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How to Use AcCoRD

This page provides basic instructions on how to use AcCoRD. It is up to date for version 1.1. The instructions assume that you have already downloaded and installed AcCoRD. If not, then please refer to the AcCoRD Downloads page.

Some of the content on this page is adapted from the paper “Simulating with AcCoRD: Actor-Based Communication via Reaction-Diffusion”. To access this paper, please visit the AcCoRD Publications page. The publications page also includes links to other papers that describe or use AcCoRD.

How to Use AcCoRD (Summary)

Here is a summary for using AcCoRD on a personal computer. This summary is also a quick start guide. More details for all of these steps can be found on the linked pages.

  1. Prepare a configuration file – Many sample files are included with the AcCoRD Download and discussed on the AcCoRD Examples page. Choose a sample file and modify it as desired. See AcCoRD Configuration for more details, or visit the AcCoRD Configuration Parameters page for a detailed listing of all possible simulation parameters.
  2. Run AcCoRD – Open a command line window and navigate to the AcCoRD “bin” directory. Enter the command to run the simulation. If your OS is Windows and your config file is MY_CONFIG.txt, then you can enter “accord_win.exe MY_CONFIG.txt”. This uses 1 as the default seed number for the random number generator. If your simulation output parameter was set to MY_OUTPUT, then the files MY_OUTPUT_SEED1.txt and MY_OUTPUT_SEED1_summary.txt will be created and placed in the “bin/results” directory. See Running Simulations for more details.
  3. Import Output in MATLAB – Set the current directory to the AcCoRD “matlab” directory. If your simulation output parameter was set to MY_OUTPUT and written to the “bin/results” directory, then call accordImport(‘../bin/results/MY_OUTPUT’, 1, true). The mat-file MY_OUTPUT_out.mat will be created. See Reading Output for more details.
  4. Process the Output – Read the “data” and “config” variables in the file MY_OUTPUT_out.mat as desired for post-processing. To plot a figure showing a passive actor signal, modify and run a copy of the file accordPlotMakerWrapper.m. To make a video showing the environment and molecules (IF you saved molecule locations in your configuration), modify and run a copy of accordVideoMakerWrapper. See Post-Processing for more details.