Putting-the-theory-into-burstlet-theory

Model code for bioRxiv preprint "Putting the theory into ‘burstlet theory’: A biophysical model of bursts and burstlets in the respiratory preBötzinger complex" doi: https://doi.org/10.1101/2021.11.19.469304

1. Copy ip3.cc file to new directory and create subdirectory labeled "data"

2. Compile code using g++ compiler (ver. 9.3.0) using the command:

   g++ -std=c++0x -O2 ip3.cc -o ip3
   

3. Run simulations executing the commands in the file labeled "do". The commands with in the "do" file contains commads for generating the example traces from Fig. 1, Fig. 2 and Fig.4 of the paper. For example the following command will run one simulations for 300 seconds of simulation time with the full population of 400 neurons and kbath=5.5mM and Psynca=6%:

   ./ip3 -dt .025 -DT 20 -d .3 .3 -s 400 -fc 1.0 1.0 -T 300 -w 0.15 -prob 0.13 -kbath 5.5  -fsca 0.06 0.06 data/net/1.sp -o  >data/net/1.hst 2>data/net/1.ca
   

   The first part of the line ./ip3 runs simulations. The flags - determine the model parameters. For example -dt .025 sets the integration step size to 0.025ms, -DT 20 sets bin size to 20ms population spiking histograms, -d .3 .3 sets the tonic drive (g_{Tonic}) to 0.3nS (if -d .3 .4 was used then g_{tonic} would linearly ramp from 0.3nS to 0.4nS over the course of the simulation time), -s 400 sets the population size, -w 0.15 and -prob 0.13 set the synatic weight and the synaptic connection probability between the rhythm to generating neurons 0.15nS and 13%, -kbath 5.5 set the bath potassium concentration to 5.5mM, and -fsca 0.06 0.06 sets the parameter P_{SynCa} in the paper (fsca in the code) to 0.06 or 6%. Finally data/net/1.sp, >data/net/1.hst and 2>data/net/1.ca are the directory that the output files 1.sp, 1.hst, and 1.ca will be written to. For the output of the simulation to be written to file, the folder containing the "ip3.cc" code must include a folder called "data" which must contain the subdirectories "square", "2cell", and "net".

4. Plot Figures. Figures were plotted using gnuplot (Ver. 5.2 patchlevel 8). See http://www.gnuplot.info/ for information and installation instructions. The figures "Fig01_sq_wave.pdf", "Fig02_2cell.pdf" and "Fig04_net.pdf" can be generated by running the gnuplot plotting files "square.plot", "2cell.plot" and "net.plot". With gnuplot installed on Ubuntu 20.04.3 LTS, these gnuplot files can be executed in command line by typing the following command:

   gnuplot square.plot
   

Alternatively, the simulation output can be plotted using any graphing software. All output data is organized into columns in the .sp files where column 1 in all simulations is time in seconds. For the Ca2+ square wave simulations, column 3 is the Ca2+ pulse, column 4 is [Ca]_i, Column 5 is [Ca]_ER. For the two cell simulations column 2 is the membrane potential for neuron 1 (rhythmogenic) and column 3 is the membrane potential for neuron 2 (pattern) in mV. For the network simulations column 2 is the population histogram spikes/bin/N.