Scripts used for the single-compartment simulations of the plasticity in the post-synaptic spine using NeuroRD simulator. Contains also the scripts for printing the Table of reactions.

N.B. The NeuroRD simulations are run from the Python script runmodel_parallel.py, on line 157, after the script has created all necessary xml files: `java -jar neurord-3.2.3-all-deps.jar -Dneurord.writers=text model_XXX.xml` (where model_XXX.xml is the main xml file made by the python script) This may not work on all systems. I ran it this way on a CentOS Linux machine where Java 1.8.0_131 was installed. However, on another machine (macOS) I had to use a slightly different command: `java --add-modules java.se.ee -jar neurord-3.2.3-all-deps.jar -Dneurord.writers=text model_XXX.xml` The important thing is that in both cases I used the -Dneurord.writers=text flag, which bypasses the jhdf5 and uses txt outputs. If you use jhdf5 (which is actually recommended as it saves a lot of space), you'll have to rewrite the parts of the script that read the model outputs.

Files included:
IC_oldCaM.xml

- Initial concentrations in the simulations that used the old calmodulin binding rules

IC_singlecompartment.xml

- Initial concentrations used in the main set of simulations. N.B. these values are not steady-state values. To get proper reaction dynamics, the script runsteadystate.sh has to be run - this script saves a .mat file that will be used for creating an IC file with steady-state concentrations.

Model_template.xml

- A template for the main NeuroRD simulations

Morphology.xml

- Dimension of the modelled spine

Reactions.xml

- Set of reactions

Reactions_oldCaM.xml

- Set of reactions with the old calmodulin binding rules

Stimulations_template.xml

- A template for the stimulations used in NeuroRD simulations

analyzeoutfile.py

- A file needed for extracting data from .mat file into and IC file

mesh_general.out

- A mesh file

neurord-3.2.3-all-deps.jar

- The NeuroRD java jar file

printtab1.py

- A python script for printing Tab. 1

runmodel_parallel.py

- The main python script for running the NeuroRD simulations. Makes the needed .xml files based on the Reactions.xml, the IC file and the template xml files and runs the simulation. Deletes the temporary .xml files afterwards (and the huge out files) and saves interpolated results into a .mat file.

runfig2_nrd.sh

- A script that runs the NeuroRD simulations of steady-state inputs needed for Fig. 2

runfig3-4_nrd.sh

- A script that runs the HFS and LFS simulations needed for Fig. 3 and 4

runsteadystate.sh

- A script that simulates the steady state solution in the absence of any inputs. This should be run before any other NeuroRD simulations.