Individual-based modeling of soil organic matter in NetLogo: Transparent, user-friendly, and open

Authored by Marta Ginovart, Anna Gras, Thomas Banitz

Date Published: 2015

DOI: 10.1016/j.envsoft.2015.05.007

Sponsors: Spanish Ministries German Academic Exchange Service (DAAD)

Platforms: NetLogo

Model Documentation: ODD Flow charts Mathematical description

Model Code URLs: http://ars.els-cdn.com/content/image/1-s2.0-S1364815215001541-mmc2.zip

Abstract

Soil organic matter dynamics are essential for terrestrial ecosystem functions as they affect biogeochemical cycles and, thus, the provision of plant nutrients or the release of greenhouse gases to the atmosphere. Most of the involved processes are driven by microorganisms. To investigate and understand these processes, individual-based models allow analyzing complex microbial systems' behavior based on rules and conditions for individual entities within these systems, taking into account local interactions and individual variations. Here, we present a streamlined, user-friendly and open version of the individual-based model INDISIM-SOM, which describes the mineralization of soil carbon and nitrogen. It was implemented in NetLogo, a widely used and easily accessible software platform especially designed for individual-based simulation models. Including powerful means to observe the model behavior and a standardized documentation, this increases INDISIM-SOM's range of potential uses and users, and facilitates the exchange among soil scientists as well as between different modeling approaches. (C) 2015 Elsevier Ltd. All rights reserved.

Tags

Simulation parameterization carbon Populations Sensitivity-analysis Complex Components Nitrogen dynamics Microbiology Mineralization