Introduction

SPARK, or Simple Platform for Agent-based Representation of Knowledge, is an agent based modeling (ABM) framework which includes the Java library for implementing agent based models and the runtime engine for executing these models. SPARK was written by Alexey Solovyev with additional help from Maxim Mikheev. The project leader is Qi Mi.

The official SPARK website: http://www.mirmresearch.net/spark/default.asp

License

SPARK largely uses the MIT License. For details see the LICENSE file.

SPARK contains several third-party libraries. Information about these libraries and about their licenses can be found in the spark/Licenses folder.

How to Run

JDK (Java Development Kit) 1.8 or higher is required to run SPARK. A free and open source version of JDK can be downloaded at https://adoptopenjdk.net/releases.html.

To make sure that JDK is properly installed, run the following command in the command line: javac -version. This command should print the version of the installed JDK.

Download the latest SPARK release. Unzip the archive into any folder on your computer. (Note for macOS users: do not unzip the SPARK distribution into a restricted folder such as Documents, Downloads, or Desktop.) Double click SPARK_Manager.jar in a file manager to run SPARK. If it does not work then run SPARK from the command line:

macOS/Linux:

cd 'name of SPARK directory'
bin/spark-manager

Windows:

cd 'name of SPARK directory'
bin\spark-manager

Documentation

Documentation can be found at http://www.mirmresearch.net/spark/documentation/documentation.asp

Note: the documentation is not updated yet and it may contain outdated information.

Building from Source Code

Clone the repository and run

./gradlew sparkInstall

A compiled version of SPARK with all dependencies will be created in spark/build/spark.

Alternatively, the command ./gradlew sparkDist will create a zip archive in spark/build/sparkDist.

Publications

1. Solovyev, A., Mikheev, M., Zhou, L., Dutta-Moscato, J., Ziraldo, C., An, G., Vodovotz, Y., & Mi, Q. (2010). SPARK: A Framework for Multi-Scale Agent-Based Biomedical Modeling. International journal of agent technologies and systems, 2(3), 18–30. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3806198/

2. Solovyev, A., Mi, Q., Tzen, Y. T., Brienza, D., & Vodovotz, Y. (2013). Hybrid equation/agent-based model of ischemia-induced hyperemia and pressure ulcer formation predicts greater propensity to ulcerate in subjects with spinal cord injury. PLoS computational biology, 9(5), e1003070. https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003070

3. Dutta-Moscato, J., Solovyev, A., Mi, Q., Nishikawa, T., Soto-Gutierrez, A., Fox, I. J., & Vodovotz, Y. (2014). A Multiscale Agent-Based in silico Model of Liver Fibrosis Progression. Frontiers in bioengineering and biotechnology, 2, 18. https://www.frontiersin.org/articles/10.3389/fbioe.2014.00018/full

4. Ziraldo, C., Solovyev, A., Allegretti, A., Krishnan, S., Henzel, M. K., Sowa, G. A., Brienza, D., An, G., Mi, Q., & Vodovotz, Y. (2015). A Computational, Tissue-Realistic Model of Pressure Ulcer Formation in Individuals with Spinal Cord Injury. PLoS computational biology, 11(6), e1004309. https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004309

Feedback and Troubleshooting

Please open issues at https://github.com/monadius/spark-abm/issues