Biomek User s Guide. Beckman Part No AA April 1998

Transcription

1 Beckman Part No AA April 1998 Biomek 2000 User s Guide Beckman Instruments, Inc N. Harbor Blvd., Fullerton, CA Copyright 1998 Beckman Instruments, Inc. Printed in U.S.A.

2 Copyright Copyright, Licenses and Trademarks Beckman Instruments, Inc., All rights reserved. No part of this publication may be reproduced, transcribed, transmitted, or translated into any language in any form by any means without the 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 authorization from Beckman Instruments.

3 User s Guide Table of Contents Notice Safety Notice Safety During Installation...vii Electrical Safety...vii Safety Against Risk of Fire...viii Chemical and Biological Safety...viii Moving Parts...viii Cleaning...ix Maintenance...ix Accessory 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 Intended Use Theory of Operation Workstation Components Automation Features Modular Platform for Easy Upgrades Pipette and Wash Tools Accessories BioWorks Interconnect Diagrams Safety Features Biomek 2000 i

4 User s Guide Table of Contents Safety Precautions Safety During Installation Electrical Safety Safety Against Risk of Fire Chemical and Biological Safety Moving Parts Cleaning Maintenance Accessory Safety Side Loader (SL) SL Incubator High-Density Replicating System Plate Reader Wash System Heater-Cooler Block Biomek 2000 Safety Features Principles of Operation General Information The Edit Module Creating a Method Setup, Initial Configuration, and Default Configuration Setup Initial Configuration Default Configuration Placing Labware on the Worksurface Specifying a Method Step (Action) Error Messages During Labware Placement Pipette Transfers Source Destination Tool Options Tip Handling Options Advanced Options Printing Methods Mix and Serial Transfer Pipetting Functions Mix Serial Transfer Tip Handling Functions Tip Change Reset Tip Rack Wash Tool Functions Wash ii Biomek 2000

5 Table of Contents User s Guide Aspirate Bulk Dispense Purge Labware Moves Manual Moves Automatic Moves Editing Existing Methods Saving Methods Running a Method Alarms and Suppress All Alarms Verify Configuration Save Preferences Dry Run Stop and Quit Functions Functional Verification and Self Diagnostics Performance Characteristics and Specifications Basic Operating Procedures Basic Operating Procedures Editing the BioWorks Demo Method Changing the Initial Configuration Viewing and Editing a Transfer Function Adding a Transfer Function Inserting Messages and Pauses Saving a Method Running a Method Recommended Maintenance Procedures Maintenance Procedures General Information Weekly Perform a Position Calibrate Perform Check Disk Verify the Alignment Points Check Finger Pads for Wear Monthly Semi-Annually (Every Six Months) Calibrate Pipetting Tools Biomek 2000 iii

6 Table of Contents User s Guide Parts, Supplies and Accessories Diagnostics Overview General Information United States Sales Telephone Number World Wide Web Biomek 2000 iv

7 Notice Notice This equipment has been tested and found to comply with the limits for a Class A digital device, pursuant to part 15 of the FCC rules. These limits are designed to provide reasonable protection against harmful interference with the equipment is operated in a commercial environment. This equipment generates, uses, and can radiate radio frequency energy and, if not installed and used in accordance with the instruction manual, may cause harmful interference to radio 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 without prior consent, in writing, from Beckman Instruments, Inc. Biomek and Beckman are registered trademarks of Beckman Instruments, Inc. BioWorks and BioScript are trademarks of Beckman Instruments, Inc. Microsoft and MS-DOS are registered trademarks and Windows is a trademark of Microsoft Corporation. Biomek 2000 v

8 Notice vi Biomek 2000

9 Safety Safety Notice The exclamation mark (contained in a triangle) is an international symbol displayed to indicate to the user that all safety instructions should be read and understood before installation and operation are attempted. When you see the safety notice symbol on the instrument or on one of its accessories, you should refer to this manual for specific safety information that applies. If the product is used in a manner other than specified in the manual, the safety and performance of the equipment could be impaired. Any installation or service procedures not described in this manual must be performed by qualified service personnel. Safety During Installation Do not lift the Biomek 2000 by the bridge. Two people are 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 receptacle is properly wired and 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 than the type supplied for the accessory for the Biomek 2000, as appropriate for the country where it is installed. Biomek 2000 vii

10 Safety Safety Against Risk of Fire Certain electrical circuits within this equipment are protected by fuses against over-current conditions. For continued protection against risk of fire, replace fuses only with the same type and rating specified. Chemical and Biological Safety Normal operation of this equipment sometimes involves the use of reagents which are toxic, flammable, or biologically harmful. When using such reagents, observe the following precautions: Infectious samples must be handled according to good laboratory procedures and methods to prevent the spread of disease Observe all cautionary information printed on the original solution containers prior to their use All waste solutions must be disposed of according to your facility's waste disposal procedures Liquid transfers may generate aerosols. Operate the Biomek in an appropriate enclosure and take all necessary precautions when using biohazardous, pathologic, toxic, or radioactive materials Objects dropped onto plates, accidental tool release, or other accidental collisions may result 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 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 exchange labware, reagents, or tools while the instrument is operating, as indicated by the amber safety light at the end of the bridge. When the light is on, the workstation is in operation and may move suddenly and rapidly at any moment. A beep sounds just prior to initial movement to provide additional warning Never attempt to physically restrict the movement of the head and bridge assembly. 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 Run window to stop the instrument if the stop is not an emergency viii Biomek 2000

11 Safety Because the parts of the Biomek move automatically, keep clear of the head assembly during operation. Also, keep the area around the workstation clear (including the expansion area) to prevent obstructing the movement of the instrument Always check the position of the tools and labware before beginning any stage of the method to ensure that their locations on the worksurface match those given on the window. Also, check that the labware is properly seated on the worksurface before beginning an operation. Cleaning You may clean the spill trays of the Biomek worksurface and the nozzles of the Wash tools. Please observe the following precautions: Be careful when handling the Wash tools as the nozzles are sharp. Contact your laboratory safety officer and refer to the guidelines in the section titled "Chemical and Biological Safety" if you will be cleaning spill trays that may have been exposed to hazardous solutions. Maintenance 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. 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 requesting service by a Beckman Field Service Representative or returning parts to Beckman for repair. Beckman will NOT accept any items which have not been decontaminated where it is appropriate to do so. If any parts are returned, they must be enclosed in a sealed plastic bag stating that the contents are safe to handle and are not contaminated. Do not replenish bleach in a sterilization reservoir using the aspirate and bulk dispense transfers, as the bleach may damage the Wash tool. Accessory Safety Follow the appropriate safety instructions for the accessories listed below in addition to the standard safety precautions for the Biomek Biomek 2000 ix

12 Safety Side Loader (SL) Verify that the voltage selector is set for current voltage by a Beckman Representative at the time of installation. During method operation, DO NOT touch, change, or otherwise interfere with labware on the worksurface, stacks, or in the SL hand unless the system tells you to. The arm can move suddenly. Stay clear of the arm and hand during operation. Keep the area around the SL clear of any obstructions to avoid collisions. There is a Stop switch at the base of each Stack Area. If an emergency stop is required, pressing this on each stack area of your SL switch will freeze the SL instantly. CAUTION The Stop switch on the SL will not stop the workstation, nor will the Stop switch on the workstation stop the SL. NOTE: You may lose data and be forced to quit the run in progress if you press the SL Stop switch. Use of the SL stop switch may result in spillage 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 emergency. SL Incubator Operating the incubator at 4 C for longer than twenty-four hours may result in ice formation within the chamber, adversely affecting temperature equilibrium and assay results. Do NOT place the incubator in stack location "C" as the incubator may inhibit access to the Stop switch of the SL in the event of an emergency. Allow enough time for the incubator to reach the desired temperature to ensure reliable assay results (typically less than one hour, depending on the circulator and desired temperature). Use 50% polyethylene glycol and 50% water as the conductive fluid in the water circulator. Maximum inlet pressure to the SL Incubator is 5 psig (34.5 kpa). When cleaning the incubator wear protective gloves and eyewear. x Biomek 2000

13 Safety High-Density Replicating System The High-Density Replicating (HDR) System is not autoclaveable, nor should you use organic solvents to clean the system. However, you can autoclave the pins of the HDR Tool and use organic solvents to clean the pins. If you are using the bleach tray within the tool holder, remove the HDR Tool from the bleach tray and rinse thoroughly after each session. Do NOT store or let the HDR Tool stand in the tool holder with its pins immersed in bleach when not in use. Extended contact with bleach will result in corrosion of the metal pins. Plate Reader Refer to the Plate Reader User's Manual from the original manufacturer (Molecular Devices Corp.) for maintenance and service information. There are no user-serviceable components under the cover. Change lamps only with the power off. Never touch any of the fiber optic cables or their housing, manifold, or rotor connections. These fibers are extremely delicate and critical to the performance of the Plate Reader. Use only 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 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 Switch of the SL in the event of an emergency. Use only locations 1F1 or 2F1 on the SL. To prevent fluid from dripping off the microplate when it is in the reading chamber onto any sensitive optical elements, and to minimize potential biohazard exposure to other Plate Reader users, observe the following precautions: When reading microplates that may have fluid on the underside of the microplate, damp-dry the underside using a dry paper towel (or equivalent) before putting the microplate on the drawer. Alternatively, place a clear sheet (such as a Molecular Devices blanking template) underneath the microplate when inserting it in the drawer. Biomek 2000 xi

14 Safety Wash System Never run the 6-Port Valve dry. Liquid should always run through the 6-Port Valve. Failure to do so can result in damage to the valve. Strong acids, strong bases, oxidizers, radioactive and biohazardous liquids should not be run through the Wash Unit. Each laboratory must qualify this instrument with its unique application(s). Plug any unused port with the plugs provided with the 6-Port valve. Otherwise liquid may spill through exposed ports when the 6-Port valve is used. When using a Wash tool, make sure a quarter reservoir is installed properly in the support block under the tool. Heater/Cooler Block Failure to provide cooling water to the Heater/Cooler Block (HCB) will cause excessive and potentially dangerous 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 Block 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 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 front of the instrument. Press this switch to stop the Biomek. Also the warning light at the top of the bridge warns you that the instrument is operating, and emits a beep before the initial movement in a method. When this light is on do NOT attempt to change labware. Summary of Warning Information This manual is provided to help you establish safe conditions for performing the maintenance and servicing of your equipment. Specific considerations and precautions are also described in the manual, but appear in the form of Warnings, Cautions, and Notes. It is important that you service your equipment in accordance with this instruction manual and any additional information which may be provided by Beckman. Address any questions regarding the safe and proper maintenance and servicing of your equipment to your nearest Beckman Sales and Service Center. xii Biomek 2000

15 Chapter 1 Introduction User s Guide Chapter 1 One Introduction Intended Use The Biomek 2000 Laboratory Automation Workstation is designed to meet the needs of rapidly changing life science technology with simple, intelligent automation of liquid-handling tasks. Pipetting, diluting and dispensing operations are performed quickly, easily and automatically. The modular platform allows expansion of system capability to include plate heating and cooling, plate washing, high-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 laboratory techniques All methods are validated for consistency System configurations are automatically verified Potential conflicts are detected by the software Workstation Components The major components of the Biomek Workstation are shown in the diagram on the following page. Biomek

16 User s Guide Chapter 1 Figure 1: Biomek 2000 Laboratory Automation Workstation 1 Head Assembly 5 Worksurface 2 Back Support 6 Bridge 3 Side Module (both sides) 7 Safety Light 4 Front Rail Automation Features The Biomek provides the following features which simplify and automate routine and repetitive laboratory operations: Automatically monitors and tracks pipette tip usage, both between and within runs 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 1-2 Biomek 2000

17 Chapter 1 User s Guide Modular Platform for Easy Upgrades Worksurface capacity expands by up to 50% with optional side modules Workstation fits in a laminar flow or fume hood for sterile or hazardous operations Options such as the Plate Reader are directly controlled by the Biomek workstation The high-capacity Side Loader (SL) System and SL Incubator provide maximum capacity, temperature control and extended periods of unattended operation Communication ports and software communication links provided Pipette and Wash Tools The 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 provide effective tracking of liquid levels using a patented sonic liquid-sensing technology. This method accurately detects microliter volumes of both conductive and non-ionic liquids. Single and multichannel wash tools, when used with the Biomek Wash system, provide an efficient and automated method of dispensing bulk quantities of reagents and replenishing reservoirs. Biomek

18 User s Guide Chapter 1 Tools are summarized in the table below: Pipette Tools Nom. Volume Range Max. Reach P20 Single-Tip Tool 1-20µL 100 mm P200L Single-Tip Tool 5-200µL 100 mm P1000L Single-Tip Tool µL 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 Wash-8 Eight-Channel Tool 1 x 50µL to 1 x 150 ml 8 x 50µL to 8 x ml 40 mm 40 mm HDR Tools Pin Diameter Nominal Sample Density* 96-Pin HDRT 384-Pin HDRT or in. 3,456 (small pin) or 1,536 (large pin) or in. 3,456 (small pin) or 1,536 (large pin) *Number of samples spotted onto a microplate-sized area (approximately 9 x 13 cm). For complete operating specifications and application information, contact your Beckman Representative. 1-4 Biomek 2000

19 Chapter 1 User s Guide Accessories A variety of options are available to customize the operation of the Biomek to suit your laboratory's specific requirements. You can select options for handling of large volumes of samples, high-density replication transfers, collection of optical density data, incubation of samples, filtration applications, or any combination of the above. Optional side modules can be added to expand the worksurface capacity by up to 50%. The Side Loader System automates high volume sample handling, and when used with the optional incubator, provides temperature control for unattended operation. A Plate Reader may be mounted on the Side Loader or workstation for reading microplates. Filter plates may be processed with the Vacuum Valve Unit and the 96-Filtration System. Options provided by Beckman are directly controlled by the Biomek workstation. Communication 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 user interface which is used to design, run, and monitor methods. Other integrated modules provide alignment, diagnostic, and troubleshooting functions. Context-sensitive help screens are available for most functions and general help is provided for all modules. All methods are validated for consistency, system configurations are automatically verified, and potential conflicts are detected by the software. Interconnect Diagrams The following diagrams show the interconnection of the Biomek Workstation with the PC controller, and other additional options. Refer to the Biomek 2000 Hardware and Software Installation Manual for complete installation instructions, or contact your local Beckman Field Service Engineer. Biomek

20 User s Guide Chapter 1 Figure 2: Connecting the Biomek Workstation to the Computer 1-6 Biomek 2000

21 Chapter 1 User s Guide Figure 3: Connecting the Biomek Workstation to the Side Loader Controller Biomek

22 User s Guide Chapter 1 Wash Unit Plate Reader HCB Controller Figure 4: Connecting the Biomek Workstation to the Plate Reader, Wash Unit, and HCB Controller Safety Features An 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. 1-8 Biomek 2000

23 Chapter 1 User s Guide Stop Button Figure 5: Emergency Stop Switch CAUTION Never attempt 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. Biomek

24 User s Guide Chapter Biomek 2000

25 Safety Precautions User s Guide Chapter 2 Two Safety During Installation Do not lift the Biomek 2000 by the bridge. Two people are 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 receptacle is properly wired and 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 than the type supplied for the accessory for the Biomek 2000, as appropriate for the country where it is installed. Safety Against Risk of Fire Certain electrical circuits within this equipment are protected by fuses against over-current conditions. For continued protection against risk of fire, replace fuses only with the same type and rating specified. 2-1

26 User s Guide Chapter 2 Chemical and Biological Safety Normal operation of this equipment sometimes involves the use of reagents which are toxic, flammable, or biologically harmful. When using such reagents, observe the following precautions: Infectious samples must be handled according to good laboratory procedures and methods to prevent the spread of disease. Observe all cautionary information printed on the original solution containers prior to their use. All waste solutions must be disposed of according to your facility's waste disposal procedures. Liquid transfers may generate aerosols. Operate the Biomek in an appropriate enclosure and take all necessary precautions when using pathologic, toxic, or radioactive materials. Objects dropped onto plates, accidental tool release, or other accidental collisions may result 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 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 exchange labware, reagents, or tools while the instrument is operating, as indicated by the amber safety light at the end of the bridge. When the light is on, the workstation is in operation and may move suddenly and rapidly at any moment. A beep sounds just prior to initial movement to provide additional warning. Never attempt to physically restrict the movement of the head and bridge assembly. 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 Run window to stop the instrument if the stop is not an emergency. Because the parts of the Biomek move automatically, keep clear of the head assembly during operation. Also, keep the area around the workstation clear (including the expansion area) to prevent obstructing the movement of the instrument. 2-2 Biomek 2000

27 Chapter 2 User s Guide Always check the position of the tools and labware before beginning any stage of the method, to ensure that their locations on the worksurface match those given on the window. Also, check that the labware is properly seated on the worksurface before beginning an operation. Cleaning You may clean the spill trays of the Biomek worksurface and the nozzles of the Wash tools. Please observe the following precautions: Be careful when handling the Wash tools as the nozzles are sharp. Contact your laboratory safety officer and refer to the guidelines in the section titled "Chemical and Biological Safety" if you will be cleaning spill trays that may have been exposed to hazardous solutions. Maintenance 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. 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 requesting service by a Beckman Field Service Representative or returning parts to Beckman for repair. Beckman will NOT accept any items which have not been decontaminated where it is appropriate to do so. If any parts are returned, they must be enclosed in a sealed plastic bag stating that the contents are safe to handle and are not contaminated. Do not replenish bleach in a sterilization reservoir using the aspirate and bulk dispense transfers, as the bleach may damage the Wash tool. Accessory Safety Follow the appropriate safety instructions for the accessories listed below in addition to the standard safety precautions for the Biomek Biomek

28 User s Guide Chapter 2 Side Loader (SL) Verify that the voltage selector is set for correct voltage by a Beckman Representative at the time of installation. DO NOT touch, change, or otherwise interfere with labware on the worksurface, stacks, or in the SL hand unless the system instructs you to do so. The arm can move suddenly. Stay clear of the arm and hand during operation. Keep the area around the SL clear of any obstructions to avoid collisions. There is a Stop button at the base of each Stack Area. If an emergency stop is required, pressing this on each stack area of your SL button will freeze the SL instantly. CAUTION The Stop button on the SL will not stop the workstation, nor will the Stop button on the workstation stop the SL. NOTE You may lose 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 window 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 affecting temperature equilibrium and assay results. Do NOT place the incubator in stack location "C" as the incubator may inhibit access to the Stop button of the SL in the event of an emergency. Allow enough time for the incubator to reach the desired temperature to ensure reliable assay results (typically less than one hour, depending on the circulator and desired temperature). Use 50% polyethylene glycol and 50% water as the conductive fluid in the water circulator. Maximum inlet pressure to the SL Incubator is 5 psig (34.5 kpa). When cleaning the incubator wear protective gloves and eyewear. 2-4 Biomek 2000

29 Chapter 2 User s Guide High-Density Replicating System The High-Density Replicating System (HDR System) is not autoclaveable, nor should you use organic solvents to clean the system. However, you can autoclave the pins of the HDR Tool and use organic solvents to clean the pins. If you are using the bleach tray within the tool holder, remove the HDR Tool from the bleach tray and rinse thoroughly after each session. Do NOT store or let the HDR Tool stand in the tool holder with its pins immersed in bleach when not in use. Extended contact with bleach will result in corrosion of the metal pins. Plate Reader Never touch any of the fiber optic cables or their housing, manifold, or rotor connections. These fibers are extremely delicate and critical to the performance of the Plate Reader. Use only 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 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 Button of the SL in the event of an emergency. To prevent fluid from dripping off the microplate when it is in the reading chamber onto any sensitive optical elements, and to minimize potential biohazard exposure to other Plate Reader users, observe the following precautions: When reading microplates that may have fluid on the underside of the microplate, damp-dry the underside using a dry paper towel (or equivalent) before putting the microplate on the drawer. Alternatively, place a clear sheet (such as a Molecular Devices blanking template) underneath the microplate when inserting it in the drawer. When reading filter bottom microplates where fluid may drip off the filter membrane, place a clear sheet under the microplate (such as a Molecular Devices blanking template) when inserting it in the drawer. Biomek

30 User s Guide Chapter 2 Wash System Never run the 6-Port Valve dry. Liquid should always run through the 6-Port Valve. Failure to do so can result in damage to the valve. Strong acids, strong bases, oxidizers, radioactive and biohazardous liquids should not be run through the Wash Unit. Each laboratory must qualify this instrument with its unique application(s). Plug any unused port with the plugs provided with the 6-Port valve. Otherwise liquid may spill through exposed ports when the 6-Port valve is used. When using a Wash tool, make sure a quarter reservoir is installed properly in the support block under the tool. Heater-Cooler Block Failure to provide cooling water to the heater/cooler block will cause excessive and potentially dangerous 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 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 button is located on the front of the instrument. Press this button to stop the Biomek. Also, the warning light at the top of the bridge warns you that the instrument is operating, and emits a beep before the initial movement in a method. When this light is on, do NOT attempt to change labware. 2-6 Biomek 2000

31 Chapter 3 Principles of Operation User s Guide Chapter 3 Three General Information The following sections are intended to provide an overview of the operation of the Biomek Workstation. They are not meant as a comprehensive reference of features and functionality, but rather as an introductory reference to help you become familiar with the operational principles. For complete information on each of the software features, refer to the BioWorks Software Reference Manual. Note: When running Biomek methods, do not import or export methods 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 deleted using the Lab Book Manager only. The Edit Module The Biomek uses methods to define the actions that the workstation performs. These methods are created using the Edit module, within the BioWorks program group. Biomek

32 User s Guide Chapter 3 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. 3-2 Biomek 2000

33 Chapter 3 User s Guide You can select one of the methods provided with the software by selecting Method 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. Biomek

34 User s Guide Chapter 3 Method List of Actions Function Palette/ Labware Bar Setup Button Biomek 2000 Worksurface Creating a Method When you create a method, you specify the actions that the workstation will perform using the Edit module. You use the function buttons on the Function Palette to specify a function (such as a pipetting 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. 3-4 Biomek 2000

35 Chapter 3 User s Guide When you specify a function in this manner, you are usually presented with a dialog which you then use to define the specifics of the operation. For example, if you are defining a pipetting operation, you will indicate the volume to be pipetted in the dialog. Setup, Initial Configuration, and Default Configuration Setup The Setup function is used to identify (to the software and the Biomek) which accessories, 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, Disposal units, or a Plate Reader. Note The Setup button allows you to change the configuration for a specific method. If you want to make a more global change to all of the methods in a lab book, use the Install program, available from the BioWorks Program Group. Biomek

36 User s Guide Chapter 3 As an example, you may add a Plate Reader to your system, or you may want to move it from a location on the left side of the worksurface, to a position on the Side Loader. This is done through Setup. You may also want to take the Side Loader out of the setup for a particular method because it is not being used for that particular 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 method is always Initial Configuration. When you highlight this line in the method window, the starting layout of the labware is shown on the worksurface window. Initial Configuratiom 3-6 Biomek 2000

37 Chapter 3 User s Guide The workstation setup can only be changed when you are in the Initial Configuration of the method (that is, you have highlighted the Initial Configuration line). If you change the workstation setup at any other time, the system will assume that it is a manual or automatic move and add the step to 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: Default Configuratiom Worksurface The worksurface is then displayed. Place the items that you want to appear in the Default Configuration on the worksurface just as you would for a method. Biomek

38 User s Guide Chapter 3 To save this configuration as the Default Configuration, go to the Method menu and choose Save As. Verify that the method name is specified as Default Config. The name must be typed exactly as shown for BioWorks to recognize this as a default configuration. Click OK to save the configuration. When you open a new method, you will be 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 within that category. Specifying a Method Step (Action) First, click the desired function icon on the Function palette. In this example, the Mix at Location icon is selected. Mix at Location Icon 3-8 Biomek 2000

39 Chapter 3 User s Guide 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. Biomek

40 User s Guide Chapter 3 The resulting method steps will appear in the Method List of Actions, as demonstrated below: Method List of Actions Error Messages During Labware Placement When you are placing labware on the worksurface, you may see a number of different types of messages, regarding 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 specific volume of liquid from one place on the worksurface to another Biomek 2000

41 Chapter 3 User s Guide The Pipette Transfer icon button is shown below and is found on the Function Palette: Pipette Transfer Icon When you have placed 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. Biomek

42 User s Guide Chapter 3 Information pertaining to the source labware (used for aspiration) is on the left of the screen, and information pertaining to the destination labware (or destination) is on the right. Transfer volume, tool and tip options are located in the center of the screen. The fields that you will edit on this screen are summarized below: Source Aspirate Height sets the height the tip goes into the labware. The range is from -10% to 110%, where 0% is at the bottom of the labware well and 100% is at the top. Some tool and tip combinations cannot go all the way to the bottom of certain types of labware, in which case the range will be limited by BioWorks. Liquid Level options are Fixed, Liquid Level Sensing, or Liquid-Level Tracking. Fixed means that on each visit to the source labware, the tip will go to the programmed aspirate height. Sensing will determine where the liquid is in a well, then aspirate the volume just below the surface (miniscus). Sensing is only available with the P200L and P1000L tools. These tools sense the liquid level and automatically determine the aspirate height. Sensing is used on each visit 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 aspirate in the Depth field. This may be useful to aspirate the lower level of a two-phase solution. Sensing also detects whether or not a tip is present, and will also reject dirty tips. Always use clean tips with liquid sensing. Hint You should usually use a tip depth of 5mm to 10mm to ensure that only liquid is aspirated from the well. A setting of 0mm can cause problems due to aspiration of air. Tracking means that on the first visit to the well, the tip goes to the programmed height. On subsequent visits, the system will calculate the distance to move down based on the volume of liquid it aspirated on the previous visit, and the shape of the labware. This feature is useful if a full tube is to be emptied with multiple aspirations, because no liquid will remain on the tip, and the liquid will not be spilled out on the first visit. Hint Set the first height well below the actual level to ensure that all liquid is aspirated, and to avoid aspiration of air Biomek 2000

43 Chapter 3 User s Guide Aspirate Rate can be set from 1 to 10. Note that the scale is logarithmic, with lower numbers being slower. A setting of 6 is quite slow. Prewet causes the system to pipette extra liquid into and out of the pipette tip before aspirating the specified volume. This can reduce surface tension between the liquid and the pipette tip. The actual volume used for prewetting is programmed in the Tool Edit window. Tip Touch is used to remove liquid from the outside of the tip after the aspiration by touching the tip to the side of the well. Tip touch is done at a height which is preset for each individual type of labware. Mix settings are on a pop up window which appears when you click Mix Values. The mix feature aspirates and dispenses for a specified number of times (cycles) to mix solutions. Selecting Mix allows you to specify a mix routine function in either the source or destination range. The Mix occurs prior to aspiration. For many liquids, you should aspirate from the bottom of the well and dispense near to the top at a rate of 10 to optimize mixing. Ranges and Patterns are used to set the wells that the tool will visit in the source labware. Range is a contiguous set of wells. You specify the sequence of wells with a direction 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 the destination range has been filled. Repeat Same Labware can be used at both the source and the destination. Repeat Next Labware completes the range at the source then waits for the next piece of labware on the worksurface at the same location. (This does not mean that the source range is repeated at the labware next to the original source.) Move the next piece of labware into position using either a manual move or an automatic move (with a Set Shelf command) if a Side Loader is present. Marks are used to tell the system where the last transfer finished in the range so that the system can resume the range on subsequent transfers and not return to the beginning of the range. You can use the following options for setting marks: Use no Marks is the default setting. Set a New Mark marks the well where the next pipetting function at that piece of labware is to begin. Use an Existing Mark starts the system at the current mark. This does not move the mark after the transfer is complete. Use then Set New Mark starts the system at the current mark and moves the mark after the transfer. Biomek

44 User s Guide Chapter 3 Marks are invisible to the user. Marks stay with the labware, no matter where the labware is moved. This is particularly useful when a Side Loader or Gripper Tool is used to move labware on the worksurface. Marks cannot be used with a serial transfer. Destination Most functions at the destination are similar to the corresponding source functions. By default, there are three different tool types (categories) for each pipetting tool: contain, deliver and repeat. Note: Make sure the tool type matches the delivery type selected at the destination. Each tool type has been optimized for a specific delivery type. The differences are noted below: Delivery Type can be selected as one of the following: To Contain causes the tip to pick up the requested volume and dispense that volume. This is usually used in conjunction with the blowout setting to ensure that all of the liquid is expelled from the tip. Please note that the tool name "contain" is 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 Blowout provide the most accurate delivery. Another related option, Repeat Pipette, is controlled from the Advanced screen, discussed later. Replicates are used to dispense to multiple wells from a single source well (or set of wells for multi-tip tools). Replicates are entered using the spin box. The highlighted wells on the range are linked by a line indicating the replicates chosen. The replicate number must be divisible into the total range selected. For single tip tools, the replicate number is linked to repeat pipetting (discussed later). The direction of the pipetting action selected will influence the direction of the replicates. Marks are handled the same at the destination, as at the source. All marks can be cleared using the Clear Marks icon on the function palette, as shown on the next page Biomek 2000

45 Chapter 3 User s Guide Tool Options Tool shows the default tool selected by the system based on the tools available in the initial configuration and the labware in use. For example, a multi-tip tool will not be used by default if a 24 tube rack is used as the source. If multiple compatible tools are available, then the first compatible tool in the tool list (alphabetically) is the default. Hint To select a specific tool before calling up the pipetting screen, click on the tool in the tool rack before clicking on the source and destination. This tool will then be 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 for all transfers After Transfer changes the tip after each transfer At End of Row/Column changes the tip when the end of the a row or column is reached, whichever comes first. For a multi tip tool, this is identical to After Transfer At New Replicate changes the tip before a new replicate Discard Tips releases the tips into the Disposal chute after use. Otherwise, tips are returned to the tip rack. Biomek

46 User s Guide Chapter 3 Tip Source allows you to select the label of a tip rack to use. Tip racks are used from left to right, and from an A row to a B row by default. 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 Biomek 2000

47 Chapter 3 User s Guide The following Advanced screen contains the options for delays and repeat pipetting. To return to the Basic options, click on the Basic button near the bottom of the screen. Repeat Pipetting is a single pick-up, multi-dispense mode of pipetting. The volume entered is the volume of each delivery, not the total volume to be delivered. For single-tip tools, the repeat count may be less than or equal to the replicate number but can be no greater than the replicate number. Also, the number used for Repeat Count multiplied by the volume per tip must be less than or equal to 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 to which all subsequent delays are compared and all subsequent transfers are to begin on the beat. For example, if the biomek arrives at the start of a transfer early, it waits for the next beat, which is balance of of the delay from the start of the last transfer. If the biomek is late (i.e., because it changed tips) it executes the transfer immediately. If it is still late, it executes transfers until it catches up with the beat. Biomek

48 User s Guide Chapter 3 Printing Methods A method must be saved in order for the latest changes to be printed. Mix and Serial Transfer Pipetting Functions Mix These specialized pipetting functions are also available from the function palette. These are described below. 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 Biomek 2000

49 Chapter 3 User s Guide Serial Transfer The Serial Transfer icon button is shown below: Serial transfers occur only within one 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: Biomek

50 User s Guide Chapter 3 Tip Handling Functions The following tip handling functions are also available from the function palette. Tip Change The Tip Change icon button is shown below: A tip change can be programmed between functions rather than included within a pipetting function. This allows you to specify a tip change function between two consecutive functions that do not include a tip change. If the second function has a tip change programmed within it and the first does not, then 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 optimize tip usage. You use the Reset Tip Rack dialog to indicate how many tips in the rack have been used. Tips are numbered starting with tip #1 as the tip in the upper left-hand corner, tip #2 immediately below it in the same column, and so on. Setting this value to zero causes the system to use all of the tips in the rack as new Biomek 2000

51 Chapter 3 User s Guide Wash Tool Functions There are four icons related to Wash Tool functions. These icons are only active if the Wash Unit has been selected through Setup in the Initial Configuration (see pg. 3-5). Wash The Wash icon button is shown below: The Wash function allows you to wash a plate using either the Wash 1 or the Wash 8 tool. If the Six Port Valve option is installed, then a specific buffer can also be selected for the wash operation. Many of the operations controlled from the Wash dialog are similar to the Pipette Transfer dialog. Those that are not are described below. Source Reagent specifies a reagent 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. Aspirate Height and Dispense Height are the same as for pipetting, except that the values refer to the height of the longer aspirate needle on the tool. Aspirate The Aspirate icon button is shown below: The Aspirate function uses the wash tools to remove liquid from a plate or tubes using the vacuum source. Duration controls the length of time that the valve is open and liquid is removed from the source. (The Aspirate function is based on time, not on volume.) Biomek

52 User s Guide Chapter 3 All of the other parameters are the same as for pipetting and wash operations. Bulk Dispense The Bulk Dispense icon button is shown below: Bulk dispense uses the wash tool to dispense liquid to a plate or a tube. The volume dispensed in a bulk dispense operation is not as accurate as with a pipette transfer, but it is quicker because the tool does not have to visit the source labware. Aspirate Excess turns on the vacuum briefly to bring 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 buffer. To use this function, click the Purge icon in the Function Palette, then click the tool in the Tool Rack to be purged. Source Reagent indicates which buffer the tool is to be purged with. Purge Volume controls the volume of buffer to purge with. Purge Rate sets the rate of the peristaltic pump Biomek 2000

53 Chapter 3 User s Guide Labware Moves The Move icon button is shown below: All labware moves in a method, whether manual or automatic, are controlled by the Move icon on the Function Palette. If a Side Loader or Gripper Tool is present, then the system assumes an automatic move, if the labware and locations are compatible. Manual Moves This section describes manual moves, which require an operator intervention to move, remove, or replace labware. Automatic Moves are covered in the next section. To add a manual move to a method, click on the Move icon then click the piece of labware to be moved. Then click the destination for the labware. If you want to remove a piece of labware from the worksurface, use the Remove icon on the labware bar (in the Other group) to perform this function. Automatic Moves When a Gripper Tool is present on the system, you 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 also use the Side Loader to remove lids, and to dispose of used labware and lids into the SL Disposal unit. All of these functions are added to a method through the Move icon. First you click the Move icon, then click the labware to be moved, then click the destination. If you selected a piece of labware which currently has a lid, you will be prompted to select whether you want to move only the lid or to move the lid and labware. Other prompts may also appear to allow you to further specify exactly what you want to move. Both the Gripper Tool and the Side Loader are also capable of moving plates to and from the optional Plate Reader when it is installed in a compatible location. Biomek

54 User s Guide Chapter 3 Editing Existing Methods One of the simplest ways to write a method is to copy an existing one, then change it to suit your needs. The following guidelines apply to editing methods: Open the method you want to edit and then use the Method/Save As command to save a copy of it under another name. This keeps the original method intact. When adding a step to a method, use the highlight line (in the method edit window) to select the step which will follow your new step(s). When you add a step to a method, it is always added above the line which is highlighted. If you want to change the setup of the method, you must highlight the Initial Configuration line of the method. 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 will also notice a check box at the bottom of the Save dialog labeled Save Unvalidated. Validation is a system of internal checks done on a method to ensure that there are no conflicts with tools, labware, or other problems. When this box is unchecked (the default) the Biomek automatically validates each method when it is saved. If you are making an interim save (that is, the method is not yet complete but you want to save what you have so far) you should check this box so that the system does not attempt to validate the method Biomek 2000

55 Chapter 3 User s Guide If validation fails, the method is not saved and a message is displayed to explain the source of the failure. You must correct the problem before you will be able to validate the method. Note that you must successfully validate a method before it can be run. Running a Method The Run icon button is shown below. This icon is found on the icon bar at the top of the BioWorks Edit window. Once you have saved your method and validated it, you can run it using the Run module. If you are in the Edit module, you can simply click the Run icon button in the toolbar to bring up the Run dialog and begin running the method. Note: After the method is run, a ".txt" file will be created in the root- BioWorks directory. 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 alarms when an error occurs that causes the system to shut down (such as a collision). Method Fatal alarms when the method must be aborted, such as when a stall is detected. Method Halt alarms when the method has stopped but can be restarted after a user intervenes (to provide more tips, for example). Method Pause alarms when the method has paused for a programmed user intervention. Warnings alarms when a warning message is posted. No intervention is required and the method continues. Select the Suppress All Alarms option if you want to disable all of the alarms. Biomek

56 User s Guide Chapter 3 Verify Configuration When this option is enabled, the user will be prompted to verify the setup of the labware and tools on the worksurface when a run begins. (A view of the worksurface is displayed when the Start button is clicked to begin a run.) Save Preferences All the settings for the above options can be saved so that they are used for each method run by selecting this option. Dry Run This turns off the Tool Type identification and liquid level sensing for the run. This allows you to test the method run without reagents. Stop and Quit Functions You can stop (pause) or quit a method from the run display. Stop stops the method at the point 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 immediately. Functional Verification and Self Diagnostics The power-up software performs the following diagnostic checks: confirms connection of the cable between the workstation and the computer verification of the checksum for the EPROM performs a check of the ROM checks the first 1 MB of RAM If an error is detected, an error code is displayed through the diagnostic LEDs located on the workstation. Contact an authorized Beckman service engineer for additional information if a power-up error is detected Biomek 2000

57 Chapter 3 User s Guide Performance Characteristics and Specifications Performance characteristics for the pipette tools are shown below: Tool 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 Pipetting Precision Biomek

58 User s Guide Chapter Biomek 2000

59 Chapter 4 Basic Operating Procedures User s Guide Chapter 4 Four Basic Operating Procedures Note This manual does not attempt to address all of the functionality available with the BioWorks operating software for the Biomek Rather, this section provides a number of tutorial examples 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 Edit icon in the BioWorks program group. This displays the Edit window, as shown on the next page. Biomek

60 User s Guide Chapter 4 The name 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. 4-2 Biomek 2000

61 Chapter 4 User s Guide Select Lab Book Biomek

62 User s Guide Chapter 4 This displays the Select Lab 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. 4-4 Biomek 2000

63 Chapter 4 User s Guide Biomek

64 User s Guide Chapter 4 BioWorks loads the method, then displays the Method, Function Palette, and Worksurface windows, as shown below. Before we begin editing the method, let s review some important features of the Edit window and its "child" windows: Make sure that the Initial Configuration line in the Method window is highlighted before you begin placing or moving labware on the worksurface. 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 specific item. Then place the labware on the desired location on the Worksurface window. To delete an item of labware from the Worksurface, click on the item, then press the Delete key. (You will be prompted for confirmation.) 4-6 Biomek 2000

65 Chapter 4 User s Guide When adding or placing labware on the worksurface, you may receive a Possible Collision error message. If this occurs, this does not necessarily mean that you cannot use that position for that labware. However, you should carefully consider whether or not the adjacent labware will cause a conflict based on the information in the warning message. If in doubt, consider using another arrangement. If you add, delete, or remove labware when any other line of the method is highlighted, BioWorks will consider this a labware move, and will function accordingly. 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 the Method is highlighted. Then, click on the Plates button of the Labware bar, then scroll through the list and select the 96-well flat bottom plate. The cursor becomes a rectangle (to represent the plate). Place the rectangle on position B4 to add a third plate to the initial configuration. The new configuration, with the 96-well plate located in position B4 of the worksurface, is shown on the following screen. Biomek

66 User s Guide Chapter 4 Viewing and 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. 4-8 Biomek 2000

67 Chapter 4 User s Guide In this function, 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. Biomek

68 User s Guide Chapter 4 Double-click on the second function (the third line) of the method to display 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% 4-10 Biomek 2000

69 Chapter 4 User s Guide When you are done, click on OK to exit this dialog, then click on OK again from the Pipette Transfer 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. Biomek

70 User s Guide Chapter 4 The cursor s shape changes to a pipette symbol. Click on location A2 to designate the source, then click on location B4 for the destination. The Pipette Transfer dialog is displayed. Set the options on the dialog as follows: Make sure the Tool is set to P200L Set the volume to 100µl per tip Set the Source Labware Action to Range and the Direction to By Row. Use the cursor to highlight the top row of wells on 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 source wells (to fill each with a different source) or change the Source End Action to Repeat Same Labware (which would reuse the source wells until all of the destination wells were filled). Select a Tip Touch at the source and at the destination Select Fixed for Liquid Level 4-12 Biomek 2000

71 Chapter 4 User s Guide The dialog should look like the one shown on the following screen (patterns for the destination plate may be different). Click OK to add this step to the method. Inserting Messages and Pauses You can also insert 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 System button (shown on the next page), located on the function pallette. Biomek

72 User s Guide Chapter 4 This displays the System Pause/Message dialog. Select the dialog items 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.) 4-14 Biomek 2000

73 Chapter 4 User s Guide Now, insert the system pause between the message and the next pipette transfer. Highlight the second pipette transfer line in the method (note that 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 finished. Biomek

74 User s Guide Chapter 4 Saving a Method Before proceeding, 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 Biomek 2000

75 Chapter 4 User s Guide Running a Method Before you run a method for the first time on a new Biomek, you must perform an alignment check and re-align the Biomek (and Side Loader) if necessary. Refer to the Biomek 2000 Hardware and Software Installation Guide for alignment instructions. 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 set up your worksurface appropriately, click on the Accept All button to accept the worksurface configuration. Biomek

76 User s Guide Chapter 4 The method will begin, and the Method Run screen will be displayed, showing a list of actions performed during the method run Biomek 2000