This is the public homepage for AcCoRD (Actor-based Communication via Reaction-Diffusion). AcCoRD is a molecular communication simulator and designed as a generic reaction-diffusion solver for flexible system configuration. Actors are placed as sources (i.e., transmitters) or observers (i.e., receivers) of molecules. Environments can be defined with a combination of microscopic and mesoscopic regions. Here are some sample videos generated from AcCoRD output:
AcCoRD has a very simple installation procedure. A complete installation has the following:
Detailed installation instructions can be found in the AcCoRD User Manual, which is included in every download as of version 1.3 and also applies to older releases.
The latest stable release of AcCoRD is v1.4.2 (2020-02-12). Pre-compiled versions:
Source code:
You can also find the latest and older releases on the Github AcCoRD Releases page. However, the releases on the Github page keep the executables separate from the source code, so you will need to put the executables in the "bin" folder yourself.
Note: More detailed instructions are included in the AcCoRD User's Manual, which is included with every download as of version 1.3.
This section provides a basic summary of how to use AcCoRD. It is up to date for version 1.4. The instructions assume that you have already downloaded and installed AcCoRD. If not, then please refer to the AcCoRD Downloads section. Some of the content in this section is adapted from the paper “Simulating with AcCoRD: Actor-Based Communication via Reaction-Diffusion”.
Here is a summary for using AcCoRD on a personal computer. This summary is also a quick start guide.
This section 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 section and the AcCoRD User's Manual (included with every download as of version 1.3). The examples here 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. Besides the versions included in the download section, more old versions of AcCoRD can be found on Github.
The AcCoRD journal paper, "Simulating with AcCoRD: Actor-Based Communication via Reaction-Diffusion", 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 includes 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.
Here is a link to the published videos themselves.
The tutorial "Molecular Communication: Methods, Simulations, and Experiments" was presented at IEEE GLOBECOM 2018 on 9 December 2018. It included a demo of AcCoRD. Here is a zip directory of the unique files used to build the demo example. It includes a readme file with instructions on how to generate the outputs using a Windows installation, as well as copies of the output files. The files were written for use with version 1.4.
The tutorial "Simulation Methods for Molecular Communication" was presented at the 4th Workshop on Molecular Communication in Linz, Austria, on 17 April 2019. It included a demo of AcCoRD. Here is a zip directory of the unique files used to build the demo examples and process the results, and here is a PDF of the slide presentation (which is also listed on the Media and Resources page's presentation section). The files were written for use with version 1.4.1.
This section lists AcCoRD publications, including papers that describe AcCoRD or used it for simulations. If you use AcCoRD in your own work, then please cite the primary reference. We would also be happy to add a link to your work here.
The paper "Simulating with AcCoRD: Actor-Based Communication via Reaction-Diusion" (also available from arXiv) is the primary reference for AcCoRD. There's also a YouTube Video Abstract. If you use AcCoRD in your work, then please cite this paper. It provides an overview of AcCoRD, including:
This paper is in the March 2017 issue of Nano Communication Networks (vol. 11, pp. 44-75). It includes videos in the supplementary materials. A playlist of these videos is also available on YouTube.
Papers that describe new features added to AcCoRD:
Portion's of AcCoRD's design was initially motivated in the following papers:
The following papers did not discuss AcCoRD's implementation but used it for some or all of their simulations:
AcCoRD is in on-going development. The code is open source and available with the "New BSD" license. The latest code and development branches can be found on the Github AcCoRD project page. Existing bugs and planned features are described on the Github AcCoRD Issues page. To report a bug or suggest a feature, you can post on the Issues page or contact us directly.