affectors
Class TxnLeakyCyceAff

java.lang.Object
  affectors.Affector
      affectors.TxnLeakyCyceAff

All Implemented Interfaces:

java.lang.Cloneable

public class TxnLeakyCyceAff

extends Affector

TxnLeakyCyce implements leaky transcriptional activation under the control of two equivalent activators and one inhibitor. The activation is a sigmoidal curve based on the sum of the two activators. The inhibitor is a noncompetetive inhibitor of transcription. The activator and inhibitor are cytoplasmic. There is a basal rate of transcription which is not affected by the activator, but which is inhibited by the repressor. This is used for the transcription of cyce in the endocycle.

Formula
dcyce/dt = 1/Hcyce (base+(1-base)(((ACT1+ACT2)/K_Act)^nu_Act/(1+(((ACT1+ACT2)/K_Act))^nu_Act+(INH/K_Inh)^nu_Inh))) Psi[INH, K_Inh, nu_Inh]

Parameters

Half life of cyce [Hcyce]	Half life of cyce
Basal transcription rate [base]	The basal transcription rate of cyce in absence of activator
Activator 1 [ACT1]	The first activator node of cyce transcription
Activator 2 [ACT2]	The second activator node of cyce transcription
Inhibitor [INH]	The inhibitor node of cyce transcription
Half maximal activation level [K_Act]	The concentration of activator at which transcription proceeds at half its maximal rate
Half maximal inhibition level [K_Inh]	The concentration of inhibitor at which transcription is half of what it would be otherwise
Activation cooperativity [nu_Act]	The non-linearity of the activating function. The higher the value, the sharper the curves in the S-shaped activation function
Inhibition cooperativity [nu_Inh]	The non-linearity of the inhibition function. The higher the value, the sharper the curves in the S-shaped inhibition function

Usage
&cyce

&TxnLeakyCyceAff ACT1 ACT2 INH H_cyce base K_Act K_Inh nu_Act nu_Inh

&endcyce

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

TxnLeakyCyceAff()

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

TxnLeakyCyceAff

public TxnLeakyCyceAff()

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