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Open-source code for simulating anatomically realistic distributions of RyR clusters in relation to cardiac cell contractile machinery.
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input-files
output-files
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visualization
README.md
ryr-simulator-parallel.R

README.md

RyR-simulator

An R-statistics package script for simulating anatomically realistic distributions of RyR clusters around mitochondria and the contractile machinery. Published in PLoS Computational Biology: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004417.

Visitors interested in using the finite element geometric model (and associated FE reaction-diffusion simulation codes) can obtain all the codes and mesh inputs at https://github.com/vraj004/cardiac_ecc

required Applications/Packages

R - statistics package available from http://www.r-project.org

MATLAB - optional: only used for point pattern visualization

FOLDER INFORMATION

input-files/:

master-cell/

  • directory consisting of all the input files necessary for generating statistics on nearest neighborhood distances between RyR clusters and axial and radial distances of RyR clusters from the z-disc. Folder currently contains data extracted from Cell 1 of submitted paper.

target-cell/

  • directory of same input files as those in master-cell but with information from target cell onto which RyR clusters must be simulated. Folder currently contains data extracted from Cell 1 of submitted paper.

target-tomo-cell/

  • directory of input files of an electron tomogram derived image stack of myofibrils and mitochondria for RyR cluster simulation.

output-files/:

target-cell/

  • The RyR cluster patterns simulated on the target cell along with the histograms of the observed ryr cluster nearest-neighborhood distances and the axial and radial distances to the z-discs. Current simulations reconstruct RyR cluster distributions on Cell 1 from the observed data on Cell 1 from submitted paper.

target-tomo-cell/

  • directory of output files of RyR cluster distributions on a tomogram-derived template of myofibrils and mitochondria.

source/:

contains all the source files for running in R.

ryr-simulator.R: The main program to run the RyR cluster simulator.

ryr-simulator-parallel.R: The main program to run the RyR cluster simulator with parallel processing.

nnd-calculators.R: A bunch of calculators of nearest-neighborhood distances; currently using CGW version which measures torus distance.

EXPERIMENTAL DATA

The electron microscopy data and confocal microscopy data used for this study have been shared online at https://dx.doi.org/10.4225/49/55B622EBE2D4C

RUNNING ONE OF THE SCRIPTS

The main program is the script ryr-simulator.R . To run the script we recommend using the source() command at the R prompt:

source('/path-to-distribution/RyR-simulator/source/ryr-simulator.R', chdir = TRUE)

NOTE:

  1. replace /path-to-distribution/RyR-simulator with the proper path to the top level directory of the RyR-simulator distribution
  2. IMPORTANT: use the chdir = TRUE option of the source command - otherwise it will not work!

This procedure has been tested on OS X with R 2.15.0 GUI 1.51 (Leopard build 64-bit (6148)) and R 3.0.1 "Good Sport" which is current as of this writing. You can obtain R for OS X at http://cran.r-project.org/bin/macosx/. Again, on OS X you can just drag ryr-simulator.R from the Finder into the command line window of the R app and it will automagically generate the proper source() command at the prompt.

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