affectors
Class TxnSiteInhibitorAff

java.lang.Object
  affectors.Affector
      affectors.TxnSiteInhibitorAff

All Implemented Interfaces:

java.lang.Cloneable

public class TxnSiteInhibitorAff

extends Affector

Use for multiplicative inhibition of transcription. Formula is 1 minus our standard activation s-shaped curve, giving an upside-down s-shaped curve (our Psi function) with a half-maximal inhibition at K and the degree of non-linearity controlled by nu. This Affector is designed to work inside of a ProductAff. It inhibits if multiplied by another term - the value of this affector is positive, so it will not inhibit if you add it to another term. You should only use this Affector inside of an EnhancerRegion.

Formula
dnodex/dt = INHIBITOR^nu / (K^nu + INHIBITOR^nu)

Parameters

Inhibitor [INHIBITOR]	The inhibitor Node.
Half-maximal inhibition level [K_INHIBITORnodex]	The concentration of inhibitor at which transcription is reduced by half.
Cooperativity [nu_INHIBITORnodex]	The non-linearity of the inhibiting function. The higher the value, the sharper the curves in the S-shaped inhibition function.

Usage
&nodex

&EnhancerRegionAff H_nodex

&ProductAff

&TxnSiteActivatorAff ACTIVATOR K_ACTIVATORnodex nu_ACTIVATORnodex &TxnSiteInhibitorAff INHIBITOR K_INHIBITORnodex nu_INHIBITORnodex

&endProductAff

&endEnhancerRegion

&endnodex

Field Summary

Fields inherited from class affectors.Affector

ADesc, affectorType, CC, CERTIFICATION, CONVERSION, copyNumber, DEGRADATION, FF, firstFreeParam, GG, GUI_CAPABLE, HH, KK, MATHTYPE, NDesc, PDesc, PRODUCTION, RETURNS_DERIV, RETURNS_PARTIALS, TERMTYPE, TT, Type, UNSPECIFIED

Constructor Summary

TxnSiteInhibitorAff()

Method Summary

float	getValue(Node which_node)
protected void	setLabelsAndTypes()
void	setParameterNumbers(int[] param_nums)

Methods inherited from class affectors.Affector

addDefaultParam, Chi, clearStatic, copy_, copy, doesContainTarget, findOrCreateParam, findParam, fixNodes, getNCValue, getNodes, getNumNodes, getNumParameters, getOtherSide, getParameter, getParameter, getParamName, getParamPos, getParamValue, getParamValue, getParamVariationMode, init, isLinearInTarget, Phi, Psi, setContainsTarget, setDescriptions, setParameter, setParamRange, setParamRange, setParamValue, setParamValue, setSide, setSided

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

TxnSiteInhibitorAff

public TxnSiteInhibitorAff()

Method Detail

setLabelsAndTypes

protected void setLabelsAndTypes()

Specified by:

setLabelsAndTypes in class Affector

setParameterNumbers

public void setParameterNumbers(int[] param_nums)

Specified by:

setParameterNumbers in class Affector

getValue

public float getValue(Node which_node)

Overrides:

getValue in class Affector