Biomek 3 Migration Guide

1
Biomek 3 Migration Guide

• For Migrating From Biomek FX Software To Biomek 3
  Software

2
Biomek 3 Migration Guide

• Table Of Contents
• Support necessary for Biomek 3
• PC requirements
• SQL Server Personal Edition
• Operating system and Internet Explorer version
• Administration rights

3
Biomek 3 Migration Guide

• Table of Contents (continued)
• Whats new with Biomek 3
• New Features with brief summary
• Snapshot of differences
• Where are files located at now?
• 21 CFR Part 11 Compliance Overview
• Structure of Project file and Methods
• Converting Biomek Techniques, labware, etc to
  Biomek 3

4
Biomek 3 Migration Guide

• Table of Contents (continued)
• Converting Biomek FX methods to Biomek 3 methods
• Wizards and AAO
• Custom Integrations, Custom Scripts, and Core
  Systems
• Multiple Workspaces
• FAQ
• Accounts and Permissions

5
Support Necessary For Biomek 3

• Minimum PC required to support Biomek 3 software
• Pentium IV 2.0 GHz
• 512 Mb of memory
• Video card capable of displaying 1024 x 768
• 100 Mb of hard drive space
• Networking enabled

6
Support Necessary For Biomek 3

• Windows NT4 sp6a and IE 5.5 with scripting
  enabled
• -or-
• Windows XP sp1 and IE 6.0 with scripting enabled
• SQL Server Personal edition
• SQL Server 2000 provides a powerful and
  comprehensive data management platform
• Personal Edition is ideal for stand-alone
  applications that require local SQL Server data
  storage on a client computer
• This is installed on new Beckman Coulters
  Controllers otherwise, it is the customers
  responsibility to provide this
• Administrator rights necessary for the
  installation of the Biomek 3 software only

7
Whats New With Biomek 3

• Operating system
• Windows NT, Windows XP
• Administrator password rights is required for
  installation only, but no longer needed to run
  the software
• Backwards compatibility with Biomek FX

8
Whats New With Biomek 3

• 21 CFR Part 11 Compliance Option
• The password protect scheme for Biomek FX is
  replaced with a new protection feature complying
  to 21 CFR part 11 specification
• Other features added are
• Better collision avoidance
• Integrated HDR support
• Easier sample tracking and reporting
• Aspirating and Dispense speeds in ?l/s
• Hardware setup now a part of the editor

9
Whats New With Biomek 3

• The Workspace has been replaced with a separate
  Instrument file and a Project file
• The Instrument file is specific to the hardware
  of the instrument (pod settings, deck framing,
  etc.)
• The Project file contains the methods, labware
  definitions, techniques, and the rest of the
  support information

10
Differences
11
Where Are The Files In NT4
12
Where Are The Files In XP
13
21 CFR Part 11

• Beckman Coulter Accounts Permissions are an
  integrated set of features built into Beckman
  Coulter software that assists users in complying
  with 21 CFR Part 11 requirements for closed
  systems
• Support is extended only for the Biomek
  instrument devices integrated with the Biomek
  instrument are not supported unless specified in
  separate documentation

14
21 CFR Part 11

• A separate installation program is provided to
  enable Accounts and Permissions support
• Beckman Coulter Accounts Permissions support
  may be installed before or after the Biomek
  software is installed on the system
• Users require a separate account for each system
  they need to access
• It is the Customers responsibility to have
  processes in place to govern all system
  administration activities, as specified in the 21
  CFR Part 11 regulation

15
21 CFR Part 11

• For more information on 21 CFR Part 11 features
  please refer to the Biomek Software Users Manual,
  Section 2.1 Using Accounts and Permissions
• For more information on 21 CFR Part 11
  specifications please visit the following
  website
• http//www.FDA.gov/cdrh/aboutcfr.html

16
Workspace

• The Workspace file that contained all Biomek FX
  settings is now separated into two files in
  Biomek 3 software
• Instrument file
• Project file

17
Instrument File

• The Instrument file contains files specific to
  the hardware of the instrument
• Deck Layout
• Framing tools
• Pod settings
• For more information about the Instrument file,
  see Using Instrument Files and Setting, Section
  3.1 of the Biomek Software Users Manual

18
Importing Instrument Parameters

• To transfer the Instrument settings from one PC
  to another, use the Import/Export Utility located
  in the the Instrument menu
• For more information, see Using the Import/
  Export Utility, Section 3.4 Sharing Instrument
  Settings of the Biomek Software Users Manual

19
Importing Instrument Parameters Precautions

• When importing from the Biomek FX workspace, it
  will be necessary to do two imports, one for the
  decks and one for Biomek FX system parameters
• DO NOT import any of the other Instrument
  settings such as Framing tools and Pod settings
  at this time. The installation service engineer
  should have already completed this task

20
Importing Biomek FX Decks

• Launch Biomek 3 Software
• Click Instrument gt Import/Export Utility

21
Importing Biomek FX Decks

• Click Open
• Select the import file you wish to use
• Click Open

• Select the decks to import
• Click Import

22
Project File

• The Project file is a database that contains the
  following Biomek FX system information
• Labware and tip type definitions
• Well patterns
• Pipetting techniques, liquid types and pipetting
  templates
• Methods
• For more information on Projects, see
  Understanding and Using Project Files , Section 6
  of the Biomek Software Users Manual

23
Importing Biomek FX Parameters

• Labware definitions, technique settings, etc.
  created in Biomek FX Software can be transferred
  from one system to another using the Import
  Project and Export Project located in the the
  Project menu
• The default Project is called BiomekFX

24
Importing Biomek FX System Parameters
Precautions

• DO NOT import the entire WORLD file. It will
  overwrite the changes made in Biomek 3 software
• It is not possible to export system parameters
  created in Biomek 3 into older versions of the
  Biomek FX software

25
Importing Biomek FX Parameters

• Launch Biomek 3 Software
• Click Project gt Import Project

26
Importing Biomek FX Parameters

• Select the import file to use click Open

27
Importing Biomek FX Parameters

• Select the individual items to import by clicking
  on the box in front of the item
• When finished selecting, click OK

28
Whats new with Biomek 3 Pipetting Speeds in
?l/sec

• It is necessary to convert the aspirate and
  dispense speeds on ALL techniques and liquid
  types which you imported
• In Biomek FX 2.5 software, aspirate and dispense
  speeds were in percents
• To convert to ?l/sec, multiply the percentage
  times the 1 ?l per sec speed
• (Ex. 60 x 1.486(1 speed for P200 head) 88.8
  ul per sec on an AP96/P200 head)
• The next slide provides the minimum and maximum
  speed for the different heads and syringe sizes

29
Pipetting Speed for Biomek FX Systems
30
Whats New With Biomek 3 Methods

• In Biomek 3 Software, all Biomek FX Methods are
  part of the Project File
• Methods are no longer separate files
• Do not reside in C\Program Files\Biomek
  FX\Methods
• Methods created in Biomek FX software can be
  transferred from one system to another using
  Import located in the the File menu
• For more information on Importing Methods, see
  Importing Methods to a Project File, Section
  12.16.3 of the Biomek Software Users Manual

31
Methods created in Biomek FX Software
Precautions

• Biomek FX methods imported into Biomek 3 software
  should be verified after importing
• If your Biomek FX methods are password protected,
  it will not cause any problems when importing
  them. Biomek 3 import will ignore the password
  protection when importing the method
• It is not possible to export methods created in
  Biomek 3 into older versions of the Biomek FX
  software

32
Converting Biomek FX Methods

• Launch Biomek 3 Software
• Click on File gt Import

33
Converting Biomek FX Methods

• On the file name line, type .bmt and then press
  enter
• Select the methods to import
• Click Open

34
Converting Biomek FX Methods

• Click Yes to import the methods to the current
  project

35
Converting Biomek FX Methods

• Click Yes to import the corresponding project
  items for each method
• Note Imported Biomek 2.x methods will not have
  project items linked to them. So you can answer
  either yes or no

36
Biomek FX Methods created by third party vendors

• If you have obtained Biomek FX methods created by
  third party vendors, please contact them directly
  to verify the software version
• If methods need to be converted to Biomek 3
  software, all methods should be verified after
  importing

37
Whats New With Biomek 3 Creating and Saving
Methods

• Methods are created and executed in the same
  manner as in previous versions of the software
• Methods are not saved as a separate file (.bmt)
  and are now part of the current project
• Saving a method will only save the method and not
  any current version labware or other project
  items associated with it
• For more information on Creating and Saving
  Methods, see Creating and Using Methods, Section
  12 of the Biomek Software Users Manual

38
File gt Save

• Similar to File gt Save in Biomek FX v2.5
• Saves current method to the Project database
  overwrites the existing saved method
• Changes made to project items after the method is
  saved will be utilized by the method the next
  time its opened

39
File gt Save As

• Similar to File gt Save As in Biomek FX v2.5
• Saves a method to the Project database
• Changes made to project items after the method is
  saved will be utilized by the method the next
  time its opened

40
Opening a Saved Method

• Similar to File gt Open in Biomek FX v2.5
• Changes made to project items will be utilized by
  the method

41
Exporting Saved Methods

• Saved methods can be exported using the Export
  command
• Select File gt Export

42
Whats New With Biomek 3 Check In Methods

• The Check In feature will do the following
• Save the method
• Creates a new revision of the method
• Saves selected Project items such as labware
  definitions techniques with the method
• For more information on Creating and Saving
  Methods, see Creating and Using Methods, Section
  12 of the Biomek Software Users Manual

43
Check In Methods

• Methods can be checked into a Project file by
  selecting File gt Check In
• Changes made to project items after the method is
  saved will NOT be utilized by the method the next
  time its opened

44
Method History

• Method history can be viewed for methods that
  have been checked into the Project File
• Select File gt History

45
Opening a Checked In Method

• Similar to File gt Open in Biomek FX v2.5
• Changes made to project items will NOT be
  automatically utilized by the method

46
Opening a Checked In Method

• If project items has been changed since the
  method was checked in, there are three options
• Get Latest
• Opens method using the most recent project items
• Open Read-Only
• Opens method in read-only mode using the saved
  project items
• Method can only be run, not edited in read-only
  mode
• Cancel
• Method is not opened

47
What Is New With Biomek 3 Saving vs. Check In
Methods
48
Check Out Methods

• Methods that are checked into a Project File can
  be checked out by selecting File gt Check Out
• Allows any revision of the method to be opened in
  a read-only mode

49
Exporting Checked Out Methods

• Select File gt Export
• Save methods as .bmf files

50
What Is New With Biomek 3 Home All Axes

• Home All Axes option in the Instrument Menu
• initializes the Biomek FX system
• Home All Axes is still an option under Manual
  Control in the Hardware Setup

51
What Is New With Biomek 3 Hardware Setup

• The Hardware Setup is now located within the
  Biomek FX software
• No longer have to close the Biomek FX software to
  access the Hardware Setup

52
What Is New With Biomek 3 Hardware Setup

• Users cannot access the following options within
  Hardware Setup
• Manual Control
• Deck Editor
• Device Editor
• Import/Export Utility
• For more information on the Hardware Setup, see
  Configuring Hardware Setup, Section 4 of the
  Biomek Software Users Manual

53
What Is New With Biomek 3 Simulator Software

• The simulator software is now part of Biomek 3
  software
• To access the simulation display, click on the
  following icon

54
What Is New With Biomek 3 Technique Browser-Group

• In the Technique Browser, you can add a file
  folder called a Group to assist in organizing
  pipetting techniques
• For more information on the Technique Brower
  Group, see Understanding and Creating Techniques,
  Section 9 of the Biomek Users Manual

55
What Is New With Biomek 3 Error Options

• Located in Options gt Preferences
• Upon a error during a run, a user can specify two
  options
• play a sound
• Launch a program

56
Things that Have Moved Project Menu

• The following options that used to reside in the
  Tools menu in Biomek FX software is now located
  in the Project Menu

57
Things that Have Moved Instrument Menu

• The following options that used to reside in the
  Tools menu in software is now located in the
  Instrument Menu

58
Things that Have Moved Execution Menu

• The following option that used to reside in the
  Tools menu in software is now located in the
  Execution Menu

59
Things that Have Moved Options Menu

• The following options that used to reside in the
  Tools menu in software is now located in the
  Options Menu

60
No Longer Available Pod Editor

• If you want to alter the Pod settings, select
  Instrument gt Hardware Setup
• Select the Pod and click on Additional Pod
  Settings
• Configure the Pod as Needed

61
No Longer Available Method Tool Passwords

• Method and Tool Passwords are no longer available
  in Biomek 3 software
• It has been replaced with 21 CFR Part 11
  compliance tool
• Account and permissions

62
Wizards

• The following Wizards are no longer supported in
  Biomek 3 software
• Hit Picking Wizard
• Plate Replication Wizard
• Promega Single Plate Plasmid DNA Miniprep Wizard
• Promega 1-2 Plate Plasmid DNA Miniprep Wizard
• Promega 12 Plate Plasmid DNA Miniprep Wizard
• QIAGEN Single Plate Plasmid DNA Miniprep Wizard
• Quantitation Normalization Wizard

63
Wizards

• The following will have new wizards created
  specifically for Biomek 3 software
• Hit Picking
• Quantitation Normalization
• Contact your Beckman Coulter representative to
  check on availability

64
AAOFX

• AAOFX version 1.0 will not function with Biomek 3
  software
• A new version will be developed for Biomek 3
• Contact your Beckman Coulter representative to
  check on availability

65
eLab Notebook Biomek FX Methods

• Biomek FX methods available on eLab Notebook are
  currently not validated for Biomek 3 software
• When available, new methods for Biomek 3 software
  will be posted on the eLab Notebook website

66
eLab Notebook Biomek FX Software Downloads

• The following Biomek FX software download files
  available on eLab Notebook have not been
  validated for 3 software
• Additional Beckman Pump Installation
• Simulator Software (2.5 and earlier)
• OCX Software
• When available, new download files for Biomek 3
  software will be posted on the eLab Notebook
  website

67
Biomek 3 Core System Integration

• Biomek 3 requires a new SILASTM module to
  interface with the SAMI software
• Contact your Beckman Coulter representative to
  check on availability

68
Biomek 3 Device Integrations

• Cytomat, SPECTRAmax and ELx405 integrations
  require new installation modules to support
  Biomek 3
• Contact your Beckman Coulter representative to
  check on availability

69
Biomek 3 Custom Integrations

• Custom device integrations developed on previous
  versions will not operate on Biomek 3
• Contact Beckman Coulter Sales to explore your
  options

70
Biomek 3 Scripting

• With changes made in Biomek 3 software scripts
  created in previous versions will not function
  properly
• Scripting support is provided by your Beckman
  Coulter Project Manager

71
Reference Manual

• Refer to the Biomek Software Users Manual for
  more details and descriptions of the features
  listed in the Migration Guide
• Manual can be found at
• Start/Sagian Software/Biomek Software Users
  Manual

72
FAQ

• Error message encountered during migration and
  how to respond to them

73
FAQs Device Question 1

• Question My Cytomat hotel does not seem to work
  with my Biomek 3 software. Why is this
  happening?
• Answer A new step installation is required for
  Biomek 3 software. Please contact your local
  Beckman Coulter representative to check on
  availability of the new step.

74
FAQs Labware Question 1

• Question I created labware in Biomek FX
  software and imported into the Project folder,
  but now I cant find it. Why is this happening?
• Answer The labware may have been imported into
  a different Project file. To check to see if
  other Project files contain the labware in
  question, click on Project gt Open Project. Open
  a different Project folder and then select
  Project gt Project Contents. Check to see if the
  labware resides in this project folder, if not
  continue searching through the remaining Project
  files. Once the labware has been located, you
  will want to export the labware to your desired
  Project file.

75
FAQs Methods Question 1

• Question I have a method created in Biomek FX
  software. When I double click on the file to
  launch the software, Biomek 3 software will
  launch but my method does not appear. Why is
  this happening?
• Answer This is occurring since Biomek FX
  methods are now part of the Project File. To
  open Biomek FX methods, you must use the Import
  option located in the File Menu. This will
  import your method into a Biomek 3 method.

76
FAQs Methods Question 2

• Question When I use the File gt Open option, I
  cannot locate my method or browse for my method.
  Why is this happening?
• Answer Two possible reasons
• Method has not been imported into the Project
  File
• If this is the case, use the Import option
  located in the File Menu. This will convert your
  method into a Biomek 3 method.
• Method is located in a different Project File

77
FAQs Methods Question 3

• Question I cannot find my method when I go into
  C\Program Files\Biomek FX\Methods. Where are
  they?
• Answer This is occurring since Methods are now
  part of the Project File. You must use the Open
  option located in the File Menu.

78
FAQs Methods Question 4

• Question I have a method created in Biomek FX
  software that contains script. I imported the
  method over and the script step is no longer
  working. Why is this happening?
• Answer Scripting is not a supported feature and
  with the changes made in Biomek 3 software, there
  is no way to guarantee that custom scripting will
  still function as intended. Please check with
  the creator of the custom script for assistance.

79
FAQs Methods Question 5

• Can you convert methods from Biomek FX 1.5 to
  Biomek 3 software?
• Answer Yes, you can using the Import option in
  the File menu.

80
FAQs Operating System 1

• Can you use Windows 2000 with Biomek 3 software?
• Answer Windows 2000 service pack 3 and IE 5.5
  with scripting enabled.

81
FAQs Wizard Question 1

• Question My Hit Picking Wizard does not appear
  when I select File gt Method Wizard. Why is this
  happening?
• Answer This is occurring since Biomek 3
  software does not support this version of the Hit
  Picking wizards. Please contact your local
  Beckman Coulter representative to check on
  availability.

82
FAQs Wizard Question 2

• Question My Promega 1-2 Plate Plasmid DNA
  Miniprep Wizard does not appear when I select
  File gt Method Wizard. Why is this happening?
• Answer This is occurring since Biomek 3
  software does not support this version of the
  wizards. Biomek FX version 2.5 software will
  support software wizards. Please contact your
  local Beckman Coulter representative for
  assistance in converting back to Biomek FX
  version 2.5 software.

83
FAQs World Question 1

• Question I imported my entire World file into
  Biomek 3 software and it doesnt seem to be
  working. Why is this happening?
• Answer The world file has overwritten the
  changes made in Biomek 3 software. Please contact
  your local Beckman Coulter representative for
  assistance.

84
FAQs World Question 2

• Question I currently have multiple workspaces,
  what can I do to keep this information separate
  in Biomek 3 software?
• Answer You can still have them except now they
  will be called Projects. The one exception to
  this is that when importing the decks they should
  all be put in the same Instrument file.

85
Accounts and Permissions

• An integrated set of features built into the
  Beckman Coulter software that assist users in
  complying with 21 CFR Part 11 requirements for a
  closed system
• For more information on Account and Permissions,
  see Using Accounts and Permissions, Section 2 of
  the Biomek Software Users Manual

86
AP Support Options

• No Support
• User login not utilized
• Accounts and Permissions
• User login required with password
• Accounts and Permissions with password
• User login required with password
• Signature security enabled for database write
  access.

87
AP Administrator

• Administrator Access
• Administrative Tools\Beckman Coulter Accounts
  Permissions Administrator

88
AP Administrator Login

• Administrator Login
• Password protected
• Only one administrator account supported

89
AP Account Management

• Accounts Tab
• Create and configure user accounts permissions

90
AP Global Settings

• Settings Tab
• Configure global account options

91
AP Audit Log

• Audit Tab
• Account Manager history log

92
AP User Login

• Start the Biomek Software
• Enter the User name and Password

93
AP User Log Off

• Select to log off user