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Heterosynaptic Calcium Buffering
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images
Fig2.py
Fig5.py
Fig5_3d.py
Fig5_Feb2019.py
Fig6.py
Fig6_generate_data.py
NN_mapk14.g
README.html
README.md
SuppExamples.zip
SupplementaryData.ods
SupplementaryMaterial.pdf
TabulatedChemElecModels.docx
VHC-neuron.CNG.swc
abstrModelEqns9.py
abstrModelEqns9.pyc
proto21.py
proto21.pyc

README.md

MOOSE

Heterosynaptic Calcium Buffering 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 fig 2

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

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.)

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

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