affectors
Class TxnSiteActivatorAff

java.lang.Object
  affectors.Affector
      affectors.TxnSiteActivatorAff

All Implemented Interfaces:

java.lang.Cloneable

Direct Known Subclasses:

TxnSiteActivator1Aff

public class TxnSiteActivatorAff

extends Affector

Use for activation of transcription. Activates according to an S-shaped function (Phi function) with a half maximal activation level K and a cooperativity nu. This is identical to the Txn1Aff except that it is designed to work inside of a meta-affector. You should only use this Affector inside of an EnhancerRegion.

Formula
dnodex/dt = (ACTIVATOR/K)^nu / (1 + (ACTIVATOR/K)^nu)

Parameters

Activator [ACTIVATOR]	The transcriptional activator Node
Half-max activation level [K_ACTIVATORnodex]	The concentration of activator at which transcription proceeds at half its maximal rate
Cooperativity [nu_ACTIVATORnodex]	The non-linearity of the activating function. The higher the value, the sharper the curves in the S-shaped activation function

Usage
&nodex

&EnhancerRegion H_nodex

&TxnSiteActivatorAff ACTIVATOR K_ACTIVATORnodex nu_ACTIVATORnodex

&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

TxnSiteActivatorAff()

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

TxnSiteActivatorAff

public TxnSiteActivatorAff()

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