BatchKi Reference Manual

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[Output]

This section of the initialization file controls some aspects of producing the program's output. The default settings are as follow:

[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

Parameter AllProgressCurves

This parameter can have two possible values:

• AllProgressCurves = yes
• AllProgressCurves = no

When AllProgressCurves is set to `yes', the software will generate a separate image file for each reaction progress curve. This can considerably increase the total number of files generated over time, and the total amount of storage space. It is important to realize that certain operating systems (e.g., Microsoft Windows) do have an intrinsic limits on the number of files in the given directory (approximately 50,000 in the case of Windows-2000).

When AllProgressCurves is set to `no', the software will generate only a summary graphical representation of all progress curves on the given plate.

Parameter GraphicFormat

This parameter can have two possible values:

• GraphicFormat = GIF
• GraphicFormat = SVG

When GraphicFormat is set to `GIF', all generated graphics will be in the GIF format.

When GraphicFormat is set to `SVG', all generated graphics will be in Adobe's Scalable Vector Graphics (SVG) format. Viewing SVG graphics within a web browser requires a special SVG browser plug-in, available free of charge from Adobe Systems Inc. (www.adobe.com).

Parameter GraphicProgress

This parameter can have two possible values:

• GraphicProgress = yes
• GraphicProgress = no

When GraphicProgress is set to `yes', the program will generate SVG graphic files for all progress curves found in the plate-reader data set, and the associated residual plots. The generation of these graphical files can slow down the batch processing of very large amounts of data (typically hundreds of plate-reader data sets). If processing speed during batch execution is important, the user might choose to set the parameter to `no'. In this case all other (non-graphical) output files are still generated.

Parameter GraphsPerRow

This parameter controls how many dose-response graphs will be displayed in each row on the graphical summary page. For example, if GraphsPerRow = 3, the summary page will have three dose-response graphs per row. Changing the GraphsPerRow parameter might be useful in producing suitably sized hard copy printouts for archiving or pasting into laboratory notebooks.

Parameter GridRectangleSize

This parameter controls the size of rectangles (in pixels) used to display a panel of all reaction progress curves on each plate. The most appropriate value will depend (a) on the resolution of the computer monitor and (b) the number of wells on each plate. A typical value is GridRectangleSize = 50.

Parameter InhibitorNameLength

This control parameter assists in the layout of the graphical summary page. The default value is InhibitorNameLength = 16. When any compound name on a given plate is longer than InhibitorNameLength, the graphical summary page showing all dose-response graphs on the plate is arranged such that inhibitor names are segregated at the bottom, below all the dose-response graphs. Such arrangement allows the graphical summary page to be more easily printed on a single sheet of paper, if a hard-copy printout is desired.

Parameter LeverageHigh

Nonlinear leverages are diagonal elements of the ``hat matrix'' $\hat{\bf H} = {\bf J} \left ( {\bf J}^T {\bf J}\right )^{-1} {\bf J}^T$, where ${\bf J}$ is the $n_D \times n_P$ matrix of first derivatives of the predicted model with respect to the adjustable model parameters ($n_D$ is the number experimental data points; $n_P$ is the number of theoretical model parameters). For a detailed discussion of leverages, see [5].

The LeverageHigh parameter is used in BatchKi in two different ways:

1. For visually marking any data points on a dose-response curve that are characterized by inappropriately high leverage, or influence on the results of fit. These data points will be marked by a bright red color (see the left-hand panel in Figure 4.1).
2. For computing the number of optimally placed data points, as shown in the Excel-style output summary file (see the right-hand panel in Figure 4.1). ``Optimal'' points are those for which the nonlinear leverages are higher than LeverageLow (see below) and lower than LeverageHigh.

The default value is LeverageHigh = 0.7.

Figure 4.1: The use of control parameters LeverageHigh and LeverageLow in the display of results of fit.

Parameter LeverageLow

This control parameter is companion to LeverageHigh explained above. All data points with nonlinear leverages (diagonal elements of the ``hat matrix'' $\hat{\bf H} = {\bf J} \left ( {\bf J}^T {\bf J}\right )^{-1} {\bf J}^T$) lower LeverageLow will be shown in the output files with a distinct color (see the left-hand panel in Figure 4.1).

The default value is LeverageLow = 0.001.

Parameter LogPotency

This parameter can have two possible values:

• LogPotency = yes
• LogPotency = no

The value of this parameter controls how the main measure of inhibitory potency (either $K_i^{\rm (app)}$ or $IC_{50}$, depending on the chosen fitting model) will be displayed in the output files. If LogPotency = no (the default value), then all either $K_i^{\rm (app)}$ or $IC_{50}$ will be reported in moles per liter (micromoles per liter in some displays. If LogPotency = yes, then regardless of the fitting model the inhibitory potency will be displayed in logarithmic units.

Parameter OnlySummarySpreadsheet

This parameter can have two possible values:

• OnlySummarySpreadsheet = yes
• OnlySummarySpreadsheet = no

When this parameter is set to `yes', the only generated output file is the tab-delimited text file index.xls in the directory output. No other output is generated. This setting might be useful only when executing the program from the command line (see below) and when processing very large number of data files in the batch run. For example, upon processing 500 plate-reader data files in a single run, the disk space required to hold all the output files is approximately 200 MB. The generation of all output files also significantly slows down the program execution, approximately by a factor of three to five.

When OnlySummarySpreadsheet is set to `no', which is the default value, the program will generate HTML files, XML files, and SVG graphics files for all inhibitors on all plates being processed in the given run.

Parameter OnlyVelocities

This parameter can have two possible values:

• OnlyVelocities = yes
• OnlyVelocities = no

When this parameter is set to `yes', the computation is terminated immediately after the determination of initial reaction velocities. The program does not proceed to compute inhibition constants. This feature is useful in a preliminary examination of experimental data. The default value of this control parameter is `no'.

Parameter ReportIC50

This parameter can have two possible values:

• ReportIC50 = yes
• ReportIC50 = no

When this parameter is set to `yes', the inhibitory potency will be expressed in terms of $IC_{50}$ even when the fitting model is the Morrison equation, in which case the primary measure of inhibitory potency is the apparent inhibition constant $K_{i}^{(app)}$. This option is useful for comparing BatchKi results with historical data or results from other software packages, which might not generate $K_{i}^{(app)}$ values. The mathematical relationship between the two measures of potency is is $IC_{50} = K_{i}^{(app)} + [E]_0/2$, where $[E]_0$ is the total or analytical enzyme concentration.

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Petr Kuzmic | Jul 12 2008