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//creation and loading of a help file
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proc mkHELP() {
xpanel("HELP_FILE")
xlabel("Welcome to the vlPAG/DRN DA neuron model!") 
xlabel("-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------")
xlabel("The computer model consists of a single compartment spherical (15 micm diameter) neuron, the vlPAG/DRN DA neuron, which is endowed with eight conductances [NaT, NaP, kA, kDR, kM, H, CaHVA, CaLVA]")
xlabel("and a linear leak conductance. All data and simulations described below have been presented in:")
xlabel("Dougalis, A.G., Matthews, G.A.C., Liss, B. & Ungless, M.A. (2017). Ionic currents influencing autorhythmicity and pacemaking in dopamine neurons of the ventrolateral periaquaductal gray and")
xlabel("dorsal raphe nucleus (vlPAG/DRN): a voltage-clamp and computational modeling study. Journal of Computational Neuroscience, doi: 10.1007/s10827-017-0641-0. [Apr 3-2017. Epub ahead of print]")
xlabel("-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------")
xlabel("How to START running simulations [manuscript Figures 7-10 and online material 5]")
xlabel("Using the -RunControl- panelbox, press -Init&Run- to run simulations. You should be able to observe the results of the simulations in three appropriate graphic windows. The Graphic windows are labelled with")
xlabel("the parameter that is being monitored in time (in ms), i.e. v(0.5) is vlPAG/DRN DA neuron voltage (in mV), ina_NaP is the current carried by the persistent sodium current (mA/cm2). The three main graphic windows are loaded") 
xlabel("automatically and replicate the panels A-C as seen in Figure 9 of the published manuscript [Figure 9: Contribution of individual ionic currents to interspike interval (ISI) repolarisation in model DA neuron].")
xlabel("The three graphs depict [top to bottom as shown in Figure 9A-C] the voltage-time series(mV-ms)for the vlPAG/DRN DA neuron (TOP) and the current-time series (mA/cm2-ms) for inward (MIDDLE) and outward (BOTTOM)")                  
xlabel("ionic currents flowing through the vlPAG/DRN DA neuron during spontaneous firing.")
xlabel("Using the -I/V Clamp Electrode- panelbox select the option -IClamp- and dial appropriate durations (500-1000ms) and amplitude (+/- 0.12 nA) for injecting current into the vlPAG/DRN DA neuron. These actions would") 
xlabel("help the user to replicate the results presented in Figure 7 and 10 of the published manuscript investigating, respectively, the voltage-sag & delayed repolarisation following incremental hyperpolarising injections") 
xlabel("and instantaneous/sustained firing & Depolarisation Block [DB] following incremental depolarising current injections [Figure 7: Electrophysiological properties of model DA neuron; Figure 10: Contribution of individual") 
xlabel("ionic currents to depolarization block (DB) in model DA neuron]. To investigate the impact of individual conductances on the firing rate on the vlPAG/DRN DA neuron as shown in Figure 8 of the published manuscript, use")
xlabel("the -Conductance Parameter- panelbox to selectively change the properties (e.g. Ionic reversal potential[erev], Ionic Maximal conductance[gbar], Steady-state extent of Activation/Inactivation midpoint[vhalf] and slope)")  
xlabel("of any current desired and observe the changes in the electrophysiological behavior of the vlPAG/DRN DA model neuron.Finally, if other parameters, other than the ones contained in the parameter boxes supplied, need to") 
xlabel("be manipulated for simulations [e.g. midpoints and slope of the rate of Activation/Inactivation of conductances],these further parameters can be accessed/called from the NEURON menu through the following path:")
xlabel(" --Tools--Distributed_Mechanisms--Viewer--Name_Values--Parameters.")
xlabel("-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------")
xlabel("How to SAVE simulations")
xlabel("To export the resultant traces depicted in graphs 1, 2 & 3 simply press the button -Yes Save my data- on the panelbox named -Saving Simulations- appearing on your screen automatically upon loading the simulations.")
xlabel("This would save automatically the, voltage time-series of the vlPAG/DRN DA neurons and the current-time series of all ionic currents for the whole duration of the simulations [set at 5s] to a file called")
xlabel("vlPAG_DRN Analysis.dat. Rename the file as .txt and import it to other software for analysis if required (e.g. Spike2 CED) at a 40KHz reconstruction frequency (simulation step 25 mics). With appropriate modifications")
xlabel("in the vlPAG_DRN DA model.hoc file, one can add any other variables desired to be saved directly to that file (e.g. gating Activation/Inactivation variables, m & h, for sodium transient conductance, m_NaT & h_NaT).")
xlabel("-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------")
xlabel("This model and files will be updated when necessary by the modeller and implementer.For any queries or problems with this model please contact me on antoniosdougalis@hotmail.com")
xlabel("Have fun with modelling!")
xlabel("")
xlabel("Dr. Antonios Dougalis, April 2017, Berlin")
xlabel("antoniosdougalis@hotmail.com")
xpanel(200,50)
}