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

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