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COPASI
COPASI (COmplex PAthway SImulator) is an open-source software application for creating and solving mathematical models of biological processes such as metabolic networks, cell-signaling pathways, regulatory networks, infectious diseases, and many others. History COPASI is based on the Gepasi simulation software that was developed in the early 1990s by Pedro Mendes. The initial development of COPASI was funded by the Virginia Bioinformatics Institute, and the Klaus Tschira Foundation. Current development efforts are supported by grants from the National Institutes of Health, the BBSRC, and the German Ministry of Education. Development team COPASI is the result of an international collaboration between the University of Manchester (UK), the University of Heidelberg (Germany), and the Virginia Bioinformatics Institute (USA). The project principal investigators are Pedro Mendes and Ursula Kummer. The chief software architects are Stefan Hoops and Sven Sahle. Features COPASI in ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Pedro Pedrosa Mendes
Pedro Pedrosa Mendes is a professor of Systems Biology, computational systems biology in the Department of Computer Science, University of Manchester, Department of Computer Science at the University of Manchester. He is a member of the Manchester Centre for Integrative Systems Biology, Manchester Centre for Integrative Systems Biology (MCISB), the Machine learning, Machine Learning and Optimization (MLO) group. He is also a professor at the University of Connecticut Health Center. Education Mendes did his undergraduate degree in biochemistry at the University of Lisbon. He then moved to the UK and was awarded a PhD, Doctor of Philosophy from Aberystwyth University in 1994 for work on computer simulation of metabolic pathways. Career Following his PhD, Mendes moved to the National Center for Genome Resources for a year then on to the Virginia Bioinformatics Institute (VBI) of Virginia Polytechnic Institute and State University, Virginia Polytechnic Institute and State University (V ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
List Of Systems Biology Modeling Software
Systems biology relies heavily on building mathematical models A mathematical model is a description of a system using mathematical concepts and language. The process of developing a mathematical model is termed mathematical modeling. Mathematical models are used in the natural sciences (such as physics, ... to help understand and make predictions of biological processes. Specialized software to assist in building models has been developed since the arrival of the first digital computers. The following list gives the currently supported software applications available to researchers. The vast majority of modern systems biology modeling software support SBML, which is the de facto standard for exchanging models of biological cellular processes. Some tools also support CellML, a standard used for representing physiological processes. The advantage of using standard formats is that even though a particular software application may eventually become unsupported and even unusabl ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ordinary Differential Equations
In mathematics, an ordinary differential equation (ODE) is a differential equation whose unknown(s) consists of one (or more) function(s) of one variable and involves the derivatives of those functions. The term ''ordinary'' is used in contrast with the term partial differential equation which may be with respect to ''more than'' one independent variable. 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 , ..., and are arbitrary differentiable functions that do not need to be linear, and are the successive derivatives of the unknown function of the variable . Among ordinary differential equations, linear differential equations play a prominent role for several reasons. Most elementary and special functions that are encountered in physics and applied mathematics are ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Virginia Bioinformatics Institute
The Biocomplexity Institute of Virginia Tech (formerly the Virginia Bioinformatics Institute) is a research organization specializing in bioinformatics, computational biology, and systems biology. The institute has more than 250 personnel, including over 50 tenured and research faculty. Research at the institute involves collaboration in diverse disciplines such as mathematics, computer science, biology, plant pathology, biochemistry, systems biology, statistics, economics, synthetic biology and medicine. The institute develops -omic and bioinformatic tools and databases that can be applied to the study of human, animal and plant diseases as well as the discovery of new vaccine, drug and diagnostic targets. The institute's programs are supported by a variety of government and private agencies including the National Institutes of Health, National Science Foundation, U.S. Department of Defense, U.S. Department of Agriculture, and U.S. Department of Energy. Since inception, the Bio ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Metabolic Control Analysis
Metabolic control analysis (MCA) is a mathematical framework for describing metabolic, signaling, and genetic pathways. MCA quantifies how variables,elastsuch as fluxes and species concentrations, depend on network parameters. In particular, it is able to describe how network-dependent properties, called control coefficients, depend on local properties called elasticities or Elasticity Coefficients. MCA was originally developed to describe the control in metabolic pathways but was subsequently extended to describe signaling and genetic networks. MCA has sometimes also been referred to as ''Metabolic Control Theory,'' but this terminology was rather strongly opposed by Henrik Kacser, one of the founders. More recent work has shown that MCA can be mapped directly on to classical control theory and are as such equivalent. Biochemical systems theory is a similar formalism, though with rather different objectives. Both are evolutions of an earlier theoretical analysis by Joseph Higg ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Linux
Linux ( or ) is a family of open-source Unix-like operating systems based on the Linux kernel, an operating system kernel first released on September 17, 1991, by Linus Torvalds. Linux is typically packaged as a Linux distribution, which includes the kernel and supporting system software and libraries, many of which are provided by the GNU Project. Many Linux distributions use the word "Linux" in their name, but the Free Software Foundation uses the name "GNU/Linux" to emphasize the importance of GNU software, causing some controversy. Popular Linux distributions include Debian, Fedora Linux, and Ubuntu, the latter of which itself consists of many different distributions and modifications, including Lubuntu and Xubuntu. Commercial distributions include Red Hat Enterprise Linux and SUSE Linux Enterprise. Desktop Linux distributions include a windowing system such as X11 or Wayland, and a desktop environment such as GNOME or KDE Plasma. Distributions intended for ser ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Steady State (chemistry)
In chemistry, a steady state is a situation in which all state variables are constant in spite of ongoing processes that strive to change them. For an entire system to be at steady state, i.e. for all state variables of a system to be constant, there must be a flow through the system (compare mass balance). A simple example of such a system is the case of a bathtub with the tap running but with the drain unplugged: after a certain time, the water flows in and out at the same rate, so the water level (the state variable Volume) stabilizes and the system is in a steady state. The steady state concept is different from chemical equilibrium. Although both may create a situation where a concentration does not change, in a system at chemical equilibrium, the net reaction rate is zero (products transform into reactants at the same rate as reactants transform into products), while no such limitation exists in the steady state concept. Indeed, there does not have to be a reaction at all ... [...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. Particularly from the year 2000 onwards, the concept has been used widely in biology in a variety of contexts. The Human Genome Project is an example of applied systems thinking in biology which has led to new, collaborative ways of working on problems in the biological field of genetics. One of the aims of systems biology is to model and discover emergent property, emergent properties, properties of cell (biology), cells, tissue (biology), tissues and organisms functioning as a system whose theoretical description is only possible using techniques of systems biology. These typically involve metabolic networks or cell ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Heidelberg University
} Heidelberg University, officially the Ruprecht Karl University of Heidelberg, (german: Ruprecht-Karls-Universität Heidelberg; la, Universitas Ruperto Carola Heidelbergensis) is a public research university in Heidelberg, Baden-Württemberg, Germany. Founded in 1386 on instruction of Pope Urban VI, Heidelberg is Germany's oldest university and one of the world's oldest surviving universities; it was the third university established in the Holy Roman Empire. Heidelberg is one of the most prestigious and highly ranked universities in Europe and the world. Heidelberg has been a coeducational institution since 1899. The university consists of twelve faculties and offers degree programmes at undergraduate, graduate and postdoctoral levels in some 100 disciplines. The language of instruction is usually German, while a considerable number of graduate degrees are offered in English as well as some in French. As of 2021, 57 Nobel Prize winners have been affiliated with the city o ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Berkeley Madonna
Berkeley Madonna is a mathematical modelling software package, developed at the University of California at Berkeley by Robert Macey and George Oster. It numerically solves ordinary differential equations and difference equations, originally developed to execute STELLA programs. Its strength lies in a relatively simple syntax to define differential equations coupled with a simple yet powerful user interface. In particular, Berkeley Madonna provides the facility of putting parameters onto a slider that can in turn be moved by a user to change the value. Such visualizations enable quick assessments of whether or not a particular model class is suitable to describe the data to be analyzed and modeled, and, later, communicating models easily to other disciplines such as medical decision makers. Uses It has become a standard in the development and communication of pharmacometric models describing drug concentration and its effects in drug development , modeling of physiological proce ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
C (programming Language)
C (''pronounced like the letter c'') is a General-purpose language, general-purpose computer programming language. It was created in the 1970s by Dennis Ritchie, and remains very widely used and influential. By design, C's features cleanly reflect the capabilities of the targeted CPUs. It has found lasting use in operating systems, device drivers, protocol stacks, though decreasingly for application software. C is commonly used on computer architectures that range from the largest supercomputers to the smallest microcontrollers and embedded systems. A successor to the programming language B (programming language), B, C was originally developed at Bell Labs by Ritchie between 1972 and 1973 to construct utilities running on Unix. It was applied to re-implementing the kernel of the Unix operating system. During the 1980s, C gradually gained popularity. It has become one of the measuring programming language popularity, most widely used programming languages, with C compilers avail ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Lyapunov Exponent
In mathematics, the Lyapunov exponent or Lyapunov characteristic exponent of a dynamical system is a quantity that characterizes the rate of separation of infinitesimally close trajectories. Quantitatively, two trajectories in phase space with initial separation vector \delta \mathbf_0 diverge (provided that the divergence can be treated within the linearized approximation) at a rate given by : , \delta\mathbf(t) , \approx e^ , \delta \mathbf_0 , where \lambda is the Lyapunov exponent. The rate of separation can be different for different orientations of initial separation vector. Thus, there is a spectrum of Lyapunov exponents—equal in number to the dimensionality of the phase space. It is common to refer to the largest one as the maximal Lyapunov exponent (MLE), because it determines a notion of predictability for a dynamical system. A positive MLE is usually taken as an indication that the system is chaotic (provided some other conditions are met, e.g., phase space comp ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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