###### processes

- theoretical representations that simulate the behaviour or activity of biological processes or diseases . (biology-online.org)
- Model-based simulations of processes are used to explore hitherto unforeseen features and thereby suggest further profitable lines of both experimentation and theoretical study. (google.co.uk)
- It involves the use of computer simulations of biological systems, including cellular subsystems (such as the networks of metabolites and enzymes which comprise metabolism, signal transduction pathways and gene regulatory networks), to both analyze and visualize the complex connections of these cellular processes. (wikipedia.org)
- The complex network of biochemical reaction/transport processes and their spatial organization make the development of a predictive model of a living cell a grand challenge for the 21st century, listed as such by the National Science Foundation (NSF) in 2006. (wikipedia.org)
- Computer simulations have become an indispensable tool for revealing the molecular mechanism of biological processes. (uiuc.edu)
- However, since biological processes, which are normally microsecond or even millisecond long, need to be followed in computer simulations femtosecond by femtosecond, simulating such processes in every atomistic detail is computationally challenging. (uiuc.edu)
- While efforts have been made in this direction to reduce model complexity, they often prove insufficient to grasp which and when model processes play a crucial role. (springer.com)
- We detect model processes that are always inactive , or inactive on some time interval. (springer.com)
- Eliminating these processes reduces the complex dynamics of the original model to the much simpler dynamics of the core processes, in a succession of sub-models that are easier to analyse. (springer.com)
- Mathematical modelling has been used for decades as an approach to understand the functioning of biological systems in terms of their internal processes and components. (springer.com)
- Complexity arises from the high dimension of the networks, the large number of biological processes involved and their non linearity due to the complex feedback loops that regulate them. (springer.com)
- Reduction approaches have proven successful to significantly reduce model complexity, but they do not provide a mean to understand how the system dynamics emerges from the cascade of biological processes and regulatory mechanisms at work. (springer.com)
- Other models are more detailed and account for sub-cellular processes. (wikipedia.org)
- Today they continue to serve as an important model for normal human biology as well as pathological disease processes. (wikipedia.org)
- The P systems may trade space and time complexities and less often use models to explain natural processes in living cells. (wikipedia.org)
- Models allow a better understanding of how complex interactions and processes work. (wikipedia.org)
- Life is a characteristic that distinguishes physical entities that do have biological processes, such as signaling and self-sustaining processes, from those that do not, either because such functions have ceased, or because they never had such functions and are classified as inanimate. (wikipedia.org)
- Mathematical biology aims at the mathematical representation, treatment and modeling of biological processes, using techniques and tools of applied mathematics. (wikipedia.org)

###### Populations

- Another way populations models are useful are when species become endangered. (wikipedia.org)
- Late 18th-century biologists began to develop techniques in population modeling in order to understand dynamics of growing and shrinking ball populations of living organisms. (wikipedia.org)
- Population modeling became of particular interest to biologists in the 20th century as pressure on limited means of sustenance due to increasing human populations in parts of Europe were noticed by biologist like Raymond Pearl. (wikipedia.org)
- Matrix models of populations calculate the growth of a population with life history variables. (wikipedia.org)
- According to Hutchinson, he constructed "mathematical models of populations, the changing proportions of individuals of various ages, birthrate, the ecological niche, and population interaction in this technical introduction to population ecology. (wikipedia.org)

###### membranes

- Ultrafast energy flow in model biological membranes. (uva.nl)
- Membrane computing (or MC) is an area within computer science that seeks to discover new computational models from the study of biological cells, particularly of the cellular membranes. (wikipedia.org)
- Many variant models have been studied, and interest has focused on proving computational universality for systems with a small number of membranes, for the purpose of solving NP-complete problems such as Boolean satisfiability (SAT) problems and the traveling salesman problem (TSP). (wikipedia.org)
- They are based upon the structure of biological cells, abstracting from the way in which chemicals interact and cross cell membranes. (wikipedia.org)

###### organism

- In this article, we review the properties of this organism as biological model and its biotechnological applications. (diva-portal.org)
- The relatively large size of the chick as a model organism allowed scientists during this time to make these significant observations without the help of a microscope. (wikipedia.org)
- Death is the permanent termination of all biological functions which sustain an organism, and as such, is the end of its life. (wikipedia.org)

###### computational model

- A whole cell computational model for the bacterium Mycoplasma genitalium, including all its 525 genes, gene products, and their interactions, was built by scientists from Stanford University and the J. Craig Venter Institute and published on 20 July 2012 in Cell. (wikipedia.org)
- The MGS computational model is a generalisation of cellular automata, Lindenmayer systems, Paun systems and other computational formalisms inspired by chemistry and biology. (wikipedia.org)
- A P system is a computational model in the field of computer science that performs calculations using a biologically-inspired process. (wikipedia.org)
- Although inspired by biology, the primary research interest in P systems is concerned with their use as a computational model, rather than for biological modeling, although this is also being investigated. (wikipedia.org)

###### Dynamical

- Understanding the dynamical behaviour of biological systems is challenged by their large number of components and interactions. (springer.com)
- We design a method for dealing with model complexity, based on the analysis of dynamical models by means of Principal Process Analysis. (springer.com)
- In conclusion, Principal Process Analysis is a simple-to-use method, which constitutes an additional and useful tool for analysing the complex dynamical behaviour of biological systems. (springer.com)
- In this work we study three systems of biological interest: the translocation of a heterogeneously charged polymer through an infinitely thin pore, the wrapped of a rigid particle by a soft vesicle and the modification of the dynamical properties of a gel due to the presence of rigid inclusions. (umass.edu)
- This paper is concerned with stability analysis of biological networks modeled as discrete and finite dynamical systems. (springer.com)
- MGS (a General Model of Simulation) is a domain-specific language used for specification and simulation of dynamical systems with dynamical structure, developed at IBISC (Computer Science, Integrative Biology and Complex Systems) at Université d'Évry Val-d'Essonne (University of Évry). (wikipedia.org)

###### Complexity

- The Modelling Biological Complexity MRes is designed for students whishing to develop the skills to apply mathematical, computational and physical science techniques to real biological problems. (ucl.ac.uk)
- Numerous kinetic models of these networks have been developed in computational biology, of increasing complexity due to advances in modelling and parameter estimation approaches (see [ 1 , 2 ] for an example). (springer.com)
- One approach often used to tackle the problem of complexity is model reduction (see [ 3 ] for a recent review). (springer.com)
- Complex systems biology (CSB) is a branch or subfield of mathematical and theoretical biology concerned with complexity of both structure and function in biological organisms, as well as the emergence and evolution of organisms and species, with emphasis being placed on the complex interactions of, and within, bionetworks, and on the fundamental relations and relational patterns that are essential to life. (wikipedia.org)
- this is because the latter is restricted primarily to simplified models of biological organization and organisms, as well as to only a general consideration of philosophical or semantic questions related to complexity in biology. (wikipedia.org)
- A complete definition of complexity for individual organisms, species, ecosystems, biological evolution and the biosphere has eluded researchers, and still is an ongoing issue. (wikipedia.org)
- however, such approaches are not focused on, or do not include, the conceptual part of complexity related to organization and topological attributes or algebraic topology, such as network connectivity of genomes, interactomes and biological organisms that are very important. (wikipedia.org)
- The hierarchy of complexity levels of organization in the biosphere is also recognized in modern classifications of taxonomic ranks, such as: biological domain and biosphere, biological kingdom, Phylum, biological class, order, family, genus and species. (wikipedia.org)
- Tessellation or cellular automata provide however an intuitive, visual/computational insight into the lower levels of complexity, and have therefore become an increasingly popular, discrete model studied in computability theory, applied mathematics, physics, computer science, theoretical biology/systems biology, cancer simulations and microstructure modeling. (wikipedia.org)

###### simulation

- Using a Blue Gene supercomputer running Michael Hines's NEURON software, the simulation does not consist simply of an artificial neural network, but involves a partially biologically realistic model of neurons. (wikipedia.org)
- The unit will also introduce time series analysis, Bayesian approaches to modelling data, and simulation models including explicitly spatial and individual-based models. (edu.au)
- The models significantly reduce computational cost and, thereby, enhance the speed of simulation. (uiuc.edu)
- Hans L.M. Vangheluwe is a professor and researcher in the domain of Computer simulation and Modelling. (wikipedia.org)
- He then was called up for military service, where he served as one of the two detaches in the "Beheerseenheid van het Mathematisch Model van de Noordzee en het Schelde Estuarium (BMM)" of the Belgian Navy, showing his proficiency in Simulation of the physical world. (wikipedia.org)
- Simulation: Transactions of the Society for Modeling and Simulation International, 80(9):433-450, September 2004. (wikipedia.org)
- Special Issue: Grand Challenges for Modeling and Simulation. (wikipedia.org)
- Integrating Base Object Model components into DEVS-based simulation. (wikipedia.org)
- Journal of Defense Modeling and Simulation, April 2010. (wikipedia.org)
- In numerical simulation or modeling of real systems, error analysis is concerned with the changes in the output of the model as the parameters to the model vary about a mean. (wikipedia.org)

###### biomedical

- It has both theoretical and practical applications in biological, biomedical and biotechnology research. (wikipedia.org)

###### Laboratory

- The high growth rates, cell yields of the cultures, and the constitutive expression of an impressively efficient natural competence apparatus, amongst other properties, make some strains of the genus excellent laboratory models to study the molecular basis of thermophilia. (diva-portal.org)
- The probabilistic description taken by the models in this category was inspired from laboratory experiments involving either natural or pharmacological stimulation which exhibit variability in the resulting spike pattern. (wikipedia.org)
- Since 2010 At the technion he also heads the Enterprise Systems Modeling Laboratory. (wikipedia.org)

###### mathematical model

- A population model is a type of mathematical model that is applied to the study of population dynamics. (wikipedia.org)

###### ecological

- With massive increases in the availability of ecological and other kinds of biological data, skill in developing models to describe and understand relationships in data and extrapolate beyond existing data, and an understanding of the nuances of particular kinds of data, is fundamental in modern biological research. (edu.au)
- Ecological population modeling is concerned with the changes in parameters such as population size and age distribution within a population. (wikipedia.org)
- The logistic population model, the Lotka-Volterra model of community ecology, life table matrix modeling, the equilibrium model of island biogeography and variations thereof are the basis for ecological population modeling today. (wikipedia.org)
- Systems ecology focuses on interactions and transactions within and between biological and ecological systems, and is especially concerned with the way the functioning of ecosystems can be influenced by human interventions. (wikipedia.org)
- Systems ecology seeks a holistic view of the interactions and transactions within and between biological and ecological systems. (wikipedia.org)

###### experimental

- Structural superpositions between two type of structures show that experimental structures (red) were well reproduced by simulations (blue) with the hybrid model. (uiuc.edu)
- We find that the negative feedback loop involving proteins PER, CRY, CLOCK-BMAL1 is the main oscillator, in agreement with previous modelling and experimental studies. (springer.com)
- Accordingly, an important aspect of biological neuron models is experimental validation, and the use of physical units to describe the experimental procedure associated with the model predictions. (wikipedia.org)
- The most extensive experimental inquiry in this category of models was made by Hodgkin-Huxley in the early 1950s using an experimental setup that punctured the cell membrane and allowed to force a specific membrane voltage/current. (wikipedia.org)

###### dynamics

- This volume develops a unifying approach to population studies that emphasizes the interplay between modeling and experimentation and that will provide mathematicians and biologists with a framework within which population dynamics can be fully explored and understood. (google.co.uk)
- We quantify by means of global relative errors the extent to which the simplified models reproduce the main features of the original system dynamics and apply global sensitivity analysis to test the influence of model parameters on the errors. (springer.com)
- The analysis of the sub-model dynamics allows us to identify the source of circadian oscillations. (springer.com)
- Population models are used to determine maximum harvest for agriculturists, to understand the dynamics of biological invasions, and for environmental conservation. (wikipedia.org)
- Work in this area dates back to the 19th century, and even as far as 1798 when Thomas Malthus formulated the first principle of population dynamics, which later became known as the Malthusian growth model. (wikipedia.org)

###### system's response

- The goal is to create accurate real-time models of a system's response to environmental and internal stimuli, such as a model of a cancer cell in order to find weaknesses in its signalling pathways, or modelling of ion channel mutations to see effects on cardiomyocytes and in turn, the function of a beating heart. (wikipedia.org)
- Once those parameters are established, they can be used to create a model to predict the system's response under different conditions. (bio-medicine.org)

###### system

- It is understood that an unexpected emergent property of a complex system is a result of the interplay of the cause-and-effect among simpler, integrated parts (see biological organisation). (wikipedia.org)
- Modeling a biological system relies in part on defining parameters f. (bio-medicine.org)
- Modeling a biological system relies, in part, on defining parameters for that system, which correspond to how the system functions under normal conditions. (bio-medicine.org)
- This makes it easier for optimization routines to identify a functional working set of parameters that can then be used to predict the activity of the modeled system. (bio-medicine.org)
- A biological neuron model, also known as a spiking neuron model, is a mathematical description of the properties of certain cells in the nervous system that generate sharp electrical potentials across their cell membrane, roughly one millisecond in duration, as shown in Fig. 1. (wikipedia.org)
- It is worth noting that not all the cells of the nervous system produce the type of spike that define the scope of the spiking neuron models. (wikipedia.org)
- Ultimately, biological neuron models aim to explain the mechanisms underlying the operation of the nervous system for the purpose of restoring lost control capabilities such as perception (e.g. deafness or blindness), motor movement decision making, and continuous limb control. (wikipedia.org)
- To date, the P systems are nearly all theoretical models that have never been reduced to practice, although a practical system is given in. (wikipedia.org)
- An updated list of publications of theoretical biologist Robert Rosen Theory of Biological Anthropology (Documents No. 9 and 10 in English) Drawing the Line Between Theoretical and Basic Biology, a forum article by Isidro A. T. Savillo Synthesis and Analysis of a Biological System[permanent dead link], by Hiroyuki Kurata, 1999. (wikipedia.org)
- Variations on the P system model led to the formation of a branch of research known as 'membrane computing. (wikipedia.org)
- Just as in a biological cell, where a chemical reaction may only take place upon the chance event that the required chemical molecules collide and interact (possibly also with a catalyst), the rules in a P system are applied at random. (wikipedia.org)
- There are three (in the basic P system model) distinct ways in a rule may handle its output objects. (wikipedia.org)

###### Units

- Neuron models can be divided into two categories according to the physical units of the interface of the model. (wikipedia.org)
- The input stage of these models is not electrical, but rather has either pharmacological (chemical) concentration units, or physical units that characterize an external stimulus such as light, sound or other forms of physical pressure. (wikipedia.org)

###### Chemicals

- Chemicals are modeled by symbols, or alternatively by strings of symbols. (wikipedia.org)

###### spatial

- spatial effects are investigated by developing models that highlight the consequences that geographical restriction and species mobility may have on population development. (google.co.uk)

###### simulations

- Despite ever-growing computing power, computer simulations cannot be used for the modeling of large biomolecular systems over time scales long enough to be of biological interest. (uiuc.edu)
- As reported recently , we have significantly improved the model for simulations of protein folding by re-parameterizing hydration of protein backbones, a critical factor for controlling the balance between unfolded and folded states of proteins. (uiuc.edu)

###### ecology

- Modeling Nature: Episodes in the History of Population Ecology. (wikipedia.org)

###### Quantitative

- This unit builds on the foundation provided in Quantitative Methods in Biology to familiarise students with more advanced model building techniques including generalised linear, mixed and additive models, regression trees, bootstrapping methods, and non-linear regression. (edu.au)

###### mechanisms

- Many of the included examples are characterised by highly complex, nonlinear, and supercomplex mechanisms, as it is being increasingly recognised that the result of such interactions may only be understood through a combination of mathematical, logical, physical/chemical, molecular and computational models. (wikipedia.org)

###### neural

- So far the physics engine Gepetto has been built and models of the neural connectome and a muscle cell have been created in the NeuroML format. (wikipedia.org)
- In that sense, biological neural models differ from artificial neuron models that do not presume to predict the outcomes of experiments involving the biological neural tissue (although artificial neuron models are also concerned with execution of perception and estimation tasks). (wikipedia.org)

###### parameters

- Researchers at North Carolina State University have developed a new method for estimating the parameters used in such models which may advance modeling in research areas ranging from cancer to fertility. (bio-medicine.org)
- The method we've developed should expedite the development of more accurate parameters, which can be used to create more precise and predictable models of oscillatory biological systems. (bio-medicine.org)
- Researchers then try to identify the parameters that would result in the closest 'fit' to those concentrations when plugged into the model. (bio-medicine.org)

###### interplay

- Biological systems manifest many important examples of emergent properties in the complex interplay of components. (wikipedia.org)

###### stochastic

- Phylogenetics is an area that deals with the reconstruction and analysis of phylogenetic (evolutionary) trees and networks based on inherited characteristics Traditional population genetic models deal with alleles and genotypes, and are frequently stochastic. (wikipedia.org)

###### systems biology

- Modelling biological systems is a significant task of systems biology and mathematical biology. (wikipedia.org)
- Computational systems biology aims to develop and use efficient algorithms, data structures, visualization and communication tools with the goal of computer modelling of biological systems. (wikipedia.org)
- By far the most widely accepted standard format for storing and exchanging models in the field is the Systems Biology Markup Language (SBML) The SBML.org website includes a guide to many important software packages used in computational systems biology. (wikipedia.org)
- Creating a cellular model has been a particularly challenging task of systems biology and mathematical biology. (wikipedia.org)

###### theoretical biology

- The field is sometimes called mathematical biology or biomathematics to stress the mathematical side, or theoretical biology to stress the biological side. (wikipedia.org)
- Theoretical biology focuses more on the development of theoretical principles for biology while mathematical biology focuses on the use of mathematical tools to study biological systems, even though the two terms are sometimes interchanged. (wikipedia.org)

###### Theory

- A Continuum Theory of Multiphase Mixtures for Modelling Biological Growth. (umich.edu)
- This dissertation presents a continuum treatment of growth in biological tissue developed within the context of modern mixture theory. (umich.edu)
- To accelerate the convergence to a unified theory, we list several models in each category, and where applicable, also references to supporting experiments. (wikipedia.org)
- Thus, MC is not merely a theory related to a specific model, it is a framework for devising compartmentalized models. (wikipedia.org)

###### stimulus

- Traditional study of biological systems requires reductive methods in which quantities of data are gathered by category, such as concentration over time in response to a certain stimulus. (wikipedia.org)
- Natural or pharmacological input neuron models - The models in this category connect between the input stimulus which can be either pharmacological or natural, to the probability of a spike event. (wikipedia.org)

###### 20th century

- Great advances in immunology and oncology continued to characterize the 20th century, for which we indebted to the chicken model. (wikipedia.org)

###### cellular model

- It is a sub-task of creating a cellular model. (wikipedia.org)

###### Discrete

- The feasibility of our approach is demonstrated by the analysis of stability and bifurcations of several discrete biological models using implementations of algebraic methods. (springer.com)
- Allen L.J.: Some discrete-time SI, SIR, and SIS epidemic models. (springer.com)

###### reproduce

- To alleviate the reliance on native structures, several coarse-grained protein models have been parametrized to reproduce peptide folding or have been built on knowledge-based statistical potentials, achieving even in some cases predictive capabilities. (uiuc.edu)

###### computer

- Student performance is assessed by essays, mini projects, oral and poster presentations, a computer programming and biological database task, web development, the research project and an end-of-year viva. (ucl.ac.uk)
- A dynamic computer model of intracellular signaling was the basis for Merrimack Pharmaceuticals to discover the target for their cancer medicine MM-111. (wikipedia.org)
- He was a co-founder of Modelica, a language for the acausal modelling of complex systems and Computer Automated Multiparadigm Modeling. (wikipedia.org)
- Computer Automated Multi-Paradigm Modeling: An Introduction. (wikipedia.org)

###### fundamental

- How proteins fold into their native structures is a fundamental but mysterious biological process. (uiuc.edu)

###### Understanding

- Modeling of dynamic interactions in nature can provide a manageable way of understanding how numbers change over time or in relation to each other. (wikipedia.org)

###### context

- Driving forces in a biological context are usually referred to as rhythms, pulses or clocks. (uleth.ca)

###### species

- Population models can track the fragile species and work and curb the decline. (wikipedia.org)
- Together, Lotka and Volterra formed the Lotka-Volterra model for competition that applies the logistic equation to two species illustrating competition, predation, and parasitism interactions between species. (wikipedia.org)
- The equilibrium model of island biogeography describes the number of species on an island as an equilibrium of immigration and extinction. (wikipedia.org)

###### analysis

- Computers are critical to analysis and modelling of these data. (wikipedia.org)

###### studies

- The coarse-grained models are limited, therefore, in their use in studies of folding, aggregation, large conformational changes of proteins, or conformational features of intrinsically disordered proteins. (uiuc.edu)
- Tremendous efforts have been spent in parameterizing the hybrid model in order to make it accurate enough for computational studies of proteins. (uiuc.edu)
- Furthermore, the availability of plasmids and up to four thermostable antibiotic selection markers allows its use in physiological studies as a model for ancient bacteria. (diva-portal.org)
- The studies devise models that may at least theoretically be implemented on hardware. (wikipedia.org)

###### Growth

- One of the most basic and milestone models of population growth was the logistic model of population growth formulated by Pierre François Verhulst in 1838. (wikipedia.org)
- The logistic model takes the shape of a sigmoid curve and describes the growth of a population as exponential, followed by a decrease in growth, and bound by a carrying capacity due to environmental pressures. (wikipedia.org)

###### precise

- This requires precise mathematical models. (wikipedia.org)

###### patterns

- Many patterns can be noticed by using population modeling as a tool. (wikipedia.org)

###### interest

- A range of interdisciplinary research-driven projects follow in which students gain experience of different research techniques and a range of areas of biological interest. (ucl.ac.uk)

###### scientists

- Modeling biological systems can provide key insights for scientists an. (bio-medicine.org)
- Modeling biological systems can provide key insights for scientists and medical researchers, but periodic cycles that repeat themselves so-called oscillatory systems pose some key challenges. (bio-medicine.org)

###### complex systems

- He has published in the fields of conceptual modeling of complex systems, systems architecture and design. (wikipedia.org)

###### physical

- Foundation courses use innovative teaching methods for interdisciplinary research to provide essential background knowledge in computational, mathematical and physical techniques and a broad introduction to core biological concepts and systems. (ucl.ac.uk)
- Systems that require a driving force of some kind are very common in physical and biological settings. (uleth.ca)

###### describe

- The models in this category describe the relationship between neuronal membrane currents at the input stage, and membrane voltage at the output stage. (wikipedia.org)

###### approach

- ERP modeling: a comprehensive approach" (PDF). (wikipedia.org)

###### research

- Chickens (Gallus gallus domesticus) and their eggs have been used extensively as research models throughout the history of biology. (wikipedia.org)

###### particularly

- MGS is particularly aimed at modelling biological systems. (wikipedia.org)

###### function

- Each category could be further divided according to the abstraction/detail level: Electrical input-output membrane voltage models - These models produce a prediction for membrane output voltage as function of electrical stimulation at the input stage (either voltage or current). (wikipedia.org)

###### Proceedings

- Proceedings of the International Conference on Model-Based Systems Engineering (MBSE'09). (wikipedia.org)

###### important

- Various models of the spread of infections have been proposed and analyzed, and provide important results that may be applied to health policy decisions. (wikipedia.org)

###### details

- By following this idea, a hybrid model with its components represented at different levels of details has been developed. (uiuc.edu)
- The various models in this category differ in the exact functional relationship between the input current and the output voltage and in the level of details. (wikipedia.org)