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.
Visit this new site to learn more about Humboldt State's
Mathematical Modeling graduate program!
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New Individual- and agent-based modeling textbook.
Steve Railsback and Volker Grimm are preparing a new
text on individual-based (or "agent-based") modeling in science. The text is designed for
courses in which instructors as well as students are new to this kind of modeling.
The book is not specific to ecology, but general to all scientific fields. It
teaches basic concepts of modeling, the design of individual-based models,
how to program models in the NetLogo platform, and analysis of models to
solve scientific problems and develop theory.
Draft chapters are now available
for download and evaluation at the book's web site.
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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 are 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.
See the course web site
for information.
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inSTREAM used in McCloud River Project instream flow studies.
Our individual-based trout model was used as one of several instream flow
assessment methods in the
regulatory process to update the operating license
of the McCloud River hydroelectric project. This was the first completely non-research
application of inSTREAM. The model predicted that higher instream flows
in summer could increase the relative abundance of brown vs. rainbow trout, but
high winter flows could have the opposite effect.
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inSTREAM training opportunities.
We occasionally provide training in our inSTREAM individual-based trout model.
Classes are usually but not always here in Arcata.
Contact Steve Railsback if you are interested.
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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.
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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.
- "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.
- "Pattern-oriented modeling of agent-based complex
systems: lessons from ecology" appears in Science.
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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
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NEW: Two-dimensional hydraulic simulation.
Simulated stream trout move in response to a flow event at our South Fork Eel
River study site, where habitat was simulated using a two-dimension hydrodynamic
model. Habitat cells are shaded by water depth (lighter cells deeper);
blue dots indicate cells containing fish. Stay tuned for more details soon. |
WebMASTER:
krf20@humboldt.edu
Last Updated: 23 Dec. 2009