Biology and Ecology


The basic immune simulator – was developed with RePast . The agents were created to represent the basic cell types of the immune system.

Zone 1 represents the parenchymal cells (yellow dots) or the functional cells of any tissue.

BioSystems Group at UCSF. “Research in the Biosystems group can be broadly characterized as a blend of Bioengineering, Computational Biology (including Bioinformatics and Computational Therapeutics), Systems Biology, and Therapeutic Engineering. It is uniquely interdisciplinary. Our goal is to use and create computational and informatic approaches to discover useful new biological knowledge. We seek novel approaches that will accelerate drug development and enable therapeutic advances, optimization, and individualization.”


Modeling the Collective Behavior of Hepatocytes in Clearing Toxins

Center for Cell Dynamics.  “The Center for Cell Dynamics fosters research in cell and developmental biology that fuses experimental approaches with realistic, mechanistic computational models. The computational pursuit focuses both on high-resolution imaging methods for visualizing the interactions of molecular building blocks, and on creating computer simulations that capture systems-level properties of gene networks, the cytoskeleton, and cellular interaction, on the basis of known properties of the molecular building blocks of life.


Simulation Videos

Complex Biosystems Modeling Laboratory (CBML). Work at CBML is highly interdisciplinary with multiple national and international collaborations. CBML’s collaborative contributions to the field of integrative cancer research range from innovative agent-based modeling and the application of game theory and scaling laws to in silico work on genetic instability and carrying capacity. Through CViT, CBML is also involved in IT infrastructure development for in silico cancer research.


Modeling Tumor Growth and Invasion

Multicellular system biology – focuses on the understanding of tissue formation on different time and length scales. It pursues projects on the development of models to permit realistic simulations of multicellular organization processes, and on the analysis of data that occur during this process.

Multicellular systems biology

Multicellular systems biology

SBiE – Laboratory for Systems Biology and Bio-Inspired Engineering.


ATLSS.  “The Everglades and Big Cypress Swamp of South Florida are characterized by complex patterns of spatial heterogeneity and temporal variability, with water flow being the major factor controlling the trophic dynamics of the system. A key objective of modeling studies for these systems is to compare the future effects of alternative hydrologic scenarios on the biotic components of the systems. Due to the varying scales at which trophic interactions occur, and the importance of population structure and individual behavior for population prediction in higher trophic level organisms, use of a single modeling approach is not appropriate. We are developing a set of models designed to integrate three approaches for different trophic levels of the system: (1) process models for lower trophic levels (including benthic insects, periphyton and zooplankton), (2) structured population models for five functional groups of fish and macroinvertebrates, and (3) individual-based models for large consumers (wood storks, great blue herons, white ibis, American alligators, white-tailed deer, and Florida panther). These are integrated across the freshwater landscape of the Everglades and Big Cypress Swamp and coupled to GIS maps for cover type. Spatial scales of resolution for the models are as small as 100 m, with the capability to vary this based upon the scale of available input data. The system is then coupled to a hydrology model, and used to assess the effects of alternative proposed restoration scenarios on trophic structure.”


Across Trophic Level System Simulation

Collaborative Research: Agent-based modeling and observation of intra-population variability in phytoplankton – The goal of the proposed project is to investigate and evaluate the ABM approach for simulating intra-population variability in nutrient contents.

FEARLUS – Framework for Evaluation and Assessment of Regional Land Use Scenarios.

Individual-Based Ecological Modeling. “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.”

The Modelling Group.  “Our methodological philosophy is to combine explicit physical and biological mechanisms, operating at the level of individuals, with evolutionary forces to let patterns and predictions emerge.”

NIMBios: “National Institute for Mathematical and Biological synthesis.  “A major goal of mathematical models and analysis in biology is to provide insight into the complexities arising from the non-linearity and hierarchical nature of biological systems. Primary goals of NIMBioS will be to foster the maturation of cross-disciplinary approaches in mathematical biology and foster the development of a cadre of researchers who are capable of conceiving and engaging in creative and collaborative connections across disciplines to address fundamental and applied biological questions. Our vision for NIMBioS is to efficiently utilize NSF funding: 1) to address key biological questions by facilitating the assembly and productive collaboration of interdisciplinary teams; and 2) to foster development of the critical and essential human capacity to deal with the complexities of the multi-scale systems that characterize modern biology.”

TIEM:  The Institute for Environmental Modeling.  “The purpose of TIEM is to do basic research on significant environmental problems that impact the State of Tennessee and have national and international implications. The focus of the Institute is on experimental design, environmental model formulation together with mathematical and statistical analyses of the models, projection of the analysis for use by decision makers, development of theoretical and computational tools for studying the environment as well as development of hardware and software (such as parallel computing and visualization graphics) to implement and analyze the models. TIEM is housed in the Division of Biology and is directed by Louis J. Gross.”