Averages and rescales values to couple different kinds of simulation
void (shared message field) This is a shared message to receive Process message from the scheduler.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Input message to the adaptor. If multiple inputs are received, the system averages the inputs.
(destination message field) Handles ‘process’ call
(destination message field) Handles ‘reinit’ call
double (source message field) Sends the output value every timestep.
void (source message field) Sends out the request. Issued from the process call.
Pd (source message field) Sends out a request to a generic double field. Issued from the process call.Works for any number of targets.
double (value field) Offset to apply to input message, before scaling
double (value field) Offset to apply at output, after scaling
double (value field) Scaling factor to apply to input
double (value field) This is the linearly transformed output.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
double (value field) x field. Typically display coordinate x
double (value field) y field. Typically display coordinate y
double (value field) z field. Typically display coordinate z
string (value field) A string to hold some text notes about parent object
string (value field) A string to hold a text string specifying display color.Can be a regular English color name, or an rgb code rrrgggbbb
string (value field) A string to hold a text string specifying color for text labelthat might be on the display for this object.Can be a regular English color name, or an rgb code rrrgggbbb
string (value field) A string to specify icon to use for display
void (shared message field) Shared message for process and reinit
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Handles argument 1. This just assigns it
(destination message field) Handles argument 2. This just assigns it
(destination message field) Handles argument 3. This sums in each input, and clears each clock tick.
(destination message field) Handles process call
(destination message field) Handles reinit call
double (source message field) Sends out the computed value
string (value field) Arithmetic function to perform on inputs.
double (value field) Value of output as computed last timestep.
double (value field) Value of arg1 as computed last timestep.
unsigned int,double (lookup field) Value of any of the internal fields, output, arg1, arg2, arg3,as specified by the index argument from 0 to 3.
void (shared message field) Shared message for process and reinit
(destination message field) Handles process call
(destination message field) Handles reinit call
CaConc: Calcium concentration pool. Takes current from a channel and keeps track of calcium buildup and depletion by a single exponential process.
void (shared message field) Shared message to receive Process message from scheduler
(destination message field) Handles process call
(destination message field) Handles reinit call
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Calcium Ion current, due to be converted to conc.
(destination message field) Fraction of total Ion current, that is carried by Ca2+.
(destination message field) Any input current that increases the concentration.
(destination message field) Any input current that decreases the concentration.
(destination message field) Synonym for assignment of basal conc.
double (source message field) Concentration of Ca in pool
double (value field) Calcium concentration.
double (value field) Basal Calcium concentration.
double (value field) Basal Calcium concentration, synonym for CaBasal
double (value field) Settling time for Ca concentration
double (value field) Volume scaling factor
double (value field) Thickness of Ca shell.
double (value field) Ceiling value for Ca concentration. If Ca > ceiling, Ca = ceiling. If ceiling <= 0.0, there is no upper limit on Ca concentration value.
double (value field) Floor value for Ca concentration. If Ca < floor, Ca = floor
ChanBase: Base class for assorted ion channels.Presents a common interface for all of them.
void (shared message field) This is a shared message to couple channel to compartment. The first entry is a MsgSrc to send Gk and Ek to the compartment The second entry is a MsgDest for Vm from the compartment.
void (shared message field) Message to Goldman-Hodgkin-Katz object
(destination message field) Handles Vm message coming in from compartment
(destination message field) Handles Vm message coming in from compartment
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
double,double (source message field) Sends channel variables Gk and Ek to compartment
double (source message field) Conductance term going out to GHK object
double (source message field) Channel current. This message typically goes to concenobjects that keep track of ion concentration.
double (value field) Maximal channel conductance
double (value field) Reversal potential of channel
double (value field) Channel conductance variable
double (value field) Channel current variable
Pure virtual base class for chemical compartments
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Tells ChemCompt derived class to build a default mesh with thespecified volume and number of meshEntries.
(destination message field) Changes volume but does not notify any child objects.Only works if the ChemCompt has just one voxel.This function will invalidate any concentration term inthe model. If you don’t know why you would want to do this,then you shouldn’t use this function.
(destination message field) Resets the diffusion stencil to the core stencil that only includes the within-mesh diffusion. This is needed prior to building up the cross-mesh diffusion through junctions.
(destination message field) Assigns number of field entries in field array.
(destination message field) Requests number of field entries in field array.The requesting Element must provide a handler for the returned value.
double (value field) Volume of entire chemical domain.Assigning this only works if the chemical compartment hasonly a single voxel. Otherwise ignored.This function goes through all objects below this on thetree, and rescales their molecule #s and rates as per thevolume change. This keeps concentration the same, and alsomaintains rates as expressed in volume units.
vector<double> (value field) Vector of volumes of each of the voxels.
unsigned int (value field) Number of spatial dimensions of this compartment. Usually 3 or 2
unsigned int,double (lookup field) Volume of specified voxel.
unsigned int,vector<double> (lookup field) vector of diffusion rates in the stencil for specified voxel.The identity of the coupled voxels is given by the partner field ‘stencilIndex’.Returns an empty vector for non-voxelized compartments.
unsigned int,vector<unsigned int> (lookup field) vector of voxels diffusively coupled to the specified voxel.The diffusion rates into the coupled voxels is given by the partner field ‘stencilRate’.Returns an empty vector for non-voxelized compartments.
Class information object.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
string (value field) Documentation
string (value field) Name of base class
Clock: Clock class. Handles sequencing of operations in simulations.Every object scheduled for operations in MOOSE is connected to oneof the ‘Tick’ entries on the Clock.The Clock manages ten ‘Ticks’, each of which has its own dt,which is an integral multiple of the base clock dt_. On every clock step the ticks are examined to see which of themis due for updating. When a tick is updated, the ‘process’ call of all the objects scheduled on that tick is called.The default scheduling (should not be overridden) has the following assignment of classes to Ticks:0. Biophysics: Init call on Compartments in EE method1. Biophysics: Channels2. Biophysics: Process call on Compartments3. Undefined 4. Kinetics: Pools, or in ksolve mode: Mesh to handle diffusion5. Kinetics: Reacs, enzymes, etc, or in ksolve mode: Stoich/GSL6. Stimulus tables7. More stimulus tables8. Plots9. Postmaster. This must be called last of all and nothing else should use this Tick. The Postmaster is automatically scheduled at set up time. The Tick should be given the longest possible value, typically but not always equal to one of the other ticks, so as to batch the communications. For spiking-only communications, it is usually possible to space the communication tick by as much as 1-2 ms which is the axonal + synaptic delay.
void (shared message field) Controls all scheduling aspects of Clock, usually from Shell
void (shared message field) Shared proc/reinit message
void (shared message field) Shared proc/reinit message
void (shared message field) Shared proc/reinit message
void (shared message field) Shared proc/reinit message
void (shared message field) Shared proc/reinit message
void (shared message field) Shared proc/reinit message
void (shared message field) Shared proc/reinit message
void (shared message field) Shared proc/reinit message
void (shared message field) Shared proc/reinit message
void (shared message field) Shared proc/reinit message
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Sets off the simulation for the specified duration
(destination message field) Sets off the simulation for the specified # of steps
(destination message field) Halts the simulation, with option to restart seamlessly
(destination message field) Zeroes out all ticks, starts at t = 0
void (source message field) Signal for completion of run
PK8ProcInfo (source message field) Process for Tick 0
PK8ProcInfo (source message field) Reinit for Tick 0
PK8ProcInfo (source message field) Process for Tick 1
PK8ProcInfo (source message field) Reinit for Tick 1
PK8ProcInfo (source message field) Process for Tick 2
PK8ProcInfo (source message field) Reinit for Tick 2
PK8ProcInfo (source message field) Process for Tick 3
PK8ProcInfo (source message field) Reinit for Tick 3
PK8ProcInfo (source message field) Process for Tick 4
PK8ProcInfo (source message field) Reinit for Tick 4
PK8ProcInfo (source message field) Process for Tick 5
PK8ProcInfo (source message field) Reinit for Tick 5
PK8ProcInfo (source message field) Process for Tick 6
PK8ProcInfo (source message field) Reinit for Tick 6
PK8ProcInfo (source message field) Process for Tick 7
PK8ProcInfo (source message field) Reinit for Tick 7
PK8ProcInfo (source message field) Process for Tick 8
PK8ProcInfo (source message field) Reinit for Tick 8
PK8ProcInfo (source message field) Process for Tick 9
PK8ProcInfo (source message field) Reinit for Tick 9
double (value field) Base timestep for simulation
double (value field) Duration to run the simulation
double (value field) Current simulation time
unsigned int (value field) Number of steps to advance the simulation, in units of the smallest timestep on the clock ticks
unsigned int (value field) Number of clock ticks
unsigned int (value field) Current simulation step
vector<double> (value field) Utility function returning the dt (timestep) of all ticks.
bool (value field) Utility function to report if simulation is in progress.
Compartment object, for branching neuron models.
CompartmentBase object, for branching neuron models.
void (shared message field) This is a shared message to receive Process messages from the scheduler objects. The Process should be called _second_ in each clock tick, after the Init message.The first entry in the shared msg is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.
void (shared message field) This is a shared message to receive Init messages from the scheduler objects. Its job is to separate the compartmental calculations from the message passing. It doesn’t really need to be shared, as it does not use the reinit part, but the scheduler objects expect this form of message for all scheduled output. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a dummy MsgDest for the Reinit operation. It also uses ProcInfo.
void (shared message field) This is a shared message from a compartment to channels. The first entry is a MsgDest for the info coming from the channel. It expects Gk and Ek from the channel as args. The second entry is a MsgSrc sending Vm
void (shared message field) This is a shared message between asymmetric compartments. axial messages (this kind) connect up to raxial messages (defined below). The soma should use raxial messages to connect to the axial message of all the immediately adjacent dendritic compartments.This puts the (low) somatic resistance in series with these dendrites. Dendrites should then use raxial messages toconnect on to more distal dendrites. In other words, raxial messages should face outward from the soma. The first entry is a MsgSrc sending Vm to the axialFuncof the target compartment. The second entry is a MsgDest for the info coming from the other compt. It expects Ra and Vm from the other compt as args. Note that the message is named after the source type.
void (shared message field) This is a raxial shared message between asymmetric compartments. The first entry is a MsgDest for the info coming from the other compt. It expects Vm from the other compt as an arg. The second is a MsgSrc sending Ra and Vm to the raxialFunc of the target compartment.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) The injectMsg corresponds to the INJECT message in the GENESIS compartment. Unlike the ‘inject’ field, any value assigned by handleInject applies only for a single timestep.So it needs to be updated every dt for a steady (or varying)injection current
(destination message field) Sends a random injection current to the compartment. Must beupdated each timestep.Arguments to randInject are probability and current.
(destination message field) The injectMsg corresponds to the INJECT message in the GENESIS compartment. Unlike the ‘inject’ field, any value assigned by handleInject applies only for a single timestep.So it needs to be updated every dt for a steady (or varying)injection current
(destination message field) Message for organizing compartments into groups, calledcables. Doesn’t do anything.
(destination message field) Handles ‘process’ call
(destination message field) Handles ‘reinit’ call
(destination message field) Handles Process call for the ‘init’ phase of the CompartmentBase calculations. These occur as a separate Tick cycle from the regular proc cycle, and should be called before the proc msg.
(destination message field) Handles Reinit call for the ‘init’ phase of the CompartmentBase calculations.
(destination message field) Handles conductance and Reversal potential arguments from Channel
(destination message field) Handles Raxial info: arguments are Ra and Vm.
(destination message field) Handles Axial information. Argument is just Vm.
double (source message field) Sends out Vm value of compartment on each timestep
double (source message field) Sends out Vm value of compartment to adjacent compartments,on each timestep
double,double (source message field) Sends out Raxial information on each timestep, fields are Ra and Vm
double (value field) membrane potential
double (value field) Membrane capacitance
double (value field) Resting membrane potential
double (value field) Current going through membrane
double (value field) Current injection to deliver into compartment
double (value field) Initial value for membrane potential
double (value field) Membrane resistance
double (value field) Axial resistance of compartment
double (value field) Diameter of compartment
double (value field) Length of compartment
double (value field) X coordinate of start of compartment
double (value field) Y coordinate of start of compartment
double (value field) Z coordinate of start of compartment
double (value field) x coordinate of end of compartment
double (value field) y coordinate of end of compartment
double (value field) z coordinate of end of compartment
: Base class for mass-action enzymes in which there is an explicit pool for the enzyme-substrate complex. It models the reaction: E + S <===> E.S —-> E + P
void (shared message field) Connects to enzyme pool
void (shared message field) Connects to enz-sub complex pool
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Handles # of molecules of Enzyme
(destination message field) Handles # of molecules of enz-sub complex
double,double (source message field) Sends out increment of molecules on product each timestep
double,double (source message field) Sends out increment of molecules on product each timestep
double (value field) Forward reaction from enz + sub to complex, in # units.This parameter is subordinate to the Km. This means thatwhen Km is changed, this changes. It also means that whenk2 or k3 (aka kcat) are changed, we assume that Km remainsfixed, and as a result k1 must change. It is only whenk1 is assigned directly that we assume that the user knowswhat they are doing, and we adjust Km accordingly.k1 is also subordinate to the ‘ratio’ field, since setting the ratio reassigns k2.Should you wish to assign the elementary rates k1, k2, k3,of an enzyme directly, always assign k1 last.
double (value field) Reverse reaction from complex to enz + sub
double (value field) Forward rate constant from complex to product + enz
double (value field) Ratio of k2/k3
double (value field) K1 expressed in concentration (1/millimolar.sec) unitsThis parameter is subordinate to the Km. This means thatwhen Km is changed, this changes. It also means that whenk2 or k3 (aka kcat) are changed, we assume that Km remainsfixed, and as a result concK1 must change. It is only whenconcK1 is assigned directly that we assume that the user knowswhat they are doing, and we adjust Km accordingly.concK1 is also subordinate to the ‘ratio’ field, sincesetting the ratio reassigns k2.Should you wish to assign the elementary rates concK1, k2, k3,of an enzyme directly, always assign concK1 last.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
bool (value field) Flag. True when the mesh should be toroidal, that is,when going beyond the right face brings us around to theleft-most mesh entry, and so on. If we have nx, ny, nzentries, this rule means that the coordinate (x, ny, z)will map onto (x, 0, z). Similarly,(-1, y, z) -> (nx-1, y, z)Default is false
bool (value field) Flag. When it is true, the numbers nx, ny, nz remainunchanged when x0, x1, y0, y1, z0, z1 are altered. Thusdx, dy, dz would change instead. When it is false, thendx, dy, dz remain the same and nx, ny, nz are altered.Default is true
bool (value field) Flag. When it is true, the mesh matches up sequential mesh entries for diffusion and chmestry. This is regardless of spatial location, and is guaranteed to set up at least the home reaction systemDefault is false
double (value field) X coord of one end
double (value field) Y coord of one end
double (value field) Z coord of one end
double (value field) X coord of other end
double (value field) Y coord of other end
double (value field) Z coord of other end
double (value field) X size for mesh
double (value field) Y size for mesh
double (value field) Z size for mesh
unsigned int (value field) Number of subdivisions in mesh in X
unsigned int (value field) Number of subdivisions in mesh in Y
unsigned int (value field) Number of subdivisions in mesh in Z
vector<double> (value field) Set all the coords of the cuboid at once. Order is:x0 y0 z0 x1 y1 z1 dx dy dzWhen this is done, it recalculates the numEntries since dx, dy and dz are given explicitly.As a special hack, you can leave out dx, dy and dz and use a vector of size 6. In this case the operation assumes that nx, ny and nz are to be preserved and dx, dy and dz will be recalculated.
vector<unsigned int> (value field) Array in which each mesh entry stores spatial (cubic) index
vector<unsigned int> (value field) Array in which each space index (obtained by linearizing the xyz coords) specifies which meshIndex is present.In many cases the index will store the EMPTY flag if there isno mesh entry at that spatial location
vector<unsigned int> (value field) Array specifying surface of arbitrary volume within the CubeMesh. All entries must fall within the cuboid. Each entry of the array is a spatial index obtained by linearizing the ix, iy, iz coordinates within the cuboid. So, each entry == ( iz * ny + iy ) * nx + ixNote that the voxels listed on the surface are WITHIN the volume of the CubeMesh object
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
double (value field) x coord of one end
double (value field) y coord of one end
double (value field) z coord of one end
double (value field) Radius of one end
double (value field) x coord of other end
double (value field) y coord of other end
double (value field) z coord of other end
double (value field) Radius of other end
double (value field) Length constant to use for subdivisionsThe system will attempt to subdivide using compartments oflength diffLength on average. If the cylinder has different enddiameters r0 and r1, it will scale to smaller lengthsfor the smaller diameter end and vice versa.Once the value is set it will recompute diffLength as totLength/numEntries
vector<double> (value field) All the coords as a single vector: x0 y0 z0 x1 y1 z1 r0 r1 diffLength
unsigned int (value field) Number of diffusive compartments in model
double (value field) Total length of cylinder
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
int (value field) The stride is the increment to the src DataId that gives thedest DataId. It can be positive or negative, but bounds checkingtakes place and it does not wrap around.
DifShell object: Models diffusion of an ion (typically calcium) within an electric compartment. A DifShell is an iso-concentration region with respect to the ion. Adjoining DifShells exchange flux of this ion, and also keep track of changes in concentration due to pumping, buffering and channel currents, by talking to the appropriate objects.
- process_0¶
void (shared message field) Here we create 2 shared finfos to attach with the Ticks. This is because we want to perform DifShell computations in 2 stages, much as in the Compartment object. In the first stage we send out the concentration value to other DifShells and Buffer elements. We also receive fluxes and currents and sum them up to compute ( dC / dt ). In the second stage we find the new C value using an explicit integration method. This 2-stage procedure eliminates the need to store and send prev_C values, as was common in GENESIS.
- process_1¶
void (shared message field) Second process call
- buffer¶
void (shared message field) This is a shared message from a DifShell to a Buffer (FixBuffer or DifBuffer). During stage 0:
During stage 1: - DifShell advances concentration C This scheme means that the Buffer does not need to be scheduled, and it does its computations when it receives a cue from the DifShell. May not be the best idea, but it saves us from doing the above computations in 3 stages instead of 2.
- innerDif¶
void (shared message field) This shared message (and the next) is between DifShells: adjoining shells exchange information to find out the flux between them. Using this message, an inner shell sends to, and receives from its outer shell.
- outerDif¶
void (shared message field) Using this message, an outer shell sends to, and receives from its inner shell.
- getC()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- setCeq()¶
(destination message field) Assigns field value.
- getCeq()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- setD()¶
(destination message field) Assigns field value.
- getD()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- setValence()¶
(destination message field) Assigns field value.
- getValence()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- setLeak()¶
(destination message field) Assigns field value.
- getLeak()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- setShapeMode()¶
(destination message field) Assigns field value.
- getShapeMode()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- setLength()¶
(destination message field) Assigns field value.
- getLength()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- setDiameter()¶
(destination message field) Assigns field value.
- getDiameter()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- setThickness()¶
(destination message field) Assigns field value.
- getThickness()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- setVolume()¶
(destination message field) Assigns field value.
- getVolume()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- setOuterArea()¶
(destination message field) Assigns field value.
- getOuterArea()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- setInnerArea()¶
(destination message field) Assigns field value.
- getInnerArea()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- process()¶
(destination message field) Handles process call
- reinit()¶
(destination message field) Reinit happens only in stage 0
- process()
(destination message field) Handle process call
- reinit()
(destination message field) Reinit happens only in stage 0
- reaction()¶
(destination message field) Here the DifShell receives reaction rates (forward and backward), and concentrations for the free-buffer and bound-buffer molecules.
- fluxFromOut()¶
(destination message field) Destination message
- fluxFromIn()¶
(destination message field)
- influx()¶
(destination message field)
- outflux()¶
(destination message field)
- fInflux()¶
(destination message field)
- fOutflux()¶
(destination message field)
- storeInflux()¶
(destination message field)
- storeOutflux()¶
(destination message field)
- tauPump()¶
(destination message field)
- eqTauPump()¶
(destination message field)
- mmPump()¶
(destination message field)
- hillPump()¶
(destination message field)
- concentrationOut¶
double (source message field) Sends out concentration
- innerDifSourceOut¶
double,double (source message field) Sends out source information.
- outerDifSourceOut¶
double,double (source message field) Sends out source information.
- C¶
double (value field) Concentration C is computed by the DifShell and is read-only
- Ceq¶
double (value field)
- D¶
double (value field)
- valence¶
double (value field)
- leak¶
double (value field)
- shapeMode¶
unsigned int (value field)
- length¶
double (value field)
- diameter¶
double (value field)
- thickness¶
double (value field)
- volume¶
double (value field)
- outerArea¶
double (value field)
- innerArea¶
double (value field)
A difference amplifier. Output is the difference between the total plus inputs and the total minus inputs multiplied by gain. Gain can be set statically as a field or can be a destination message and thus dynamically determined by the output of another object. Same as GENESIS diffamp object.
void (shared message field) This is a shared message to receive Process messages from the scheduler objects.The first entry in the shared msg is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Destination message to control gain dynamically.
(destination message field) Positive input terminal of the amplifier. All the messages connected here are summed up to get total positive input.
(destination message field) Negative input terminal of the amplifier. All the messages connected here are summed up to get total positive input.
(destination message field) Handles process call, updates internal time stamp.
(destination message field) Handles reinit call.
double (source message field) Current output level.
double (value field) Gain of the amplifier. The output of the amplifier is the difference between the totals in plus and minus inputs multiplied by the gain. Defaults to 1
double (value field) Saturation is the bound on the output. If output goes beyond the +/-saturation range, it is truncated to the closer of +saturation and -saturation. Defaults to the maximum double precision floating point number representable on the system.
double (value field) Output of the amplifier, i.e. gain * (plus - minus).
Variable for storing values.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
double (value field) Variable value
void (shared message field) Shared message for process and reinit
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Builds junctions between NeuroMesh, SpineMesh and PsdMesh
(destination message field) Handles process call
(destination message field) Handles reinit call
Id (value field) Stoichiometry object for handling this reaction system.
string (value field) Path of reaction system. Must include all the pools that are to be handled by the Dsolve, can also include other random objects, which will be ignored.
Id (value field) Reac-diff compartment in which this diffusion system is embedded.
unsigned int (value field) Number of voxels in the core reac-diff system, on the current diffusion solver.
unsigned int (value field) Number of voxels in the core reac-diff system, on the current diffusion solver.
unsigned int (value field) Number of molecular pools in the entire reac-diff system, including variable, function and buffered.
unsigned int,vector<double> (lookup field) vector of # of molecules along diffusion length, looked up by pool index
Abstract base class for enzymes.
void (shared message field) Connects to substrate molecule
void (shared message field) Connects to product molecule
void (shared message field) Shared message for process and reinit
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Handles # of molecules of Enzyme
(destination message field) Handles # of molecules of substrate
(destination message field) Handles # of molecules of product. Dummy.
(destination message field) Handles process call
(destination message field) Handles reinit call
(destination message field) Tells the MMEnz to recompute its numKm after remeshing
double,double (source message field) Sends out increment of molecules on product each timestep
double,double (source message field) Sends out increment of molecules on product each timestep
double (value field) Michaelis-Menten constant in SI conc units (milliMolar)
double (value field) Michaelis-Menten constant in number units, volume dependent
double (value field) Forward rate constant for enzyme, units 1/sec
unsigned int (value field) Number of substrates in this MM reaction. Usually 1.Does not include the enzyme itself
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
string (value field) Name of field handled by Finfo
string (value field) Documentation for Finfo
string (value field) RTTI type info for this Finfo
vector<string> (value field) Subsidiary SrcFinfos. Useful for SharedFinfos
vector<string> (value field) Subsidiary DestFinfos. Useful for SharedFinfos
Func: general purpose function calculator using real numbers. It can
parse mathematical expression defining a function and evaluate it
and/or its derivative for specified variable values.
The variables can be input from other moose objects. In case of
arbitrary variable names, the source message must have the variable
name as the first argument. For most common cases, input messages to
set x, y, z and xy, xyz are made available without such
requirement. This class handles only real numbers
pi=3.141592...,
e=2.718281...
void (shared message field) This is a shared message to receive Process messages from the scheduler objects.The first entry in the shared msg is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Handle value for specified variable coming from other objects
(destination message field) Handle value for variable named x. This is a shorthand. If the
expression does not have any variable named x, this the first variable in the sequence vars.
- yIn()¶
(destination message field) Handle value for variable named y. This is a utility for two/three
variable functions where the y value comes from a source separate from that of x. This is a shorthand. If the
expression does not have any variable named y, this the second variable in the sequence vars.
- zIn()¶
(destination message field) Handle value for variable named z. This is a utility for three
variable functions where the z value comes from a source separate from that of x or y. This is a shorthand. If the expression does not have any variable named y, this the second variable in the sequence vars.
- xyIn()¶
(destination message field) Handle value for variables x and y for two-variable function
- xyzIn()¶
(destination message field) Handle value for variables x, y and z for three-variable function
- process()
(destination message field) Handles process call, updates internal time stamp.
- reinit()
(destination message field) Handles reinit call.
- valueOut¶
double (source message field) Evaluated value of the function for the current variable values.
- derivativeOut¶
double (source message field) Value of derivative of the function for the current variable values
- value¶
double (value field) Result of the function evaluation with current variable values.
- derivative¶
double (value field) Derivative of the function at given variable values.
- mode¶
unsigned int (value field) Mode of operation:
1: only the function value will be funculated 2: only the derivative will be funculated 3: both function value and derivative at current variable values will be funculated.
- expr¶
string (value field) Mathematical expression defining the function. The underlying parser
is muParser. Hence the available functions and operators are (from muParser docs):
Functions Name args explanation sin 1 sine function cos 1 cosine function tan 1 tangens function asin 1 arcus sine function acos 1 arcus cosine function atan 1 arcus tangens function sinh 1 hyperbolic sine function cosh 1 hyperbolic cosine tanh 1 hyperbolic tangens function asinh 1 hyperbolic arcus sine function acosh 1 hyperbolic arcus tangens function atanh 1 hyperbolic arcur tangens function log2 1 logarithm to the base 2 log10 1 logarithm to the base 10 log 1 logarithm to the base 10 ln 1 logarithm to base e (2.71828...) exp 1 e raised to the power of x sqrt 1 square root of a value sign 1 sign function -1 if x<0; 1 if x>0 rint 1 round to nearest integer abs 1 absolute value min var. min of all arguments max var. max of all arguments sum var. sum of all arguments avg var. mean value of all arguments
Operators Op meaning prioroty = assignement -1 && logical and 1 || logical or 2 <= less or equal 4 >= greater or equal 4 != not equal 4 == equal 4 > greater than 4 < less than 4 + addition 5 - subtraction 5 * multiplication 6 / division 6 ^ raise x to the power of y 7
?: if then else operator C++ style syntax
expression does not have any variable named x, this the first variable in the sequence vars.
- y¶
double (value field) Value for variable named y. This is a utility for two/three
variable functions where the y value comes from a source separate from that of x. This is a shorthand. If the
expression does not have any variable named y, this the second variable in the sequence vars.
- z¶
double (value field) Value for variable named z. This is a utility for three
variable functions where the z value comes from a source separate from that of x or z. This is a shorthand. If the expression does not have any variable named z, this the third variable in the sequence vars.
- var¶
string,double (lookup field) Lookup table for variable values.
void (shared message field) Shared message for process and reinit
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Handles input values. This generic message works only in cases where the inputs are commutative, so ordering does not matter. In due course will implement a synapse type extendable, identified system of inputs so that arbitrary numbers of inputs can be unambiguaously defined.
(destination message field) Handles process call
(destination message field) Handles reinit call
double (source message field) Sends out sum on each timestep
double (value field) Outcome of function computation
Implementation of gap junction between two compartments. The shared
fields, ‘channel1’ and ‘channel2’ can be connected to the ‘channel’
message of the compartments at either end of the gap junction. The
compartments will send their Vm to the gap junction and receive the
conductance ‘Gk’ of the gap junction and the Vm of the other
compartment.
void (shared message field) This is a shared message to couple the conductance and Vm from
terminal 2 to the compartment at terminal 1. The first entry is source sending out Gk and Vm2, the second entry is destination for Vm1.
- channel2¶
void (shared message field) This is a shared message to couple the conductance and Vm from
terminal 1 to the compartment at terminal 2. The first entry is source sending out Gk and Vm1, the second entry is destination for Vm2.
- proc¶
void (shared message field) This is a shared message to receive Process messages from the scheduler objects. The Process should be called _second_ in each clock tick, after the Init message.The first entry in the shared msg is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.
- Vm1()¶
(destination message field) Handles Vm message from compartment
- Vm2()¶
(destination message field) Handles Vm message from another compartment
- setGk()¶
(destination message field) Assigns field value.
- getGk()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- process()
(destination message field) Handles ‘process’ call
- reinit()
(destination message field) Handles ‘reinit’ call
- channel1Out¶
double,double (source message field) Sends Gk and Vm from one compartment to the other
- channel2Out¶
double,double (source message field) Sends Gk and Vm from one compartment to the other
- Gk¶
double (value field) Conductance of the gap junction
void (shared message field) Shared message for process and reinit
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Handles process call
(destination message field) Handles reinit call
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
Id (value field) Stoichiometry object for handling this reaction system.
unsigned int (value field) Number of voxels in the core reac-diff system, on the current solver.
unsigned int (value field) Number of voxels in the entire reac-diff system, including proxy voxels to represent abutting compartments.
unsigned int (value field) Number of molecular pools in the entire reac-diff system, including variable, function and buffered.
bool (value field) Flag: True when using probabilistic (random) rounding. When initializing the mol# from floating-point Sinit values, we have two options. One is to look at each Sinit, and round to the nearest integer. The other is to look at each Sinit, and probabilistically round up or down depending on the value. For example, if we had a Sinit value of 1.49, this would always be rounded to 1.0 if the flag is false, and would be rounded to 1.0 and 2.0 in the ratio 51:49 if the flag is true.
unsigned int,vector<double> (lookup field) vector of pool counts
HHChannel: Hodgkin-Huxley type voltage-gated Ion channel. Something like the old tabchannel from GENESIS, but also presents a similar interface as hhchan from GENESIS.
- proc¶
void (shared message field) This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on.
The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.
- process()¶
(destination message field) Handles process call
- reinit()¶
(destination message field) Handles reinit call
- setXpower()¶
(destination message field) Assigns field value.
- getXpower()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- setYpower()¶
(destination message field) Assigns field value.
- getYpower()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- setZpower()¶
(destination message field) Assigns field value.
- getZpower()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- setInstant()¶
(destination message field) Assigns field value.
- getInstant()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- setX()¶
(destination message field) Assigns field value.
- getX()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- setY()¶
(destination message field) Assigns field value.
- getY()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- setZ()¶
(destination message field) Assigns field value.
- getZ()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- setUseConcentration()¶
(destination message field) Assigns field value.
- getUseConcentration()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- concen()¶
(destination message field) Incoming message from Concen object to specific conc to usein the Z gate calculations
- createGate()¶
(destination message field) Function to create specified gate.Argument: Gate type [X Y Z]
- setNumGateX()¶
(destination message field) Assigns number of field entries in field array.
- getNumGateX()¶
(destination message field) Requests number of field entries in field array.The requesting Element must provide a handler for the returned value.
- setNumGateY()¶
(destination message field) Assigns number of field entries in field array.
- getNumGateY()¶
(destination message field) Requests number of field entries in field array.The requesting Element must provide a handler for the returned value.
- setNumGateZ()¶
(destination message field) Assigns number of field entries in field array.
- getNumGateZ()¶
(destination message field) Requests number of field entries in field array.The requesting Element must provide a handler for the returned value.
- Xpower¶
double (value field) Power for X gate
- Ypower¶
double (value field) Power for Y gate
- Zpower¶
double (value field) Power for Z gate
- instant¶
int (value field) Bitmapped flag: bit 0 = Xgate, bit 1 = Ygate, bit 2 = ZgateWhen true, specifies that the lookup table value should beused directly as the state of the channel, rather than usedas a rate term for numerical integration for the state
- X¶
double (value field) State variable for X gate
- Y¶
double (value field) State variable for Y gate
- Z¶
double (value field) State variable for Y gate
- useConcentration¶
int (value field) Flag: when true, use concentration message rather than Vm tocontrol Z gate
HHChannel2D: Hodgkin-Huxley type voltage-gated Ion channel. Something like the old tabchannel from GENESIS, but also presents a similar interface as hhchan from GENESIS.
- proc¶
void (shared message field) This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on.
The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.
- process()¶
(destination message field) Handles process call
- reinit()¶
(destination message field) Handles reinit call
- setXindex()¶
(destination message field) Assigns field value.
- getXindex()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- setYindex()¶
(destination message field) Assigns field value.
- getYindex()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- setZindex()¶
(destination message field) Assigns field value.
- getZindex()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- setXpower()¶
(destination message field) Assigns field value.
- getXpower()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- setYpower()¶
(destination message field) Assigns field value.
- getYpower()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- setZpower()¶
(destination message field) Assigns field value.
- getZpower()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- setInstant()¶
(destination message field) Assigns field value.
- getInstant()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- setX()¶
(destination message field) Assigns field value.
- getX()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- setY()¶
(destination message field) Assigns field value.
- getY()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- setZ()¶
(destination message field) Assigns field value.
- getZ()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- concen()¶
(destination message field) Incoming message from Concen object to specific conc to useas the first concen variable
- concen2()¶
(destination message field) Incoming message from Concen object to specific conc to useas the second concen variable
- setNumGateX()¶
(destination message field) Assigns number of field entries in field array.
- getNumGateX()¶
(destination message field) Requests number of field entries in field array.The requesting Element must provide a handler for the returned value.
- setNumGateY()¶
(destination message field) Assigns number of field entries in field array.
- getNumGateY()¶
(destination message field) Requests number of field entries in field array.The requesting Element must provide a handler for the returned value.
- setNumGateZ()¶
(destination message field) Assigns number of field entries in field array.
- getNumGateZ()¶
(destination message field) Requests number of field entries in field array.The requesting Element must provide a handler for the returned value.
- Xindex¶
string (value field) String for setting X index.
- Yindex¶
string (value field) String for setting Y index.
- Zindex¶
string (value field) String for setting Z index.
- Xpower¶
double (value field) Power for X gate
- Ypower¶
double (value field) Power for Y gate
- Zpower¶
double (value field) Power for Z gate
- instant¶
int (value field) Bitmapped flag: bit 0 = Xgate, bit 1 = Ygate, bit 2 = ZgateWhen true, specifies that the lookup table value should beused directly as the state of the channel, rather than usedas a rate term for numerical integration for the state
- X¶
double (value field) State variable for X gate
- Y¶
double (value field) State variable for Y gate
- Z¶
double (value field) State variable for Y gate
HHGate: Gate for Hodkgin-Huxley type channels, equivalent to the m and h terms on the Na squid channel and the n term on K. This takes the voltage and state variable from the channel, computes the new value of the state variable and a scaling, depending on gate power, for the conductance.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Set up both gates using 13 parameters, as follows:setupAlpha AA AB AC AD AF BA BB BC BD BF xdivs xmin xmaxHere AA-AF are Coefficients A to F of the alpha (forward) termHere BA-BF are Coefficients A to F of the beta (reverse) termHere xdivs is the number of entries in the table,xmin and xmax define the range for lookup.Outside this range the returned value will be the low [high]entry of the table.The equation describing each table is:y(x) = (A + B * x) / (C + exp((x + D) / F))The original HH equations can readily be cast into this form
(destination message field) Identical to setupAlpha, except that the forms specified bythe 13 parameters are for the tau and m-infinity curves ratherthan the alpha and beta terms. So the parameters are:setupTau TA TB TC TD TF MA MB MC MD MF xdivs xmin xmaxAs before, the equation describing each curve is:y(x) = (A + B * x) / (C + exp((x + D) / F))
(destination message field) Dummy function for backward compatibility. It used to convertthe tables from alpha, beta values to alpha, alpha+betabecause the internal calculations used these forms. Notneeded now, deprecated.
(destination message field) Dummy function for backward compatibility. It used to convertthe tables from tau, minf values to alpha, alpha+betabecause the internal calculations used these forms. Notneeded now, deprecated.
(destination message field) Sets up one gate at a time using the alpha/beta form.Has 9 parameters, as follows:setupGate A B C D F xdivs xmin xmax is_betaThis sets up the gate using the equation:y(x) = (A + B * x) / (C + exp((x + D) / F))Deprecated.
vector<double> (value field) Parameters for voltage-dependent rates, alpha:Set up alpha term using 5 parameters, as follows:y(x) = (A + B * x) / (C + exp((x + D) / F))The original HH equations can readily be cast into this form
vector<double> (value field) Parameters for voltage-dependent rates, beta:Set up beta term using 5 parameters, as follows:y(x) = (A + B * x) / (C + exp((x + D) / F))The original HH equations can readily be cast into this form
vector<double> (value field) Parameters for voltage-dependent rates, tau:Set up tau curve using 5 parameters, as follows:y(x) = (A + B * x) / (C + exp((x + D) / F))
vector<double> (value field) Parameters for voltage-dependent rates, mInfinity:Set up mInfinity curve using 5 parameters, as follows:y(x) = (A + B * x) / (C + exp((x + D) / F))The original HH equations can readily be cast into this form
double (value field) Minimum range for lookup
double (value field) Minimum range for lookup
unsigned int (value field) Divisions for lookup. Zero means to use linear interpolation
vector<double> (value field) Table of A entries
vector<double> (value field) Table of alpha + beta entries
bool (value field) Flag: use linear interpolation if true, else direct lookup
vector<double> (value field) Set up both gates using 13 parameters, as follows:setupAlpha AA AB AC AD AF BA BB BC BD BF xdivs xmin xmaxHere AA-AF are Coefficients A to F of the alpha (forward) termHere BA-BF are Coefficients A to F of the beta (reverse) termHere xdivs is the number of entries in the table,xmin and xmax define the range for lookup.Outside this range the returned value will be the low [high]entry of the table.The equation describing each table is:y(x) = (A + B * x) / (C + exp((x + D) / F))The original HH equations can readily be cast into this form
double,double (lookup field) lookupA: Look up the A gate value from a double. Usually doesso by direct scaling and offset to an integer lookup, usinga fine enough table granularity that there is little error.Alternatively uses linear interpolation.The range of the double is predefined based on knowledge ofvoltage or conc ranges, and the granularity is specified bythe xmin, xmax, and dV fields.
double,double (lookup field) lookupB: Look up the B gate value from a double.Note that this looks up the raw tables, which are transformedfrom the reference parameters.
HHGate2D: Gate for Hodkgin-Huxley type channels, equivalent to the m and h terms on the Na squid channel and the n term on K. This takes the voltage and state variable from the channel, computes the new value of the state variable and a scaling, depending on gate power, for the conductance. These two terms are sent right back in a message to the channel.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
vector< vector<double> > (value field) Table of A entries
vector< vector<double> > (value field) Table of B entries
double (value field) Minimum range for lookup
double (value field) Minimum range for lookup
unsigned int (value field) Divisions for lookup. Zero means to use linear interpolation
double (value field) Minimum range for lookup
double (value field) Minimum range for lookup
unsigned int (value field) Divisions for lookup. Zero means to use linear interpolation
double (value field) Minimum range for lookup
double (value field) Minimum range for lookup
unsigned int (value field) Divisions for lookup. Zero means to use linear interpolation
double (value field) Minimum range for lookup
double (value field) Minimum range for lookup
unsigned int (value field) Divisions for lookup. Zero means to use linear interpolation
vector<double>,double (lookup field) lookupA: Look up the A gate value from two doubles, passedin as a vector. Uses linear interpolation in the 2D tableThe range of the lookup doubles is predefined based on knowledge of voltage or conc ranges, and the granularity is specified by the xmin, xmax, and dx field, and their y-axis counterparts.
vector<double>,double (lookup field) lookupB: Look up B gate value from two doubles in a vector.
void (shared message field) Handles ‘reinit’ and ‘process’ calls from a clock.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Handles ‘process’ call: Solver advances by one time-step.
(destination message field) Handles ‘reinit’ call: Solver reads in model.
Id (value field) Use this field to specify path to a ‘seed’ compartment, that is, any compartment within a neuron. The HSolve object uses this seed as a handle to discover the rest of the neuronal model, which means all the remaining compartments, channels, synapses, etc.
string (value field) Specifies the path to a compartmental model to be taken over. This can be the path to any container object that has the model under it (found by performing a deep search). Alternatively, this can also be the path to any compartment within the neuron. This compartment will be used as a handle to discover the rest of the model, which means all the remaining compartments, channels, synapses, etc.
double (value field) The time-step for this solver.
int (value field) This flag determines how current flowing into a calcium pool is computed. A value of 0 means that the membrane potential at the beginning of the time-step is used for the calculation. This is how GENESIS does its computations. A value of 1 means the membrane potential at the middle of the time-step is used. This is the correct way of integration, and is the default way.
int (value field) Specifies number of divisions for lookup tables of voltage-sensitive channels.
double (value field) Specifies the lower bound for lookup tables of voltage-sensitive channels. Default is to automatically decide based on the tables of the channels that the solver reads in.
double (value field) Specifies the upper bound for lookup tables of voltage-sensitive channels. Default is to automatically decide based on the tables of the channels that the solver reads in.
int (value field) Specifies number of divisions for lookup tables of calcium-sensitive channels.
double (value field) Specifies the lower bound for lookup tables of calcium-sensitive channels. Default is to automatically decide based on the tables of the channels that the solver reads in.
double (value field) Specifies the upper bound for lookup tables of calcium-sensitive channels. Default is to automatically decide based on the tables of the channels that the solver reads in.
void (shared message field) Shared message for process and reinit
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Handles process call
(destination message field) Handles reinit call
double (source message field) Sends out spike events
double (value field) Membrane potential
double (value field) charging time-course
double (value field) firing threshold
double (value field) Minimum time between successive spikes
double (value field) Duration of spike buffer.
Interpol: Interpolation class. Handles lookup from a 1-dimensional array of real-numbered values.Returns ‘y’ value based on given ‘x’ value. Can either use interpolation or roundoff to the nearest index.
void (shared message field) Shared message for process and reinit
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Interpolates using the input as x value.
(destination message field) Handles process call, updates internal time stamp.
(destination message field) Handles reinit call.
double (source message field) respond to a request for a value lookup
double (value field) Minimum value of x. x below this will result in y[0] being returned.
double (value field) Maximum value of x. x above this will result in y[last] being returned.
double (value field) Looked up value.
Interpol2D: Interpolation class. Handles lookup from a 2-dimensional grid of real-numbered values. Returns ‘z’ value based on given ‘x’ and ‘y’ values. Can either use interpolation or roundoff to the nearest index.
void (shared message field) This is a shared message for doing lookups on the table. Receives 2 doubles: x, y. Sends back a double with the looked-up z value.
(destination message field) Looks up table value based on indices v1 and v2, and sendsvalue back using the ‘lookupOut’ message
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
double (source message field) respond to a request for a value lookup
double (value field) Minimum value for x axis of lookup table
double (value field) Maximum value for x axis of lookup table
unsigned int (value field) # of divisions on x axis of lookup table
double (value field) Increment on x axis of lookup table
double (value field) Minimum value for y axis of lookup table
double (value field) Maximum value for y axis of lookup table
unsigned int (value field) # of divisions on y axis of lookup table
double (value field) Increment on y axis of lookup table
vector< vector<double> > (value field) Get the entire table.
vector<unsigned int>,double (lookup field) Lookup an entry on the table
vector<double>,double (lookup field) Interpolated value for specified x and y. This is provided for debugging. Normally other objects will retrieve interpolated values via lookup message.
Izhikevich model of spiking neuron (Izhikevich,EM. 2003. Simple model of spiking neurons. Neural Networks, IEEE Transactions on 14(6). pp 1569-1572).
dVm/dt = 0.04 * Vm^2 + 5 * Vm + 140 - u + inject
du/dt = a * (b * Vm - u)
if Vm >= Vmax then Vm = c and u = u + d
Vmax = 30 mV in the paper.
void (shared message field) Shared message to receive Process message from scheduler
void (shared message field) This is a shared message from a IzhikevichNrn to channels.The first entry is a MsgDest for the info coming from the channel. It expects Gk and Ek from the channel as args. The second entry is a MsgSrc sending Vm
(destination message field) Handles process call
(destination message field) Handles reinit call
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Injection current into the neuron.
(destination message field) Destination message to modify parameter c at runtime.
(destination message field) Destination message to modify parameter d at runtime.
(destination message field) Destination message to modify parameter b at runtime
(destination message field) Destination message modify parameter a at runtime.
(destination message field) Handles conductance and reversal potential arguments from Channel
double (source message field) Sends out Vm
double (source message field) Sends out spike events
double (source message field) Sends out Vm
double (value field) Maximum membrane potential. Membrane potential is reset to c whenever it reaches Vmax. NOTE: Izhikevich model specifies the PEAK voltage, rather than THRSHOLD voltage. The threshold depends on the previous history.
double (value field) Reset potential. Membrane potential is reset to c whenever it reaches Vmax.
double (value field) Parameter d in Izhikevich model. Unit is V/s.
double (value field) Parameter a in Izhikevich model. Unit is s^{-1}
double (value field) Parameter b in Izhikevich model. Unit is s^{-1}
double (value field) Parameter u in Izhikevich equation. Unit is V/s
double (value field) Membrane potential, equivalent to v in Izhikevich equation.
double (value field) Total current going through the membrane. Unit is A.
double (value field) External current injection into the neuron
double (value field) Hidden coefficient of input current term (I) in Izhikevich model. Defaults to 1e9 Ohm/s.
bool (value field) True if this neuron is an accommodating one. The equation for recovery variable u is special in this case.
double (value field) This is used for accommodating neurons where recovery variables u is computed as: u += tau*a*(b*(Vm-u0))
double (value field) Initial membrane potential. Unit is V.
double (value field) Initial value of u.
double (value field) Coefficient of v^2 in Izhikevich equation. Defaults to 0.04 in physiological unit. In SI it should be 40000.0. Unit is V^-1 s^{-1}
double (value field) Coefficient of v in Izhikevich model. Defaults to 5 in physiological unit, 5000.0 for SI units. Unit is s^{-1}
double (value field) Constant term in Izhikevich model. Defaults to 140 in both physiological and SI units. unit is V/s.
void (shared message field) Shared message for process and reinit
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Handles process call
(destination message field) Handles reinit call
string (value field) Integration method, using GSL. So far only explict. Options are:rk5: The default Runge-Kutta-Fehlberg 5th order adaptive dt methodgsl: alias for the aboverk4: The Runge-Kutta 4th order fixed dt methodrk2: The Runge-Kutta 2,3 embedded fixed dt methodrkck: The Runge-Kutta Cash-Karp (4,5) methodrk8: The Runge-Kutta Prince-Dormand (8,9) method
double (value field) Absolute permissible integration error range.
double (value field) Relative permissible integration error range.
Id (value field) Stoichiometry object for handling this reaction system.
Id (value field) Diffusion solver object handling this reactin system.
Id (value field) Compartment in which the Ksolve reaction system lives.
unsigned int (value field) Number of voxels in the core reac-diff system, on the current solver.
unsigned int (value field) Number of voxels in the entire reac-diff system, including proxy voxels to represent abutting compartments.
unsigned int (value field) Number of molecular pools in the entire reac-diff system, including variable, function and buffered.
unsigned int,vector<double> (lookup field) vector of pool counts. Index specifies which voxel.
Leakage: Passive leakage channel.
void (shared message field) This is a shared message to receive Process message from the scheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on.
The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.
- process()
(destination message field) Handles process call
- reinit()
(destination message field) Handles reinit call
Variable for storing values.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
long (value field) Variable value
MarkovChannel : Multistate ion channel class.It deals with ion channels which can be found in one of multiple states, some of which are conducting. This implementation assumes the occurence of first order kinetics to calculate the probabilities of the channel being found in all states. Further, the rates of transition between these states can be constant, voltage-dependent or ligand dependent (only one ligand species). The current flow obtained from the channel is calculated in a deterministic method by solving the system of differential equations obtained from the assumptions above.
void (shared message field) This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.
(destination message field) Handles process call
(destination message field) Handles reinit call
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Deals with incoming messages containing information of ligand concentration
(destination message field) Deals with incoming message from MarkovSolver object containing state information of the channel.
double (value field) Ligand concentration.
double (value field) Membrane voltage.
unsigned int (value field) The number of states that the channel can occupy.
unsigned int (value field) The number of states which are open/conducting.
vector<double> (value field) This is a row vector that contains the probabilities of finding the channel in each state.
vector<double> (value field) This is a row vector that contains the probabilities of finding the channel in each state at t = 0. The state of the channel is reset to this value during a call to reinit()
vector<string> (value field) Labels for each state.
vector<double> (value field) A row vector containing the conductance associated with each of the open/conducting states.
void (shared message field) Shared message for process and reinit
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Initialize solver parameters.
(destination message field) Handles information regarding the instantaneous rate matrix from the MarkovRateTable class.
(destination message field) Handles process call
(destination message field) Handles reinit call
vector<double> (source message field) Sends updated state to the MarkovChannel class.
bool (value field) True if the message has come in to set solver parameters.
string (value field) Numerical method to use.
double (value field) Accuracy criterion
double (value field) Another accuracy criterion
double (value field) internal timestep to use.
void (shared message field) This message couples the rate table to the compartment. The rate table needs updates on voltage in order to compute the rate table.
void (shared message field) This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.
(destination message field) Handles incoming message containing voltage information.
(destination message field) Handles process call
(destination message field) Handles reinit call
(destination message field) Initialization of the class. Allocates memory for all the tables.
(destination message field) Handles incoming message containing ligand concentration.
(destination message field) Setting up of 1D lookup table for the (i,j)’th rate.
(destination message field) Setting up of 2D lookup table for the (i,j)’th rate.
(destination message field) Setting a constant value for the (i,j)’th rate. Internally, this is stored as a 1-D rate with a lookup table containing 1 entry.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
vector< vector<double> > (source message field) Sends out instantaneous rate information of varying transition ratesat each time step.
double (value field) Membrane voltage.
double (value field) Ligand concentration.
vector< vector<double> > (value field) Instantaneous rate matrix.
unsigned int (value field) Dimension of the families of lookup tables. Is always equal to the number of states in the model.
void (shared message field) This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.
(destination message field) Handles process call
(destination message field) Handles reinit call
void (shared message field) This message couples the MarkovSolverBase to the Compartment. The compartment needs Vm in order to look up the correct matrix exponential for computing the state.
void (shared message field) This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.
(destination message field) Handles incoming message containing voltage information.
(destination message field) Handles process call
(destination message field) Handles reinit call
(destination message field) Handles incoming message containing ligand concentration.
(destination message field) Setups the table of matrix exponentials associated with the solver object.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
vector<double> (source message field) Sends updated state to the MarkovChannel class.
vector< vector<double> > (value field) Instantaneous rate matrix.
vector<double> (value field) Current state of the channel.
vector<double> (value field) Initial state of the channel.
double (value field) Minimum value for x axis of lookup table
double (value field) Maximum value for x axis of lookup table
unsigned int (value field) # of divisions on x axis of lookup table
double (value field) Reciprocal of increment on x axis of lookup table
double (value field) Minimum value for y axis of lookup table
double (value field) Maximum value for y axis of lookup table
unsigned int (value field) # of divisions on y axis of lookup table
double (value field) Reciprocal of increment on y axis of lookup table
void (shared message field) Shared message for process and reinit
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Handle arg1
(destination message field) Handle arg2
(destination message field) Handle arg3
(destination message field) Handle arg4
(destination message field) Handle process call
(destination message field) Handle reinit call
double (source message field) Sends out result of computation
string (value field) MathML version of expression to compute
string (value field) function is for functions of form f(x, y) = x + y
double (value field) result value
One voxel in a chemical reaction compartment
void (shared message field) Shared message for process and reinit
void (shared message field) Shared message for updating mesh volumes and subdivisions,typically controls pool volumes
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Handles process call
(destination message field) Handles reinit call
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
double,unsigned int,unsigned int,vector<unsigned int>,vector<double> (source message field) Tells the target pool or other entity that the compartment subdivision(meshing) has changed, and that it has to redo its volume and memory allocation accordingly.Arguments are: oldvol, numTotalEntries, startEntry, localIndices, volsThe vols specifies volumes of each local mesh entry. It also specifieshow many meshEntries are present on the local node.The localIndices vector is used for general load balancing only.It has a list of the all meshEntries on current node.If it is empty, we assume block load balancing. In this secondcase the contents of the current node go from startEntry to startEntry + vols.size().
void (source message field) Tells connected enz or reac that the compartment subdivision(meshing) has changed, and that it has to redo its volume-dependent rate terms like numKf_ accordingly.
double (value field) Volume of this MeshEntry
unsigned int (value field) number of dimensions of this MeshEntry
unsigned int (value field) The MeshType defines the shape of the mesh entry. 0: Not assigned 1: cuboid 2: cylinder 3. cylindrical shell 4: cylindrical shell segment 5: sphere 6: spherical shell 7: spherical shell segment 8: Tetrahedral
vector<double> (value field) Coordinates that define current MeshEntry. Depend on MeshType.
vector<unsigned int> (value field) Indices of other MeshEntries that this one connects to
vector<double> (value field) Diffusion area for geometry of interface
vector<double> (value field) Diffusion scaling for geometry of interface
MgBlock: Hodgkin-Huxley type voltage-gated Ion channel. Something like the old tabchannel from GENESIS, but also presents a similar interface as hhchan from GENESIS.
- proc¶
void (shared message field) This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on.
The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.
- process()¶
(destination message field) Handles process call
- reinit()¶
(destination message field) Handles reinit call
- origChannel()¶
(destination message field)
- setKMg_A()¶
(destination message field) Assigns field value.
- getKMg_A()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- setKMg_B()¶
(destination message field) Assigns field value.
- getKMg_B()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- setCMg()¶
(destination message field) Assigns field value.
- getCMg()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- setIk()¶
(destination message field) Assigns field value.
- getIk()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- setZk()¶
(destination message field) Assigns field value.
- getZk()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- KMg_A¶
double (value field) 1/eta
- KMg_B¶
double (value field) 1/gamma
- CMg¶
double (value field) [Mg] in mM
- Ik¶
double (value field) Current through MgBlock
- Zk¶
double (value field) Charge on ion
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
Id (value field) Id of source Element.
Id (value field) Id of source Element.
vector<string> (value field) Names of SrcFinfos for messages going from e1 to e2. There arematching entries in the destFieldsOnE2 vector
vector<string> (value field) Names of DestFinfos for messages going from e1 to e2. There arematching entries in the srcFieldsOnE1 vector
vector<string> (value field) Names of SrcFinfos for messages going from e2 to e1. There arematching entries in the destFieldsOnE1 vector
vector<string> (value field) Names of destFinfos for messages going from e2 to e1. There arematching entries in the srcFieldsOnE2 vector
ObjId,ObjId (lookup field) The element adjacent to the specified element
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
string (value field) Access function for entire Mstring object.
string (value field) Access function for value field of Mstring object,which happens also to be the entire contents of the object.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Set internal conc of ion, and immediately send out the updated E
(destination message field) Set external conc of ion, and immediately send out the updated E
double (source message field) Computed reversal potential
double (value field) Computed reversal potential
double (value field) Temperature of cell
int (value field) Valence of ion in Nernst calculation
double (value field) Internal conc of ion
double (value field) External conc of ion
double (value field) Voltage scale factor
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Tells NeuroMesh to mesh up a subpart of a cell. For nowassumed contiguous.The first argument is the cell Id. The second is the wildcardpath of compartments to use for the subpart.
Id,vector<Id>,vector<Id>,vector<unsigned int> (source message field) Request SpineMesh to construct self based on list of electrical compartments that this NeuroMesh has determined are spine shaft and spine head respectively. Also passes in the info about where each spine is connected to the NeuroMesh. Arguments: Cell Id, shaft compartment Ids, head compartment Ids,index of matching parent voxels for each spine
Id,vector<double>,vector<unsigned int> (source message field) Tells PsdMesh to build a mesh. Arguments: Cell Id, Coordinates of each psd, index of matching parent voxels for each spineThe coordinates each have 8 entries:xyz of centre of psd, xyz of vector perpendicular to psd, psd diameter, diffusion distance from parent compartment to PSD
Id (value field) Id for base element of cell model. Uses this to traverse theentire tree of the cell to build the mesh.
vector<Id> (value field) Set of compartments to model. If they happen to be contiguousthen also set up diffusion between the compartments. Can alsohandle cases where the same cell is divided into multiplenon-diffusively-coupled compartments
bool (value field) Flag: when separateSpines is true, the traversal separates any compartment with the strings ‘spine’, ‘head’, ‘shaft’ or ‘neck’ in its name,Allows to set up separate mesh for spines, based on the same cell model. Requires for the spineListOut message tobe sent to the target SpineMesh object.
unsigned int (value field) Number of cylindrical/spherical segments in model
unsigned int (value field) Number of diffusive compartments in model
vector<unsigned int> (value field) Vector of indices of parents of each voxel.
double (value field) Diffusive length constant to use for subdivisions. The system willattempt to subdivide cell using diffusive compartments ofthe specified diffusion lengths as a maximum.In order to get integral numbersof compartments in each segment, it may subdivide more finely.Uses default of 0.5 microns, that is, half typical lambda.For default, consider a tau of about 1 second for mostreactions, and a diffusion const of about 1e-12 um^2/sec.This gives lambda of 1 micron
string (value field) Policy for how to interpret electrical model geometry (which is a branching 1-dimensional tree) in terms of 3-D constructslike spheres, cylinders, and cones.There are three options, default, trousers, and cylinder:default mode: - Use frustrums of cones. Distal diameter is always from compt dia. - For linear dendrites (no branching), proximal diameter is diameter of the parent compartment - For branching dendrites and dendrites emerging from soma, proximal diameter is from compt dia. Don’t worry about overlap. - Place somatic dendrites on surface of spherical soma, or at ends of cylindrical soma - Place dendritic spines on surface of cylindrical dendrites, not emerging from their middle.trousers mode: - Use frustrums of cones. Distal diameter is always from compt dia. - For linear dendrites (no branching), proximal diameter is diameter of the parent compartment - For branching dendrites, use a trouser function. Avoid overlap. - For soma, use some variant of trousers. Here we must avoid overlap - For spines, use a way to smoothly merge into parent dend. Radius of curvature should be similar to that of the spine neck. - Place somatic dendrites on surface of spherical soma, or at ends of cylindrical soma - Place dendritic spines on surface of cylindrical dendrites, not emerging from their middle.cylinder mode: - Use cylinders. Diameter is just compartment dia. - Place somatic dendrites on surface of spherical soma, or at ends of cylindrical soma - Place dendritic spines on surface of cylindrical dendrites, not emerging from their middle. - Ignore spatial overlap.
Neuron - A compartment container
Neutral: Base class for all MOOSE classes. Providesaccess functions for housekeeping fields and operations, messagetraversal, and so on.
(destination message field) Message from Parent Element(s)
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
int (source message field) Message to child Elements
Neutral (value field) Access function for entire object
string (value field) Name of object
ObjId (value field) ObjId for current object
ObjId (value field) Parent ObjId for current object
vector<Id> (value field) vector of ObjIds listing all children of current object
string (value field) text path for object
string (value field) Class Name of object
unsigned int (value field) # of Data entries on Element.Note that on a FieldElement this does NOT refer to field entries,but to the number of DataEntries on the parent of the FieldElement.
unsigned int (value field) For a FieldElement: number of entries of self.For a regular Element: One.
vector<string> (value field) List of all value fields on Element.These fields are accessed through the assignment operations in the Python interface.These fields may also be accessed as functions through the set<FieldName> and get<FieldName> commands.
vector<string> (value field) List of all source fields on Element, that is fields that can act as message sources.
vector<string> (value field) List of all destination fields on Element, that is, fieldsthat are accessed as Element functions.
vector<ObjId> (value field) Messages going out from this Element
vector<ObjId> (value field) Messages coming in to this Element
string,vector<Id> (lookup field) Ids of Elements connected this Element on specified field.
string,vector<ObjId> (lookup field) ObjIds receiving messages from the specified SrcFinfo
string,vector<string> (lookup field) Matching function names for each ObjId receiving a msg from the specified SrcFinfo
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
unsigned int (value field) DataId of source Element.
PID feedback controller.PID stands for Proportional-Integral-Derivative. It is used to feedback control dynamical systems. It tries to create a feedback output such that the sensed (measured) parameter is held at command value. Refer to wikipedia (http://wikipedia.org) for details on PID Controller.
void (shared message field) This is a shared message to receive Process messages from the scheduler objects.The first entry in the shared msg is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Command (desired value) input. This is known as setpoint (SP) in control theory.
(destination message field) Sensed parameter - this is the one to be tuned. This is known as process variable (PV) in control theory. This comes from the process we are trying to control.
(destination message field) Destination message to control the PIDController gain dynamically.
(destination message field) Handle process calls.
(destination message field) Reinitialize the object.
double (source message field) Sends the output of the PIDController. This is known as manipulated variable (MV) in control theory. This should be fed into the process which we are trying to control.
double (value field) This is the proportional gain (Kp). This tuning parameter scales the proportional term. Larger gain usually results in faster response, but too much will lead to instability and oscillation.
double (value field) Bound on the permissible range of output. Defaults to maximum double value.
double (value field) The command (desired) value of the sensed parameter. In control theory this is commonly known as setpoint(SP).
double (value field) Sensed (measured) value. This is commonly known as process variable(PV) in control theory.
double (value field) The integration time constant, typically = dt. This is actually proportional gain divided by integral gain (Kp/Ki)). Larger Ki (smaller tauI) usually leads to fast elimination of steady state errors at the cost of larger overshoot.
double (value field) The differentiation time constant, typically = dt / 4. This is derivative gain (Kd) times proportional gain (Kp). Larger Kd (tauD) decreases overshoot at the cost of slowing down transient response and may lead to instability.
double (value field) Output of the PIDController. This is given by: gain * ( error + INTEGRAL[ error dt ] / tau_i + tau_d * d(error)/dt )
Where gain = proportional gain (Kp), tau_i = integral gain (Kp/Ki) and tau_d = derivative gain (Kd/Kp). In control theory this is also known as the manipulated variable (MV)
- error¶
double (value field) The error term, which is the difference between command and sensed value.
- integral¶
double (value field) The integral term. It is calculated as INTEGRAL(error dt) = previous_integral + dt * (error + e_previous)/2.
- derivative
double (value field) The derivative term. This is (error - e_previous)/dt.
- e_previous¶
double (value field) The error term for previous step.
(destination message field) Increments mol numbers by specified amount. Can be +ve or -ve
(destination message field) Decrements mol numbers by specified amount. Can be +ve or -ve
Abstract base class for pools.
void (shared message field) Connects to reaction
void (shared message field) Shared message for process and reinit
void (shared message field) Shared message for connecting to species objects
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Handles reaction input
(destination message field) Handles process call
(destination message field) Handles reinit call
(destination message field) Separate finfo to assign molWt, and consequently diffusion const.Should only be used in SharedMsg with species.
double (source message field) Sends out # of molecules in pool on each timestep
void (source message field) Requests Species object for mol wt
double (value field) Number of molecules in pool
double (value field) Initial value of number of molecules in pool
double (value field) Diffusion constant of molecule
double (value field) Motor transport rate molecule. + is away from soma, - is towards soma. Only relevant for ZombiePool subclasses.
double (value field) Concentration of molecules in this pool
double (value field) Initial value of molecular concentration in pool
double (value field) Volume of compartment. Units are SI. Utility field, the actual volume info is stored on a volume mesh entry in the parent compartment.This mapping is implicit: the parent compartment must be somewhere up the element tree, and must have matching mesh entries. If the compartment isn’tavailable the volume is just taken as 1
unsigned int (value field) Species identifier for this mol pool. Eventually link to ontology.
void (shared message field) Shared message for process and reinit
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Handles process call
(destination message field) Handles reinit call
unsigned int (value field) Returns number of nodes that simulation runs on.
unsigned int (value field) Returns index of current node.
unsigned int (value field) Size of the send a receive buffers for each node.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Specifies the geometry of the spine,and the associated parent voxelArguments: cell container, disk params vector with 8 entriesper psd, parent voxel index
double (value field) An assumed thickness for PSD. The volume is computed as thePSD area passed in to each PSD, times this value.defaults to 50 nanometres. For reference, membranes are 5 nm.
PulseGen: general purpose pulse generator. This can generate any number of pulses with specified level and duration.
- proc¶
void (shared message field) This is a shared message to receive Process messages from the scheduler objects.The first entry in the shared msg is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.
- getOutputValue()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- setBaseLevel()¶
(destination message field) Assigns field value.
- getBaseLevel()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- setFirstLevel()¶
(destination message field) Assigns field value.
- getFirstLevel()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- setFirstWidth()¶
(destination message field) Assigns field value.
- getFirstWidth()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- setFirstDelay()¶
(destination message field) Assigns field value.
- getFirstDelay()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- setSecondLevel()¶
(destination message field) Assigns field value.
- getSecondLevel()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- setSecondWidth()¶
(destination message field) Assigns field value.
- getSecondWidth()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- setSecondDelay()¶
(destination message field) Assigns field value.
- getSecondDelay()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- setCount()¶
(destination message field) Assigns field value.
- getCount()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- setTrigMode()¶
(destination message field) Assigns field value.
- getTrigMode()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- setLevel()¶
(destination message field) Assigns field value.
- getLevel()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- setWidth()¶
(destination message field) Assigns field value.
- getWidth()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- setDelay()¶
(destination message field) Assigns field value.
- getDelay()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- input()¶
(destination message field) Handle incoming input that determines gating/triggering onset.
- levelIn()¶
(destination message field) Handle level value coming from other objects
- widthIn()¶
(destination message field) Handle width value coming from other objects
- delayIn()¶
(destination message field) Handle delay value coming from other objects
- process()¶
(destination message field) Handles process call, updates internal time stamp.
- reinit()¶
(destination message field) Handles reinit call.
- output¶
double (source message field) Current output level.
- outputValue¶
double (value field) Output amplitude
- baseLevel¶
double (value field) Basal level of the stimulus
- firstLevel¶
double (value field) Amplitude of the first pulse in a sequence
- firstWidth¶
double (value field) Width of the first pulse in a sequence
- firstDelay¶
double (value field) Delay to start of the first pulse in a sequence
- secondLevel¶
double (value field) Amplitude of the second pulse in a sequence
- secondWidth¶
double (value field) Width of the second pulse in a sequence
- secondDelay¶
double (value field) Delay to start of of the second pulse in a sequence
- count¶
unsigned int (value field) Number of pulses in a sequence
- trigMode¶
unsigned int (value field) Trigger mode for pulses in the sequence.
0 : free-running mode where it keeps looping its output 1 : external trigger, where it is triggered by an external input (and stops after creating the first train of pulses) 2 : external gate mode, where it keeps generating the pulses in a loop as long as the input is high.
RC circuit: a series resistance R shunted by a capacitance C.
void (shared message field) This is a shared message to receive Process messages from the scheduler objects.The first entry in the shared msg is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Receives input to the RC circuit. All incoming messages are summed up to give the total input current.
(destination message field) Handles process call.
(destination message field) Handle reinitialization
double (source message field) Current output level.
double (value field) Initial value of ‘state’
double (value field) Series resistance of the RC circuit.
double (value field) Parallel capacitance of the RC circuit.
double (value field) Output value of the RC circuit. This is the voltage across the capacitor.
double (value field) Input value to the RC circuit.This is handled as an input current to the circuit.
Base class for reactions. Provides the MOOSE APIfunctions, but ruthlessly refers almost all of them to derivedclasses, which have to provide the man page output.
void (shared message field) Connects to substrate pool
void (shared message field) Connects to substrate pool
void (shared message field) Shared message for process and reinit
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Handles # of molecules of substrate
(destination message field) Handles # of molecules of product
(destination message field) Handles process call
(destination message field) Handles reinit call
double,double (source message field) Sends out increment of molecules on product each timestep
double,double (source message field) Sends out increment of molecules on product each timestep
double (value field) Forward rate constant, in # units
double (value field) Reverse rate constant, in # units
double (value field) Forward rate constant, in concentration units
double (value field) Reverse rate constant, in concentration units
unsigned int (value field) Number of substrates of reaction
unsigned int (value field) Number of products of reaction
(destination message field) Assigns clock ticks. Args: tick#, dt
(destination message field) create( class, parent, newElm, name, numData, isGlobal )
(destination message field) Destroys Element, all its messages, and all its children. Args: Id
(destination message field) handleCopy( vector< Id > args, string newName, unsigned int nCopies, bool toGlobal, bool copyExtMsgs ): The vector< Id > has Id orig, Id newParent, Id newElm. This function copies an Element and all its children to a new parent. May also expand out the original into nCopies copies. Normally all messages within the copy tree are also copied. If the flag copyExtMsgs is true, then all msgs going out are also copied.
(destination message field) handleMove( Id orig, Id newParent ): moves an Element to a new parent
(destination message field) Makes a msg. Arguments are: msgtype, src object, src field, dest object, dest field
(destination message field) Stops simulation running and quits the simulator
(destination message field) Deals with assignment of path to a given clock. Arguments: path, field, tick number.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
unsigned int (value field) Index of source object.
unsigned int (value field) Index of dest object.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns connectivity with specified probability and seed
(destination message field) Assigns single row,column value
(destination message field) Clears single row,column entry
(destination message field) Clears out the entire matrix
(destination message field) Transposes the sparse matrix
(destination message field) Fills entire matrix using pairs of (x,y) indices to indicate presence of a connection. If the target is a FieldElement itautomagically assigns FieldIndices.
(destination message field) Fills entire matrix using triplets of (x,y,fieldIndex) to fully specify every connection in the sparse matrix.
unsigned int (value field) Number of rows in matrix.
unsigned int (value field) Number of columns in matrix.
unsigned int (value field) Number of Entries in matrix.
double (value field) connection probability for random connectivity.
long (value field) Random number seed for generating probabilistic connectivity.
void (shared message field) Connects to pools of this Species type
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Handle requests for molWt.
double (source message field) returns molWt.
double (value field) Molecular weight of species
SpikeGen object, for detecting threshold crossings.The threshold detection can work in multiple modes.
If the refractT < 0.0, then it fires an event only at the rising edge of the input voltage waveform
void (shared message field) Shared message to receive Process message from scheduler
(destination message field) Handles process call
(destination message field) Handles reinit call
(destination message field) Handles Vm message coming in from compartment
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
double (source message field) Sends out a trigger for an event.
double (value field) Spiking threshold, must cross it going up
double (value field) Refractory Time.
double (value field) Absolute refractory time. Synonym for refractT.
bool (value field) True if SpikeGen has just fired
bool (value field) When edgeTriggered = 0, the SpikeGen will fire an event in each timestep while incoming Vm is > threshold and at least abs_refracttime has passed since last event. This may be problematic if the incoming Vm remains above threshold for longer than abs_refract. Setting edgeTriggered to 1 resolves this as the SpikeGen generatesan event only on the rising edge of the incoming Vm and will remain idle unless the incoming Vm goes below threshold.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Specifies the list of electrical compartments for the spine,and the associated parent voxelArguments: cell container, shaft compartments, head compartments, parent voxel index
vector<unsigned int> (value field) Vector of indices of proximal voxels within this mesh.Spines are at present modeled with just one compartment,so each entry in this vector is always set to EMPTY == -1U
void (shared message field) Shared message for process and reinit
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Handles process call
(destination message field) Handles reinit call
(destination message field) Handles process call
(destination message field) Handles reinit call
double (value field) Mean of all sampled values.
double (value field) Standard Deviation of all sampled values.
double (value field) Sum of all sampled values.
unsigned int (value field) Number of all sampled values.
SteadyState: works out a steady-state value for a reaction system. It uses GSL heavily, and isn’t even compiled if the flag isn’t set. It finds the ss value closest to the initial conditions, defined by current molecular concentrations.If you want to find multiple stable states, use the MultiStable object,which operates a SteadyState object to find multiple states.If you want to carry out a dose-response calculation, use the DoseResponse object.If you want to follow a stable state in phase space, use the StateTrajectory object.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) This function initializes and rebuilds the matrices used in the calculation.
(destination message field) Finds the nearest steady state to the current initial conditions. This function rebuilds the entire calculation only if the object has not yet been initialized.
(destination message field) Finds the nearest steady state to the current initial conditions. This function rebuilds the entire calculation
(destination message field) Utility function to show the matrices derived for the calculations on the reaction system. Shows the Nr, gamma, and total matrices
(destination message field) Generate random initial conditions consistent with the massconservation rules. Typically invoked in order to scanstates
Id (value field) Specify the Id of the stoichiometry system to use
bool (value field) Bool: True if there is a problem with the stoichiometry
bool (value field) True if the model has been initialized successfully
unsigned int (value field) Number of iterations done by steady state solver
string (value field) Status of solver
unsigned int (value field) Max permissible number of iterations to try before giving up
double (value field) Fractional accuracy required to accept convergence
unsigned int (value field) Number of variable molecules in reaction system.
unsigned int (value field) Number of independent molecules in reaction system
unsigned int (value field) 0: stable; 1: unstable; 2: saddle; 3: osc?; 4: one near-zero eigenvalue; 5: other
unsigned int (value field) Number of negative eigenvalues: indicates type of solution
unsigned int (value field) Number of positive eigenvalues: indicates type of solution
unsigned int (value field) 0: Good; 1: Failed to find steady states; 2: Failed to find eigenvalues
unsigned int,double (lookup field) Totals table for conservation laws. The exact mapping ofthis to various sums of molecules is given by the conservation matrix, and is currently a bit opaque.The value of ‘total’ is set to initial conditions whenthe ‘SteadyState::settle’ function is called.Assigning values to the total is a special operation:it rescales the concentrations of all the affectedmolecules so that they are at the specified total.This happens the next time ‘settle’ is called.
unsigned int,double (lookup field) Eigenvalues computed for steady state
void (shared message field) Shared message for process and reinit
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Handles process call, updates internal time stamp.
(destination message field) Handles reinit call.
double (source message field) Sends out tabulated data according to lookup parameters.
double (value field) Start time used when table is emitting values. For lookupvalues below this, the table just sends out its zero entry.Corresponds to zeroth entry of table.
double (value field) Time to stop emitting values.If time exceeds this, then the table sends out its last entry.The stopTime corresponds to the last entry of table.
double (value field) If looping, this is the time between successive cycle starts.Defaults to the difference between stopTime and startTime, so that the output waveform cycles with precisely the same duration as the table contents.If larger than stopTime - startTime, then it pauses at the last table value till it is time to go around again.If smaller than stopTime - startTime, then it begins the next cycle even before the first one has reached the end of the table.
double (value field) Increment in lookup (x) value on every timestep. If it isless than or equal to zero, the StimulusTable uses the current timeas the lookup value.
double (value field) Current value of lookup (x) value.If stepSize is less than or equal to zero, this is set tothe current time to use as the lookup value.
bool (value field) Flag: Should it loop around to startTime once it has reachedstopTime. Default (zero) is to do a single pass.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Restore all zombies to their native state
string (value field) Wildcard path for reaction system handled by Stoich
Id (value field) Id of Kinetic reaction solver class that works with this Stoich. Must be of class Ksolve, or Gsolve (at present) Must be assigned before the path is set.
Id (value field) Id of Diffusion solver class that works with this Stoich. Must be of class Dsolve If left unset then the system will be assumed to work in a non-diffusive, well-stirred cell. If it is going to be used it must be assigned before the path is set.
Id (value field) Id of chemical compartment class that works with this Stoich. Must be derived from class ChemCompt. If left unset then the system will be assumed to work in a non-diffusive, well-stirred cell. If it is going to be used it must be assigned before the path is set.
double (value field) Estimated timestep for reac system based on Euler error
unsigned int (value field) Number of time-varying pools to be computed by the numerical engine
unsigned int (value field) Total number of pools handled by the numerical engine. This includes variable ones, buffered ones, and functions
vector<unsigned int> (value field) Map to look up the index of the pool from its Id.poolIndex = poolIdMap[ Id::value() - poolOffset ] where the poolOffset is the smallest Id::value. poolOffset is passed back as the last entry of this vector. Any Ids that are not pools return EMPTY=~0.
unsigned int (value field) Total number of rate terms in the reaction system.
vector<int> (value field) The non-zero matrix entries in the sparse matrix. Theircolumn indices are in a separate vector and the rowinformatino in a third
vector<unsigned int> (value field) Column Index of each matrix entry
vector<unsigned int> (value field) Row start for each block of entries and column indices
SumFunc object. Adds up all inputs
SymCompartment object, for branching neuron models. In symmetric
compartments the axial resistance is equally divided on two sides of
you must use a fixed-width font like Courier for correct rendition of the diagrams below.]
In case of branching, the B-C part of the parent’s axial resistance
forms a Y with the A-B part of the children.
As per basic circuit analysis techniques, the C node is replaced using
star-mesh transform. This requires all sibling compartments at a
branch point to be connected via ‘sibling’ messages by the user (or
by the cell reader in case of prototypes). For the same reason, the
child compartment must be connected to the parent by
distal-proximal message pair. The calculation of the
coefficient for computing equivalent resistances in the mesh is done
at reinit.
void (shared message field) This is a shared message between symmetric compartments.
It goes from the proximal end of the current compartment to distal end of the compartment closer to the soma.
- distal¶
void (shared message field) This is a shared message between symmetric compartments.
The Ra values collected from children and sibling nodes are used for computing the equivalent resistance between each pair of nodes using star-mesh transformation. Mathematically this is the same as the proximal message, but the distinction is important for traversal and clarity.
- sibling¶
void (shared message field) This is a shared message between symmetric compartments.
Conceptually, this goes from the proximal end of the current compartment to the proximal end of a sibling compartment on a branch in a dendrite. However, this works out to the same as a ‘distal’ message in terms of equivalent circuit. The Ra values collected from siblings and parent node are used for computing the equivalent resistance between each pair of nodes using star-mesh transformation.
- sphere¶
void (shared message field) This is a shared message between a spherical compartment
(typically soma) and a number of evenly spaced cylindrical compartments, typically primary dendrites. The sphere contributes the usual Ra/2 to the resistance between itself and children. The child compartments do not connect across to each other through sibling messages. Instead they just connect to the soma through the ‘proximalOnly’ message
- cylinder¶
void (shared message field) This is a shared message between a cylindrical compartment
(typically a dendrite) and a number of evenly spaced child compartments, typically dendritic spines, protruding from the curved surface of the cylinder. We assume that the resistance from the cylinder curved surface to its axis is negligible. The child compartments do not need to connect across to each other through sibling messages. Instead they just connect to the parent dendrite through the ‘proximalOnly’ message
- proximalOnly¶
void (shared message field) This is a shared message between a dendrite and a parent
compartment whose offspring are spatially separated from each other. For example, evenly spaced dendrites emerging from a soma or spines emerging from a common parent dendrite. In these cases the sibling dendrites do not need to connect to each other through ‘sibling’ messages. Instead they just connect to the parent compartment (soma or dendrite) through this message
- raxialSym()¶
(destination message field) Expects Ra and Vm from other compartment.
- sumRaxial()¶
(destination message field) Expects Ra from other compartment.
- raxialSym()
(destination message field) Expects Ra and Vm from other compartment.
- sumRaxial()
(destination message field) Expects Ra from other compartment.
- raxialSym()
(destination message field) Expects Ra and Vm from other compartment.
- sumRaxial()
(destination message field) Expects Ra from other compartment.
- raxialSphere()¶
(destination message field) Expects Ra and Vm from other compartment. This is a special case when
other compartments are evenly distributed on a spherical compartment.
- raxialCylinder()¶
(destination message field) Expects Ra and Vm from other compartment. This is a special case when
other compartments are evenly distributed on the curved surface of the cylindrical compartment, so we assume that the cylinder does not add any further resistance.
- raxialSphere()
(destination message field) Expects Ra and Vm from other compartment. This is a special case when
other compartments are evenly distributed on a spherical compartment.
- proximalOut¶
double,double (source message field) Sends out Ra and Vm on each timestep, on the proximalend of a compartment. That is, this end should be pointed toward the soma. Mathematically the same as raxialOutbut provides a logical orientation of the dendrite.One can traverse proximalOut messages to get to the soma.
- sumRaxialOut¶
double (source message field) Sends out Ra
- distalOut¶
double,double (source message field) Sends out Ra and Vm on each timestep, on the distal endof a compartment. This end should be pointed away from thesoma. Mathematically the same as proximalOut, but givesan orientation to the dendrite and helps traversal.
- sumRaxialOut
double (source message field) Sends out Ra
- distalOut
double,double (source message field) Sends out Ra and Vm on each timestep, on the distal endof a compartment. This end should be pointed away from thesoma. Mathematically the same as proximalOut, but givesan orientation to the dendrite and helps traversal.
- sumRaxialOut
double (source message field) Sends out Ra
- distalOut
double,double (source message field) Sends out Ra and Vm on each timestep, on the distal endof a compartment. This end should be pointed away from thesoma. Mathematically the same as proximalOut, but givesan orientation to the dendrite and helps traversal.
- cylinderOut¶
double,double (source message field) Sends out Ra and Vm to compartments (typically spines) on thecurved surface of a cylinder. Ra is set to nearly zero,since we assume that the resistance from axis to surface isnegligible.
- proximalOut
double,double (source message field) Sends out Ra and Vm on each timestep, on the proximalend of a compartment. That is, this end should be pointed toward the soma. Mathematically the same as raxialOutbut provides a logical orientation of the dendrite.One can traverse proximalOut messages to get to the soma.
void (shared message field) Shared message to receive Process message from scheduler
(destination message field) Handles process call
(destination message field) Handles reinit call
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Sometimes we want to continuously activate the channel
(destination message field) Modulate channel response
double (value field) Decay time constant for the synaptic conductance, tau1 >= tau2.
double (value field) Rise time constant for the synaptic conductance, tau1 >= tau2.
bool (value field) Flag. If true, the overall conductance is normalized by the number of individual synapses in this SynChan object.
SynChanBase: Base class for assorted ion channels.Presents a common interface for all of them.
void (shared message field) This is a shared message to couple channel to compartment. The first entry is a MsgSrc to send Gk and Ek to the compartment The second entry is a MsgDest for Vm from the compartment.
void (shared message field) Message to Goldman-Hodgkin-Katz object
(destination message field) Handles Vm message coming in from compartment
(destination message field) Handles Vm message coming in from compartment
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
double,double (source message field) Sends channel variables Gk and Ek to compartment
double (source message field) Conductance term going out to GHK object
double (source message field) Channel current. This message typically goes to concenobjects that keep track of ion concentration.
double (value field) Maximal channel conductance
double (value field) Reversal potential of channel
double (value field) Channel conductance variable
double (value field) Channel current variable
double (value field) Duration of spike buffer.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns number of field entries in field array.
(destination message field) Requests number of field entries in field array.The requesting Element must provide a handler for the returned value.
unsigned int (value field) Number of synapses on SynHandler. Duplicate field for num_synapse
Synapse using ring buffer for events.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Handles arriving spike messages, inserts into event queue.
double (value field) Synaptic weight
double (value field) Axonal propagation delay to this synapse
void (shared message field) Shared message for process and reinit
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Fills data into table. Also handles data sent back following request
(destination message field) Fills spike timings into the Table. Signal has to exceed thresh
(destination message field) Handles process call, updates internal time stamp.
(destination message field) Handles reinit call.
Pd (source message field) Sends request for a field to target object
double (value field) threshold used when Table acts as a buffer for spikes
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Linearly scales and offsets data. Scale first, then offset.
(destination message field) Dumps table contents to xplot-format file. Argument 1 is filename, argument 2 is plotname
(destination message field) Dumps table contents to single-column ascii file. Uses scientific notation. Argument 1 is filename
(destination message field) Reads a single column from a CSV file. Arguments: filename, column#, starting row#, separator
(destination message field) Reads a single plot from an xplot file. Arguments: filename, plotnameWhen the file has 2 columns, the 2nd column is loaded.
(destination message field) Reads a single plot from an xplot file, and selects a subset of points from it. Arguments: filename, plotname, startindex, endindexUses C convention: startindex included, endindex not included.When the file has 2 columns, the 2nd column is loaded.
(destination message field) Reads a plot from an xplot file and compares with contents of TableBase.Result is put in ‘output’ field of table.If the comparison fails (e.g., due to zero entries), the return value is -1.Arguments: filename, plotname, comparison_operationOperations: rmsd (for RMSDifference), rmsr (RMSratio ), dotp (Dot product, not yet implemented).
(destination message field) Compares contents of TableBase with a vector of doubles.Result is put in ‘output’ field of table.If the comparison fails (e.g., due to zero entries), the return value is -1.Arguments: Other vector, comparison_operationOperations: rmsd (for RMSDifference), rmsr (RMSratio ), dotp (Dot product, not yet implemented).
(destination message field) Handles request to clear the data vector
vector<double> (value field) vector with all table entries
double (value field) Output value holding current table entry or output of a calculation
unsigned int (value field) size of table. Note that this is the number of x divisions +1since it must represent the largest value as well as thesmallest
unsigned int,double (lookup field) Value of table at specified index
TimeTable: Read in spike times from file and send out eventOut messages
at the specified times.
void (shared message field) Shared message for process and reinit
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Handle process call
(destination message field) Handles reinit call
double (source message field) Sends out spike time if it falls in current timestep.
string (value field) File to read lookup data from. The file should be contain two columns
separated by any space character.
- method¶
int (value field) Method to use for filling up the entries. Currently only method 4
(loading from file) is supported.
- state¶
double (value field) Current state of the time table.
Variable for storing values.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
unsigned long (value field) Variable value
Voltage clamp object for holding neuronal compartments at a specific voltage. This implementation uses a builtin RC circuit to filter the
command input and then use a PID to bring the sensed voltage (Vm from
compartment) to the filtered command potential.
Connect the currentOut source of VClamp to injectMsgdest of Compartment. Connect the VmOut source of Compartment to
set_sensed dest of VClamp. Either set command field to a
fixed value, or connect an appropriate source of command potential
(like the outputOut message of an appropriately configured
PulseGen) to set_command dest.
The default settings for the RC filter and PID controller should betime constant of RC filter, tau = 5 * dt
proportional gain of PID, gain = Cm/dt where Cm is the membrane
capacitance of the compartmentintegration time of PID, ti = dt
derivative time of PID, td = 0
- proc¶
void (shared message field) Shared message to receive Process messages from the scheduler
- getCommand()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- getCurrent()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- getSensed()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- setMode()¶
(destination message field) Assigns field value.
- getMode()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- setTi()¶
(destination message field) Assigns field value.
- getTi()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- setTd()¶
(destination message field) Assigns field value.
- getTd()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- setTau()¶
(destination message field) Assigns field value.
- getTau()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- setGain()¶
(destination message field) Assigns field value.
- getGain()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- sensedIn()¶
(destination message field) The VmOut message of the Compartment object should be connected
here.
- commandIn()¶
(destination message field) The command voltage source should be connected to this.
- process()¶
(destination message field) Handles ‘process’ call on each time step.
- reinit()¶
(destination message field) Handles ‘reinit’ call
- currentOut¶
double (source message field) Sends out current output of the clamping circuit. This should be connected to the injectMsg field of a compartment to voltage clamp it.
- command¶
double (value field) Command input received by the clamp circuit.
- current¶
double (value field) The amount of current injected by the clamp into the membrane.
- sensed¶
double (value field) Membrane potential read from compartment.
- mode¶
unsigned int (value field) Working mode of the PID controller.
mode = 1, derivative action based on command input mode = 2, proportional action and derivative action are based on command input.
- ti¶
double (value field) Integration time of the PID controller. Defaults to 1e9, i.e. integral
action is negligibly small.
- td¶
double (value field) Derivative time of the PID controller. This defaults to 0,
i.e. derivative action is unused.
- tau¶
double (value field) Time constant of the lowpass filter at input of the PID
controller. This smooths out abrupt changes in the input. Set it to 5 * dt or more to avoid overshoots.
- gain¶
double (value field) Proportional gain of the PID controller.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
unsigned int (value field) Number of divisions.
double (value field) Minimum value in table.
double (value field) Maximum value in table.
double (value field) Maximum value in table.
vector<double> (value field) The lookup table.
double,double (lookup field) Lookup function that performs interpolation to return a value.
unsigned int,double (lookup field) Lookup function that returns value by index.
void (shared message field) Shared message to receive Process message from scheduler
(destination message field) Handles process call
(destination message field) Handles reinit call
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Assigns field value.
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
(destination message field) Calcium Ion current, due to be converted to conc.
(destination message field) Fraction of total Ion current, that is carried by Ca2+.
(destination message field) Any input current that increases the concentration.
(destination message field) Any input current that decreases the concentration.
(destination message field) Synonym for assignment of basal conc.
double (source message field) Concentration of Ca in pool
double (value field) Calcium concentration.
double (value field) Basal Calcium concentration.
double (value field) Basal Calcium concentration, synonym for CaBasal
double (value field) Settling time for Ca concentration
double (value field) Volume scaling factor
double (value field) Thickness of Ca shell.
double (value field) Ceiling value for Ca concentration. If Ca > ceiling, Ca = ceiling. If ceiling <= 0.0, there is no upper limit on Ca concentration value.
double (value field) Floor value for Ca concentration. If Ca < floor, Ca = floor
Compartment object, for branching neuron models.
- proc¶
void (shared message field) This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on.
The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.
- process()¶
(destination message field) Handles process call
- reinit()¶
(destination message field) Handles reinit call
- setGbar()¶
(destination message field) Assigns field value.
- getGbar()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- setEk()¶
(destination message field) Assigns field value.
- getEk()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- setGk()¶
(destination message field) Assigns field value.
- getGk()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- getIk()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- setXpower()¶
(destination message field) Assigns field value.
- getXpower()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- setYpower()¶
(destination message field) Assigns field value.
- getYpower()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- setZpower()¶
(destination message field) Assigns field value.
- getZpower()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- setInstant()¶
(destination message field) Assigns field value.
- getInstant()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- setX()¶
(destination message field) Assigns field value.
- getX()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- setY()¶
(destination message field) Assigns field value.
- getY()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- setZ()¶
(destination message field) Assigns field value.
- getZ()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- setUseConcentration()¶
(destination message field) Assigns field value.
- getUseConcentration()¶
(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.
- concen()¶
(destination message field) Incoming message from Concen object to specific conc to usein the Z gate calculations
- createGate()¶
(destination message field) Function to create specified gate.Argument: Gate type [X Y Z]
- setNumGateX()¶
(destination message field) Assigns number of field entries in field array.
- getNumGateX()¶
(destination message field) Requests number of field entries in field array.The requesting Element must provide a handler for the returned value.
- setNumGateY()¶
(destination message field) Assigns number of field entries in field array.
- getNumGateY()¶
(destination message field) Requests number of field entries in field array.The requesting Element must provide a handler for the returned value.
- setNumGateZ()¶
(destination message field) Assigns number of field entries in field array.
- getNumGateZ()¶
(destination message field) Requests number of field entries in field array.The requesting Element must provide a handler for the returned value.
- Gbar¶
double (value field) Maximal channel conductance
- Ek¶
double (value field) Reversal potential of channel
- Gk¶
double (value field) Channel conductance variable
- Ik¶
double (value field) Channel current variable
- Xpower¶
double (value field) Power for X gate
- Ypower¶
double (value field) Power for Y gate
- Zpower¶
double (value field) Power for Z gate
- instant¶
int (value field) Bitmapped flag: bit 0 = Xgate, bit 1 = Ygate, bit 2 = ZgateWhen true, specifies that the lookup table value should beused directly as the state of the channel, rather than usedas a rate term for numerical integration for the state
- X¶
double (value field) State variable for X gate
- Y¶
double (value field) State variable for Y gate
- Z¶
double (value field) State variable for Y gate
- useConcentration¶
int (value field) Flag: when true, use concentration message rather than Vm tocontrol Z gate