This is the readme for simulations for the paper:

Bhalla US (2017) Synaptic input sequence discrimination on behavioral
time-scales mediated by reaction-diffusion chemistry in
dendrites. Elife

This archive was contributed by Dr U. Bhalla

This zipfile contains the following files:
README.html: this file
Fig2.py:		Script for generating Figure 2.
abstrModelEqns9.py:	Script defining abstract models for Figure 2

Fig5.py			Script for generating panels BCEF of Figure 5
Fig5_Feb2019.py         Updated version of Fig5.py that works with the
                        current (20190219) version of MOOSE. Due to a
                        change in the random-number generator system
                        the exact shape of the response is a little
                        different however the qualitative outcome is still
                        the same.
Fig5_3d.py		Script for generating panel D of Figure 5

Fig6_generate_data.py	Script for generating data files for Figure 6
Fig6.py			Script for making panels B-J of Figure 6.

NN_mapk14.g		GENESIS chemical model definition file for Figure 6
proto21.py		Channel prototypes for Figure 6
VHC-neuron.CNG.swc	Morphology file for Figure 6

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To generate the figures:

Figure 2:	(takes about 10 seconds)
python Fig2.py


Figure 5:	(takes about 30 seconds)
python Fig5.py


python Fig5_3d.py	(This will only work if you have Moogli installed. It
			generates the 3-D view of the modeled dendrite.)


Figure 6:	(takes about 6 hours for each generation run, 
		and 5 seconds for the final figure)
python Fig6_generate_data.py --fnumber 0 --sequence 1234

python Fig6_generate_data.py --fnumber 2 --sequence 40312

python Fig6.py	
	( This assumes that the files 
		Fig6_data.0.1234.xplot and Fig6_data.2.40312.xplot
	have been generated from the previous two commands.
	Note that I have explicitly embedded the results from a big
		parallel run for the tuning matrices into the script file.)

=============================================================================

20190219 This archive revised to include a new file Fig5_Feb2019.py from
Upinder Bhalla. See notes above for file description.