Skip to content

CellSMB/RyR-simulator

master
Switch branches/tags

Name already in use

A tag already exists with the provided branch name. Many Git commands accept both tag and branch names, so creating this branch may cause unexpected behavior. Are you sure you want to create this branch?
Code

Latest commit

 

Git stats

Files

Permalink
Failed to load latest commit information.
Type
Name
Latest commit message
Commit time
 
 
 
 
 
 
 
 

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.

About

Open-source code for simulating anatomically realistic distributions of RyR clusters in relation to cardiac cell contractile machinery.

Topics

Resources

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published