affectors
Class Txn2bAff

java.lang.Object
  affectors.Affector
      affectors.Txn2bAff

All Implemented Interfaces:

java.lang.Cloneable

public class Txn2bAff

extends Affector

Txn2b implements transcriptional activation under the control of one extracellular activator expressed on neighboring cells and one cytoplasmic inhibitor, the latter of which competetively inhibits the activator. The inhibitor behaves as if it titrates away the activator according to some dose-response curve; another way to look at it is that the inhibitor raises the threshhold for activation.

Formula
EFFECTIVE_ACT = ACTIVATOR(neighbors) * ( 1 - INHIBITOR^nu_INHIB / (K_INHIBITOR^nu_INHIB + INHIBITOR^nu_INHIB))
dnodex/dt = (1 / H_nodex) * EFFECTIVE_ACT^nu_ACT / (K_ACT^nu_ACT + EFFECTIVE_ACT^nu_ACT)

Parameters

Inhibitor [INHIBITOR]	The inhibitor Node
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
Activator 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
Half-max inhibition level [K_INHIBITOR]	The concentration of inhibitor at which transcription proceeds at half the rate it would have otherwise
Inhibition Cooperativity [nu_INHIBITOR]	The non-linearity of the inhibiting function. The higher the value, the sharper the curves in the upside-down S-shaped inhibition function

Usage
&nodex

&Txn2bAff INHIBITOR ACTIVATOR K_ACTIVATORnodex nu_ACTIVATORnodex H_nodex K_INHIBITORnodex nu_INHIBITORnodex

&endnodex

NOTE - you can accomplish this same function using the meta-enhancers, and those are a more general framework for putting together transcription terms.

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

Txn2bAff()

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

Txn2bAff

public Txn2bAff()

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