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13. Messages

Elements within a GENESIS simulation communicate by a system of links called ``messages'', which allow one element to access the data fields of another element. Once the message link to or from an element have been established, the element is able to receive or send information each time its state is updated during the simulation.

Messages have no time delay and serve to unify a large number of elements into a single computational unit. They are used, for example, in detailed compartmental models of cells to link together membrane compartments and channels into a single electrical entity. The section on Synaptic Connections describes how messages are used for communication between neurons.

It is not feasible to summarize all of the GENESIS messages here, because the message name and parameters are specific to the object that receives the message. An element can send any message, and will not complain even if the message is not a valid GENESIS message. However, the destination element will check to see that it is a valid message name for that object and that it has the correct number of parameters. If the showobject command, or the documentation for an object is inadequate to explain what a given message really does, look at the MSGLOOP section of the source code for that object.

The GENESIS routines used for establishing and working with messages include the following:

Routine Description
addmsg Establishes message links between two elements.
deletemsg Deletes a message link between two elements.
dd3dmsg Establishes message links between dendrodendritic synapses.
gen3dmsg Establishes message links between elements (identified in two
lists) that are within a certain range of each other.
getmsg Returns information about a message into or out of element.
resetfastmsgVariation of reset command for use with kinetics library.
showmsg Displays list of incoming and outgoing messages of an element.

For example, at each step of a simulation, one asymmetric compartment connected to another asymmetric compartment needs to send both its axial resistance Ra and its membrane potential as of the previous simulation step (previous_state) to the second compartment. This allows the second compartment to calculate the current entering from the first.

You establish such a message link using the addmsg command. In the following command the dendrite compartment is linked to the soma with a message of the type RAXIAL, and a message link is established whereby two value fields, Ra and previous_state, will be sent from the dendrite to the soma at each simulation step:

  addmsg /cell/dend /cell/soma RAXIAL Ra previous_state
This establishes the information flow from the dendrite to the soma. In the reverse direction, the dendrite needs to receive the value of the soma's previous membrane potential in order to update its own state (the dendrite already knows its own axial resistance to the soma, and so the message need not include information regarding axial resistance). This link can be set up as follows:
  addmsg /cell/soma /cell/dend AXIAL  previous_state
Messages do not have to be between computational elements only. The following example shows how the soma would plot the value of its Vm field (the membrane potential) by sending a PLOT message to the xgraph element /graphs/Vmgraph (the last two arguments give the label and color to be used in plotting this field):
  addmsg /cell/soma /graphs/Vmgraph PLOT Vm *voltage *red
To find out the allowed message types and and associated fields for an element type, you use the showobject routine. For example:
  showobject compartment
This routine produces, along with other information, the following list of valid messages for objects of the type compartment:
        [6] EREST                : Em
        [3] INJECT               : inject
        [2] AXIAL                : Vm
        [1] RAXIAL               : Ra Vm
        [0] CHANNEL              : Gk Ek
In order to determine which messages have been established for a specific element, you can use the showmsg routine, which lists the incoming and outgoing messages for an element. For example, showmsg produces the following results when you run the Neuron tutorial in Scripts/neuron:
  genesis > showmsg /cell/dend1
  MSG 0 from '/cell/soma'  type [2] 'AXIAL' < Vm = 0 >
  MSG 1 from '/cell/dend2'  type [1] 'RAXIAL' < Ra = 7960 > < Vm = 0 >
  MSG 2 from '/cell/dend1/Ex_channel'  type [0] 'CHANNEL' < Gk = 0 >
        < Ek = -10 >
  MSG 3 from '/cell/dend1/Inh_channel'  type [0] 'CHANNEL' < Gk = 0 >
        < Ek = -80 >
  MSG 4 from '/input/injectpulse/dend1curr'  type [3] 'INJECT' < inject = 0 >

  MSG 0 to '/cell/soma' type [1] 'RAXIAL' < Ra = 7960 > < Vm = 0 >
  MSG 1 to '/cell/dend2' type [2] 'AXIAL' < Vm = 0 >
  MSG 2 to '/cell/dend1/Ex_channel' type [0] 'VOLTAGE' < Vm = -70 >
  MSG 3 to '/cell/dend1/Inh_channel' type [0] 'VOLTAGE' < Vm = -70 >
  MSG 4 to '/output/dend1graphs/dend1Vm_grf' type [0] 'PLOT' < data = -70 >
        < name = dend1 > < color = black >
Although showmsg is useful for providing debugging information when used interactively at the GENESIS prompt, its output is not in a convenient form for use within a script. In this case, you would use the getmsg routine. Here are some examples using getmsg:
  genesis > echo { getmsg /cell/dend1 -outgoing -type 1 }

  genesis > echo { getmsg /cell/dend1 -outgoing -source 1}

  genesis > echo { getmsg /cell/dend1 -out -destination 1 }

  genesis > echo { getmsg /cell/dend1 -out -count }

The deletemsg command removes message links. For example, to remove the input to the to the dend1 compartment from the channel Inh_channel, you would remove incoming message 3 and outgoing message 3, of the messages listed above. This would be done with the statements:

  deletemsg /cell/dend1 3 -incoming
  deletemsg /cell/dend1 3 -outgoing
The PLOT message from a compartment /cell/soma to a graph /data/voltage could be located and deleted with:
  deletemsg /data/voltage -in 0 -find /cell/soma PLOT

The various options for addmsg , showmsg , getmsg , and deletemsg are described in the Command Reference section.

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