Table of contents
Classes
- Brain
The core brain structure
- Cell
This object is a container for the compartments
- CellManager
Used to keep cells sorted based on cluster and location
- Channel
This object is used to represent the channels that are
present in the cell membrane - specifically the
Sodium (Na), Calcium (Ca), and Potassium (K) channels
- Column
Container for the layers
- Compartment
This object is the primary until of measure in the program
The compartment is also a container for channels and spikeshapes
The compartment is responsible for calculating membrane potential and
for generating an Action Potential
- CompartmentDelay
Message from a compartment to be sent after a number of timeticks have elapsed
- ConnectionManager
This object is for handling all of the connections between cells
it is owned by the InitManager, and it is responsible for making
the connectione between cells and making the synapses that connected
the pair of cells
- InitManager
from Reading in values, to validating input data, to instantiating
object classes and making them a permanent part of the Brain object
- Layer
The layer object is a container structure for the kind and quantity of cell types
within this layer
- LearnTable
this synapse component stores the tabulated values for the synaptic learning
- Message
this object is for passing data back and forth between the cells
and between the Stimulus, Reports and the Cells
- MessageBus
This object handles all of the message passing between
cells
- MessageManager
the purpose of this object is to hold a pool of Message objects, in creating all of the messages at
one time, or in increments of CHUNK_SIZE (chosen arbitrarily for now, but a multiple of 2), its purpose is to
increase performance of the overall system by avoiding allocation and deallocation of
large quantities of messages on the fly
- Report
Handles the gathering of data for a particular report into a
buffer
- Stimulus
Emulates the background noise in the brain
by firing messages to the cells on its list
- Synapse
models the communication between cells
- SynapseData
This object is component of the Synapses, it holds generic data information
such as the delay, SynapseReversal, Maximum conductance, etc
- SynapseDelay
Synapse activity delayed for some time is stored into an list
- SynapseLearning
This synapse component holds data about short and long term learning for the synapse
it is now owned by the brain so that the synpase bject is optimized for size
it is basically a tabulation of values for the positive and negative hebbian learning
updates to the USE value - when a spike shape arrives at a synapse, and a resulting
PSG influences (whether positively or negatively) a resulting spike shape in the
connected (receiving) cell, then the USE of this synapse is modified by some functional
amount
- SynapsePSG
This is a component of the synapses, it is owned by the brain
- SynapseRSE
This object is a component of the Synapse object
Functions, Macros
- getTreeIndex
Return the symbol table index of a given name
- makeBrConn
Synapse connections made inside a brain definition section
- makeCellConn
Synapse connections made within a cell definition section
- makeColConn
Synapse connections made within a column definition section
- makeLayConn
Synapse connections made within a layer definition section
- makeSymTree
Makes a tree structure from all the element names in the input file
- printtree
Recursive function used to display the contents of the Symbol Table Tree
- TreePrint
Helper function to output tree information to the screen
Enums, Unions, Structs
- Address
Each compartment within the active brain is addressed by a triple of numbers
- ARRAYS
Structure to hold pointers to data created from input file
- BRAIN
Initial Brain structure
- CellCmpConnect
Helper object for the Cell and Compartment classes
- MPI_MessageStruct
various structures for MPI messages
this is the required envelope
- SynapsePSGOutgoing
This is a component of the synapse object
- T_BRAIN
Intermediate brain object
- T_CELL
Intermediate Cell object
- T_CHANNEL
Intermediate Channel object
- T_CMPCONNECT
Object containing information for synapse connections between compartments
- T_COLUMN
Intermediate Column Object
- T_COMPART
Intermediate Compartment object
- T_CONNECT
Object containing information for synapse connections
- T_CSHELL
Intermediate Column Shell Object
- T_LAYER
Intermediate Layer object
- T_LSHELL
Layer Shell Object
- T_REPORT
Intermediate Report object
- T_SPIKE
Intermediate Spike object
- T_STIMULUS
Intermediate Stimulus object
- T_STINJECT
Intermediate Stimulus inject object
- T_SYN_FD
Intermediate FD (RSE) object for Short Term Synaptic Dynamics
- T_SYNAPSE
Intermediate Synapse object
- T_SYNDATA
Intermediate Synapse Data Object
- T_SYNLEARN
Intermediate Synapse Learning object
- T_SYNPSG
Intermediate Post synaptic Object
- Treenode
tree node structure
hierarchy of classes
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(c)opyright by Malte Zöckler, Roland Wunderling
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