Individual-Based Ecological Modeling at Humboldt State University

Research on the use of individual-based models (IBMs) for applied and theoretical ecology is affiliated with the Mathematical Modeling Program, HSU Mathematics Department. This research is a collaboration of mathematicians, ecologists and biologists, environmental engineers, and software professionals. See below for our research goals.

What's New

• inSTREAM training opportunities, summer of 2008. We will be providing training in our inSTREAM individual-based trout model on at least two occasions in upcoming months. In the last week of March we will be at Oregon State University. In early July we will conduct a class here in Arcata. Contact Steve Railsback if you are interested.
  
  
• Summer short courses in individual- and agent-based modeling, 2008-2010. The Institute of Forest Growth and Forest Computer Sciences of Technical University Dresden, Germany, received funding to conduct one-week intensive courses in individual- and agent-based simulation modeling, in the summers of 2008, 2009, and 2010. The courses will be taught in English at a lovely small town in the "Switzerland of Saxony" park area near Dresden. Instructors will include Uta Berger of TU Dresden, Volker Grimm, and Steve Railsback of our Humboldt State program. The 2008 class is already filled; applications for the 2009 class will be accepted in next winter. See the course web site for information.
  
  
• Evaluation of nonlinear, interactive effects of temperature, turbidity, and channel shape on trout populations. Bret Harvey conducted a simulation analysis of whether these three stressors have cumulative effects on trout populations that are stronger than we would expect if they acted independently. The study recently was published in Fisheries. See the Products and Publications page for details.
  
  
• Execution time improvements for inSTREAM completed and published. We implemented a minor change in formulation that reduces execution time of our individual-based trout model by about one third, with negligible effect on results. See the inSTREAM page for details.
  
  
• inSTREAM, our individual-based Stream Trout Research and Assessment Model, is available in new versions. Version 4.2 is designed for public use; the release includes software, example input, and a new, complete documentation set. Two other versions support alternative hydraulic simulation methods; one is inSTREAM-2D, which uses two-dimensional hydrodynamic modeling. See the inSTREAM page for additional information and downloads.
  
  
• Sensitivity Analysis Methods for large IBMs developed. For his MS thesis, Paul Cunningham developed a three-phase strategy for parameter sensitivity analysis of large, complex IBMs and demonstrated it on inSTREAM. A draft publication on the strategy is on our publications and products page.
  
  
• Trait-mediated indirect interactions and non-consumptive effects emerge from our approach to modeling adaptive behavior. TMIIs and NCEs are exciting new areas of ecological research because they illustrate the effects of individual adaptive behavior on population and community dynamics. In a new manuscript, we describe the approach to theory of adaptive behavior we use and illlustrate its ability to reproduce a wide range of TMIIs and NCEs observed in empirical experiments. See the publications and products page.
  
  
• CALFED post-doctoral fellowship awarded to Annjanette Dodd. Annje Dodd was recently awarded a CALFED Science Fellows post-doc grant for a salmon out-migration modeling project and is now at work with us. Her bio and project abstract are here.
  
  
• "Pattern-oriented modeling of agent-based complex systems: lessons from ecology" appears in Science. This paper by Volker Grimm and others (including Steve Railsback) discusses the use of individual-based models and observed patterns in studying complex systems. Patterns can be used to design models, test theory for how system phenomena emerge from individual traits, and parameterize models. See our publications and products page for the citation and access to this paper.
  
  
• Individual-based Modeling and Ecology, by Volker Grimm and Steve Railsback. This is the first major monograph on IBMs and how they can be used productively in theoretical and applied science. It is available from Princeton University Press, Amazon, or your favorite bookstore. Click here for additional information, including the draft Table of Contents and Introduction.
  
  

Goals:

• Developing a conceptual and theoretical basis for individual-based ecology. Differential calculus provides the conceptual basis for classical ecological models, but IBMs lack such a basis. We find the new science of Complex Adaptive Systems to be a fruitful source of concepts for thinking about and designing IBMs.
• Applying fish IBMs to river management issues. We developed several generations of stream salmonid IBM to address such management questions as: How do the magnitude and timing of instream flow releases affect populations? What are the cumulative effects of changes in flow and temperature on fish populations? What effects do habitat alterations (e.g., loss of pools, increased turbidity), competition, predation, and habitat connectivity have on population dynamics?
• Using IBMs to test and develop ecological theory. We use IBMs as 'virtual ecosystems' for testing ecological theory and linking behavioral ecology to population ecology.
• Developing software and software engineering approaches for IBMs. Software engineering is much more important for IBMs than for other ecological models. We develop software engineering guidance, flexible and re-usable code for stream fish models, and a library of Swarm-based code for IBMs.
• Integrating individual-based approaches in ecological and modeling education. We integrate IBMs in ecological modeling courses at HSU, and gladly offer software and guidance to instructors at other institution

 

WebMASTER:  amd2@humboldt.edu
Last Updated:  06 March 2008