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LEECH HEART INTERNEURON 8-CELL TUTORIAL HELP
Andrew Hill, Steve Van Hooser, Ron Calabrese
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This tutorial allows one to study a network model of the
leech heart interneuron by Andrew Hill and Ron Calabrese.
Note: This help describes how to run the model, perform
experiments, and view the results. For a general
introduction to the leech heart interneuron circuit or
a technical description of the model, please see the
"Introduction". For help using one of the specific
experiment tools, use the "Help" button on its window.
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TABLE OF CONTENTS:
(1). Viewing the introductory material
(2). Showing, hiding, and viewing graphs
(3). Experiments
(4). Running the model and setting initial conditions
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(1). VIEWING THE INTRODUCTORY MATERIAL
The "Introduction" is an HTML document which can be viewed
in a web browser. Clicking on the introduction button
brings up a small window with a text field that says:
"netscape <filename>", where <filename> is the name of the
introduction document. If you use a different web browser,
simply change the name from "netscape" to the name of your
browser. If you do not have an web browser at all, please
see the Calabrese lab FTP site for a postscript version of
the introduction. Use username "anonymous" and get the file
pub/tutorials/intro.ps on calabreselx.biology.emory.edu.
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(2). SHOWING, HIDING, and VIEWING GRAPHS
There are six windows containing graphs of the activity
of the network which can be alternatively shown and hidden.
Two contain membrane voltage traces, and four contain
current traces for the various currents in HN cell 4L
(this cell was arbitrarily chosen).
To show the membrane voltage for all of the left or right
cells, click "Show Left Vm's" or "Show Right Vm's". A
window will pop up with the appropriate voltage traces,
and the button will change its name to
"Hide <Left/Right> Vm's". Clicking on "Hide..." will
hide the window.
To show the ionic current flowing in HN cell 4L, click
on either "Show 4L INa, IK" or "Show 4L Ih, ICa, IP".
The former shows the fast sodium current and the three
potassium currents, and the later shows the current
activated by hyperpolarization, the fast and slow calcium
currents, and the persistent sodium current. Clicking on
the button again will hide the window, just like the
membrane voltage windows above.
To show the synaptic current flowing into cell 4L, click
on either "Show 4R->4L currents" or "Show 1,2L->4L currents".
These show the synaptic currents to cell 4L from cell 4R or
from cells 1,2L, respectively. Clicking on the button again
will hide the window, just like the above windows.
All of the graphs have several features in common. First,
all graphs have a "scale" button which can be used to
change the minimum and maximum values for the x- and y-axes.
Second, there is a button on the top of the set of graphs
labeled "Autoscale", which will automatically adjust the
time axes to run from time 0 to until the end of the
currently-running simulation (as determined by the value
in the "Time (sec)" field). Finally, one can adjust the
scale of an axis graphically by clicking on the maximal or
minimal label, holding down, and dragging to a new value.
For example, to change the voltage axis to be from (0..-0.060)
to (0..-0.030), simply click on the label "-0.060", drag
until hitting the value -0.030 on the axis, and release.
The graph will redraw with the new scale. To change it back,
simply grab onto the "-0.030" label, and drag off the graph
until hitting -0.060 and release.
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(3). EXPERIMENTS
At present, one can perform three manipulations on the
model. First, one may change its parameters using the
"Parameter Editor"--simply click on the button to use
it. The Parameter Editor has its own help feature, so
look there for detailed information on using the editor.
Second, one may inject current into any of the cells by
clicking on the "Current Injection" button and adjusting
the value for each cell. Remember that the units are in
Amps, and that typical current injections for neurons are
in the tenths of a nano-Amp range. To inject 0.1e-9 into
the HN cell 4L, simply edit the text field next to "cell_4L"
to read 0.1e-9, and then either press return or click on
the label "cell_4L".
Finally, one may disable cells and synapses. While in
principle one may set the synaptic weights of any cell in
which one is not interested to zero to remove its
contribution, one can save time by not computing the
activity of that cell at all. The "Disable Cells and
Synapses" tool allows one to "disable" these cells so they
are not updated in the simulation. Further, it is common
to set the value of a synaptic weight to zero and then return
it to its original value. One can do this by entering the
specific values in the "Parameter Editor", but a feature
to do this more quickly has been added in the "Disable
Cells and Synapses" tool. See that tool's help button for
more information. Special note: If you disable a cell,
be sure to disable the synapses leading away from the cell
because otherwise the disabled cell will continue to output
the same synaptic current it did the instant it was disabled.
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(4). RUNNING THE MODEL AND SETTING INITIAL CONDITIONS
To run the model, simply specify how long the simulation
should last in the "Time" field and then click "Run".
Clicking "Stop" during a simulation will stop the simulation.
Clicking "Reset" will reset the simulation clock and return
the values of the simulation components to the original initial
values. (Note that this leaves the parameters of the model
untouched, but returns variables such as the current flowing
into the cell and the membrane voltage to their original initial
values.) Clicking "Exit Tutorial" will quit the program and
GENESIS.
The "Kick" button and the "Initial Cond" button allow the
initial conditions to be adjusted for different model
parameters. This is important for two reasons: first,
it is possible to start two cells which normally fire out
of phase in exactly the same state, and, since this is a
computer simulation without noise, the model doesn't start
oscillating. Second, even if the cells are started at
slightly different values, it may take a long time before
the cells settle into their oscillation pattern.
The "Kick" command solves both of these problems--it briefly
injects negative current into all of the cells to quiet
them, and then releases one group of cells which fire
together in the animal. It runs, in total, for 0.4 sec, and
restores any previous injection value when it is finished.
If one is using a set of parameters that take a long time
to settle down, one may want to let the system settle down
one time and then save the state of the network for later
restoration. Pressing "Initial Cond" exposes a hidden set
of buttons that allow the user to do just this. Simply type
the name of a file to save and either press return or click
the label of the text edit box. To restore a set of
conditions that were saved, enter the name in the "Restore"
text box and either press return or click the text box label.
To restore the default initial condition, simply click the
button with that label. Clicking "Initial Cond" again will
hide the buttons from the user.
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