|
Rule-based Modeling
Rule-based modeling is a modeling approach that uses a set of rules that indirectly specifies a mathematical model. The rule-set can either be translated into a model such as Markov chains or differential equations, or be treated using tools that directly work on the rule-set in place of a translated model, as the latter is typically much bigger. Rule-based modeling is especially effective in cases where the rule-set is significantly simpler than the model it implies, meaning that the model is a repeated manifestation of a limited number of patterns. An important domain where this is often the case is biochemical models of living organisms. Groups of mutually corresponding substances are subject to mutually corresponding interactions. BioNetGen is a suite of software tools used to generate mathematical models consisting of ordinary differential equations without generating the equations directly. For example below is an example rule in the BioNetGen format: A(a,a) + B(b) -> A(a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Conceptual Model
The term conceptual model refers to any model that is formed after a wikt:concept#Noun, conceptualization or generalization process. Conceptual models are often abstractions of things in the real world, whether physical or social. Semantics, Semantic studies are relevant to various stages of process of concept formation, concept formation. Semantics is fundamentally a study of concepts, the meaning that thinking beings give to various elements of their experience. Overview Concept models and conceptual models The value of a conceptual model is usually directly proportional to how well it corresponds to a past, present, future, actual or potential state of affairs. A concept model (a model of a concept) is quite different because in order to be a good model it need not have this real world correspondence. In artificial intelligence, conceptual models and conceptual graphs are used for building expert systems and knowledge-based systems; here the analysts are concerned to repres ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Markov Chains
In probability theory and statistics, a Markov chain or Markov process is a stochastic process describing a sequence of possible events in which the probability of each event depends only on the state attained in the previous event. Informally, this may be thought of as, "What happens next depends only on the state of affairs ''now''." A countably infinite sequence, in which the chain moves state at discrete time steps, gives a discrete-time Markov chain (DTMC). A continuous-time process is called a continuous-time Markov chain (CTMC). Markov processes are named in honor of the Russian mathematician Andrey Markov. Markov chains have many applications as statistical models of real-world processes. They provide the basis for general stochastic simulation methods known as Markov chain Monte Carlo, which are used for simulating sampling from complex probability distributions, and have found application in areas including Bayesian statistics, biology, chemistry, economics, finance, i ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ordinary Differential Equation
In mathematics, an ordinary differential equation (ODE) is a differential equation (DE) dependent on only a single independent variable (mathematics), variable. As with any other DE, its unknown(s) consists of one (or more) Function (mathematics), function(s) and involves the derivatives of those functions. The term "ordinary" is used in contrast with partial differential equation, ''partial'' differential equations (PDEs) which may be with respect to one independent variable, and, less commonly, in contrast with stochastic differential equations, ''stochastic'' differential equations (SDEs) where the progression is random. Differential equations A linear differential equation is a differential equation that is defined by a linear polynomial in the unknown function and its derivatives, that is an equation of the form :a_0(x)y +a_1(x)y' + a_2(x)y'' +\cdots +a_n(x)y^+b(x)=0, where a_0(x),\ldots,a_n(x) and b(x) are arbitrary differentiable functions that do not need to be linea ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
GNU GPL
The GNU General Public Licenses (GNU GPL or simply GPL) are a series of widely used free software licenses, or ''copyleft'' licenses, that guarantee end users the freedom to run, study, share, or modify the software. The GPL was the first copyleft license available for general use. It was originally written by Richard Stallman, the founder of the Free Software Foundation (FSF), for the GNU Project. The license grants the recipients of a computer program the rights of the Free Software Definition. The licenses in the GPL series are all copyleft licenses, which means that any derivative work must be distributed under the same or equivalent license terms. The GPL is more restrictive than the GNU Lesser General Public License, and even more distinct from the more widely used permissive software licenses such as BSD, MIT, and Apache. Historically, the GPL license family has been one of the most popular software licenses in the free and open-source software (FOSS) domain. Promi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Computer Simulation
Computer simulation is the running of a mathematical model on a computer, the model being designed to represent the behaviour of, or the outcome of, a real-world or physical system. The reliability of some mathematical models can be determined by comparing their results to the real-world outcomes they aim to predict. Computer simulations have become a useful tool for the mathematical modeling of many natural systems in physics (computational physics), astrophysics, climatology, chemistry, biology and manufacturing, as well as human systems in economics, psychology, social science, health care and engineering. Simulation of a system is represented as the running of the system's model. It can be used to explore and gain new insights into new technology and to estimate the performance of systems too complex for analytical solutions. Computer simulations are realized by running computer programs that can be either small, running almost instantly on small devices, or large-scale ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Virtual Cell
Virtual Cell (VCell) is an open-source software platform for modeling and simulation of living organisms, primarily cells. It has been designed to be a tool for a wide range of scientists, from experimental cell biologists to theoretical biophysicists. Concept Virtual Cell is an advanced software platform for modeling and simulating reaction kinetics, membrane transport and diffusion in the complex geometries of cells and multicellular tissues. VCell models have a hierarchical tree structure. The trunk level is the "Physiology" consisting of compartments, species and chemical reactions, and reaction rates that are functions of concentrations. Given initial concentrations of species, VCell can calculate how these concentrations change over time. How these numerical simulations are performed, is determined through a number of "Applications", which specify whether simulations will be deterministic or stochastic, and spatial or compartmental; multiple "Applications" can also spec ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Systems Biology
Systems biology is the computational modeling, computational and mathematical analysis and modeling of complex biological systems. It is a biology-based interdisciplinary field of study that focuses on complex interactions within biological systems, using a holistic approach (holism instead of the more traditional reductionist, reductionism) to biological research. This multifaceted research domain necessitates the collaborative efforts of chemists, biologists, mathematicians, physicists, and engineers to decipher the biology of intricate living systems by merging various quantitative molecular measurements with carefully constructed mathematical models. It represents a comprehensive method for comprehending the complex relationships within biological systems. In contrast to conventional biological studies that typically center on isolated elements, systems biology seeks to combine different biological data to create models that illustrate and elucidate the dynamic interactions with ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Biology
Molecular biology is a branch of biology that seeks to understand the molecule, molecular basis of biological activity in and between Cell (biology), cells, including biomolecule, biomolecular synthesis, modification, mechanisms, and interactions. Though cells and other microscopic structures had been observed in living organisms as early as the 18th century, a detailed understanding of the mechanisms and interactions governing their behavior did not emerge until the 20th century, when technologies used in physics and chemistry had advanced sufficiently to permit their application in the biological sciences. The term 'molecular biology' was first used in 1945 by the English physicist William Astbury, who described it as an approach focused on discerning the underpinnings of biological phenomena—i.e. uncovering the physical and chemical structures and properties of biological molecules, as well as their interactions with other molecules and how these interactions explain observ ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Stochastic Simulation
A stochastic simulation is a simulation of a system that has variables that can change stochastically (randomly) with individual probabilities.DLOUHÝ, M.; FÁBRY, J.; KUNCOVÁ, M.. Simulace pro ekonomy. Praha : VŠE, 2005. Realizations of these random variables are generated and inserted into a model of the system. Outputs of the model are recorded, and then the process is repeated with a new set of random values. These steps are repeated until a sufficient amount of data is gathered. In the end, the distribution of the outputs shows the most probable estimates as well as a frame of expectations regarding what ranges of values the variables are more or less likely to fall in. Often random variables inserted into the model are created on a computer with a random number generator (RNG). The U(0,1) uniform distribution outputs of the random number generator are then transformed into random variables with probability distributions that are used in the system model. Etymology ''St ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
