Plotting states with stochastic ion channels-Channel Builder
Plotting states with stochastic ion channels-Channel Builder
Is there a way to plot the number of channels in each state of a stochastic model built with the channel builder? The only information I can get about the channels in each state is from the Point Process Viewer ("real time"), is there anyway to access/save this information?
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Re: Plotting states with stochastic ion channels-Channel Builder
Very good question!
STATEs of NMODL-specified mechanisms are automatically range variables, therefore visible to hoc with the appropriate syntax (suffix for density mechanisms, dot notation for point processes). The same is true for mechanisms constructed with the Channel Builder.
Imagine a stochastic channel mechanism called Nahh (upper case name because it's a point process, hence the name of an object class), which has states called mihj where i = 0..3 and j = 0..1. Suppose there is a model with multiple instances of this class, with the instances having names of the form nahh[k] where k = 0, 1, . . .. Then the states of any particular instance will be known to hoc as nahh[k].mihj, e.g. nahh[2].m0h1. The numeric value of each state will be the number of channels in that state.
Just like any other variable, Channel Builder states can be plotted in graphs (it is most convenient to use NEURON Main Menu / Graph / State axis, then use this new graph's "Plot what?" tool--see "Q: How do I plot something other than membrane potential?" in the FAQ list http://www.neuron.yale.edu/neuron/faq/general-questions), or captured with the Vector class's record() method (see http://www.neuron.yale.edu/neuron/stati ... tml#record) for subsequent plotting, analysis, or writing to files.
STATEs of NMODL-specified mechanisms are automatically range variables, therefore visible to hoc with the appropriate syntax (suffix for density mechanisms, dot notation for point processes). The same is true for mechanisms constructed with the Channel Builder.
Imagine a stochastic channel mechanism called Nahh (upper case name because it's a point process, hence the name of an object class), which has states called mihj where i = 0..3 and j = 0..1. Suppose there is a model with multiple instances of this class, with the instances having names of the form nahh[k] where k = 0, 1, . . .. Then the states of any particular instance will be known to hoc as nahh[k].mihj, e.g. nahh[2].m0h1. The numeric value of each state will be the number of channels in that state.
Just like any other variable, Channel Builder states can be plotted in graphs (it is most convenient to use NEURON Main Menu / Graph / State axis, then use this new graph's "Plot what?" tool--see "Q: How do I plot something other than membrane potential?" in the FAQ list http://www.neuron.yale.edu/neuron/faq/general-questions), or captured with the Vector class's record() method (see http://www.neuron.yale.edu/neuron/stati ... tml#record) for subsequent plotting, analysis, or writing to files.