org.primordion.cellontro.app.sbml

Class XhDimericMWCstiff

java.lang.Object

org.primordion.xholon.base.Xholon

org.primordion.xholon.base.XholonWithPorts

org.primordion.cellontro.app.sbml.XhAbstractSbml

org.primordion.cellontro.app.sbml.XhDimericMWCstiff

All Implemented Interfaces:

java.io.Serializable, java.lang.Comparable, IBioXholon, IXholon, XholonMarker

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.

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
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.sbml.XhAbstractSbml

pheneVal, roleName

Fields inherited from class org.primordion.xholon.base.XholonWithPorts

port

Fields inherited from interface org.primordion.xholon.base.IXholon

DEFAULT_SIZE_MSG_Q, DEFAULT_SIZE_SYSTEM_MSG_Q, GETNAME_DEFAULT, GETNAME_LOCALPART_ID, GETNAME_NOROLENAME, GETNAME_ROLENAME_OR_CLASSNAME, GETNAME_ROLENAMESEP_, GETNAME_SIZE_TEMPLATE, NINCLUDE_PSC, NINCLUDE_PSx, NINCLUDE_PxC, NINCLUDE_Pxx, NINCLUDE_xSC, NINCLUDE_xSx, NINCLUDE_xxC, NINCLUDE_xxx, XHOLON_ID_DEFAULT, XHOLON_ID_NULL

Constructor Summary

Constructors

Constructor and Description
XhDimericMWCstiff()

Method Summary

Methods

Modifier and Type	Method and Description
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)

Methods inherited from class org.primordion.cellontro.app.sbml.XhAbstractSbml

configure, decPheneVal, getPheneVal, getRoleName, getVal, incPheneVal, initialize, preAct, setPheneVal, setRoleName, setVal, toString, toXmlAttributes

Methods inherited from class org.primordion.xholon.base.XholonWithPorts

configurePorts, getPort, getPort, isActiveObject, isBound, isContainer, isPassiveObject, postConfigure, setPort, setPort, setPorts, terminate

Methods inherited from class org.primordion.xholon.base.Xholon

actNr, appendChild, appendChild, appendChild, appendsOwnChildren, bindPorts, cleanup, compareTo, configure, consoleLog, decVal, decVal, depth, doAction, equals, findFirstChildWithXhClass, findFirstChildWithXhClass, forwardMessage, forwardSyncMessage, getActionList, getAllPorts, getAnnotation, getApp, getAttributeNodeXh, getAttributeXh, getChildNodes, getClassNode, getClassNode, getFactory, getFirstChild, getFirstSibling, getId, getInteraction, getInteractionsEnabled, getIQueueImplName, getLastChild, getLastSibling, getLogger, getMsgQ, getName, getName, getNeighbors, getNextSibling, getNthChild, getNthSibling, getNumChildren, getNumLevels, getNumSiblings, getParentNode, getPreviousSibling, getRootNode, getSelfAndSiblings, getSelfAndSiblingsIndex, getService, getSiblings, getSystemMsgQ, getUid, getUri, getVal_boolean, getVal_byte, getVal_char, getVal_double, getVal_float, getVal_int, getVal_long, getVal_Object, getVal_short, getVal_String, getXhc, getXhcId, getXhcName, getXholon2Xml, getXhType, getXml2Xholon, getXPath, handleNodeSelection, handleNodeSelection, hasAncestor, hasAnnotation, hasAttributeXh, hasChildNodes, hasChildOrSiblingNodes, hasNextSibling, hasParentNode, hasSiblingNodes, height, incVal, incVal, initStatics, inOrderPrint, insertAfter, insertAfter, insertAfter, insertBefore, insertBefore, insertBefore, insertFirstChild, isAttributeHandler, isExternal, isInternal, isLeaf, isRootNode, isUniqueSibling, isUniqueSiblingRoleName, performActivity, performActivity, performBooleanActivity, performBooleanActivity, performDoubleActivity, performGuard, performVoidActivity, postAct, postOrderPrint, postReconfigure, preConfigure, preOrderPrint, preReconfigure, print, println, processMessageQ, processReceivedMessage, processReceivedSyncMessage, processSystemMessageQ, reconfigure, registerMessageForwardee, remove, removeAttributeNodeXh, removeAttributeXh, removeChild, replaceNode, searchForReferencingNodes, searchForReferencingNodesRecurse, sendMessage, sendMessage, sendMessage, sendSyncMessage, sendSyncMessage, sendSyncMessage, sendSystemMessage, sendSystemMessage, setActionList, setAnnotation, setApp, setAttributeNodeXh, setAttributeVal, setAttributeXh, setFirstChild, setId, setName, setNextSibling, setParentChildLinks, setParentNode, setParentSiblingLinks, setUid, setUri, setVal_boolean, setVal_byte, setVal_char, setVal_double, setVal_float, setVal_int, setVal_long, setVal_Object, setVal_short, setVal_String, setVal, setVal, setVal, setVal, setVal, setVal, setVal, setVal, setVal, setXhc, showAnnotation, swapNode, toXml, toXmlAttribute, toXmlText, treeSize, visit

Methods inherited from class java.lang.Object

getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.primordion.xholon.base.IXholon

actNr, appendChild, appendChild, appendChild, appendsOwnChildren, bindPorts, cleanup, configure, consoleLog, decVal, decVal, depth, doAction, findFirstChildWithXhClass, findFirstChildWithXhClass, forwardMessage, forwardSyncMessage, getActionList, getAllPorts, getAnnotation, getApp, getAttributeNodeXh, getAttributeXh, getChildNodes, getClassNode, getClassNode, getFirstChild, getFirstSibling, getId, getLastChild, getLastSibling, getName, getName, getNeighbors, getNextSibling, getNthChild, getNthSibling, getNumChildren, getNumLevels, getNumSiblings, getParentNode, getPort, getPort, getPreviousSibling, getRootNode, getSelfAndSiblings, getSelfAndSiblingsIndex, getService, getSiblings, getUid, getUri, getVal_boolean, getVal_byte, getVal_char, getVal_double, getVal_float, getVal_int, getVal_long, getVal_Object, getVal_short, getVal_String, getXhc, getXhcId, getXhcName, getXholon2Xml, getXhType, getXml2Xholon, handleNodeSelection, handleNodeSelection, hasAncestor, hasAnnotation, hasAttributeXh, hasChildNodes, hasChildOrSiblingNodes, hasNextSibling, hasParentNode, hasSiblingNodes, height, incVal, incVal, initStatics, inOrderPrint, insertAfter, insertAfter, insertAfter, insertBefore, insertBefore, insertBefore, insertFirstChild, isActiveObject, isAttributeHandler, isBound, isContainer, isExternal, isInternal, isLeaf, isPassiveObject, isRootNode, isUniqueSibling, isUniqueSiblingRoleName, performActivity, performActivity, performBooleanActivity, performBooleanActivity, performDoubleActivity, performGuard, performVoidActivity, postAct, postConfigure, postOrderPrint, postReconfigure, preConfigure, preOrderPrint, preReconfigure, print, println, processMessageQ, processReceivedMessage, processReceivedSyncMessage, processSystemMessageQ, reconfigure, registerMessageForwardee, remove, removeAttributeNodeXh, removeAttributeXh, removeChild, replaceNode, searchForReferencingNodes, sendMessage, sendMessage, sendMessage, sendSyncMessage, sendSyncMessage, sendSyncMessage, sendSystemMessage, sendSystemMessage, setActionList, setAnnotation, setApp, setAttributeNodeXh, setAttributeVal, setAttributeXh, setFirstChild, setId, setName, setNextSibling, setParentChildLinks, setParentNode, setParentSiblingLinks, setPort, setPort, setPorts, setUid, setUri, setVal_boolean, setVal_byte, setVal_char, setVal_double, setVal_float, setVal_int, setVal_long, setVal_Object, setVal_short, setVal_String, setVal, setVal, setVal, setVal, setVal, setVal, setVal, setVal, setVal, setXhc, showAnnotation, swapNode, terminate, toXml, toXmlAttribute, toXmlText, treeSize, visit

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

Returns:

Maximum number of reactants.

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

Parameters:

numR - Maximum number of reactants.

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

Returns:

Maximum number of products.

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

Parameters:

numP - Maximum number of products.

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

Returns:

Maximum number of modifiers.

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

Parameters:

numM - Maximum number of modifiers.

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)

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