simecol: An Object-Oriented Framework for Ecological Modeling in R

The simecol package provides an open structure to implement, simulate and share ecological models. A generalized object-oriented architecture improves readability and potential code re-use of models and makes simecol-models freely extendable and simple to use. The simecol package was implemented in the S4 class system of the programming language R. Reference applications, e.g. predator-prey models or grid models are provided which can be used as a starting point for own developments. Compact example applications and the complete code of an individual-based model of the water flea Daphnia document the efficient usage of simecol for various purposes in ecological modeling, e.g. scenario analysis, stochastic simulations and individual based population dynamics. Ecologists are encouraged to exploit the abilities of simecol to structure their work and to use R and object-oriented programming as a suitable medium for the distribution and share of ecological modeling code.

Sequential Predation: A Multi-model Study

In many ecosystems food resources are available sequentially. The paper analyses a situation with two competing prey species both of which are consumed by a common predator species. Within a season the two prey species are available sequentially, although there may be an overlap. Three modelling methodologies are applied to this system] discrete dynamical systems (difference equations), individual-oriented event-driven simulations and cellular automata. The presence of the predator is shown to have a strong impact on the outcome of the prey species competition. The system of coexisting prey species changes to a system of founder-controlled competition. It appears that sequential predation can even have counterintuitive evolutionary consequences for the prey species. The species which appears later in the season will be more successful in its competition with the early species if it favours the predator; for example, by a high leaf palatability. Spatial structuring and topological issues are found to play a crucial role in both the ecological and evolutionary dynamics. The advantages of a multi!model approach are discussed

Red Queen Coevolution on Fitness Landscapes

Species do not merely evolve, they also coevolve with other organisms. Coevolution is a major force driving interacting species to continuously evolve ex- ploring their fitness landscapes. Coevolution involves the coupling of species fit- ness landscapes, linking species genetic changes with their inter-specific ecological interactions. Here we first introduce the Red Queen hypothesis of evolution com- menting on some theoretical aspects and empirical evidences. As an introduction to the fitness landscape concept, we review key issues on evolution on simple and rugged fitness landscapes. Then we present key modeling examples of coevolution on different fitness landscapes at different scales, from RNA viruses to complex ecosystems and macroevolution.Comment: 40 pages, 12 figures. To appear in "Recent Advances in the Theory and Application of Fitness Landscapes" (H. Richter and A. Engelbrecht, eds.). Springer Series in Emergence, Complexity, and Computation, 201

Oscillatory dynamics in a model of vascular tumour growth -- implications for chemotherapy

Background\ud \ud Investigations of solid tumours suggest that vessel occlusion may occur when increased pressure from the tumour mass is exerted on the vessel walls. Since immature vessels are frequently found in tumours and may be particularly sensitive, such occlusion may impair tumour blood flow and have a negative impact on therapeutic outcome. In order to study the effects that occlusion may have on tumour growth patterns and therapeutic response, in this paper we develop and investigate a continuum model of vascular tumour growth.\ud Results\ud \ud By analysing a spatially uniform submodel, we identify regions of parameter space in which the combination of tumour cell proliferation and vessel occlusion give rise to sustained temporal oscillations in the tumour cell population and in the vessel density. Alternatively, if the vessels are assumed to be less prone to collapse, stable steady state solutions are observed. When spatial effects are considered, the pattern of tumour invasion depends on the dynamics of the spatially uniform submodel. If the submodel predicts a stable steady state, then steady travelling waves are observed in the full model, and the system evolves to the same stable steady state behind the invading front. When the submodel yields oscillatory behaviour, the full model produces periodic travelling waves. The stability of the waves (which can be predicted by approximating the system as one of λ-ω type) dictates whether the waves develop into regular or irregular spatio-temporal oscillations. Simulations of chemotherapy reveal that treatment outcome depends crucially on the underlying tumour growth dynamics. In particular, if the dynamics are oscillatory, then therapeutic efficacy is difficult to assess since the fluctuations in the size of the tumour cell population are enhanced, compared to untreated controls.\ud Conclusions\ud \ud We have developed a mathematical model of vascular tumour growth formulated as a system of partial differential equations (PDEs). Employing a combination of numerical and analytical techniques, we demonstrate how the spatio-temporal dynamics of the untreated tumour may influence its response to chemotherapy.\ud Reviewers\ud \ud This manuscript was reviewed by Professor Zvia Agur and Professor Marek Kimmel

Multiscale modeling in biology

The 1966 science-fction film Fantastic Voyage captured the public imagination with a clever idea: what fantastic things might we see and do if we could minaturize ourselves and travel through the bloodstream as corpuscles do? (This being Hollywood, the answer was that we'd save a fellow scientist from evildoers.

An exploration and validation of computer modeling of evolution, natural selection, and evolutionary biology with cellular automata for secondary students.

The Evolutionary Tool Kit, a new software package, is the prototype of a concept simulator providing an environment for students to create microworlds of populations of artificial organisms. Its function is to model processes, concepts and arguments in natural selection and evolutionary biology, using either Mendelian asexual or sexual reproduction, or counterfactual systems such as \u27paint pot\u27 or blending inheritance. In this environment students can explore a conceptual What if? in evolutionary biology, test misconceptions and deepen understanding of inheritance and changes in populations. Populations can be defined either with typological, or with populational thinking, to inquire into the role and necessity of variation in natural selection. The approach is generative not tutorial. The interface is highly graphic with twenty traits set as icons that are moved onto the \u27phenotypes\u27. Activities include investigations of evolutionary theory of aging, reproductive advantage, sexual selection and mimicry. Design of the activities incorporates Howard Gardner\u27s Theory of Multiple Intelligences. Draft of a teacher and student manual are included

Genetic evolution and equivalence of some complex systems: fractals, cellular automata and lindenmayer systems

Tesis doctoral inédita leída en la Universidad Autónoma de Madrid. Escuela Politécnica Superior, Departamento de Ingeniería informática.26-04-200