This page contains links to and descriptions of configuration and post-processing file examples to run in the AcCoRD simulator. To run these examples yourself, you will need to download and install AcCoRD. For more information on how to use these files, you can refer to the How to Use AcCoRD page and the AcCoRD User's Manual (included with every download as of version 1.3). The examples are sorted into two main categories. The configuration files of the latest release examples are included with every download of AcCoRD and are kept up to date to run on the latest release. The specific release examples are maintained for a specific version and are intended to recreate results from a specific publication or demonstrate a new feature associated with that release.
There is a set of configuration files that are kept up to date for the latest version of AcCoRD. To limit execution times, most of these simulations only run a single realization. Descriptions are included in the AcCoRD User Manual. To access these files, you can download the latest version of AcCoRD.
The following configuration files were written for a specific version of AcCoRD. Old versions of AcCoRD can be found here.
Sample Videos in the AcCoRD Journal Paper
The AcCoRD journal paper, "Simulating with AcCoRD: Actor-Based Communication via Reaction-Diffusion" (and which can be accessed here), refers to a series of 8 videos. The simulations were run using version 0.7 and 0.7.0.1, and the videos were generated using version 1.0, but they can all be re-created using just 1.0.
Here are configuration files that can be used to run the simulations.
- This configuration directory also include a MATLAB m-file ("accord_config_journal_video_1_draw_environment.m") that will draw the regions defined for the first video without needing to run a simulation. This script should be placed in the AcCoRD matlab directory to run properly.
Here are Video Maker wrappers that can be used to build the videos once the simulation output has been imported into MATLAB.
Last but not least, here are the videos themselves: https://www.youtube.com/playlist?list=PLZ7uYXG-7XF8UyhFrIuQIiZig1XA89e3i