affectors
Class TxnSiteActInhibitAff

java.lang.Object
  affectors.Affector
      affectors.TxnSiteActInhibitAff

All Implemented Interfaces:

java.lang.Cloneable

public class TxnSiteActInhibitAff

extends Affector

Use for activation + inhibition of transcription. Activates according to an S-shaped function (Phi function) with a half maximal activation level K and a cooperativity nu. Inhibits by multiplying an upside down-S shaped inhibition function (Psi function) into both the top and bottom of the Phi function. This models a situation in which the inhibitor reduces the effectiveness of bound activator, rather than reducing the effective concentration of the activator (see TxnSiteActInhibit2Aff for this option) or throttling the activator's effect by multiplying Phi by Psi (see TxnSiteActInhibit3Aff for this option). This family is designed to work inside of a meta-affector. You should only use this Affector inside of an EnhancerRegion.

Formula
inhibit_term = 1 - [(INHIBITOR/K_inhibit)^nu_inhibit * / (1 + (INHIBITOR/K_inhibit)^nu_inhibit)]
dnodex/dt = (ACTIVATOR/K_act)^nu * inhibit_term / (1 + (ACTIVATOR/K)^nu * inhibit_term)

Parameters

Activator [ACTIVATOR]	The transcriptional activator Node
Inhibitor [INHIBITOR]	The transcriptional inhibitor Node
Half-max activation level of activator [K_ACTIVATORnodex]	The concentration of activator at which transcription proceeds at half the maximal rate this particular "site" is capable of driving, absent inhibition
Cooperativity of activator [nu_ACTIVATORnodex]	The non-linearity of the activating function. The higher the value, the sharper the curves in the S-shaped activation function
Half-max inhibition level of inhibitor [K_INHIBITORnodex]	The concentration of inhibitor at which it has a half-maximal effect on effectiveness of the activator
Cooperativity of inhibitor [nu_INHIBITORnodex]	The non-linearity of the inhibition function. The higher the value, the sharper the curves in the S-shaped inhibition function

Usage
&nodex

&EnhancerRegion H_nodex

&TxnSiteActivatorAff ACTIVATOR INHIBITOR K_ACTIVATORnodex nu_ACTIVATORnodex K_INHIBITORnodex nu_INHIBITORnodex

&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

TxnSiteActInhibitAff()

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

TxnSiteActInhibitAff

public TxnSiteActInhibitAff()

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