Modelling of an in vitro Neuromodulatory Co-culture System

This project is implemented using the NEURON simulation environment version 8.0 on Windows. All of NMODL mechanism files are included in the mechanism folder while the raster plots which represent neural events are included in the raster_plot folder in this repository.

Please contact the author on the simulation results, if needed.

Update (August 4, 2021) on task3-4.hoc:

• Enhanced multi_run() procedure which automated the run() and exported data files according to the number specified by the user.
• The electric pulse stimulations were set to occur at the 1st, 5th and 25th millisecond, at the top left (axon of neuron[9], neuron[10], neuron[11]), top right (axon neuron[0], neuron[1], neuron[2]), and bottom right (axon neuron[3], neuron[4], neuron[5]) corners of the multielectrode array, respectively.

Update (July 31, 2021) on task3-3.hoc:

• Modified the .hoc code so that it is able to export voltages measured at the axon (normalised distance of 0.25 from the distal end) of all 12 neurons automatically.
• Compatible with session file task3-3.ses.

Update (July 27, 2021) on task3-3.hoc:

• Corrected the errors of producing and classifying intranodal synapses.
• Saved Gfluct.mod random values, intranodal and internodal synaptic weights, and their respective quantities into separated files.
• Defined multi_run() procedure which automated the run() and data exportation processes.
• Composed seed_generator.py which uses random.randrange(sys.maxsize) to export a seed.dat file which is comprised of 1000 randomly generated values to compensate the default pseudo-randomess of .hoc code. Afterwards, task3-3.hoc will scan seed.dat and take an integer as seed value.
• The seed value taken will affect the number of synapses, weights, and the normrand() function in Gfluct.mod.

Update (July 22, 2021) on task3-2.hoc:

• All Gfluct.mod parameters relating to inhibitory synapses in the .hoc file were set to zero.
• Reduced the standard deviation of the exhibitory conductance std_e in order to obtain results which reflected in vitro simulations more realistically.
• The train of spikes were reduced from 100 to 5.
• Modified the mechanism file Gfluct.mod in order to record the random numbers generated from further analysis purposes.
• Tuning the facilitation variable U.
• Analysing the unrealistic burst in continuous current spikes.

Update (July 17, 2021) on task4-1.ipynb:

• Created a Jupyter notebook to visualize the simulation results via raster plots (event plots).
• A sample graph was provided in the raster_plot folder.
• Please refer to the README.md file in the folder for more details.
• Some minor modifications on the parameters of the mechanisms in task3-2.hoc.

Update (June 28, 2021) on task3-2.hoc:

• Inserted tmgsyn.mod which simulates short-term (excitatory) synaptic plasticity to the axon of all 12 neurons in the system.
• Inserted ipulse1.mod which includes current clamps (point processes) that deliver a sequence of current pulses at regular intervals.
• Removed the single pulse current clamps.
• Optimisation on neurons' geometric alignment and the insertion of intranodal and internodal synapses.
• Hodgkin–Huxley model in all compartments were restored to default values.
• Composed a script named find_signal_peaks.py to find the peaks of the neuronal transmission voltage.

Update (June 23, 2021) on task3-1.hoc:

• Inserted Gfluct.mod NMODL mechanism to the axon of all 12 neurons in the system.
• The IClamp point process was limited at the axon of the first neuron in the first node and spiked only once at the beginning of the simulation.
• Number of internodal and internodal synapses were decreased to 20 each and the possibilities for zero weight (no connection) were considered.
• For the intranodel synapses, the number of synapses for even permutations of connection (0 -> 1 -> 2) and odd permutations of connection (1 -> 0 -> 2) was restricted to a maximum of 10 each with randomness applied. Therefore, there would be a maximum of 20 synapses when all 10 odd and even permutations of connection were present, respectively.
• Increased randomness for the synaptic transmisson delay (1-5 ms) and the weight (0-1) using the uniform distribution.
• Synaptic transmission voltage threshold increased to -55 mV from -65 mV.
• Modified the number of segments of the neurons' compartments.