org.primordion.cellontro.app.sbml
Class XhDimericMWCstiff

java.lang.Object
  extended byorg.primordion.xholon.base.Xholon
      extended byorg.primordion.xholon.base.XholonWithPorts
          extended byorg.primordion.cellontro.app.XhAbstractSbml
              extended byorg.primordion.cellontro.app.sbml.XhDimericMWCstiff
All Implemented Interfaces:
IBioXholon, IXholon

public class XhDimericMWCstiff
extends XhAbstractSbml

Example of very stiff biochemical model

This is a model of an allosteric enzyme following the MWC dimeric model, in which the substrate S interacts only with the enzyme species in the R-state. The system of ODEs of this model is very stiff, and correct results can only be obtained with a stiff ODE solver.

This example comes from Hayashi, K. and Sakamoto, N. (1986) Dynamic Analysis of Enzyme Systems, Japan Scientific Societies Press, Tokyo.

Example for: Time course simulation, plotting

Actions:

  1. examine the model (under Model-Biochemical and Model-Mathematical)
  2. run a time course simulation: go to Tasks-Time Course and press the Run button.
  3. There is a trajectory plot already defined with all variables this will appear when the simulation finished (very fast). Note that the S and P variables have values much higher than the other chemical species, to see the others in the plot, press the buttons for [S] and [P], and the graph rescales.


Field Summary
static int P_SM_PRD1
           
static int P_SM_PRD2
           
static int P_SM_SUB1
           
static int P_SM_SUB2
           
static int timeStepMultiplier
           
 
Fields inherited from class org.primordion.cellontro.app.XhAbstractSbml
pheneVal, roleName, securityException
 
Fields inherited from class org.primordion.xholon.base.XholonWithPorts
port
 
Fields inherited from class org.primordion.xholon.base.Xholon
DEFAULT_LEVEL, interaction, interactionsEnabled
 
Fields inherited from interface org.primordion.xholon.base.IXholon
DEFAULT_SIZE_MSG_Q, NINCLUDE_PSC, NINCLUDE_PSx, NINCLUDE_PxC, NINCLUDE_Pxx, NINCLUDE_xSC, NINCLUDE_xSx, NINCLUDE_xxC, NINCLUDE_xxx
 
Constructor Summary
XhDimericMWCstiff()
           
 
Method Summary
 void act()
          Do some action during this time step.
 int getNumModifiers()
          Get maximum number of modifiers (activator, inhibitor) that any xholon instance may have in this model.
 int getNumProducts()
          Get maximum number of products that any xholon instance may have in this model.
 int getNumReactants()
          Get maximum number of reactants (substrates) that any xholon instance may have in this model.
 int getTimeStepMultiplier()
          Get the time step multiplier, needed for numerical integration.
 void setNumModifiers(int numM)
          Set maximum number of modifiers (activator, inhibitor) that any xholon instance may have in this model.
 void setNumProducts(int numP)
          Set maximum number of products that any xholon instance may have in this model.
 void setNumReactants(int numR)
          Set maximum number of reactants (substrates) that any xholon instance may have in this model.
static void setTimeStepMultiplier(int tms)
          Set the time step multiplier, needed for numerical integration.
 
Methods inherited from class org.primordion.cellontro.app.XhAbstractSbml
configure, decPheneVal, getPheneVal, getRoleName, getVal, incPheneVal, initialize, preAct, setRoleName, toString
 
Methods inherited from class org.primordion.xholon.base.XholonWithPorts
getMaxPorts, getPort, isActiveObject, isBound, isContainer, isPassiveObject, postConfigure, setMaxPorts, setPorts, terminate
 
Methods inherited from class org.primordion.xholon.base.Xholon
appendChild, appendChild, appendChild, cleanup, configure, createStructure, decVal, decVal, depth, draw, getChildNodes, getFirstChild, getFirstSibling, getId, getLastChild, getLastSibling, getName, getNeighbors, getNextId, getNextSibling, getNthChild, getNthSibling, getNumChildren, getNumSiblings, getParentNode, getPreviousSibling, getRootNode, getSiblings, getSizeMessageQ, getUid, getVal_boolean, getVal_byte, getVal_char, getVal_double, getVal_float, getVal_int, getVal_long, getVal_Object, getVal_short, getVal_String, getXhc, getXhcId, getXhcName, getXhType, handleNodeSelection, hasAncestor, hasChildNodes, hasChildOrSiblingNodes, hasNextSibling, hasParentNode, height, incVal, incVal, initStatics, inOrderPrint, insertAfter, insertBefore, insertFirstChild, isExternal, isInternal, isLeaf, isRootNode, performActivity, performActivity, performBooleanActivity, performBooleanActivity, performDoubleActivity, performGuard, performVoidActivity, postAct, postOrderPrint, postReconfigure, preConfigure, preOrderPrint, preReconfigure, print, println, processMessageQ, processReceivedMessage, reconfigure, remove, removeChild, resetNextId, sendMessage, sendMessage, sendMessage, setAttributeVal, setFactory, setFirstChild, setId, setNextSibling, setParentChildLinks, setParentNode, setParentSiblingLinks, setSizeMessageQ, setUid, setVal, setVal, setVal, setVal, setVal, setVal, setVal, setVal, setVal, setVal, setVariableValue, setXhc, swapNode, treeSize, writeXml
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
 
Methods inherited from interface org.primordion.xholon.base.IXholon
appendChild, appendChild, appendChild, cleanup, configure, createStructure, decVal, decVal, depth, draw, getChildNodes, getFirstChild, getFirstSibling, getId, getLastChild, getLastSibling, getName, getNeighbors, getNextSibling, getNthChild, getNthSibling, getNumChildren, getNumSiblings, getParentNode, getPort, getPreviousSibling, getRootNode, getSiblings, getUid, getVal_boolean, getVal_byte, getVal_char, getVal_double, getVal_float, getVal_int, getVal_long, getVal_Object, getVal_short, getVal_String, getXhc, getXhcId, getXhcName, getXhType, handleNodeSelection, hasAncestor, hasChildNodes, hasChildOrSiblingNodes, hasNextSibling, hasParentNode, height, incVal, incVal, initStatics, inOrderPrint, insertAfter, insertBefore, insertFirstChild, isActiveObject, isBound, isContainer, isExternal, isInternal, isLeaf, isPassiveObject, isRootNode, performActivity, performActivity, performBooleanActivity, performBooleanActivity, performDoubleActivity, performGuard, performVoidActivity, postAct, postConfigure, postOrderPrint, postReconfigure, preConfigure, preOrderPrint, preReconfigure, print, println, processMessageQ, processReceivedMessage, reconfigure, remove, removeChild, sendMessage, sendMessage, sendMessage, setAttributeVal, setFirstChild, setId, setNextSibling, setParentChildLinks, setParentNode, setParentSiblingLinks, setPorts, setUid, setVal, setVal, setVal, setVal, setVal, setVal, setVal, setVal, setVal, setVal, setVariableValue, setXhc, swapNode, terminate, treeSize, writeXml
 

Field Detail

P_SM_SUB1

public static final int P_SM_SUB1
See Also:
Constant Field Values

P_SM_SUB2

public static final int P_SM_SUB2
See Also:
Constant Field Values

P_SM_PRD1

public static final int P_SM_PRD1
See Also:
Constant Field Values

P_SM_PRD2

public static final int P_SM_PRD2
See Also:
Constant Field Values

timeStepMultiplier

public static int timeStepMultiplier
Constructor Detail

XhDimericMWCstiff

public XhDimericMWCstiff()
Method Detail

getNumReactants

public int getNumReactants()
Description copied from interface: IBioXholon
Get maximum number of reactants (substrates) that any xholon instance may have in this model.

Specified by:
getNumReactants in interface IBioXholon
Specified by:
getNumReactants in class XhAbstractSbml

setNumReactants

public void setNumReactants(int numR)
Description copied from interface: IBioXholon
Set maximum number of reactants (substrates) that any xholon instance may have in this model.

Specified by:
setNumReactants in interface IBioXholon
Specified by:
setNumReactants in class XhAbstractSbml

getNumProducts

public int getNumProducts()
Description copied from interface: IBioXholon
Get maximum number of products that any xholon instance may have in this model.

Specified by:
getNumProducts in interface IBioXholon
Specified by:
getNumProducts in class XhAbstractSbml

setNumProducts

public void setNumProducts(int numP)
Description copied from interface: IBioXholon
Set maximum number of products that any xholon instance may have in this model.

Specified by:
setNumProducts in interface IBioXholon
Specified by:
setNumProducts in class XhAbstractSbml

getNumModifiers

public int getNumModifiers()
Description copied from interface: IBioXholon
Get maximum number of modifiers (activator, inhibitor) that any xholon instance may have in this model.

Specified by:
getNumModifiers in interface IBioXholon
Specified by:
getNumModifiers in class XhAbstractSbml

setNumModifiers

public void setNumModifiers(int numM)
Description copied from interface: IBioXholon
Set maximum number of modifiers (activator, inhibitor) that any xholon instance may have in this model.

Specified by:
setNumModifiers in interface IBioXholon
Specified by:
setNumModifiers in class XhAbstractSbml

getTimeStepMultiplier

public int getTimeStepMultiplier()
Description copied from class: XhAbstractSbml
Get the time step multiplier, needed for numerical integration.

Overrides:
getTimeStepMultiplier in class XhAbstractSbml
Returns:
Time step multiplier.

setTimeStepMultiplier

public static void setTimeStepMultiplier(int tms)
Description copied from class: XhAbstractSbml
Set the time step multiplier, needed for numerical integration.


act

public void act()
Description copied from interface: IXholon
Do some action during this time step. Typically all nodes in the tree will do their pre-actions (optional), then all will do their actions, and then all will do their post-actions (optional).

Specified by:
act in interface IXholon
Overrides:
act in class Xholon