BatchKi Reference Manual

  Index

Contents

• Introduction
  • Purpose of BatchKi
  • Computational Methods
  • Graphical User Interface
  
  
• Installation
  • System Requirements
    • Microsoft Windows
    • Linux and Unix-like systems
    • Other operating systems
  • Installing Prerequisites
    • Install Perl on Microsoft Windows
    • Install Apache Web Server on MS Windows
  • Downloading BatchKi
  • Installing BatchKi
    • Configuring the BatchKi installer
    • Performing the installation
    • Testing the installation
    • Installing the license file
  
  
• Program Execution
  • Command Line Interface
    • Default initialization file
    • Specified initialization file
    • Specified output directory
    • Specified output directory and initialization file
  • Common Gateway Interface (CGI)
  
  
• Control Settings and Templates
  • [Confidence Intervals]
    • Parameter Exact
    • Parameter FixedEnzyme
    • Parameter Level
  • [Enzyme concentration]
    • Parameter Optimize
    • Parameter Multiple
    • Parameter Limits
  • [Output]
    • Parameter AllProgressCurves
    • Parameter GraphicFormat
    • Parameter GraphicProgress
    • Parameter GraphsPerRow
    • Parameter GridRectangleSize
    • Parameter InhibitorNameLength
    • Parameter LeverageHigh
    • Parameter LeverageLow
    • Parameter LogPotency
    • Parameter OnlySummarySpreadsheet
    • Parameter OnlyVelocities
    • Parameter ReportIC50
  • [Progress]
    • Parameter Model
    • Parameter MaxDegree
    • Parameter AutomaticDegree
    • Parameter AutomaticDegreeTuning
    • Parameter RobustRegression
    • Parameter ExcludeFirstPoint
    • Parameter Extrapolate
    • Parameter MaxSeconds
    • Parameter MinSeconds
  • [Velocities]
    • Parameter AdjustVoInitialEstimate
    • Parameter Model
    • Parameter ExcludeLargeSquares
    • Parameter MultipleOfMedianSquare
    • Parameter ExcludeNegativeRates
    • Parameter AverageReplicates
    • Parameter ConstantWeights
    • Parameter RelativeWeights
    • Parameter RequireNegativeControl
    • Parameters related to optimized baseline rate
    • Parameter AutoBaseline
    • Parameter AutoBaselineCutoff
    • Parameter NegativeBaselineLimit
    • Parameter OptimizePositiveBackground
    • Parameter BackgroundTolerance
    • Parameters related to robust regression analysis
  • Template Files
    • Template File Customization
  
  
• Input Data
  • Single or Multiple Data Sets
  • Plate Size and Unique ID
    • The id attribute
    • The rows attribute
    • The columns attribute
  • Additional Information (Optional)
  • Plate Layout
    • The identical attribute
    • The external attribute
    • Reserved inhibitor labels
  • Concentrations
    • The identical attribute
    • The unit attribute
    • The external attribute
  • Plate Reader Output
    • The <Data...> element
    • The type attribute
    • The header attribute
    • The external attribute
    • The format attribute
    • The background attribute
  
  
• Output Files
  • Run Summary Files
    • HTML Output File
    • ASCII Delimited (Excel) File
  • Plate Summary Files
    • `Plate Summary (Text)' page
    • `Plate Summary (Graph)' page
    • `Plate Data' page
    • XML Output Files
  • Inhibitor Output Files
    • HTML Output Files
    • XML and Excel Output Files
  
  
• DTD for BatchKi Input File
  • Single Plate Reader Data File
  • Multiple Plate Reader Data Files
  
  
• Chebyshev Orthogonal Polynomials
  • Mathematical properties
  • Sample evaluation code
  
  
• List of Figures
• List of Tables
• Bibliography
• Index

  Index

biokin.com/batchki/manual/reference/html/node1.html
Petr Kuzmic | Jul 12 2008