BatchKi Reference Manual

  Contents

Index

$IC_{50}$

reporting

$IC_{50}$

relationship with $K_{i}^{(app)}$

<Concentration> element

<Concentration> element

unit attribute

<ConcEnzyme> element

external attribute

<ConcEnzyme> element

identical attribute

<ConcInhibitor> element

external attribute

<ConcInhibitor> element

identical attribute

<ConcSubstrate> element

external attribute

<ConcSubstrate> element

identical attribute

<Data> element

<Data> element

background attribute

<Data> element

external attribute

<Data> element

format attribute

<Data> element

,

<Data> element

type attribute

<Enzyme> element

external attribute

<Enzyme> element

identical attribute

<Inhibitor> element

external attribute

<Inhibitor> element

identical attribute

<Plate> element

<Plate> element

columns attribute

<Plate> element

id attribute

<Plate> element

rows attribute

<Plate> element

optional information

<Substance> element

<Substrate> element

external attribute

<Substrate> element

identical attribute

[Confidence Intervals] initialization

[Confidence Intervals] initialization

Exact parameter

[Confidence Intervals] initialization

FixedEnzyme parameter

[Confidence Intervals] initialization

Level parameter

[Enzyme concentration] initialization

[Enzyme concentration] initialization

Limits parameter

[Enzyme concentration] initialization

Multiple parameter

[Enzyme concentration] initialization

Optimize parameter

[Output] initialization

[Output] initialization

AllProgressCurves parameter

[Output] initialization

GraphicFormat parameter

[Output] initialization

GraphicProgress parameter

[Output] initialization

GraphsPerRow parameter

[Output] initialization

GridRectangleSize parameter

[Output] initialization

InhibitorNameLength parameter

[Output] initialization

LeverageHigh parameter

[Output] initialization

LeverageLow parameter

[Output] initialization

LogPotency parameter

[Output] initialization

OnlySummarySpreadsheet parameter

[Output] initialization

OnlyVelocities parameter

[Output] initialization

ReportIC50 parameter

[Progress] initialization

[Progress] initialization

AutomaticDegree parameter

[Progress] initialization

AutomaticDegreeTuning parameter

[Progress] initialization

ExcludeFirstPoint parameter

[Progress] initialization

Extrapolate parameter

[Progress] initialization

MaxDegree parameter

[Progress] initialization

MaxSeconds parameter

[Progress] initialization

,

[Progress] initialization

MinSeconds parameter

[Progress] initialization

,

[Progress] initialization

Model parameter

[Progress] initialization

RobustRegression parameter

[Velocities] initialization

[Velocities] initialization

AdjustVoInitialEstimate parameter

[Velocities] initialization

AutoBaseline parameter

[Velocities] initialization

AutoBaselineCutoff parameter

[Velocities] initialization

AverageReplicates parameter

[Velocities] initialization

BackgroundTolerance parameter

[Velocities] initialization

ConstantWeightRange parameter

[Velocities] initialization

ConstantWeights parameter

[Velocities] initialization

DeleteSingleOutlier parameter

[Velocities] initialization

ExcludeLargeSquares parameter

[Velocities] initialization

ExcludeNegativeRates parameter

[Velocities] initialization

HuberTuningConstant parameter

[Velocities] initialization

MaximumFractionOfOutliers parameter

[Velocities] initialization

MinimumRobustWeight parameter

[Velocities] initialization

MinimumWeightsRatio parameter

[Velocities] initialization

Model parameter

[Velocities] initialization

MultipleOfMedianSquare parameter

[Velocities] initialization

NgativeBaselineLimit parameter

[Velocities] initialization

OptimizePositiveBackground parameter

[Velocities] initialization

RelativeWeights parameter

[Velocities] initialization

RequireNegativeControl parameter

[Velocities] initialization

RobustRegression parameter

AdjustVoInitialEstimate parameter

[Velocities] initialization

AllProgressCurves parameter

[Output] initialization

AutoBaseline parameter

[Velocities] initialization

AutoBaselineCutoff parameter

[Velocities] initialization

AutomaticDegree parameter

[Progress] initialization

AutomaticDegreeTuning parameter

[Progress] initialization

AverageReplicates parameter

[Velocities] initialization

background attribute

<Data> element

BACKGROUND label

BackgroundTolerance parameter

[Velocities] initialization

columns attribute

<Plate> element

ConstantWeightRange parameter

[Velocities] initialization

ConstantWeights parameter

[Velocities] initialization

CONTROL label

DeleteSingleOutlier parameter

[Velocities] initialization

EMPTY label

Exact parameter

[Confidence Intervals] initialization

ExcludeFirstPoint parameter

[Progress] initialization

ExcludeLargeSquares parameter

[Velocities] initialization

ExcludeNegativeRates parameter

[Velocities] initialization

external attribute

<ConcEnzyme> element

external attribute

<ConcInhibitor> element

external attribute

<ConcSubstrate> element

external attribute

<Data> element

external attribute

<Enzyme> element

external attribute

<Inhibitor> element

external attribute

<Substrate> element

Extrapolate parameter

[Progress] initialization

FixedEnzyme parameter

[Confidence Intervals] initialization

format attribute

<Data> element

format attribute

,

GraphicFormat parameter

[Output] initialization

GraphicProgress parameter

[Output] initialization

GraphsPerRow parameter

[Output] initialization

GridRectangleSize parameter

[Output] initialization

HuberTuningConstant parameter

[Velocities] initialization

id attribute

<Plate> element

identical attribute

<ConcEnzyme> element

identical attribute

<ConcInhibitor> element

identical attribute

<ConcSubstrate> element

identical attribute

<Enzyme> element

identical attribute

<Inhibitor> element

identical attribute

<Substrate> element

InhibitorNameLength parameter

[Output] initialization

Level parameter

[Confidence Intervals] initialization

LeverageHigh parameter

[Output] initialization

LeverageLow parameter

[Output] initialization

Limits parameter

[Enzyme concentration] initialization

LogPotency parameter

[Output] initialization

MaxDegree parameter

[Progress] initialization

MaximumFractionOfOutliers parameter

[Velocities] initialization

MaxSeconds parameter

[Progress] initialization

MaxSeconds parameter

,

MinimumRobustWeight parameter

[Velocities] initialization

MinimumWeightsRatio parameter

[Velocities] initialization

MinSeconds parameter

[Progress] initialization

MinSeconds parameter

,

Model parameter

[Progress] initialization

Model parameter

[Velocities] initialization

Multiple parameter

[Enzyme concentration] initialization

MultipleOfMedianSquare parameter

[Velocities] initialization

NegativeBaselineLimit parameter

[Velocities] initialization

OnlySummarySpreadsheet parameter

[Output] initialization

OnlyVelocities parameter

[Output] initialization

Optimize parameter

[Enzyme concentration] initialization

OptimizePositiveBackground parameter

[Velocities] initialization

RelativeWeights parameter

[Velocities] initialization

ReportIC50 parameter

[Output] initialization

RequireNegativeControl parameter

[Velocities] initialization

RobustRegression parameter

[Progress] initialization

RobustRegression parameter

[Velocities] initialization

rows attribute

<Plate> element

type attribute

<Data> element

unit attribute

<Concentration> element

adjusted regression coefficient

tab-delimited output

Apache server

Apache server

most recent version

ver. 2.0.x

apparent inhibition constant

tab-delimited output

ASCII format

assays

cell-based

continuous

end-point

baseline velocity

standard error

tab-delimited output

BatchKi

binary distribution

binary executable file

configuration files

purpose

source code distribution

template files

Bio-Rad format

Bio-Tek format

CGI

Perl

script files

coefficient of variation

tab-delimited output

color scheme

signal offset

concentration

scientific notation

units

confidence interval limits

tab-delimited output

confidence intervals , ,

confidence intervals

control settings

desired level

levels

linear approximation

lower limit

linear approximation

profile-t method , ,

Student-t statistics

tab-delimited output

upper limit

upper limit

confidence level reached

linear approximation

profile-t method

continuous enzyme assays

control settings

confidence intervals

default

control velocity

standard error

data filter

data filter

excluding first data point

degrees of freedom

tab-delimited output

demonstration files

end-point enzyme assays

enzyme assays

continuous ,

end-point ,

single-point

enzyme concentration

enzyme concentration

adjustable

automatic determination

fixed

optimization example

optimization limits

rules for optimization

standard error

tab-delimited output

enzyme I.D.

tab-delimited output

enzyme inhibition

apparent inhibition constants

IC50

enzyme inhibition¡`classical''

enzyme inhibition¡`tight-binding''

Equation

Morrison

three-parameter logistic

exponential fit

exponential fit

Legendre polynomials

extrapolation to zero time

fitted control velocity

tab-delimited output

fitted enzyme concentration

tab-delimited output

fitting model

for reaction progress

for reaction velocities

progress curves

four-parameter logistic equation

gcc compiler

graph

residuals of fit

graphical user interface (GUI)

GUI (graphical user interface)

HTML

output files

template files

inhibitor I.D.

tab-delimited output

inhibitor labels

BACKGROUND

CONTROL

EMPTY

prohibited characters

reserved

inhibitors

BACKGROUND label

CONTROL label

EMPTY label

initial rate

extrapolated to zero time

initial velocities

input data

input data

cell-based assays

continuous assays

end-point assays

installation ,

installation

Appache server

Appache server

cgi-bin root

document root

command window

configuration file

configuration file

Apache

CGIdir

HTMLdir

Login ,

OperatingSystem ,

Password ,

Perl

PreserveUserData ,

Server

gunzip

I.P. address

license

license file

Perl interpreter

server name

temporary directory

test

WinZip

license file

license

installation

Linux ,

Macintosh OS X ,

Macintosh OS X

compilation

modified Makefile

mathematical model

four-parameter logistic equation

median square deviation

Microsoft Excel

output files

Morrison equation ,

negative reaction rates

negative reaction rates

selecting for optimization

noisy progress curves

exclusion from analysis

nonlinear regression

Marquardt method

outlier detection

outliers

output directory

output files ,

output files

color scheme for inhibition constants

HTML ,

per inhibitor

per plate

per plate

graphical summary

numerical summary

XML

per program run

per program run

Excel

HTML

plate data

plate data

plate layout

progress curves

randomness of residuals

relative velocities

residuals

signal offset

sum of squares

plate summary page

progress curves

residuals of fit

run summary page

standard deviation of fit

suppressing graphic output

SVG ,

tab-delimited

adjusted regression coefficient

apparent inhibition constant

baseline velocity

coefficient of variation

confidence interval limits

confidence intervals

degrees of freedom

enzyme concentration

enzyme I.D.

fitted control velocity

fitted enzyme concentration

inhibitor I.D.

plate I.D.

relative standard deviation of fit

standard deviation of fit

standard error of baseline velocity

standard error of control velocity

standard error of enzyme concentration

standard error of $K_i^{\rm app}$

substrate concentration

substrate I.D.

templates

templates

customization

XML ,

Perl

Perl programming language

Perl

ActiveState.COM

CGI

ver. 5.8.x for Linux

ver. 5.8.x for Windows

plate I.D.

tab-delimited output

plate layout ,

plate layout

BACKGROUND label

CONTROL label

EMPTY label

output files

plate reader

Bio-Rad format ,

Bio-Tek format ,

format

raw data

raw data

format

SoftMax column format

SoftMax format

SoftMax plate format

Two-column format ,

Universal format ,

polynomial degree

automatic selection

progress curves

polynomial fit

fine-tuning

prerequisites

primary data

initial velocities

reaction progress

profile-t method

confidence intervals

upper limit

program execution

CGI

command line

web interface

progress curves

combination of parameters

exclusion of noisy data

exponential fit

fitting model

median square deviation

output files

polynomial degree

selecting

program initialization

residuals of fit

quadratic parabola

randomness of residuals

output files

reaction progress

regression coefficient

adjusted

relative standard deviation of fit

tab-delimited output

relative velocities

color scheme

output files

residuals of fit

output files

progress curves

robust fit

robust regression ,

robust regression

Huber's Minimax method

vs. least-squares regression

settings

default

signal baseline

as adjustable parameter

signal offset

color scheme

output files

single-point enzyme assays

SoftMax format

source code

standard deviation

standard deviation of fit

tab-delimited output

standard error , ,

standard error of baseline velocity

tab-delimited output

standard error of control velocity

tab-delimited output

standard error of enzyme concentration

tab-delimited output

standard error of $K_i^{\rm app}$

tab-delimited output

standard error

baseline velocity

control velocity

enzyme concentration

straight-line fit

Student-t statistics

substrate concentration

tab-delimited output

substrate I.D.

tab-delimited output

SVG

output files

residuals of fit

system requirements

system requirements

Microsoft Windows

test

successful installation

Three-parameter logistic equation

tuning constant

polynomial fit

Two-column format

Universal format

XML

XML

acceptable subset

document type definition (DTD)

DTD (document type definition)

output files

output files

per plate

template files

  Contents

biokin.com/batchki/manual/reference/html/node41.html
Petr Kuzmic | Jul 12 2008