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'' (Connections.doc) describes
how messages are used for communication between neurons.
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.
showmsg
Displays list of incoming and outgoing messages of an
element.
getmsg
Returns information about a message into or out of
element.
gen3dmsg
Establishes message links between elements (identified in
two
lists) that are within a certain range of each other.
dd3dmsg
Establishes message links between dendrodendritic
synapses.
---------------------------------------------------------------------------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:
VALID MESSAGES
[6] EREST
[3] INJECT
[2] AXIAL
[1] RAXIAL
[0] CHANNEL
:
:
:
:
:
Em
inject
Vm
Ra Vm
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
INCOMING MESSAGES
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 >
OUTGOING
MSG 0 to
MSG 1 to
MSG 2 to
MSG 3 to
MSG 4 to
70 >
MESSAGES
'/cell/soma' type [1] 'RAXIAL' < Ra = 7960 > < Vm = 0 >
'/cell/dend2' type [2] 'AXIAL' < Vm = 0 >
'/cell/dend1/Ex_channel' type [0] 'VOLTAGE' < Vm = -70 >
'/cell/dend1/Inh_channel' type [0] 'VOLTAGE' < Vm = -70 >
'/output/dend1graphs/dend1Vm_grf' type [0] 'PLOT' < data = -
< 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 }
AXIAL
genesis > echo { getmsg /cell/dend1 -outgoing -source 1}
/cell/dend1
genesis > echo { getmsg /cell/dend1 -out -destination 1 }
/cell/dend2
genesis > echo { getmsg /cell/dend1 -out -count }
5
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'' (addmsg.doc), ``showmsg''
(showmsg.doc), ``getmsg'' (getmsg.doc), and ``deletemsg''
(deletemsg.doc) are described in the Command Reference section.