affectors
Class Txn1Aff

java.lang.Object
  affectors.Affector
      affectors.Txn1Aff

All Implemented Interfaces:

java.lang.Cloneable

public class Txn1Aff

extends Affector

The simplest regulated transcription affector. Transcription rate is a sigmoid function of activator concentration with transcription proceeding at half its maximum possible rate when the activator concentration equals the half-max parameter, and with the rates on either side of this half-max dependent on how non-linear the sigmoid is. The activator may be either membrane-bound or intracellular, as long as it is on the same cell as the target mRNA.

Formula
dnodex/dt = (1 / H_nodex) * ACTIVATOR^nu / (K^nu + ACTIVATOR^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
mRNA Half-life [H_nodex]	The half life of the product mRNA

Usage
&nodex

&Txn1Aff ACTIVATOR K_ACTIVATORnodex nu ACTIVATORnodex H_nodex

&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

Txn1Aff()

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

Txn1Aff

public Txn1Aff()

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