affectors
Class Txn1ECAff

java.lang.Object
  affectors.Affector
      affectors.Txn1ECAff

All Implemented Interfaces:

java.lang.Cloneable

public class Txn1ECAff

extends Affector

A variant of Txn1Aff that integrates an external influence from a neighboring cell (e.g. a signalling protein) and activates transcription as a function of the total activator presented on all cell faces. Use this if you want to skip the signal transduction cascade between a ligand on neighboring cells and transcription. Everything else is the same as Txn1Aff.

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

&Txn1ECAff 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

Txn1ECAff()

Method Summary

void	fixNodes(Cell cell, java.lang.String[] node_names)
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, 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

Txn1ECAff

public Txn1ECAff()

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

fixNodes

public void fixNodes(Cell cell,
                     java.lang.String[] node_names)
              throws java.lang.Exception

Overrides:

fixNodes in class Affector

Throws:

java.lang.Exception