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.
Modifier and Type | Field and Description |
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static int |
P_SM_PRD1 |
static int |
P_SM_PRD2 |
static int |
P_SM_SUB1 |
static int |
P_SM_SUB2 |
static int |
timeStepMultiplier |
pheneVal, roleName
port
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 and Description |
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XhBrusselator() |
Modifier and Type | Method and Description |
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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) |
configure, decPheneVal, getPheneVal, getRoleName, getVal, incPheneVal, initialize, preAct, setPheneVal, setRoleName, setVal, toString, toXmlAttributes
configurePorts, getPort, getPort, isActiveObject, isBound, isContainer, isPassiveObject, postConfigure, setPort, setPort, setPorts, terminate
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
getClass, hashCode, notify, notifyAll, wait, wait, wait
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
public static final int P_SM_SUB1
public static final int P_SM_SUB2
public static final int P_SM_PRD1
public static final int P_SM_PRD2
public static int timeStepMultiplier
public int getNumReactants()
IBioXholon
getNumReactants
in interface IBioXholon
getNumReactants
in class XhAbstractSbml
public void setNumReactants(int numR)
IBioXholon
setNumReactants
in interface IBioXholon
setNumReactants
in class XhAbstractSbml
numR
- Maximum number of reactants.public int getNumProducts()
IBioXholon
getNumProducts
in interface IBioXholon
getNumProducts
in class XhAbstractSbml
public void setNumProducts(int numP)
IBioXholon
setNumProducts
in interface IBioXholon
setNumProducts
in class XhAbstractSbml
numP
- Maximum number of products.public int getNumModifiers()
IBioXholon
getNumModifiers
in interface IBioXholon
getNumModifiers
in class XhAbstractSbml
public void setNumModifiers(int numM)
IBioXholon
setNumModifiers
in interface IBioXholon
setNumModifiers
in class XhAbstractSbml
numM
- Maximum number of modifiers.public int getTimeStepMultiplier()
XhAbstractSbml
getTimeStepMultiplier
in class XhAbstractSbml
public static void setTimeStepMultiplier(int tms)
public void act()
IXholon