoir on P3 Naming Labware It is helpful to name labware particularly when you use lots of labware on the deck You can assign a name that identifies the contents of the labware or a descriptive name that fits the work being done in the laboratory Naming labware can reduce
9. Greiner384Therma Greiner36ConeHalf Greiner96ConePP anori t sneri oma Figure 3 4 NewLabwareQuickStart in Labware Type Editor Beckman Coulter Inc Using the Editors While Creating Methods 3 7 4 Double click the NewLabwareQuickStart graphic NewLabwareQuickStart appears Figure 3 5 NewLabwareQuickStart Basic Information x Y Miscellaneous Span fi 2 7762 fe 5471 cm Movement Information Orbital Shaker Height fi 4224 em Ordering Information Stacking Colors Edit Wells_1 ii Bitmap C e Description Beckman Coulter microplate with 96 round flat bottomed wells Hint The shape and general description of the There are no errors in this labware type SHSSSSSSSESE labware definition Figure 3 5 NewLabwareQuickStart Note Each piece of labware in Labware Types has its own mini editor similar to Figure 3 5 to allow specifications to be revised and saved 5 In Height enter 1 46 and choose Save You have created a new piece of labware in the Labware Type Editor 6 Choose Exit to close the Labware Type Editor Biomek 3000 Laboratory Automation Workstation Quick Start Guide 3 8 Using the Editors While Creating Methods 3 4 Creating a New Pattern The Well Pattern Editor is used to create and store patterns for accessing specific wells in methods There are also well patterns already created in Well Patterns that may be used or copied to create new patterns The patterns created and
10. an expressly authorized officer of the Company Parts replaced during the warranty period are warranted to the end of the instrument warranty Note Performance characteristics and specifications are only warranted when Beckman Coulter replacement parts are used Biomek 3000 Laboratory Automation Workstation Quick Start Guide Table of Contents Warranty and Returned Goods Requirements 00 cece cee ence eee iii Table of Contents 000 cee eee ee eee eee v 1 introducing the Biomek 3000 Laboratory Automation Workstation 1 1 Introduction days 6 6 4 8 eenaa enera rE e a a E ae eee RS 1 1 1 1 1 How to Use This Quick Start Guide onnan nananana 1 2 1 2 Biomek 3000 Laboratory Automation Workstation 00 1 3 1 2 1 RIS ss ahs ran Ses hh beh Dee aE ed aada Bed ache ole ais 1 3 22 Head Assembly 4 446 20dad nerna seie teed Renta dee k eae eades 1 4 1 23 WOO coon iteeradeetereseeenegau a a heehee eeaaenens 4 1 4 1 2 4 Labware Positioners oann ease steed p DA4e aiead pas ee eeda eee 1 4 125 NOOLROCKS 4424256244 0cn2taaburete E e E A 1 4 1 2 6 Opfional DEVICES sesde chide divide ea a E e E RE 1 5 1 3 Biomek Software nnnnn nnana unaarne 1 6 1 4 Starting the Biomek 3000 2 0 ccc cece eee eee ne eees 1 7 1 4 1 Turning On the Biomek 3000 oi csacc scans ceka eevee easavnaes 1 7 1 4 2 Launching the Software 2 462 exceeds ddsacad ere eed Geni veads 1 7 1 4 3
11. confusion 12 13 14 15 16 2 7 Learning to Create Methods for the Biomek 3000 In Name enter Resv in Labware Properties In Labware contains select Known from the pull down menu In volume enter 100000 This means that you know you have 100000 microliters of liquid in the reservoir In liquid type select Water_MP200_P200 from the pull down menu Labware Properties for the Reservoir should look like Figure 2 5 Choose OK to close Labware Properties Double click the labware on P4 and name it Dest1 in Labware Properties Choose OK to close Labware Properties Note The default settings in Labware Properties will be used for the tip box however you can refer to the Biomek Software User s Manual Chapter 15 2 5 1 Configuring Labware Properties for Tips to learn more about configuring a tip box Select Pause to confirm setup You will see a confirmation prompt when you run your method in Section 2 8 Running a Method Leave the Verify Pod Setup option as is This setup is used to inform the software of the current state of the pod for example if the pod already has a tool loaded at the start of the method Biomek 3000 Laboratory Automation Workstation Quick Start Guide 2 8 Learning to Create Methods for the Biomek 3000 Your Instrument Setup step is now configured and the main editor should look like Figure 2 6 Note To learn more about the Instrument Setup step
12. going to insert a Transfer step into the method and configure it to move liquid from your source reservoir Resv to your destination microplate Dest1 using an MP200 Multi Tip Pipette Tool Note Refer to the Biomek Software User s Manual Chapter 15 3 Configuring Transfer and Combine Steps for complete information on configuring the Transfer and Combine steps 2 4 1 To insert a Transfer step into your method Inserting a Transfer Step Drag and drop a Transfer step from the Step Palette into the Method View just below the Instrument Setup step Notice that the Current Deck Display shows the current position of all labware on the deck Figure 2 7 You will complete three sections to configure the Transfer step for this method e Section 2 4 2 Configuring Tip Handling e Section 2 4 3 Configuring Source Labware Section 2 4 4 Configuring Destination Labware Biomek Software Method1 New File Edit Project Instrument Execution Options Help PLACE DEIL Start Instrument Setup Q Transfer IB Finish Use pod for transfer Tip Handling V Load JAP96_200uL x tips and unload them x when the transfer is done I7 Change tips between sources IV Change tips between destinations Click here to add a source Stop when finished with Destinations z Replicate each well 1 E time Dispense up to fi a time per draw Aspirate at most fo uL per tr
13. new password Remember your new password you will need to enter it each time you access Biomek Software 1 Locate the power switch on the right side of the instrument Figure 1 2 Launching the Software To launch Biomek Software 1 Choose Start gt All Programs gt Beckman Coulter gt Biomek Software Biomek Software File Edit Project Instrument Execution Options Help DO amp amp 45 J Other editors are available from the Project and Instrument menus hae Lemme Step Configuration Area Method View When a step is highlighted in the The method is built step Method View the corresponding by step in this area configuration appears in this area Unload Tool Step Ey a Basic Step Palette AR Displays the steps that provide ek essential functionality meen including instrument setup and th labware manipulation C Current Deck Display Displays the status of the deck upon completion of the previous step Bulk Tae Biomek 3000 Step Palette Tiaa Displays the special steps Waste available for Biomek 3000 including those to load unload and change tools II Biomek3000 Biomek3000 Figure 1 2 Biomek Software main editor Biomek 3000 Laboratory Automation Workstation Quick Start Guide 1 8 Introducing the Biomek 3000 Laboratory Auto m ati Home All Axes Home All Axe
14. of user s manuals provided during installation These manuals include Biomek Software User 5 Manual and Biomek 3000 Laboratory Automation Workstation User s Manual Each manual contains comprehensive information about the possibilities designed into the Biomek 3000 In this chapter you ll learn e Creating a New Method Section 2 2 e Configuring the Instrument Setup Step Section 2 3 e Configuring a Transfer Step Section 2 4 Configuring a Move Labware Step Section 2 5 e Using the Finish Step Section 2 6 Saving a Method Section 2 7 e Running a Method Section 2 8 Biomek 3000 Laboratory Automation Workstation Quick Start Guide 2 2 Learning to Create Methods for the Biomek 3000 2 2 Creating a New Method if using Accounts amp In this chapter you will build a simple method that transfers liquid between labware Pemissions ii In building this method you will You must have Develop e Populate the deck with labware using the Instrument Setup step Methods permission to create methods Refer to the Biomek Software e Move labware with the Gripper Tool using a Move Labware step User s Manual Chapter 2 Aaaa Using Accounts amp Note A gripper tool rack must be installed on the Biomek 3000 deck to store a gripper tool when not in use Transfer liquid with an MP200 Multi Tip Pipette Tool using a Transfer step Permissions for more information When yo
15. required by the Company be returned to the factory transportation charges prepaid and will be returned to Purchaser with transportation charges collect unless the product is found to be defective in which case the product must be properly decontaminated of any chemical biological or radioactive hazardous material d The Company shall be released from all obligations under all warranties either expressed or implied if any product covered hereby is repaired or modified by persons other than its own authorized service personnel unless such repair by others is made with the written consent of the Company e Ifthe product is a reagent or the like it is warranted only to conform to the quantity and content and for the period but not in excess of one year stated on the label at the time of delivery It is expressly agreed that the above warranty shall be in lieu of all warranties of fitness and of the warranty of merchantability and that the company shall have no liability for special or consequential damages of any kind or from any cause whatsoever arising out of the manufacture use sale handling repair maintenance or replacement of any of the products sold under the sales agreement Representatives and warranties made by any person including dealers and representatives of the Company which are consistent or in conflict with the terms of this warranty shall not be binding upon the Company unless reduced in writing and approved by
16. stored in Well Patterns are accessible in the Transfer and Combine steps Assume that you want to create a new well pattern based on the NewLabwareQuickStart labware you created in the Labware Type Editor To create a new well pattern in the Well Pattern Editor 1 From the Project menu choose Well Pattern Editor Well Patterns appears Figure 3 6 Well Patterns D x EIE New Copy Delete Rename Save Cancel LR_quad_384 UL_quad_384 UR_quad_384 Beckman Coulter Inc To create a new pattern select wells while holding down the Shift key To deselect wells use the Ctrl key to toggle wells from selected to unselected To invert the well selection drag the mouse across the pattern while holding down the Ctrl key Figure 3 6 Well Patterns Using the Editors While Creating Methods 2 Choose New New Pattern appears Figure 3 7 New Pattern Greiner 536FlatPSLoBas a Greiner384ConePP Greiner384ConePPDeep Greiner384FlatPP Greiner384T hermalCycler GreinerS6ConeHalfDeep GreinerS6ConePP GreinerS6ConePS GreinerS6Flat GreinerS96R oundD eep GreinerS6RoundD eepS qi GreinerS6R oundPP Pick a labware type to base this pattern on SHE de oade de ie ie i i i i Saa o a a seio aio sio sio sio io aio oeio aloaia seio aio aio sio aio aio sio aoei aio aioai LD ha o a l alaale io io io io ia SE saio aio aio sio sio aio aio io ioei ainal Seod io e e a l 3 9 GreinerS6RoundPS GreinerS6T hermalCycler Gr
17. the Step Palette Builder for more information 2 Biomek 3000 Laboratory Automation Workstation 1 7 1 4 Starting the Biomek 3000 To start the Biomek 3000 you will follow the instructions in this chapter to turn on Accounts amp the instrument launch Biomek Software and home all axes Permissions When enabled Accounts 1 4 1 Turning On the Biomek 3000 amp Permissions is an integrated set of features To turn on the Biomek 3000 instrument built into the software to assist users in complying with electronic signature 2 Flip the switch to the On position The indicator light comes on in solid green requirements for closed systems The functionality for 1 4 2 Accounts amp Permissions is included in the Biomek Software installation and provides control over 2 If Accounts amp Permissions is enabled see sidebar a dialogue box appears who can create and run requesting you to log in using the user name and password assigned to you by methods and who may your system administrator Enter the required information Your account must only run validated have Develop Methods Develop Projects and Setup Instrument methods Refer to the permissions to complete all parts of this quick start guide The Biomek Software Biomek Software User 5 main editor appears Figure 1 2 Manual Chapter 2 Using Accounts amp Note Ifyou are logging into Biomek Software for the first time you must enter Permissions a
18. 0 Figure 3 13 Hardware Setup 2 In the left pane right click Tools and choose Add Device from the menu that appears A list of all the different tool types appears Biomek 3000 Laboratory Automation Workstation Quick Start Guide 3 14 Using the Editors While Creating Methods 3 Select P200L from the list A P200L tool is added to the list of tools in the left pane Note the asterisk to the right of the tool name This indicates the tool has been added or modified and changes have not been saved Biomek Hardware Setup 2 Reconnect Mf Home All Axes p Add Device s Remove Device lt Accept X lt Cancel E Biomek 3000 SN None JK Podi a R5485 Gripper The newly added P200L External Devices tool appears here Stacker Carousels Biomek3000 Figure 3 14 Hardware Setup with new tool added 4 Click on P200L in the left pane to display the tool configuration in the right pane 5 If this new tool corresponded to a physical tool that would be used with the instrument you would enter the serial number printed on the tool label in Tool Serial Number Note The other fields may be used to modify the performance of the tool However Tool Conversion Slope and Capacity should only be changed if you are instructed to do so by a Beckman Coulter support or service representative Refer to the Biomek 3000 Laboratory Automation Workstation User s Manual Chapter 12 Confi
19. 3000 or generally unfamiliar Important Concept These boxes emphasize important concepts relevant to the Biomek 3000 instrument and the Biomek Software Refer to the links in this quick start guide or the Biomek 3000 Laboratory Automation Workstation User 5 Manual or the Biomek Software User s Manual for more information on these important concepts he Biomek 3000 Laboratory Automation Workstation 1 3 1 2 Biomek 3000 Laboratory Automation Workstation Your Biomek 3000 Laboratory Automation Workstation Figure 1 1 is a multiaxis liquid handling instrument sized to fit in a laminar flow or fume hood for sterile or hazardous operations The open architecture design along with the extensible operating software provides a foundation for integrating current and future specific use components The Biomek 3000 is a single head instrument with a series of interchangeable tools Different tools provide options for performing a variety of functions including liquid transfer and plate washing operations and moving labware around the deck The modular design of the Biomek 3000 allows expansion of the instrument capabilities to include additional operations such as filtration plate shaking photometric measurement and high capacity operation Regardless of the tool configuration or operating components your Biomek 3000 workstation is controlled through the powerful Biomek Software
20. C 0 01 54 Beckman Coulter Inc Figure 2 11 Configured Move Labware step The Move Labware step configuration is complete Now move on to Section 2 6 Using the Finish Step to learn how long the method will take to run Learning to Create Methods for the Biomek 3000 2 15 2 6 Using the Finish Step Your liquid transfer is set up so you can see how long it will take to run the entire method by using the Finish step 1 Click on the Finish step in the Method View 2 Check the status bar at the bottom of the editor for a display of the Estimated Time for Completion ETC For this method the ETC is approximately 2 24 Note Your ETC may vary slightly That s OK Note Refer to the Biomek Software User s Manual Chapter 12 2 2 Configuring the Finish Step for information on configuring the Finish step 2 6 1 Handling Configuration Errors If there is a step configuration error in your method when you click on the Finish or any step that occurs after the step with error the step with the error is highlighted in red Figure 2 12 and the ETC is displayed as Failed The error message also is displayed in the status bar or when hovering the mouse over the highlighted step Use the message to correct the error and reconfigure the step Note Refer to the Biomek Software User s Manual Chapter 25 Handling and Preventing Errors Biomek Software Method1 New File Edit Project Instrument Execution O
21. C MicroMix Shaker Biomek 3000 Laboratory Automation Workstation Quick Start Guide 1 6 1 3 Beckman Coulter Inc Introducing the Biomek 3000 Laboratory Automati Biomek Software The Biomek Software is designed to Do a substantial amount of the method building work for you Allow you to take as much direct and precise control over the method building process as you want Note A method is a series of steps controlling the operations of your Biomek 3000 The main editor that appears when the software is launched Figure 1 2 is used to build and configure methods Each step is dragged and dropped from a Step Palette into the Method View refer to Chapter 2 Learning to Create Methods for the Biomek 3000 When a step in the Method View is highlighted the corresponding configuration options appear in the Step Configuration Area refer to Chapter 2 Learning to Create Methods for the Biomek 3000 The method is customized to the desired level of precise control via the editors accessed from the Project and Instrument menus refer to Chapter 3 Using the Editors While Creating Methods Step Palettes Step Palettes are panes in the Biomek main editor showing steps available for insertion in a method They are located on the left of the main editor Use the Step Palette Builder to add other step palettes Refer to the Biomek Software User s Manual Chapter 29 5 Using
22. Homing All Axes of the Biomek 3000 Pod 1 8 2 Learning to Create Methods for the Biomek 3000 2 1 OVELVIEW c 606 4564 ordie taka Ra RK REAR RERAN NEREAREN G 2 1 2 2 Creating a New Method 404 cehstadvdae Veresseew t Ea eoni EEEa EE 2 2 2 3 Configuring the Instrument Setup Step 0 0 0 0 0 00 cece cece eee 2 4 24 Configuring a Transfer Step lt 24c4200 24baneteeicieaduesageeadeeaenees 2 9 2 4 1 Inserting a Transfer Step yan se eke cg bee R ake da wk ee KAR ERS 2 9 2 4 2 Configuring Tip Handling 0 eee eee eee 2 10 2 4 3 Configuring Source Labware 00 c cece eens 2 11 2 4 4 Configuring Destination Labware 00 0000 c eee eee 2 12 2 5 Configuring a Move Labware Step 000 cece cece eee eens 2 14 Biomek 3000 Laboratory Automation Workstation Quick Start Guide vi Table of Contents 2 6 Using the Finish Step neaaa nnana ananena 2 15 2 6 1 Handling Configuration Errors 00 0 eee ee eee eee 2 15 2 7 Saving a Method g gests cp ete acta aoa oat x ace Wt ereere 2 16 26 Ronnie MeO ons ceca xd agdhedad ns heles Shana isk i eee Ee A brr Na 2 17 3 Using the Editors While Creating Methods 3 1 OVETVIEW saso aai ai eana a daaa e E aia a aa anka e E anae ha aioa aari 3 1 3 2 General Description of Editors 26 64 cid cdi den anaana rererere 3 2 3 2 1 Project MeN ey va sdd pa hea LGR eae eee oe e E E i eae Ge E 3 3 3 2 2 nstrument Ment 22cc g se4ec
23. addition to the physical deck Note Refer to the Biomek Software User 5 Manual Chapter 5 Preparing and Managing the Deck for detailed information on using the Deck Editor To create a new deck in the Deck Editor 1 Choose Instrument gt Deck Editor Deck Editor appears Figure 3 15 Deck1 Default Deck ad Ly x New Deck Delete Deck Rename Del AutoLatch BarcodeReaderLeft BarcodeReaderRight Biomek3000Position Disposal StackerCarouselLeft StackerCarouselRight b1iomek 3000 workstation deck positions Figure 3 15 Deck Editor 2 Select New Deck Choose a name for this deck appears Figure 3 16 Choose a name for this deck TwoT oolRacks Cancel Figure 3 16 Choose a name for this deck 3 Enter TwoToolRacks and choose OK TwoToolRacks appears 4 Click and hold the mouse button on ToolRack from the Devices Types List Locations capable of supporting that ALP are indicted in the Deck View by dashed boxes Biomek 3000 Laboratory Automation Workstation Quick Start Guide 3 16 Using the Editors While Creating Methods 5 Drag and drop ToolRack to any location capable of supporting it Figure 3 17 A second ToolRack has been added to the deck This deck is now the default deck and is available in the Instrument Setup step TwoToolRacks Default Deck x x e Ff w Bo amp 8 New Deck Delete Deck Rename Deck OpenDeck ClearDeck Renumber Delete ALP Properti
24. ansfer for repeated dispensing Transfer Details ors Advanced Current Deck Display Method1 Biomek3000 Biomek3000 ETC 0 00 03 Figure 2 7 Transfer step inserted into the Method View Biomek 3000 Laboratory Automation Workstation Quick Start Guide 2 10 Learning to Create Methods for the Biomek 300 0 Tip Handling Configuring Tip Handling is not always required because the Biomek 3000 locates and loads clean tips automatically during a Transfer step Refer to the Biomek Software User s Manual Chapter 15 3 1 Configuring Tip Handling for information on other tip handling options such as Change tips between destinations 2 4 2 The Transfer step automatically loads an appropriate tool if one is not already loaded However if you want to use a specific tool for the Transfer step a tool can be loaded by inserting a Load Tool step prior to the Transfer step For this quick start method it is not necessary to insert a Load Tool step since there is only one pipetting tool on the deck Configuring Tip Handling To configure tip handling 1 In Tip Handling make sure Load is checked 2 Click on the AP96_200uL tip box on ML1 in the Current Deck Display to load AP96_200uL tips as part of the Transfer step 3 Make sure unload them is selected in the next field 4 Check Change tips between sources 5 Uncheck Change tips between destinations
25. anual Chapter 14 Manually Controlling the Biomek 3000 in Biomek Software Note Refer to Section 3 8 Manually Controlling the Pod in this quick start guide to learn how to manually move a pod to another position after using Z Max to raise it to the highest configured height Import Export Utility allows you to import and export instrument settings decks framing tools pod settings as import files imp refer to the Biomek Software User s Manual Chapter 3 Using Instrument Files and Settings 3 3 Labware Definitions When creating a new labware type it is important that the labware dimensions are entered precisely per the manufacturer s specifications An incorrect labware definition could result in a number of problems including collisions gripper errors or poor pipetting performance Using the Editors While Creating Methods 3 5 Creating New Labware in the Labware Type Editor The Labware Type Editor is used to create labware definitions so you can use labware that is not predefined in Biomek Software in your methods Assume that you have new labware that is very similar to a BCFlat96 but some specifications are slightly different so you must create a new labware type in the Labware Type Editor in order to use this new type in your methods Refer to the Biomek Software User s Manual Chapter 7 Creating and Modifying Tip and Labware Types for further information on using the La
26. ation Area lt When a step is highlighted in the M verif 3 k j Ai Method View the corresponding configuration appears in this area IV Pause to M et h od Vi ew z AP96_20uL_Barier E The method is built AsIs step by step in this WN LK area SS Toggle Basic Step Palette Displays the steps ML Current Deck Display ceanal 4 available for insertion A dynamically updated te into a method representation of the devices Additional steps are and labware positioned on the available through other Biomek 3000 deck step palettes pi Method1 Biomek3000 Biomek3000 ETC 0 00 02 Figure 2 1 Biomek Software main editor for a Biomek 3000 instrument Note Your deck layout may differ slightly from the deck shown in Figure 2 1 depending on how your Biomek 3000 instrument is physically set up As you can see two steps automatically appear in every method created and executed by the Biomek Software e Start the first step in a method allows Variables 3 Start creation of global variables that are applicable i A variable is a value that to the entire method Refer to the Biomek hele esa denied 4 Software User 5 Manual Chapter 12 2 1 8 name that may be Configuring the Start Step for information on f d tedi creating variables in the Start step E PRA E during a method Refer Finish
27. bware Type Editor Note Do not run a method outside of the simulator using the labware you create here the specifications may not be accurate for the physical piece of labware you use in this tutorial method see sidebar To create new labware in the Labware Type Editor 1 From the Project menu choose Labware Type Editor Labware Types appear Figure 3 2 Labware Types D New Copy Delete Rename ABI34ellReactio AP96_20uL_Barier BCFullReservoir 26 e e o AP96_20uL_LLS BCDeep96Round o L L a BCTuberack_B3K_10m BCTuberack_B3K_12r BCTuberack_B3K_13mr SOCCCCOOOOOSD SOOCSCOCOCOOD ay BCDeep36Square BCFlat96 A i Figure 3 2 Labware Types Biomek 3000 Laboratory Automation Workstation Quick Start Guide 3 6 Using the Editors While Creating Methods 2 Click on BCFlat96 and choose Copy Copy Labware Type appears Figure 3 3 Copy Labware Type x Figure 3 3 Copy Labware Type Note To retain the dimensions of predefined labware in Biomek Software it is important to copy and then edit the copy of the labware type rather than just editing the predefined labware to meet the new labware specifications 3 Enter NewLabwareQuickStart and choose OK The copy of BCFlat96 is created with the specified name and appears in Labware Type Editor Figure 3 4 Labware Types B X E Copy Delete Rename CILI 333 E3 Greiner384ConePP Greiner384FlatPP
28. ch ML1 or auto latching AL1 tip rack holder to precisely position tip racks so that pipetting tools can accurately load and unload tips Make sure that the latch is securely holding the tip rack in position e a Reservoir to P3 e aBCFlat96 to P4 Your screen should look similar to Figure 2 3 Note To remove unwanted labware from the Deck Layout Display during setup drag and drop the labware to the Clear trash icon Biomek Software Method1 New File Edit Project Instrument Execution Options Help PEZECO CETL Start Instrume Deck Dek o oO x IV Pause to confirm setup Pause for bar code input BR nt arnt Cahn Labware Category lt Any gt x IV Verify Pod Setup Configure sewp Drag the desired labware graphic to WAJ Transfer the desired position a Tool rack Reservoir on the Deck Layout Display AP96_20uL_LLS on P3 Deck Layout Display Properties From the Deck Layout Display double click the labware graphic to i display Labware i AP96_200uL BCFlat96 on ML1 on P4 jethod1 Biomek3000 Biomek3000 ETC 0 00 02 Figure 2 3 Instrument Setup step with labware added Biomek 3000 Laboratory Automation Workstation Quick Start Guide Learning to Create Methods for the Biomek 3000 Beckman Coulter Inc 3 From the
29. controlled by a user supplied circulating bath refer to the Biomek 3000 Laboratory Automation Workstation User 5 Manual Chapter 9 Thermal Exchange Unit e Filtration System includes a vacuum valve unit that is connected to the Biomek 3000 workstation via RS 485 communication and a manifold system with interchangeable collars to allow collection of filtrates to microplates or waste The filtration system is used to run screening assays which require filtration such as receptor binding and cell based assays and plasmid DNA purification applications on the Biomek 3000 workstation refer to the Biomek 3000 Laboratory Automation Workstation User 5 Manual Chapter 10 Filtration System e Stacker Carousel provides additional labware capacity for microplates and tip boxes to the Biomek 3000 workstation It includes up to four stacks and a shuttle for transporting labware between the Biomek 3000 deck and the Stacker Carousel A Stacker Carousel may be installed on either the left side right side or both sides refer to the Biomek 3000 Laboratory Automation Workstation User s Manual Appendix B Using a Stacker Carousel e Device Integrations Several third party devices including microplate readers and shakers may be integrated into the Biomek 3000 deck and used in an automated method in conjunction with the Biomek 3000 workstation refer to the Biomek 3000 Laboratory Automation Workstation User 5 Manual Appendix C DP
30. d Move on to Section 2 8 Running a Method to run your saved Quick Start method Beckman Coulter Inc Learning to Create Methods for the Biomek 3000 2 17 2 8 Running a Method Next you will run the method you just created using the simulator The simulator allows you to watch the method on your screen without actually running the method on an instrument To run your saved method 1 If you do not see the Simulation Display button on the toolbar Figure 2 15 from the Instrument menu choose Hardware Setup Biomek Hardware Setup appears Biomek Hardware Setup Reconnect ft Home All Axes Add Device ms Remove Device J Accept gt Cancel b i T 3000 SN None erties Tr R5485 Port simulate 7 Tools oA Gripper A mpzoo Simulator Camera E Materials f External Devices f Stacker Carousels Figure 2 15 Hardware Setup 2 In Port select Simulate 3 Choose Accept to save changes and close Hardware Setup Biomek Software is now running in simulation mode Biomek 3000 Laboratory Automation Workstation Quick Start Guide 4 Click on the green arrow button on the toolbar The simulation display is automatically launched and the step configuration area is replaced with a three dimensional model of your Biomek 3000 Figure 2 16 The deck confirmation prompt Figure 2 17 appears on top of the main editor Biomek Software Quick Start Meth
31. documentation or the procedures specified in this manual regardless of foreseeability or the form of action whether in contract tort including negligence breach of warranty strict liability or otherwise and including but not limited to damages resulting from loss of data loss of anticipated profits or any special indirect incidental or consequential damages In no event shall Beckman Coulter Inc s liability to the user exceed the amount paid by the user to Beckman Coulter Inc hereunder The user assumes full responsibility for the results obtained from the use of this system and related documentation and for application of such results Beckman Coulter SAGIAN Operations Indianapolis Indiana www beckmancoulter com Biomek Beckman Coulter and the Beckman Coulter logo are registered trademarks of Beckman Coulter Inc Microsoft and MS DOS are registered trademarks and Windows is a trademark of Microsoft Corporation All other trademarks appearing in this manual are owned by their respective companies Copyright 2004 by Beckman Coulter Inc All rights reserved No part of this publication may be reproduced distributed or transmitted in any form or by any means electronic mechanical photocopying recording or otherwise or stored in a database or retrieval system without the prior written permission of Beckman Coulter Inc Beckman Coulter Inc Warranty and Returned Goods Requirements All standard Beckman Coulter I
32. earn more about the Deck Editor in the next chapter refer to Section 3 7 Creating a New Deck Biomek Software Method1 New File Edit Project Instrument Execution Options Help Deae BRS Moo a 0 ol Deck Deck Ba JV Pause to confirm setup Pause for bar code input Labware Category lt Any gt pa IV Verify Pod Setup Configure AB384WWellReactio KC A my Ay 7 APS6 200uL AP96_200ul_Barier AP96_200uL_LLS AP96 20uL Clear All Methodi Biomek3000 Biomek3000 ETC 0 00 02 Beckman Coulter Inc Figure 2 2 Instrument Setup step in the Method View Creating Labware If you want to use a labware type that does not appear in the available labware list use the Labware Type Editor to create a new labware type In Section 3 3 Creating New Labware in the Labware Type Editor you will create a new labware type in the Labware Type Editor Learning to Create Methods for the Biomek 3000 2 5 To configure the Instrument Setup step for your new method 1 In Deck make sure the default deck layout Deck1 is selected The Instrument Setup step uses a deck layout as a map for the placement of labware on the deck and external hardware devices such as stacker carousels 2 Drag and drop the following labware on the Deck Layout Display e an AP96_200uL to ML1 or AL1 Note Tip boxes must be placed in either a manual lat
33. einerFlat 5365 quare GreinerFlat3845 quare GreinerShallow384R ounce LJLShallow384R ound MJ Mictoseal 384 Pick a name for your pattern NewLabwareQuickStart NuncFlatl 5365 quare Pattern36 NuncFlat3845 quare PlasmidFilter x Cancel SBSDeep384Square gt LK Figure 3 7 New Pattern 3 Highlight NewLabwareQuickStart and choose OK Figure 3 8 appears Well Patterns D x w New Copy Delete Rename Save Cancel To create a new pattern select wells while holding down the Shift key To deselect wells use the Ctrl key to toggle wells from selected to unselected To invert the well selection drag the mouse across the pattern while holding down the Ctrl key Figure 3 8 Well Patterns based on Pattern 96 Biomek 3000 Laboratory Automation Workstation Quick Start Guide 3 10 Using the Editors While Creating Methods 4 While holding down the Shift key select the wells for the new pattern so it looks like Figure 3 9 Well Patterns D x Se New Copy Delete Rename Save Cancel LL_quad_384 LR guad 384 UL_quad_384 UR_quad_384 To create a new pattern select wells while holding down the Shift key To deselect wells use the Ctrl key to taggle wells from selected to unselected To invert the well selection drag the Mouse across the pattern while holding down the Ctrl key Figure 3 9 Wells chosen for the new pattern 5 Choose Rename to rename the new pattern Rename Pattern appears Figure 3 10
34. es Save Cancel Rack1 StackerCarouselLeft StackerCarouselRight Figure 3 17 TwoToolRacks deck with second tool rack added 6 Select Open Deck Select a Deck appears Figure 3 18 Select a Deck IV Open as default deck Figure 3 18 Select a Deck 7 Choose Deck1 to make it the default deck since it is the deck you used when you created the Quick Start Method and choose OK 8 Choose Save to exit the Deck Editor Beckman Coulter Inc Using the Editors While Creating Methods 3 17 3 8 Manually Controlling the Pod If you need to control the Biomek 3000 instrument outside of a method including moving the bridge and head assembly outside of a method you will use Manual Control Manual Control is also used to control the pod when framing the gripper tool and when recovering from errors Some devices can also be controlled outside a method using Manual Control Refer to the Biomek 3000 Laboratory Automation Workstation User 5 Manual Chapter 14 Manually Controlling the Biomek 3000 in Biomek Software for additional information Using the following instructions you will use Manual Control to move the pod to a different position on the deck You ll move the pod to the Z max height first to make sure you don t hit anything on the deck and then you l move the pod to a selected position Note Ifyou launch the simulator you can watch the pod move as you complete the following steps To move
35. g eee eden Sheeeeeee pyee eure ss 3 3 3 3 Creating New Labware in the Labware Type Editor 4 3 5 3 4 Creating a New Pattern nnnnann unanenn enere 3 8 3 5 Checking In a Method and Project File nananana nna naa eee ee eee 3 12 3 6 Using Hardware Setup sca64 lt h63taous4radbocaddhswtowentdanctstetnes 3 13 3 7 Creating a New Deck 26 4 444420d 4eeiandednns rearea 3 15 3 8 Manually Controlling the Pods i405 ce2 e 23544046 6040 4 Vn ease eens 3 17 3 9 Quick Start Guide Summary 6 0065 00400004 ns been ees a wee we wees 3 19 Beckman Coulter Inc Introducing the Biomek 3000 Laboratory Automation Workstation 1 1 Introduction Welcome to the Biomek 3000 Laboratory Automation Workstation This quick start guide is designed to help you learn to use the Biomek Software with your Biomek 3000 instrument This quick start guide includes Getting to Know the Biomek 3000 Laboratory Automation Workstation this chapter a general hardware overview on the Biomek 3000 Automated Laboratory Workstation and introduction to the Biomek Software Learning to Create Methods for the Biomek 3000 Chapter 2 an introduction to creating methods for the Biomek 3000 instrument using the Biomek Software This chapter gives instructions on creating saving running checking in and opening a small method e Using the Editors While Creating Methods Chapter 3 an introduction to using the edi
36. guring the Biomek 3000 in Hardware Setup for more information on adding and configuring tools in Hardware Setup 6 Since this tool does not correspond to a physical tool right click P200L in the left pane and select Remove Device to remove the tool from Hardware Setup 7 Choose Accept to close Hardware Setup Beckman Coulter Inc 3 7 Framing Framing teaches Biomek Software the location of the devices positioned on the deck Biomek Software uses this framing information to move the pod to the appropriate position when performing liquid handling operations and manipulating labware A Beckman Coulter Service Engineer frames the Biomek 3000 instrument during system installation It may be necessary to repeat the framing if devices are added moved or removed from the deck Refer to the Biomek 3000 Laboratory Automation Workstation User s Manual Chapter 13 Framing the Using the Editors While Creating Methods 3 15 Creating a New Deck A deck in the Biomek Software refers to the software representation of the physical Biomek 3000 instrument deck The Deck Editor is used to define and change deck configurations A deck stores framing information and device associations for each position on the deck Decks can be used for multiple methods and are stored in the Deck Editor Assume you have added a second tool rack to your deck and now must create another deck in the Deck Editor that reflects that
37. he toolbar choose Close to close the quick start method OR From the File menu choose Close The method closes and you are now ready to create a method of your own Beckman Coulter Inc Using the Editors While Creating Methods 3 19 3 9 Quick Start Guide Summary Congratulations You ve just completed this quick start guide You ve completed e a small method e steps using the editors e steps creating some new project items e steps to manually control the Biomek 3000 If you ve used the links to other manuals you ve also learned where to find hardware information on the Biomek 3000 and more information on Biomek Software Enjoy your new Biomek 3000 Laboratory Automation Workstation Biomek 3000 Laboratory Automation Workstation Quick Start Guide
38. her position Move Labware can also be used to remove labware from the deck by placing it in an appropriate disposal position or to an external hardware device without halting the Biomek 3000 instrument or the method Note Refer to the Biomek Software User s Manual Chapter 15 4 Move Labware Step To configure the Move Labware step to move your Dest1 labware at position P6 to another deck position 1 Insert a Move Labware step into the Method View Gripper Tool The gripper tool is a specialized tool that is loaded onto the head assembly and allows the Biomek 3000 workstation to grasp and move labware around the Biomek 3000 deck Refer to the Biomek 3000 Laboratory Automation Workstation User s Manual Chapter 3 Gripper Tool 2 In Move labware from select P4 from the drop down menu 3 In Move labware to select P6 from the drop down menu The main editor should now look like Figure 2 11 Biomek Software Method1 New File Edit Project Instrument Execution Options Help De ae BRS loo a gt w Start Finish m x Instrument Setup Transfer 100 uL from Move Labware from P Using pod Poa x Move labware from P4 x to Pe x Move the entire stack of labware C Move stack leaving the bottom piece of labware at the source position C Move the topmost 1 piece of labware from the stack Method1 Biomek3000 Biomek3000 ET
39. ing a Method After you ve clicked on Finish step you can save or check in your method We will just save it for now 1 Choose File gt Save from the toolbar Save Method AS appears Save Method As Enter method name Cancel Figure 2 13 Save Method As 2 Enter Quick Start Method and choose OK The method editor now looks like Figure 2 14 Biomek Software Quick Start Method Development File Edit Project Instrument Execution Options Help De ae BRS X Mloo a gt wo Start Instrument Setup Q Transfer 100 uL fr W Move Labware froi aed Fns al Vv Clear current instrument setup of all labware after the method completes Vv Clear current device setup of all labware after the method completes Vv Unload disposable tips from all pods and wash any fixed tips after the method completes IV Clear all global variables after the method completes JV Unload the current tool after the method completes No Reporting Check In Checking in a method is similar to saving a method but in addition creates a new revision of the method checks in all project items of the project file and creates new revisions for any items that have changed You will check in the method later in Section 3 5 Checking In a Method and Project File Quick Start Method Biomek3000 Biomek3000 ETC 0 02 24 Figure 2 14 Quick Start method saved and name
40. ioners or devices integrated on the left or right side of the Biomek 3000 workstation 1 2 5 Tool Racks The tool rack is a special labware positioner used to hold up to five interchangeable tools in a single deck position during a method Note The gripper tool requires a special tool rack that accommodates the gripper tool and up to two additional tools he Biomek 3000 Laboratory Automation Workstation 1 5 1 2 6 Optional Devices The following optional devices can be added to the Biomek 3000 workstation to accommodate specific operations such as tip and labware disposal plate heating and cooling microplate filtration photometric measurement and high capacity operation e Disposal Accessory provides a waste receptacle for disposing of tips and labware from the deck using the gripper tool Tip boxes or other labware may be deposited directly into the disposal accessory eliminating the need to manually dispose of waste refer to the Biomek 3000 Laboratory Automation Workstation User Manual Chapter 6 7 Disposal Accessory e Circulating Reservoir continually cycles a reagent between off deck reagent bottles and wells of a four well reservoir positioned on the Biomek 3000 deck refer to the Biomek 3000 Laboratory Automation Workstation User s Manual Chapter 8 Biomek 3000 Circulating Reservoir e Thermal Exchange Unit heats or cools a reservoir or microplate on the Biomek 3000 deck The temperature is
41. la a ia 0 00 mm from liquid 2 or Destination Dest1 06000000000 JECFIat96 x at Desti Ba ul of Water_MP200_P200 V Auto Select Customize Save As 00000000000 Technique MP200_High z 4 00 mm from bottom Alig el Overrides Technique QY 2 Click here to add a destination 4 Stop when finished with destinations Dispense up to 1 time per draw Replicate each well 1 time gt is Oa Method2 Biomek3000 Biomek3000 ETC 0 00 03 Figure 2 10 Transfer step with Destination configured Note The method view changes to reflect the amount transferred when the next step is configured The Transfer step configuration is now complete In the next section you will configure a Move Labware step to move the destination labware to a different deck position using the gripper tool If your instrument configuration does not include a gripper tool skip to Section 2 6 Using the Finish Step to learn how long the method will take to run Biomek 3000 Laboratory Automation Workstation Quick Start Guide 2 14 2 5 Learning to Create Methods for the Biomek 3000 U Configuring a Move Labware Step If your instrument configuration does not include a gripper tool you cannot move labware continue to Section 2 6 Using the Finish Step The Move Labware step automatically changes tools to the gripper tool and moves labware from one position on the Biomek 3000 instrument deck to anot
42. lates that configure the precise actions during pipetting operations refer to the Biomek Software Users Manual Chapter 10 Using the Pipetting Template Editor 3 2 2 Instrument Menu The editors on the Instrument menu Figure 3 1 allow instrument configuration to be changed They include the following e Hardware Setup if you change the configuration of your instrument it is used to install configure and remove other devices refer to the Biomek 3000 Laboratory Automation Workstation User s Manual Chapter 12 Configuring the Biomek 3000 in Hardware Setup e Deck Editor used to define and change deck configurations and frame the deck refer to the Biomek Software User s Manual Chapter 5 Preparing and Managing the Deck e Device Editor external devices may be integrated to your Biomek 3000 instrument In order to use the device it must be configured through the Device Editor refer to the Biomek Software User s Manual Chapter 22 4 1 Configuring Devices Using the Device Editor Biomek 3000 Laboratory Automation Workstation Quick Start Guide 3 4 Using the Editors While Creating Methods Beckman Coulter Inc Manual Control allows you to control the movement of the bridge head assembly and grippers independently of a method It is used to control the pod when framing the gripper tool and when recovering from errors refer to the Biomek 3000 Laboratory Automation Workstation User s M
43. mp f instrument Editors are accessed from one of two menus Permissions You must have Develop e Project menu Figure 3 1 Projects and Setup OR Instrument permissions to access the editors on the Instrument menu Figure 3 1 Project and Instrument menus Refer to the Biomek Software User 5 Manual Chapter 2 Using Accounts amp Permissions for more information Biomek Software File Edit cy on Sptions Heipr es de ee ee I 4 Project Instrument 1 Includes access to the Includes access to the fl following following Labware Type Editor Hardware Setup Tip Type Editor Deck Editor Well Pattern Editor Device Editor Technique Browser Manual Control ui Liquid Type Editor Import Export Utility Pipetting Template Editor Pause BiomekFX BiomekFx Figure 3 1 Biomek main editor Following is a brief description of the editors available from the two menus displayed in Figure 3 1 If you would like to learn more about a specific editor refer to the referenced chapter for more information You will work with four of the more commonly used editors and Manual Control in this quick start guide Beckman Coulter Inc Using the Editors While Creating Methods 3 3 3 2 1 Project Menu The editors on the Project menu Figure 3 1 allow project items to be created copied revised and renamed They include
44. multiple tool types to provide different functionality to the instrument within a method Tool types available for the Biomek 3000 head include pipetting tools single channel and eight channel tools used to aspirate and dispense liquid refer to the Biomek 3000 Laboratory Automation Workstation User s Manual Chapter 2 Pipetting Tools e gripper tool tool to grasp and move labware around the Biomek 3000 deck refer to the Biomek 3000 Laboratory Automation Workstation Users Manual Chapter 3 Gripper Tool e wash system the wash system includes single channel and eight channel tools used to perform washing and bulk dispense operations refer to the Biomek 3000 Laboratory Automation Workstation User s Manual Chapter 4 Wash System e high density replication HDR tools tools used to perform low volume liquid transfer operations by liquid adhesion using stainless steel pins Pin plates are available in 96 pin and 384 pin capacities refer to the Biomek 3000 Laboratory Automation Workstation User s Manual Chapter 5 High_ Density Replication System Note HDR tools require at least two tool racks one for the HDR tool and one for the fan unit to dry pins after sterilization 1 2 4 Labware Positioners Labware positioners are used to hold microplates tube racks reservoirs or tip racks on the Biomek 3000 deck The gripper tool can move labware to and from these labware positioners to other labware posit
45. nc policies governing returned goods apply to this product Subject to the exceptions and upon the conditions stated below the Company warrants that the products sold under this sales agreement shall be free from defects in workmanship and materials for one year after delivery of the products to the original Purchaser by the Company and if any such product should prove to be defective within such one year period the Company agrees at its option either 1 to correct by repair or at the Company s election by replacement any such defective product provided that investigation and factory inspection discloses that such defect developed under normal and proper use or 2 to refund the purchase price The exceptions and conditions mentioned above are as follows a Components or accessories manufactured by the Company which by their nature are not intended to and will not function for one year are warranted only to reasonable service for a reasonable time What constitutes a reasonable time and a reasonable service shall be determined solely by the Company A complete list of such components and accessories is maintained at the factory b The Company makes no warranty with respect to components or accessories not manufactured by it In the event of defect in any such component or accessory the Company will give reasonable assistance to Purchaser in obtaining from the manufacturer s own warranty c Any product claimed to be defective must if
46. ng to Create Methods for the Biomek 3000 2 11 2 4 3 Configuring Source Labware To configure the labware named Resv as source labware in the Transfer step Techniques Techniques allow pipetting settings to be saved globally and used in any method Biomek Software includes several predefined techniques If Auto Select is chosen in a pipetting step such as Transfer each time a method is created Biomek Software automatically selects the technique most appropriate for the pipetting operation l 2 Click on Click here to add a source Click on Resv labware sitting on P2 in the Current Deck Display Note The information you supplied during Instrument Setup is displayed in the source labware configuration Leave the Auto Select checkbox selected to use the technique selected by Biomek Software Right click on the large tip illustration next to the microplate graphic in the configuration and choose Measure from the Bottom To adjust and set the aspirate height for the depth the tip descends into the reservoir place the mouse cursor over the tip illustration When the cursor turns into a hand hold the left mouse button down to move the hand up and down until the depth is as close to 2 00 mm from bottom as you can get Then adjust the height precisely to 2 00 mm using the following note This will be your aspirate height for this transfer Note After you click on the tip you can adjust the height more
47. od Development Simulation display button Click to toggle the view of the simulator on and off Instrument Setup S Transfer 10011 fro Move Labware from IB Finish Quick Start Method Biomek3000 Biomek3000 Figure 2 16 Biomek 3000 simulator displayed Biomek Software ToolRackGripper o esv AP96_200uL The pod should have no tool loaded Does the Biomek Software deck match the above layout including the labware and their locations If yes choose OK to continue the method If no choose Abort to stop the method 1214 2003 3 51 04 PM Figure 2 17 Deck confirmation prompt for Quick Start method Beckman Coulter Inc Learning to Create Methods for the Biomek 3000 2 19 5 Choose OK The prompt closes and the method continues View the method on screen as it proceeds in the simulator The method can also be followed in the Method View as steps are highlighted in green as they are executed Note If you are running this method on your instrument instead of the simulator make sure that the physical deck layout matches the expected deck layout shown in the deck confirmation prompt before you choose OK You can proceed directly to Chapter 3 Using the Editors While Creating Methods to learn about the editors you ll use for customizing your methods Biomek 3000 Laboratory Automation Workstation Quick Start Guide Using the Editors While Creating Meth
48. ods 3 1 Overview This chapter presents step by step information to help you learn how to use the editors You can follow the instructions to use the editors or read through this chapter without performing the numbered steps Links to specific sections offer complete information on all the editors and allow you to use this chapter in conjunction with the Biomek Software User s Manual The editors allow your method to be customized to your special requirements You can go beyond the predefined project items and instrument configurations manually control the pod restore instrument settings and project files and configure external devices using specific editors The editors are accessed from the Project or Instrument menus located on the toolbar of the Biomek main editor Figure 3 1 This chapter includes the following information General Description of Editors Section 3 2 Creating New Labware in the Labware Type Editor Section 3 3 Creating a New Pattern Section 3 4 e Checking In a Method and Project File Section 3 5 e Using Hardware Setup Section 3 6 e Creating a New Deck Section 3 7 e Manually Controlling the Pod Section 3 8 Biomek 3000 Laboratory Automation Workstation Quick Start Guide 3 2 Using the Editors While Creating Methods 3 2 General Description of Editors Several editors are used to configure Biomek Software to control your Biomek 3000 If using Accounts a
49. oplate In of select Water_MP200_P200 as the liquid type if necessary Biomek Software comes with three liquid type definitions for water Water Water_MP20_P20 and Water_MP200_P200 You should always use the definition that includes the tool used for the transfer for best results Right click on the large tip illustration and choose Measure from Bottom Set the dispense height in the large tip illustration to 4 00 mm from bottom using the same technique as you used for setting the aspirate height Note If you accidentally open too many destination configurations all you have to do is right click on the title above the graphic of the plate in the configuration Click on Delete from the popup menu and the entire configuration goes away Learning to Create Methods for the Biomek 3000 2 13 The destination labware is now configured and the main editor looks like Figure 2 10 The Transfer step is now configured to transfer 100 uL from the source reservoir Resv to the destination microplate Dest1 Biomek Software Method1 New File Edit Project Instrument Execution Options Help PEACE CECE start Instrument Setup a Transfer 100 uL froi IB Finish Caption changes to reflect the amount transferred when the next step is configured 4 Use pod Podi z for transfer Load AP96_200uL tips change between sources and unload them when finished z
50. or checking in methods Enter a reason and your password to check in the method and project refer to the Biomek Software User s Manual Chapter 12 10 Checking In a Method Note Ifusing Accounts amp Permissions methods may also be validated by choosing Validate from the File menu see sidebar Using the Editors While Creating Methods 3 13 3 6 Using Hardware Setup While a Beckman Coulter Service Engineer normally installs and configures new devices in Hardware Setup it may be necessary for you to install configure and remove other devices using Hardware Setup if you change the configuration of your instrument You will also need to configure Hardware Setup if you have a new tool that you want to use with your Biomek 3000 instrument You will add a P200L Single Tip Pipette Tool to the list of tools available Adding a tool in Hardware Setup makes it available to add to a tool rack in the Instrument Setup step and use it in a method To add a new tool in Hardware Setup 1 Choose Instrument gt Hardware Setup Hardware Setup appears Figure 3 13 Biomek Hardware Setup 2 Reconnect Mf Home All Axes p Add Device s Remove Device lt Accept gt lt Cancel Biomek 3000 SN None Sanal Number OoOO O JK Podi Port T Gripper Add Device EP mp2oo Remove Device External Devices amp Stacker Carousels Reconnect Right click Tools bring up this menu Biomek300
51. precisely by using the up or down arrow keys on your keyboard while holding the Alt key You can also right click on the graphic then select from the menu that appears to adjust the height The source labware configuration is complete and the main editor now looks like Figure 2 9 Biomek Software Method1 New File Edit Project Instrument Execution Options Help PEZ BRS XBMloo a gt wi Start Q Transfer IB Finish Qik 3 2 Of o 3 5 fo z file uv we i FA o O S E Al a 2 Use pod Poat x for transfer Instrument Setup Load AP96_200uL tips change between sources and unload them when finished Source Resv Reservoir at Pesv x Using liquid type fwater_MP200_P200 x IV Auto Select Customize Saye As Technique Defaut z hay fd Stop when finished with Destinations Advanced Replicate each well 1 ae time 2 00 mm from bottom Overrides Techniquel Transfer Details Dispense up to 1 H tme per draw Aspirate at most fo pL per transfer for repeated dispensing Transfer Details Method1 Biomek3000 Biomek3000 ETC 0 00 03 Figure 2 9 Transfer step with source labware configured Biomek 3000 Laboratory Automation Workstation Quick Start Guide 2 12 Learning to Create Methods for the Biomek 3000 2 4 4 Configuring Destination Labware
52. ptions Help Dee BRS tLe oo a gt w Start Vv Clear current instrument setup of all labware Instrument Setup Clear current device setup of all labware Q ASE melOONe ig M siter the method completes Move Labware froi Vv Unload disposable tips from all pads and wash any fixed tips after the method completes after the method completes IV Clear all global variables after the method completes Error Message The error message is displayed in the status bar and as a tool tip Vu hod completes Feporting ETC Displayed as j Failed when Gh there is an error i i Tes l Error trying to aspirate from P2 Error in the Agpirate operation of theqpefault Template pipetting template Cannot liquid level sense with the current tool Method1 Biomek3000 Biomek3000 ETC Failed Jie RO our CR tun A Ue Cr Ces ree RU Me C E ele RG Figure 2 12 Quick Start method with error Biomek 3000 Laboratory Automation Workstation Quick Start Guide 2 16 2 7 Methods and Project Files Methods are saved as elements of a project file not as separate method files Saving a method only saves the current status of the method It does not create a revision or check in project items as revisions Refer to the Biomek Software Users Manual Chapter 6 Understanding and Using Project Files Learning to Create Methods for the Biomek 3001 r 6 Sav
53. s gives the instrument a point of reference from which to make subsequent moves The home position is to the left and back of the Biomek 3000 deck Beckman Coulter Inc 1 4 3 Homing All Axes of the Biomek 3000 Pod Every time the Biomek 3000 is turned on you ll have to Home All Axes This automatic process initiates the pod and defines the home position from which all subsequent moves are determined To home all axes 1 From the Instrument menu choose Home All Axes A Warning appears 2 Make sure that all warnings are addressed and choose OK The pod is homed and the instrument is now ready for use Proceed through this quick start guide while using the links to the user s manuals to learn more about the Biomek 3000 liquid handling system Learning to Create Methods for the Biomek 3000 2 1 Overview In this chapter you will be given information and instructions for building a small method using Biomek Software A method is a series of steps that control the operation of your Biomek 3000 The method you complete in this chapter represents basic operations and is intended simply to familiarize you with the Biomek 3000 and to create a basic understanding of method building opportunities Read the information in this chapter and complete the tutorial steps provided After you have completed the instructions or if you need additional information along the way use the links provided to access the suite
54. the following e Labware Type Editor allows you to add new labware types copy labware types delete labware types rename labware types and edit labware type properties refer to the Biomek Software User s Manual Chapter 7 Creating and Modifying Tip and Labware Types Note Refer to Section 3 3 Creating New Labware in the Labware Type Editor in this quick start guide to follow step by step instructions to create new piece of labware Tip Type Editor allows you to add new tips types remove tip types and change tip properties refer to the Biomek Software User s Manual Chapter 7 Creating and Modifying Tip and Labware Types Well Pattern Editor allows patterns for hitting specific wells to be created and stored refer to the Biomek Software User 5 Manual Chapter 11 Creating Well Patterns Note Refer to Section 3 4 Creating a New Pattern in this quick start guide to learn how to create a well pattern e Technique Browser allows you to customize techniques for your specific needs and save them for use in future methods refer to the Biomek Software User s Manual Chapter 9 Understanding and Creating Techniques e Liquid Type Editor allows you to create new liquid types or to modify existing liquid types refer to the Biomek Software User s Manual Chapter 8 Understanding and Creating Liquid Types Pipetting Template Editor allows you to create or modify pipetting temp
55. the pod using Manual Control To home all axes and move the head assembly using Manual Control 1 Choose Instrument gt Manual Control Manual Control appears Figure 3 19 Here is where you can choose to which position you want to move a pod Manual Control ft HH a re Advanced Controls Home All Axes Get Version Stop Exit Click on a position to move Podi to it Figure 3 19 Manual Control Biomek 3000 Laboratory Automation Workstation Quick Start Guide 3 18 Using the Editors While Creating Methods 2 Select Advanced Controls and highlight Pod1 Advanced Manual Control Pod1 appears Figure 3 20 Advanced Manual Control Pod1 Biomek 3000 Home Z XY Move Z Max i i om i tensi UnSqueeze Aspirate Sgueeze Dispense ajl Curent Postion x 53 925 cm Y 14 885 cm Z 10 74 cm D 0 23 cm Movement Vecto x fo cm Y fo cm Z jo cm D jo cm IV Auto Clear G Gea Speed 100 g Go Stop Figure 3 20 Advanced Manual Control for the Biomek 3000 head assembly 3 Select Move Z Max The head assembly moves to the highest configured height 4 Select Close Advanced Manual Control Pod1 closes 5 From Manual Control click on P5 The head assembly moves to position P5 on the deck 6 You can click on additional positions to move the pod to that position When you are finished moving the pod with Manual Control choose Exit to close Manual Control 7 From t
56. tors in the Biomek Software This chapter helps you to explore the depth of the software by giving instructions on accessing and learning more about the editors Biomek 3000 Laboratory Automation Workstation Quick Start Guide 1 2 Introducing the Biomek 3000 Laboratory Automati Beckman Coulter Inc 1 1 1 How to Use This Quick Start Guide Read through the quick start guide while using the links to the specific sections in the Biomek 3000 Laboratory Automation Workstation User s Manual and Biomek Software User 5 Manual to further investigate topics that are particularly relevant to you Moving back and forth between this guide and the user s manuals you will be able to begin to learn about the Biomek 3000 instrument and software and also become familiar with the manuals and how chapters are arranged This quick start guide can also be used as a tutorial since you ll be given instructions on creating a small method refer to Chapter 2 Learning to Create Methods for the Biomek 3000 and utilizing the editors refer to Chapter 3 Using the Editors While Creating Methods Some of the items you ll create in Chapter 3 may be viewed in the method you created in Chapter 2 In addition to the explanations graphics and links to other sources you will see other useful information in the following forms Definition These boxes contain brief definitions of material that may be specific to the Biomek
57. u create a new method by dragging a step into the Method View the Start and Finish steps appear automatically You will use an Instrument Setup Step to tell Biomek Software where you have physically placed labware on your deck Before proceeding with this quick start method make sure that e an MP200 Multi Tip Pipette Tool and Gripper Tool are added in Hardware Setup refer to Section 3 6 Using Hardware Setup e the deck layout in the Deck Editor contains at least one GripperToolRack one ManualLatch and four Biomek3000Positions refer to Section 3 7 Creating a New Deck Note If your instrument configuration does not have a gripper tool a standard ToolRack position can be used instead of the GripperToolRack e the deck is framed refer to the Biomek 3000 Laboratory Automation Workstation User s Manual Chapter 13 Framing the Biomek 3000 Beckman Coulter Inc Learning to Create Methods for the Biomek 3000 2 3 You launched Biomek Software in Chapter 1 you are now going to create a small method 1 Drag and drop an Instrument Setup into the Method View A new method is created and assigned the default name Method1 New Figure 2 1 Biomek Software Method1 New i loj x File Edit Project Instrument Execution Options Help PEZECO CETL amp Start Deck Deck x nea Instrument Setup Labware Category lt Any gt Setup IB Finish Step Configur
58. visions of project items required to run the validated method are also checked in and protected from further modification This ensures that validated method runs are reproducible Refer to the Biomek Software User s Manual Chapter 12 15 Checking Out a Method Beckman Coulter Inc Using the Editors While Creating Methods Checking In a Method and Project File Checking in a method is similar to saving a method but also creates a revision record of the method and checks in all project items of the project file and creates new revisions for any items that have changed You will check in your Quick Start method along with the new labware and well pattern you just created To check in your method with the new labware and well pattern 1 From the File menu choose Check In Check In appears with the new labware type and well pattern Select the project items to check in Project Item Modified Time E amp Labware Classes V NewlabwareQuick Labware Patterns V LabwareQuickStart Change Modified 11 21 2003 3 49 55 PM Modified me Figure 3 12 Check In 11 21 2003 3 51 02 PM 2 Choose OK to check in the new revisions of project items Notice that the method name in the Biomek main editor title bar changes to Quick Start Method Revision 1 Development If Accounts amp Permissions is enabled other dialogues appear and more steps are required f

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