org.primordion.cellontro.app.sbml
Class XhBrusselator

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.XhBrusselator
All Implemented Interfaces:
IBioXholon, IXholon

public class XhBrusselator
extends XhAbstractSbml

The famous Brusselator model in which a chemical species X catalyses its own formation. In a certain region of parameter space the Brusselator can function in a limit cycle regime around an unstable steady state. Run this simulation and then check the report file to see how Gepasi can find an unstable steady state, and calculate the eigenvalues of the Jacobian matrix.

Adapted from Copasi example, January 18, 2007, Ken Webb.


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
XhBrusselator()
           
 
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

XhBrusselator

public XhBrusselator()
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