Gourt > Science > Biology > Theoretical Biology (2)
Theoretical biology is a field of academic study and research that involves the use of quantitative tools in biology.
Many separate areas of biology fall under the concept of theoretical biology, according to the way they are studied. Some of these areas include: animal behaviour (ethology), biomechanics, biorhythms, cell biology, complexity of biological systems, ecology, enzyme kinetics, evolutionary biology, genetics, immunology, membrane transport, microbiology, molecular structures, morphogenesis, physiological mechanisms, systems biology and the origin of life. Neurobiology is an example of a subdiscipline of biology which already has a theoretical version of its own, theoretical or computational neuroscience.
The ultimate goal of the theoretical biologist is to explain the biological world using mainly mathematical and computational tools, though not necessarily. Though it is ultimately based on observations and experimental results, the theoretical biologist's product is a model or theory, and it is this that chiefly distinguishes the theoretical biologist from other biologists. Over recent years the theoretical biologist has become nearly obsolete, as tests prove the impossibility of accurate results where the environment of the observations is not homogeneous.
More on [ Theoretical biology ]
Artificial Life
Biophysics :: Biology
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A mechanistic model of infection: why duration and intensity of contacts should be included in models of disease spread
Timo Smieszek Tue, 17 Nov 2009 00:00:00 -0000
Background: Mathematical models and simulations of disease spread often assume a constant per-contact transmission probability. This assumption ignores the heterogeneity in transmission probabilities, e.g. due to the varying intensity and duration of potentially contagious contacts. Ignoring such heterogeneities might lead to erroneous conclusions from simulation results. In this paper, we show how a mechanistic model of disease transmission differs from this commonly used assumption of a constant per-contact transmission probability. Methods: We present an exposure-based, mechanistic model of disease transmission that reflects heterogeneities in contact duration and intensity. Based on empirical contact data, we calculate the expected number of secondary cases induced by an infector (i) for the mechanistic model and (ii) under the classical assumption of a constant per-contact transmission probability. The results of both approaches are compared for different basic reproduction numbers R0. Results: The outcomes of the mechanistic model differ significantly from those of the assumption of a constant per-contact transmission probability. In particular, cases with many different contacts have much lower expected numbers of secondary cases when using the mechanistic model instead of the common assumption. This is due to the fact that the proportion of long, intensive contacts decreases in the contact dataset with an increasing total number of contacts. Conclusion: The importance of highly connected individuals, so-called super-spreaders, for disease spread seems to be overestimated when a constant per-contact transmission probability is assumed. This holds particularly for diseases with low basic reproduction numbers. Simulations of disease spread should weight contacts by duration and intensity.
Computational models in plant-pathogen interactions: the case of Phytophthora infestans
Andres PinzonEmiliano BarretoAdriana BernalLuke AchenieAndres Gonzalez BarriosRaul IseaSilvia Restrepo Thu, 12 Nov 2009 00:00:00 -0000
Background: Phytophthora infestans is a devastating oomycete pathogen of potato production worldwide. This review explores the use of computational models for studying the molecular interactions between P. infestans and one of its hosts, Solanum tuberosum.Modeling and conclusionsDeterministic logistics models have been widely used to study pathogenicity mechanisms since the early 1950s, and have focused on processes at higher biological resolution levels. In recent years, owing to the availability of high throughput biological data and computational resources, interest in stochastic modeling of plant-pathogen interactions has grown. Stochastic models better reflect the behavior of biological systems. Most modern approaches to plant pathology modeling require molecular kinetics information. Unfortunately, this information is not available for many plant pathogens, including P. infestans. Boolean formalism has compensated for the lack of kinetics; this is especially the case where comparative genomics, protein-protein interactions and differential gene expression are the most common data resources.
Formal kinetics of H1N1 epidemic
Konstantin Gurevich Tue, 15 Sep 2009 00:00:00 -0000
Background: The formal kinetics of the H1N1 epidemic seems to take the form of an exponential curve. There is a good correlation between this theoretical model and epidemiological data on the number of H1N1-infected people. But this formal model leads to paradoxes about the dates when everyone becomes infected: in Mexico this will happen after one year, then in the rest of the world.Further implications of the formal modelThe general limitations of this formal kinetics model are discussed. More detailed modeling is examined and the implications are examined in the light of currently available data. The evidence indicates that not more than 10% of the population is initially resistant to the H1N1 virus. Conclusion: We are probably only at the initial stage of development of the H1N1 epidemic. Increasing the number of H1N1-resistant people in future (e.g. due to vaccination) may influence the dynamics of epidemic development. At present, the development of the epidemic depends only on the number of people in the population who are initially resistant to the virus.
Santa Fe Institute - SFI draws scientists from universities and research institutions world-wide to pursue broad research problems. Much of the work focuses on the science of complexity (emergence), which examines underlying patterns and regularities behind a wide assortment of real-world phenomena. Projects range from the communication patterns of ants to the way information spreads across economic markets.
Careers in Theoretical Biology - Guidance brochure for high school and undergraduate students. Defines theoretical biology, gives examples of its application, and provides advice on preparing for a career in the field.
Claus Emmeche - Home page of a theoretical biologist with general interests in Philosophy of Nature, Philosophy of Science, and Science Studies, and research interests in artificial life and theoretical biology. Links to online papers, other resources, and to the Center for the Philosophy of Nature and Science Studies.
Meta Description: [ I am a theoretical biologist with general interests in Philosophy of Nature, Philosophy of Science, and Science Studies, and research interests in artificial life and theoretical biology. Here are links to online papers, other ressources, and to the Center for the Philosophy of Nature and Science... ]
David Liley - Home page of a theoretical neurobiologist at Swinburne University of Technology. Papers on theoretical models of the mammalian electroencephalogram and related lecture notes (medical imaging, physiological modeling).
Department of Ecology and Evolutionary Biology, Princeton University - The Ecology and Evolutionary Biology (EEB) Department carries out research in a wide range of areas across evolution and ecology. Areas of particular interest include molecular evolution, behavioural ecology, the dynamics of communities and populations, and conservation biology.
Honig Lab at Columbia University - Research combines computational biophysics and bioinformatics to aid in understanding the structural, physical, and chemical basis of a wide range of biological phenomena, with a focus on protein structure and function. Includes publications list and information on software developed by the group.
Meta Description: [ Theoretical and computational tools to study
the structure and function of biological macromolecules ]
Molecular Information Theory - The theory of molecular machines from the NIH Laboratory of Computational and Experimental Biology.
Program in Theoretical Biology, Institute for Advanced Study - The Program in Theoretical Biology has many diverse interests, including immunology and virology, the evolution of language, evolutionary genomics, epidemiology, the evolution of cancer and the evolution of cooperation and fairness.
Random Variations to Biological Choice - Philosophical speculations on physics and biology.
Short Courses on the Mathematics of Biological Complexity - Three short courses will be held at the University of Tennessee to give biologists a rapid introduction to the mathematical and computational topics appropriate for understanding current research in biological complexity.
Theoretical Biology and Biophysics (T-10) - The Theoretical Biology and Biophysics Group (T-10) at Los Alamos National Laboratory focuses on the modeling of biological systems and the analysis and informatics of molecular and cellular biological data.
Meta Description: [ Los Alamos National Laboratory is a DOE national laboratory that applies science and technology to solve problems in national security and defense. ]
Theoretical Biology at Utrecht University, Netherlands - Formal models in ecology, spatial pattern formation, (molecular) evolution, immunology, and ethology. Formalisms range from mathematical models, cellular automata, genetic algorithms, to discrete-event individual-oriented simulation models. Bioinformatic approach typically involves spatial, multi-leveled models with many interacting entities whose behavior is determined by local information.
Theoretical Biology Groningen - Focuses on competition and natural selection, more specifically evolutionary game theory, life history theory, sexual selection, sex allocation, metapopulation genetics, resource competition, and interference competition.
University of Lund - Department of Theoretical Ecology. Members, teaching and research.
University of Vienna - Department of Theoretical Biology. Research groups and resources.
Vrije Universiteit Amsterdam - Department of Theoretical Biology. A do-it-yourself online course in 'methods in theoretical biology' and yearly organised online courses on the Dynamic Energy Budget (DEB) theory of the development and growth of organisms.
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