Each principal class corresponds to problem domain. In most cases the class contains a list of instances of the model itself. This allows different instances of the model to share components. In general they also contain further class models for describing subcomponents of the problem and the associated calculations.
| HHCell | electrically compact cell with Hodgkin-Huxley channels |
| KSCell | electrically compact cell with kinetic scheme channels, including schemes equivalent to HH models |
| ReactionKinetics | chemical reactions in a single well mixed pool |
| ReactionDiffusion | reaction diffusion systems in 1-D linear or spherical geometry |
| ReacDiff2 | reaction diffusion systems in 2-D plane parallel or axially symmetric geometry |
| CFNet | continuous firing rate network |
| IaFNet | integrate and fire networks |
| PassiveProp | passive conduction in branched neurons |
| CellGeometry | geometrical and electrical transformations of dendritic trees |
| ArtCell | growth models for simulating branching dendritic trees |
| Numerics |
This is a complete list of the data and calculation classes in Catacomb. Although they can be instantiated individually, most require connections to other catacomb class models which are best made from instances of the top level objects above.
| AppletConfig |
layout of components grouped together in a single panel for making applets
user interface: AppletConfigEditor |
| ArtCell | growth models for simulating branching dendritic trees |
| BinaryControl |
multi-channel binary signal
user interface: BinaryControlEditor |
| BranchedCell |
branched cell geometry defined by point positions, diameters, and neighbors
user interface: BranchedCellEditor |
| CalcResults |
container for the results of calculations
user interface: CalcResultsEditor |
| CalcResults3 |
3-d result data
user interface: CalcResults3Editor |
| CcmbCalc | superclass of most objects defining calculation methods |
| Catacomb |
the top of the object hierarchy, containing an overview of the current model
user interface: CatacombEditor |
| CcmbLink | superclass of possible links in CcmbNet objects |
| CcmbNet |
superclass of all node-and-link type objects
user interface: CcmbNetEditor |
| CcmbNode | a single node in a CcmbNet object or subclass thereof |
| CcmbObject |
superclass of all public Catacomb objects
user interface: CcmbObjectEditor |
| CcmbSystem | global preferences for catacomb operation and state information |
| CcmbPython | An interface object between Catacomb and the JPython interpreter. |
| CcmbPyModule | A wrapper object for JPython modules. |
| KSRateConc | concentration dependent transition for kinetic schemes |
| CellGeometry | geometrical and electrical transformations of dendritic trees |
| CellGrower | simulated dendritic branching and elongation |
| CellProps | passive electrical properties for BranchedCell objects |
| CellTransformer | electrical and geometrical transforms of branched cells |
| CFCalc | calculation methods for continuous firing rate networks |
| CFLink | a link in a continuous firing rate network |
| CFMetaWF | patterned stimulation for the members of a population in an IaFNetwork |
| CFNetwork |
a continuous firing rate network
user interface: CFNetworkEditor |
| CFNode | a node in a continuous firing rate network |
| CFStimNode | input for a continuous firing rate network |
| PointClamp | abstract superclass of voltage or current clamps for used with BranchedCell instances |
| PointClampG | conductance clamp for branched cells |
| PointClampI | current clamp for branched cells |
| PointClampR | voltage recorder for BranchedCell objects |
| PointClampV | voltage clamp for branched cells |
| ColorTable |
an indexed color table
user interface: ColorTableEditor |
| ColorTarget |
wrapper for a color as it is being modified
user interface: ColorTargetEditor |
| DataClipboard |
clipboard for manipulating imported or internally generated 2-D arrays
user interface: DataClipboardEditor |
| DiffMeasure |
measure of the difference between the results of a model and
provided data.
user interface: DiffMeasureEditor |
| DrawingMarker | properties associated with drawing elements |
| RSReacEnzyme | Michaelis Menten enzyme kinetics |
| ErrorLog |
source, time and severity log of internal errors
user interface: ErrorLogEditor |
| ExcisedPatchCalc | calculation methods for excised patches containing kinetic scheme channels |
| RSReacExternal | externally defined transition for reaction schemes |
| FieldConfig |
temporary container for an objects field visibility array
user interface: FieldConfigEditor |
| GlobalDefinitions | global definitions common to all Catacomb objects |
| ArtCellParameters | growth parameters for artificial cells |
| HelpTarget |
wrapper for the current focus of the on-line help system
user interface: HelpTargetEditor |
| HHCalc | cell environment and calculation methods for Hodgkin-Huxley equations in HHCell |
| HHCell | electrically compact cell with Hodgkin-Huxley channels |
| HHChannel |
a Hodgkin-Huxley type channel, comprising a list of gates,
and a pointer to its permeant ion
user interface: HHChannelEditor |
| HHGate | a voltage dependent gate for Hodgkin-Huxley style channels |
| HHIon | ion for use in Hodgkin-Huxley models |
| IaFCalc | calculation methods for integrate-and-fire networks |
| IaFGroupNode | a single node (population) in an integrate-and-fire network |
| IaFLink | superclass of possible link types for integrate and fire networks |
| IaFLinkDF | delta function connection between populations in an integrate and fire network |
| IaFLinkGJ | a direct electrical connection between populations in an integrate and fire network |
| IaFLinkSC | a synaptic connection between populations in an integrate and fire network |
| IaFMetaWf | patterned stimulation for the members of a population in an IaFNetwork |
| IaFNet | integrate and fire networks |
| IaFNetwork |
integrate and fire network
user interface: IaFNetworkEditor |
| IaFNode | superclass of population nodes in an integrate and fire network |
| IaFPatStim | patterned stimulation for the members of a population in an IaFNetwork |
| IaFStimNode | a stimulus node with an externally controlled potential or firing rate |
| IaFSynPars | parameters for modifiable synapses in integrate and fire networks |
| RSReacBind | binding transition for reaction schemes |
| RSLinkIdent | pseudo-reaction to indicate that pools occurring in different parts of a reaction schemes should be treated as identical |
| InfoMessage |
occasionally useful messages about what is going on
user interface: InfoMessageEditor |
| IVLaw | current-voltage relation for kinetic scheme channels |
| KSCalc | Current clamp and voltage clamp calculations with kinetic scheme channels |
| KSStateCalc | state occupancy of a set of kinetic scheme channels |
| KSChannel |
a channel defined as Kinetic Scheme - state diagram and
transition rates
user interface: KSChannelEditor |
| KSIon | ion for use with kinetic scheme channel models |
| KSRate | superclass of all possible transitions in kinetic schemes |
| KSSolution | simple solution defined by the concentrations of its ions and molecules |
| KSState | A single state of a Kinetic Scheme channel. |
| KSStateView |
Stochastic simulation of a set of kinetic scheme channels.
user interface: KSStateViewEditor |
| KSStateView |
Stochastic simulation of a set of kinetic scheme channels.
user interface: KSStateViewEditor |
| LabelledDrawing |
drawing containing labelled regions and lines
user interface: LabelledDrawingEditor |
| LinearDE2 | linear second order differential equation |
| MeshedDrawing |
labelled drawing with additional meshing information
user interface: MeshedDrawingEditor |
| MeshCtrl | variables for controlling how a mesh is built for a meshed drawing |
| LineSet |
2-D array of calculation results or imported data
user interface: LineSetEditor |
| MultiDiffMeasure |
sensitivity analysis, showing how a difference measure changes as
one parameter is systematically varied
user interface: MultiDiffMeasureEditor |
| KSRateMult | kinetic scheme transition defined in terms of multiples of the rates in another transition |
| RSReacMult | special case to simplify setting up reactions of the form nA + mB = pC. |
| CcmbListWrapper | trivial wrapper for saving and restoring lists |
| NetView |
user interface: NetViewEditor |
| ObjectInfo |
text to accompany an instance of a model for building the documentation
user interface: ObjectInfoEditor |
| ParamOptimization | tools for sensitivity analysis and parameter optimization |
| PassiveProp | passive conduction in branched neurons |
| RandomVariable | random variable with a uniform, normal or gamma distribution |
| PhaseDiffMeasure |
difference measure defined in phase space
user interface: PhaseDiffMeasureEditor |
| RSLinkPlus | connector for defining reaction or product groups in reaction schemes |
| PPCalc | calculation of voltage transients in branched cells |
| ReacDiff2Calc | Reaction Diffusion on a 2-D triangular mesh |
| ReacDiff2Results |
Movie of the results of a reaction-diffusion calculation.
user interface: ReacDiff2ResultsEditor |
| RDCalc | calculation methods for reaction-diffusion systems |
| ReactionDiffusion | reaction diffusion systems in 1-D linear or spherical geometry |
| ReactionKinetics | chemical reactions in a single well mixed pool |
| ReactionScheme |
a general reaction scheme consisting of a list of species
and the possible transitions between them
user interface: ReactionSchemeEditor |
| RSCalc | calculation methods for reaction schemes |
| RSPointProcess | point process for reaction schemes |
| RSPool | reactant or product pool for reaction scheme calculations |
| SimpleGraph |
just a graph, for exercising the mouse
user interface: SimpleGraphEditor |
| SimpleValue |
a few typical variables to show their interface components
user interface: SimpleValueEditor |
| SpikeCount | Simple spike counting for output of IaFNetwork calculations |
| SteppedProfile |
a driving Profile with possible repeats after incremental changes
user interface: SteppedProfileEditor |
| KSRateTime | time dependent transition in a kinetic scheme |
| HistogramSet |
user interface: HistogramSetEditor |
| PopGrower | simulated dendritic branching and elongation |
| KSRateVoltage | voltage dependent transition in a kinetic scheme |
| Unit | derived Unit expressed in terms of the quantities: M, L, T, charge, temperature, Avagadro's number and ten |
| KSRateVhalf | voltage dependent transition in a kinetic scheme |
| Profile |
driving Profile for any application where experimentally
a digital-to-analog conversion would be employed
user interface: ProfileEditor |