BatchKi Reference Manual

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Control Settings and Templates

The basic functionality of the program is controlled by an ASCII text file, read by the BatchKi numerical engine (batchki.exe) upon each program execution. This control settings file is a simple ASCII text file. It is used to decide on the fitting model for reaction progress curves (linear, polynomial, or exponential fit), the fitting model for the reaction velocities (Morrison equation or the four-parameter logistic equation), what type of output files should be generated (with or without graphics), and many other choices.

The default contents of the control settings file are listed below.

[Confidence Intervals]
  Exact = yes
  FixedEnzyme = yes
  Level = 99

[Enzyme Concentration]
  Limits = 5
  Multiple = 1
  Optimize = yes

[Output]
  AllProgressCurves = no
  GraphicFormat = GIF
  GraphicProgress = yes
  GraphsPerRow = 4
  GridRectangleSize = 80
  InhibitorNameLength = 16
  LeverageHigh = 0.7
  LeverageLow = 0.001
  LogPotency = no
  OnlySummarySpreadsheet = no
  OnlyVelocities = no
  ReportIC50 = no

[Progress]
  AutomaticDegree = no
  AutomaticDegreeTuning = 1.25
  ExcludeFirstPoint = no
  Extrapolate = no
  MaxDegree = 1
  MaxSeconds = 1000000000
  MinSeconds = 0
  Model = polynomial
  RobustRegression = yes

[Velocities]
  AdjustVoInitialEstimate = yes
  AutoBaseline = yes
  AutoBaselineCutoff = 0.02
  AverageReplicates = yes
  BackgroundTolerance = 0.2
  ConstantWeightRange = 2
  ConstantWeights = yes
  DeleteSingleOutlier = no
  DilutionRatioCV = 50
  DilutionRatioMax = 100
  DilutionRatioMin = 1.05
  ExcludeLargeSquares = yes
  ExcludeNegativeRates = no
  HuberTuningConstant = 1.345
  MaximumFractionOfOutliers = 0.5
  MinimumRobustWeight = 0.9
  MinimumWeightsRatio = 4
  Model = Morrison
  MultipleOfMedianSquare = 10
  NegativeBaselineLimit = 0.5
  OptimizeHillRatio = 0.5
  OptimizePositiveBackground = no
  RelativeWeights = yes
  RequireNegativeControl = yes
  RobustRegression = yes

This chapter describes the various options for locating and naming the control settings file. It also explains the meaning of each entry in the control file, and which values can be assigned to the control parameters.

By default, the control settings file is called settings.ini and resides in the directory ./system/BatchKi/. However, depending on the syntax of the command line used to invoke the numerical engine, the file can have an arbitrary name and reside in an arbitrary directory. The influence of command-line syntax on the location and naming of the control settings file is explained in section 3.1. In the following sections, the contents of the control settings file are explained.

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Petr Kuzmic | Jul 12 2008