|
Class Summary |
| Affector |
Stores the formula for how a node changes over time. |
| Affector_Template |
This should be a description of what this Affector does and where it might be used
This description will show up in the online html documentation files. |
| Cleavage2A_ICAff |
This is one half of an affector that cleaves a single node into two other
nodes. |
| Cleavage2B_ICAff |
This is one half of an affector that cleaves a single node into two other
nodes under the influence of an inhibitor. |
| CleavageA_ECAff |
This is one half of an affector that cleaves a single node into two other
nodes. |
| CleavageA_ICAff |
This is one half of an affector that cleaves a single node into two other
nodes. |
| CleavageA_ICDipAff |
Diploid version of CleaveageA_ICAff. |
| CleavageB_ECAff |
This is one half of an affector that cleaves a single node into two other
nodes. |
| CleavageB_ICAff |
This is one half of an affector that cleaves a single node into two other
nodes. |
| CleavageB_ICDipAff |
Diploid version of CleaveageB_ICAff. |
| CleaveA_Aff |
This is one half of an affector that cleaves a single cytoplasmic node into two other
cytoplasmic nodes. |
| CleaveB_Aff |
This is one half of an affector that cleaves a single cytoplasmic node into two other
cytoplasmic nodes. |
| CompAct2Aff |
The simplest regulated transcription affector. |
| ConstantInputAff |
This affector returns a constant value. |
| ConstantLevelAff |
This affector returns a constant value to cause the target node to go to
the specified final value (Final) when coupled to constant linear decay. |
| ConversionEAff |
Generalized rate-based conversion of one Node to another. |
| ConversionIAff |
Generalized rate-based conversion of one Node to another. |
| DecayAff |
This is the standard affector for decay of a Node. |
| DecayRegDownAff |
Use this for decay of a Node when the decay rate can be lowered (half life raised) by
the presence of another node. |
| DecayRegUpAff |
Use this for decay of a Node when the decay rate can be raised (half life lowered) by
the presence of another node. |
| DefinedValuesAff |
An artificial Affector which brings a Node from its initial value to a second
value starting at a specified time and taking a specified amount of time to do the
change. |
| DefinedValuesIndicatorAff |
An artificial Affector which sets nodes to specific values. |
| Dephosphor1StepA_ICAff |
This is one half of an affector that dephosphorylates a single node at a speed determined
by a phosphatase enzyme according to a sigmoid curve. |
| Dephosphor1StepB_ICAff |
This is one half of an affector that dephosphorylates a single node. |
| DephosphorylateA_Aff |
This is one half of an affector that dephosphorylates a single node assuming a constant
background phosphotase activity. |
| DephosphorylateB_Aff |
This is one half of an affector that dephosphorylates a single node assuming a constant
background phosphotase activity. |
| DephosphorylationA_ICAff |
This is one half of an affector that dephosphorylates a single node at a speed determined
by a phosphatase enzyme according to a sigmoid curve. |
| DephosphorylationB_ICAff |
This is one half of an affector that dephosphorylates a single node. |
| Dimerize_AAff |
This is the one half of a dimerization where both undimerized Nodes reside in the same cell. |
| Dimerize_BAff |
This is the one half of a dimerization where both undimerized Nodes reside in the same cell. |
| DimerizeAllMembrane_AAff |
This is one half of a dimerization where the ligand and receptor can
bind within the same membrane as well as across different faces. |
| DimerizeAllMembrane_BAff |
This is the other half of a dimerization where the ligand and receptor can
bind within the same membrane as well as across different faces. |
| DimerizeCrossMembrane_AAff |
This is one half of a membrane-bound dimerization reaction where one single Node resides
in one cell and the other single Node resides in a neighboring cell. |
| DimerizeCrossMembrane_BAff |
This is the other half of a membrane-bound dimerization reaction where one single Node resides
in one cell and the other single Node resides in a neighboring cell. |
| DimerizeCytoMem_AAff |
This is one third of a dimerization between a membrane bound and a cytoplasmic
protein, leading to a membrane bound complex. |
| DimerizeCytoMem_BAff |
This is one third of a heterodimerization between a membrane bound and a cytoplasmic
protein, leading to a membrane-bound complex. |
| DimerizeCytoMem_CAff |
This is the third half of a heterodimerization between a membrane-bound and a cytoplasmic
protein, leading to a membrane-bound complex. |
| DimerizeMemCyto_AAff |
This is one third of a dimerization between a membrane bound and a cytoplasmic
protein, leading to a cytoplasmic complex. |
| DimerizeMemCyto_BAff |
This is one third of a heterodimerization between a membrane bound and a cytoplasmic
protein, leading to a cytoplasmic complex. |
| DimerizeMemCyto_CAff |
This is the third half of a heterodimerization between a membrane-bound and a cytoplasmic
protein, leading to a cytoplasmic complex. |
| DissociationA_Aff |
One third of a triplet of affectors which mediates dissociation of protein complexes. |
| DissociationB_Aff |
One third of a triplet of affectors which mediates dissociation of protein complexes. |
| DissociationC_Aff |
One third of a triplet of affectors which mediates dissociation of protein complexes. |
| DissociationCytoMemA_Aff |
One third of a triplet of affectors which mediates dissociation of protein complexes where
one of the ligands is cytoplasmic and the other is membrane-bound. |
| DissociationCytoMemB_Aff |
One third of a triplet of affectors which mediates dissociation of protein complexes where
one of the ligands is cytoplasmic and the other is membrane-bound. |
| DissociationCytoMemC_Aff |
One third of a triplet of affectors which mediates dissociation of protein complexes where
one of the ligands is cytoplasmic and the other is membrane-bound. |
| DissociationEC_Com_Aff |
One third of a triplet of affectors which mediates dissociation of receptor-ligand complexes. |
| DissociationEC_Lig_Aff |
One third of a triplet of affectors which mediates dissociation of receptor-ligand complexes. |
| DissociationEC_Rec_Aff |
One third of a triplet of affectors which mediates dissociation of receptor-ligand complexes. |
| EndoEAff |
For endocytosis from an extracellular node - sided; use this one in the
node that is getting endocytosed. |
| EndoIAff |
For endocytosis to an intracellular node - non-sided; use this one in the
node representing the intracellular compartment. |
| EnhancerRegionAff |
EnhancerRegion surrounds other enhancers and multiplies them by the
scaling (characteristicTime / halfLife). |
| EnzymeConversionEC_Pro_Aff |
This is one half of an affector that converts a single node into another
based on some enzymatic activity. |
| EnzymeConversionEC_Sub_Aff |
This is one half of an affector that converts a single node into another
based on some enzymatic activity. |
| ExoEAff |
For exocytosis from an intracellular to a membrane-bound Node. |
| ExoIAff |
For exocytosis from an intracellular to a membrane-bound Node. |
| Formula1Aff |
A relic Affector. |
| HeatShockAff |
This is for use by Experiments to simulate a heat shock pulse of some Node. |
| HeterodimerizeA_EC_XAff |
An old name for DimerizeAllMembrane_AAff |
| HeterodimerizeA_EC2Aff |
An old name for Dimerize_AAff |
| HeterodimerizeA_ECAff |
An old name for DimerizeCrossMembrane_AAff |
| HeterodimerizeA_ECICAff |
An old name for DimerizeMemeCyto_AAff |
| HeterodimerizeA_ICAff |
An old name for Dimerize_AAff |
| HeterodimerizeB_EC_XAff |
An old name for DimerizeAllMembrane_BAff |
| HeterodimerizeB_EC2Aff |
An old name for Dimerize_BAff |
| HeterodimerizeB_ECAff |
An old name for DimerizeCrossMembrane_BAff |
| HeterodimerizeB_ECICAff |
An old name for DimerizeMemCyto_BAff |
| HeterodimerizeB_ICAff |
An old name for Dimerize_BAff |
| HeterodimerizeC_ECICAff |
An old name for DimerizeMemCyto_CAff |
| LMxferEAff |
This is one half of a pair of Affectors that moves things between
neighboring faces of a cell. |
| LMxferIAff |
This is one half of a pair of Affectors that moves things between
neighboring faces of a cell. |
| MultiEnhancerAff |
This is a meta-affector which sums together transcriptional activation terms while keeping
the total transcription rate less than or equal to 1. |
| MxferInAff |
This is one half of a pair of Affectors that moves things from a face of one
cell to the opposing face of a neighboring cell. |
| MxferOutAff |
This is one half of a pair of Affectors that moves things from a face of one
cell to the opposing face of a neighboring cell. |
| NoChangeAff |
Returns zero as the derivative; use to lock a Node at a constant level,
such as an initial condition that should persist indefinitely. |
| Phosphor1StepA_ICAff |
This is one half of an affector that phosphrylates a single node. |
| Phosphor1StepB_ICAff |
This is one half of an affector that phosphrylates a single node. |
| PhosphorylateA_Aff |
This is one half of an affector that phosphorylates a single node based on a kinase
activity. |
| PhosphorylateB_Aff |
This is one half of an affector that phosphorylates a single node based on a kinase
activity. |
| PhosphorylationA_ICAff |
This is one half of an affector that phosphorylates a single node. |
| PhosphorylationB_ICAff |
This is one half of an affector that phosphrylates a single node. |
| PlaceHolderAff |
Placeholder affector for use with creating dummy (i.e. |
| Product |
This is a special "meta-affector". |
| ProductAff |
This is a special "meta-affector". |
| PsiAff |
We call our basic upside-down sigmoid function "Psi". |
| PsiECAff |
This is similar to the Psi function except the inhibitor
is in a neighboring cell from the one that contains the target Node. |
| RecycleAAff |
One half of a pair of affectors which recycles proteins from one state back to another. |
| RecycleBAff |
The other half of a pair of affectors which recycles proteins from one state back
to another. |
| SaturationEnhancerAff |
This is the wrapper for meta-affectors which need to be put through a saturating function. |
| SumAff |
This is a special "meta-affector". |
| TlnAff |
Translation of an mRNA into protein. |
| TlnRegUpAff |
Translation of an mRNA into protein. |
| Txn1Aff |
The simplest regulated transcription affector. |
| Txn1ECAff |
A variant of Txn1Aff that integrates an external influence from a neighboring cell
(e.g. |
| Txn2aAff |
Txn2a implements transcriptional activation under the control of one activator and one
inhibitor, the latter of which competetively inhibits the activator. |
| Txn2aDipAff |
Diploid version of Txn2bAff. |
| Txn2bAff |
Txn2b implements transcriptional activation under the control of one extracellular
activator expressed on neighboring cells and one cytoplasmic inhibitor, the latter of
which competetively inhibits the activator. |
| Txn2bDipAff |
Diploid version of Txn2bAff. |
| Txn3aAff |
Txn3a takes two activators which synergize such that only in the presence of both can the
target achieve full activity. |
| Txn3bAff |
Txn3b takes two activators which synergize such that the second makes the first more potent. |
| Txn4Aff |
Txn4 takes two activators and one inhibitor which titrates away the *second* activator. |
| Txn4DipAff |
Diploid version of Txn4Aff. |
| Txn5Aff |
Txn5 takes two activators and one inhibitor that suppresses both activators equally. |
| Txn6aAff |
Txn6a takes two activators which synergize such that only in the presence of both
can the target achieve full activity, and one inhibitor which reduces the effective
concentration of the SECOND of these. |
| Txn6bAff |
Txn6b takes two activators which synergize such that only in the presence of both
can the target achieve full activity, and one inhibitor which reduces the effective
concentration of the FIRST of these. |
| TxnLeakyCyceAff |
TxnLeakyCyce implements leaky transcriptional activation under the control of two equivalent activators
and one inhibitor. |
| TxnSiteActInhibit2Aff |
Use for activation + inhibition of transcription. |
| TxnSiteActInhibit3Aff |
Use for activation + inhibition of transcription. |
| TxnSiteActInhibitAff |
Use for activation + inhibition of transcription. |
| TxnSiteActivator1Aff |
An old name for TxnSiteActivator |
| TxnSiteActivatorAff |
Use for activation of transcription. |
| TxnSiteAddInhibitorAff |
Use for inhibitor that is additive. |
| TxnSiteInhibitorAff |
Use for multiplicative inhibition of transcription. |
| VonForresterA_Aff |
This affector implements one half of a constant delay through a von Forrester equation. |
| VonForresterA_ECAff |
This affector implements one half of a constant delay through a von Forrester equation. |
| VonForresterA_ICAff |
This affector implements one half of a constant delay through a von Forrester equation. |
| VonForresterB_Aff |
This affector implements one half of a constant delay through a von Forrester equation. |
| VonForresterB_ECAff |
This affector implements one half of a constant delay through a von Forrester equation. |
| VonForresterB_ICAff |
This affector implements one half of a constant delay through a von Forrester equation. |
| WhiteNoiseAff |
Adds white noise to the concentration of a node. |
| XferInAff |
This is one half of a pair of Affectors that moves things from one cell to
neighboring cells. |
| XferOutAff |
This is one half of a pair of Affectors that moves things from one cell to
neighboring cells. |