The code was used in the following publication:
Title: Upregulated Ca2+ Release from the Endoplasmic Reticulum Leads to Impaired Presynaptic Function in Familial Alzheimer's Disease.
Authors: Temitope Adeoye (1), Syed Shah (1), David A Rabson (1), Ghanim Ullah (1), and Angelo Demuro(2),
(1) Department of Physics, University of South Florida, Tampa, FL 33620. (2) Department of Neurobiology and Behavior University of California, Irvine, CA 4550.
- data : Simulation and raw project data for AD and WT configurations as specified in methods
- docs : documentation and Markdown
- misc : Miscallaneous data, figures and codes designed for supplementary information
- results : figures, checkpoints, and tables generated by codes in scripts directory
- scripts : Matlab and Python scripts as well as .ipynb notebooks for simulations
- src : reusable Python modules imported into python scripts
Please follow the instructions belowe to reproduce the complete simulations of the manuscripts.
Note: The codes MATLAB and Python scripts were run on a research cluster with the SLURM schedular using the bash scripts in the scripts folder.
To run the codes, ensure all directories and sub-directories are present as detailed above. The ".m" and ".py" files should be availbe in the "scripts"-folder ../scripts/Matlab and ../scripts/Python respectively. Figure and data directories are automatically generated by scripts if not already present. The raw simulation data is extremely large, but still written to the specified folder specific to stimulation conditions. Single AP data will be saved to the ../data/SingleAP/ directory, AP Train (20 AP at 20 Hz) data saved to ../data/APTrain, and data for paired pulse protocol is available in ../data/Paired_Pulse.
To reproduce the complete simulations of the manuscript, run the following matlab codes in "scripts"-folder:
- solve_PPR_ODEs.m : For Paired-Pulse Protocol simulation
- solve_Train_ODEs.m: For AP train simulation
- solve_SingleAP_ODEs.m : For single AP simulation
The paramter cell_condition specifies the simulation configuration and takes care of parameter switching for WT and AD configurations.
Although several orders slower, we include and equivalent (not maintained) python code that attempts to reproduce Matlab results.
Raw data generated from either simulation is saved into "../data/", and must subsequently be processed using "data_processing.py" in "../scripts/Python/". To reproduce results/figures in the paper, the processed data can then be run with scripts prefixed with generate_figure_. Supplemental figures can also be generated using scripts prefixed with supp_figure_ that use processed data.