Bio-rad Microplate Manager Software Manual do Utilizador

P/N 4000138 RevBMicroplateManager ® 5.0 PCUser GuideBio-RadLaboratoriesLife ScienceGroup2000 Alfred Nobel DriveHercules, CA 94547

xFigure 37. Ultramark reader door controls. ...54Figure 38. Reports dialog box for endpoint an

Microplate Manager User Guide90Figure 65. Limits dialog box.Limits are assigned independently for each assay in a protocol. When there is morethan on

Chapter 6. Data Formatting and Reports91Matrix ReportFigure 66. Matrix Report.The Matrix Report is similar to the Limit Report (see above), except t

Microplate Manager User Guide92Control ReportFigure 67. Control Report.The Control Report displays absorbance or velocity data for each well as aperc

Chapter 6. Data Formatting and Reports93Normalization ReportFigure 68. Normalization Report.The Normalization Report displays absorbance or velocity

Microplate Manager User Guide94Standard Curve ReportFigure 69. Standard Curve Report.The Standard Curve Report displays the absorbances of the standa

Chapter 6. Data Formatting and Reports95defined, they are plotted together with their respective regression curves (althoughonly the external standar

Microplate Manager User Guide96Unknown Concentrations ReportFigure 70. Unknown Concentration ReportThe Unknown Concentrations Report shows the calcul

Chapter 6. Data Formatting and Reports97To change curve fit options or axis types, open the Standard Curve Report andselect the desired regression me

Microplate Manager User Guide98If there is a significant difference between standard curves that should be essentiallyidentical, the user should inves

Chapter 6. Data Formatting and Reports99quadratic, or cubic polynomial regression, because of the oscillatory nature of theresultant fit. In these ca

11. IntroductionThis manual assumes that you are familiar with your computer and standardWindows commands and functions, such as opening, closing, and

Microplate Manager User Guide100variation, and the ratio of the explained variation to total variation becomes 1.000.Or, more simply, the closer the c

1017. Data OutputThis chapter describes Microplate Manager’s functions for printing reports andexporting data.7.1 PrintingAll the reports may be prin

Microplate Manager User Guide102½ To automatically print reports immediately after a reading has been performed,click on the Reports... button in a p

Chapter 7. Data Output1037.2.1 Exporting DataAll text-based data and reports may be exported as tab-separated values or ascomma-separated values. You

Microplate Manager User Guide104Figure 73. Export to Excel dialog box.Select the Excel formatting features you want, and click on OK to export your d

Chapter 7. Data Output105Line (4 + (# of rows) * (# of cols)): <rowN:colN><tab><rowN:colN><tab>...<tab><rowN:colN>

Microplate Manager User Guide106Line ((reading# - 1)*(# of rows + 2) + row# + 4):<row1:col1><tab><row1:col2><tab>...<tab>

1078. Quick Guides8.1 Creating a New TemplateSee Chapter 4 for details.1. Choose New Template > 12 x 8 from the FILE menu.2. Choose Assay from th

Microplate Manager User Guide108a. Select Standard Curve Report or Unknown Concentration Report fromthe VIEW menu.b. Use the tabs to select the assay.

Chapter 8. Quick Guides1095. Click Analysis Options to set the kinetic analysis parameters.6. Save the protocol by choosing Save Protocol or Save Pro

Microplate Manager User Guide2Figure 1. Workflow of Microplate ManagerMicroplate Manager can perform three general types of microplate readings. Thes

Microplate Manager User Guide110c. Close the Reports dialog box to return to the kinetic protocol.5. Click on Analysis Options to set the kinetic anal

Chapter 8. Quick Guides1117. At the end of the run, save the data by choosing Save Data/Template or SaveData/Template As... from the FILE menu.8.5 C

Microplate Manager User Guide1126. Initiate the protocol by clicking on Run.7. At the end of the run, save the data by choosing Save Data/Template or

Chapter 8. Quick Guides1137. At the end of the run, save the data by choosing Save Data/Template or SaveData/Template As... from the FILE menu.8.7 C

Microplate Manager User Guide114b. Also click on Fill Labels... to enter the text to be printed along with thelabels on each report.c. Close the Repor

1159. GlossaryAssay: A set of wells grouped together for analysis.Blank: A well used for background subtraction.Endpoint analysis: Analysis based on a

11710. Ordering InformationCatalog Number Product Description170-9520 Microplate Manager, Version 5.0170-9521 PC/Microplate Reader Interface Cable Set

119IndexAnalysis options for kinetic readings, 61AssaysAnnotating, 36Defining, 34Description, 32Editing, 35Communications Setup, 9Computer and operati

Chapter 1. Introduction3Finally you take the reading. If you want to use the particular protocol you’ve createdagain, you can save it as a file.Once

Microplate Manager User Guide120Absorbance delay, 68Filenames of readings, 67Initial wait, 65Stack loader settings, 66New features, 4Outliers, identif

Index121Stack loaders, 66Standard curvesComparing external and internal, 97Description of, 98Displaying, 94Limitations, 100Standards, externalChecking

123Appendix A. MenusThe pulldown menus in Microplate Manager change depending on the particular partof the application you are using. For example, if

Microplate Manager User Guide124Close closes the current file. All windows associated with the current file areclosed. If the file has been modified,

Appendix A. Menus125Edit Standard Conc... opens a form in which you can enter concentrations ofstandards.Edit Outliers... opens a dialog box in which

Microplate Manager User Guide126FormatThis menu is available only when a template is active:Assay changes the pointer to a tool for defining the area

Appendix A. Menus127Ultramark Setup... opens a dialog box in which you can enter filters for theUltramark microplate reader.Model 550 Setup... opens

Microplate Manager User Guide128All open windows are listed at the bottom of the menu. The activewindow is indicated by a check mark. When more than n

Microplate Manager User Guide4Data FilesThe data file contains the raw data from the microplate reader. It has the extension.mpm.For an endpoint readi

Chapter 1. Introduction5• Major improvements in associating protocols and templates.• More flexibility in tagging outliers in replicate sets.• Up

72. Installation and Setup2.1 Instrument Specifications2.1.1 Host Computer and Operating SystemMicroplate Manager will run under Windows 95, Windows

Microplate Manager User Guide8A serial cable is included with the Model 550 or Benchmark and is used to connectthe instrument to the host PC. Make sur

Chapter 2. Installation and Setup92.5 Starting Microplate ManagerTo start Microplate Manager, click on the application icon on your desktop or selec

Catalog Number 170-9520Bio-Rad Technical Services DepartmentOpen Monday–Friday, 8:00 a.m. to 4:00 p.m., Pacific Standard Time.Phone: (800) 424-6723, o

Microplate Manager User Guide10When you open a protocol, Microplate Manager will look first for a reader at theserial port you select. If a reader is

Chapter 2. Installation and Setup11Click on OK to implement your changes.2.7.2 Model 550 SetupSelect Model 550 Setup from the OPTIONS menuFigure 5.

Microplate Manager User Guide12Figure 6. Preferences dialog box.In the Preferences dialog box, you can enter or select the Default File Location foro

Chapter 2. Installation and Setup13When you are finished making your selections, click on the OK button.2.9 Sample Data FilesSix sample data files a

153. Getting Started3.1 Menus, Toolbars, and Other FeaturesMenu BarMicroplate Manager has a standard menu bar with pulldown menus that include allth

Microplate Manager User Guide16Right-click CommandsYou can access many of the commands associated with the action you are currentlyperforming by using

Chapter 3. Getting Started173.2 Opening and Saving FilesMicroplate Manager has two basic file types: Protocol files and data files. Protocolfiles ha

Microplate Manager User Guide182. Open Microplate Manager.3. Under the FILE menu, select New Endpoint Protocol, New Kinetic Protocol, orNew Multiple P

Chapter 3. Getting Started19Figure 10. Performing an endpoint reading.You have a data file saved from a previous run with the template you want to u

iiiWarrantyBio-Rad Laboratories warrants that the Microplate Manager software shallsubstantially conform, in all operational features, to Bio-Rad’s cu

Microplate Manager User Guide20Scenario 2. Kinetic AssayYou want to perform a new kinetic assay. From the FILE menu, you select NewKinetic Protocol.

Chapter 3. Getting Started21Scenario 3. Using External Standards and Curve ComparisonsYou are running the same assay on many samples. To increase th

Microplate Manager User Guide22Figure 12. Comparing external and internal standards.

234. TemplatesTemplates allow you to specify the number of wells (Ultramark only) and the layoutof the standards, unknowns, controls, etc. on your mic

Microplate Manager User Guide24dialog box. Select the appropriate directory and double-click on the template file toopen it.Template files have a .mpm

Chapter 4. Templates25Creating a Custom Template Format½ This feature is only available to users of the Ultramark.If the layout of your microplate i

Microplate Manager User Guide26Figure 15. Defining the format of a plate.In the Define Plate Format dialog box, you can enter the numbers of Columns

Chapter 4. Templates27Figure 16. Entering the physical dimensions of your plate.In the Physical Dimensions dialog box, you can enter the distance in

Microplate Manager User Guide28When you have specified the physical dimensions of your plate, click on the OKbutton.4.2 Viewing the TemplateYou can d

Chapter 4. Templates29Information about Individual WellsAnother source of information about your template is the Well Info dialog box. Toopen this di

ivthis manual and the software program contained herein may not be copied, in wholeor in part, without the prior written consent of Bio-Rad, except in

Microplate Manager User Guide30Figure 19. Blank 12 x 8 template.Using the template toolbar, you define the wells that contain your standards,unknowns

Chapter 4. Templates31• Customized name for each assay.• Notes about each assay to be printed on reports.• Type of regression for each assay.• Ty

Microplate Manager User Guide32Figure 20. Example of a plate template with two different assays defined.Replicate GroupsA replicate group is a group

Chapter 4. Templates33Concentrations and Dilution FactorsConcentrations of standards and dilution factors for unknowns may also be enteredusing separ

Microplate Manager User Guide34Some additional assay-related commands are located on the EDIT and ASSAYmenus.Undo and Redo Formatting CommandsIf you m

Chapter 4. Templates35Figure 22. Defining an assay with the Assay tool.When the mouse is released, a new assay will be created, and all the wells in

Microplate Manager User Guide36Figure 23. Assay Information dialog box.Each assay will have its own tab. Click on the tab of the assay you want to ch

Chapter 4. Templates37You can then click and/or drag on your template to define your well types.Clicking on a particular well will mark that well as

Microplate Manager User Guide38Figure 25. Defining a replicate groups of unknowns.Dragging across another group of wells will assign those to a secon

Chapter 4. Templates39Figure 26. Defining multiple standard replicate groups in a row.If you drag across multiple rows or columns, the replicate gro

vTable of Contents1. Introduction...11.1 Overview of Microplate Manager...

Microplate Manager User Guide40• To undefine wells or replicate groups, click on the Format as Undefined button(or select Undefine from the FORMAT me

Chapter 4. Templates41Click on the Enter Manually button to directly input the concentrations of yourstandards. Then type in the concentrations in th

Microplate Manager User Guide42Figure 28. Edit Unknowns dialog box.Each defined assay has a tab that is labeled with the name of the assay (default n

Chapter 4. Templates43Click on Calculate when all the information is entered. The dilution factors in theDilut. column will be automatically updated.

Microplate Manager User Guide44Click on the tab of the assay you want to change, then choose the type of regressionmethod from the OPTIONS menu or fro

Chapter 4. Templates45Figure 30. External Standards dialog box.If you are already using external standards, the External Standards checkbox will bes

Microplate Manager User Guide46Select the data file containing the external standards and click on Open. The namesof all assays with defined standards

Chapter 4. Templates474.4.7 Step 7. Saving the TemplateSave the template as a data file by selecting Save Data/Template or SaveData/Template As...

495. ProtocolsProtocols contain the settings for controlling the microplate reader. To read amicroplate, you must first open a protocol and specify th

vi3.2 Opening and Saving Files...173.3 Reading Data from Other Applications...

Microplate Manager User Guide50suffixes .epr (endpoint reading), .mpr (multiple plate reading), or .kpr (kinetic platereading).½ Only one protocol ma

Chapter 5. Protocols515.1 Features Common to All ProtocolsAll three protocol types share basic reading parameters such as measurementwavelength, rea

Microplate Manager User Guide52After you select the template, it is displayed on the screen and simultaneously copiedinto the protocol file.Selecting

Chapter 5. Protocols53When a template is saved in a protocol file, it will remain there until you select adifferent template.½ If you create or edit

Microplate Manager User Guide54Figure 36. Incubator settings.The Setpoint is the temperature that the incubator will warm up to and maintainthroughou

Chapter 5. Protocols555.1.7 ReportsYou can select certain reports to be automatically displayed and/or printed after areading is taken. Click on the

Microplate Manager User Guide56before the reports have been generated, you will be prompted for the labelinginformation if it has not already been ent

Chapter 5. Protocols575.1.8 Running a ProtocolOnce all the parameters have been set, click on the Run button to begin taking areading.While the read

Microplate Manager User Guide585.2 Features Unique to Endpoint ProtocolsEndpoint protocols collect one absorbance reading for each well on a micropla

Chapter 5. Protocols59Absorbance DelayAbsorbance Delay delays data collection until a well that you select reaches aspecified level of absorbance. To

vii5.2 Features Unique to Endpoint Protocols...585.3 Features Unique to Kinetic Protocols...

Microplate Manager User Guide60To run a new kinetic protocol, select New Kinetic Protocol from the FILE menu.Figure 43. Features of a kinetic protoco

Chapter 5. Protocols61To activate a reading set, click on the checkbox next to the set number. Only sets thatare checked will be run.Enter the number

Microplate Manager User Guide62Figure 44. Analysis Options in the kinetic protocol dialog box.The settings in this dialog box will only affect the an

Chapter 5. Protocols63To set absorbance limits, select the appropriate checkbox(es) and enter ODs in theappropriate field(s).If none of the limit che

Microplate Manager User Guide645.4 Features Unique to Multiple PlateProtocolsThe multiple plate protocol will perform single endpoint readings on a s

Chapter 5. Protocols65Figure 45. Features of a Multiple Plate Protocol dialog box.The controls common to all protocols are described in section 5.1.

Microplate Manager User Guide66Stack Loader CheckboxIf you are connected to Bio-Rad’s Twister stack loader and have installed theassociated software,

Chapter 5. Protocols67After you have defined your plate types and other configurations in the Twistercontrol panel, select the appropriate plate type

Microplate Manager User Guide68a base file name for the resulting data files. File names are then constructed byappending two digits to the base file

Chapter 5. Protocols69reading is section, specify an absorbance that is above or below a certain OD value.Below will begin data collection when the m

viii8. Quick Guides...1078.1 Creating a New Template ...

716. Data Formatting andReportsAfter you have run your protocol, your data and the associated template will bedisplayed automatically. You can then o

Microplate Manager User Guide72• Normalization Report: Similar to the Limit Report, except that the readings aredisplayed as percentages relative to

Chapter 6. Data Formatting and Reports736.2 Saving Your DataData is displayed and saved with templates (see Chapter 4 for more informationabout temp

Microplate Manager User Guide74You can highlight multiple number fields by dragging your cursor over the fields.You can highlight rows and columns by

Chapter 6. Data Formatting and Reports75Figure 49. Select Outliers dialog box.Click on the checkbox next to the well number and associated value tha

Microplate Manager User Guide766.5 Editing or Replacing the Template in aData FileAfter a protocol has been run, the template from the protocol file

Chapter 6. Data Formatting and Reports776.6 ReportsWith your data displayed, select the report you want to display from the VIEWmenu. The available r

Microplate Manager User Guide78your label in the field in the pop-up box. To insert a label into the label list,select the existing label above which

Chapter 6. Data Formatting and Reports796.6.2 Raw Image Report (Ultramark only)The Raw Image Report is different from other reports in that it is an

ixList of FiguresFigure 1. Workflow of Microplate Manager...2Figure 2. Microplate Manager d

Microplate Manager User Guide80Viewing an ImageThe IMAGE menu contains special tools for viewing your images.Figure 54. Image menu.The image is displ

Chapter 6. Data Formatting and Reports81select the one to be displayed by choosing Select from the IMAGE menu andselecting the appropriate image numb

Microplate Manager User Guide82Figure 55. Close-up of a microplate image.Show Pattern on the IMAGE menu displays the area of the well used for dataco

Chapter 6. Data Formatting and Reports83dimensions for your template by selecting Physical Dimensions... See section 4.1.2for details on these featu

Microplate Manager User Guide84Absorbance ReportFigure 57. Absorbance Report.In the Absorbance Report, the mean absorbance of all the blank wells in

Chapter 6. Data Formatting and Reports85The Velocity Report displays the velocities of your well readings, based on theanalysis options you selected

Microplate Manager User Guide86Kinetic Correlation Coefficient ReportFigure 60. Kinetic Correlation Coefficient Report.The Kinetic Correlation Coeffi

Chapter 6. Data Formatting and Reports87Kinetic Plots ReportFigure 62. Kinetic Plots Report.Using the Kinetic Plots Report, you can display a plot o

Microplate Manager User Guide88Figure 63. Kinetic Zoom Plot.This window shows additional velocity information for a single well. It displays aplot of

Chapter 6. Data Formatting and Reports89Limit ReportFigure 64. Limit Report.If you have defined upper and lower limits for your data, each well is t