**processes**- 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)
- Oceans of experimental biological data generated Important intuitions captured in mental models that biologists build of biological processes How to build in silico models from all this? (coursehero.com)
- Modeling the kinetics of the processes that represent a biophysical system has long been pursued with the aim of improving our understanding of the studied system. (pubmedcentralcanada.ca)
- Due to the unique properties of biological systems, in addition to the usual difficulties faced in modeling the dynamics of physical or chemical systems, biological simulations encounter difficulties that result from intrinsic multiscale and stochastic nature of the biological processes. (pubmedcentralcanada.ca)
- Although kinetic modeling and the underlying fundamental mathematics are used in vastly different fields of science and engineering, here we will concentrate on biological kinetic networks which model cellular activities as a set of reaction processes. (pubmedcentralcanada.ca)
- The next step is building molecular models depicting principal molecular events that govern various biological processes. (eurekaselect.com)
- One of the most important aspects for all life on this planet is the act to keep their biological processes in a state where they do not reach equilibrium. (diva-portal.org)
- 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)

**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)

**neuron models**- 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)
- 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)
- 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)
- Neuron models can be divided into two categories according to the physical units of the interface of the model. (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)
- Although it is not unusual in science and engineering to have several descriptive models for different abstraction/detail levels, the number of different, sometimes contradicting, biological neuron models is exceptionally high. (wikipedia.org)
- Hence, it is not clear to what extent the electrical neuron models hold for extra-cellular stimulation (see e.g. (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)
- This chapter discusses the implications for simulation of models involving interacting species with very low copy numbers, which often occur in biological systems and give rise to significant relative fluctuations. (pubmedcentralcanada.ca)
- 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)
- 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)

**organism**- 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)

**populations**- The traditional way of modeling the time evolution of the molecular populations in a reacting system is to use a set of coupled, first order, ordinary differential equations (ODEs) called the reaction rate equations (RRE). (pubmedcentralcanada.ca)
- 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)
- Modeling Biological Populations in Space and Time. (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)

**pathways**- 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)

**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)
- This system, created in the laboratory of Jasna Brujić, an assistant professor in NYU's Department of Physics and part of its Center for Soft Matter Research, is said to be an oil-in-water solution whose surface properties reproduce those found on biological cells. (theengineer.co.uk)
- The new model performs better than the standard HMAX and comparably to a computer vision system on face detection. (mit.edu)
- Watch video lessons on the biological model of abnormality, and learn about the brain, the endocrine system, and the physiology of mental health. (study.com)
- If the biological system consists of a set of identical weakly coupled cells, stochasticity may lead to phase decoupling producing irregular spatio-temporal patterns. (royalsocietypublishing.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)
- 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)

**Membrane**- Membrane computing is the task of modelling specifically a cell membrane. (wikipedia.org)
- 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)
- 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)
- 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)
- 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)
- 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)
- Membrane computing deals with distributed and parallel computing models, processing multisets of symbol objects in a localized manner. (wikipedia.org)
- The various types of membrane systems are known as P systems after Gheorghe Păun who first conceived the model in 1998. (wikipedia.org)
- Indeed the membrane computing literature contains a very large number of models. (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)

**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)

**system's response**- 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)

**Units**- 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)
- They are based upon the structure of biological cells, abstracting from the way in which chemicals interact and cross cell membranes. (wikipedia.org)

**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)

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

**simulations**- 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)

**weaknesses**- In this chapter, our instructors will discuss the biological causes and possible treatments for abnormal behavior, as well as the strengths and weaknesses of the biological model. (study.com)
- Discuss the strengths and weaknesses of the biological model. (study.com)

**dynamics**- Travelling wave solutions of the space and time fractional models for non-linear blood flow in large vessels and Deoxyribonucleic acid (DNA) molecule dynamics defined in the sense of Jumarie's modified Riemann-Liouville derivative via the first integral method are presented in this study. (aimsciences.org)
- 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)

**researchers**- 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)
- 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)
- 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)
- The results, which matched the researchers' theoretical modelling of the process, offer a method for manipulating force and pressure in order to bind emulsions. (theengineer.co.uk)
- 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)

**conceptual**- It provides conceptual principals for building biological models and for applying the models to make predictions relevant for drug development and translational medicine. (eurekaselect.com)
- 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)
- He has published in the fields of conceptual modeling of complex systems, systems architecture and design. (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)

**experimental**- Capable of describing models that can be related to experimental data. (openwetware.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)

**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)
- 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)

**physics**- He has presided the International Council for NMR in Biological Systems, the Indian Biophysical Society, the Indian Chemical Society and has served as the vice president of the International Union of Pure and Applied Physics. (wikipedia.org)

**distinguish**- Although there are many commonalities, two aspects, in particular, distinguish biological networks from networks found in other fields: Firstly, in biological systems, copy numbers of many species are very low, which can give rise to significant relative fluctuations. (pubmedcentralcanada.ca)
- Some models in this category are black box models and distinguish only between two measured voltage levels: the presence of a spike (also known as "action potential") or a quiescent state. (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)

**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)

**networks**- This paper is concerned with stability analysis of biological networks modeled as discrete and finite dynamical systems. (springer.com)
- Fluctuations in the concentrations of biomolecules can be quite large and this may require special treatment in modeling the biological networks ( 1 - 4 ). (pubmedcentralcanada.ca)
- Knowledge networks are the first step in the process of digitizing molecular biological knowledge. (eurekaselect.com)
- Data mining in knowledge networks is the essence of building new biological models. (eurekaselect.com)

**framework**- Thus, MC is not merely a theory related to a specific model, it is a framework for devising compartmentalized models. (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)

**Sciences**- However, the complexity of biological systems has long prevented their description using general theoretical concepts taken from the physical sciences. (theengineer.co.uk)
- Thank you for your interest in spreading the word on Proceedings of the Royal Society of London B: Biological Sciences. (royalsocietypublishing.org)
- Message Body (Your Name) thought you would like to see the Proceedings of the Royal Society of London B: Biological Sciences web site. (royalsocietypublishing.org)

**molecular**- In certain such cases, as the small copy number limit is reached, differential equation-based models break down since the assumption of continuous molecular concentrations is no longer valid. (pubmedcentralcanada.ca)
- Such models contain key proteins involved in the process and can be used for prioritizing disease targets, for understanding of drug action and prevention of drug-induced toxicities, for analysis of patient predispositions and design of personalized therapies, for design of diagnostic biomarkers and analysis of patient molecular data. (eurekaselect.com)
- It provides examples for analysis of gene expression microarrays to infer biological models, to find biomarkers for drug response and for applications of high-throughput molecular profiling technologies for personalized medicine. (eurekaselect.com)

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

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

**data**- Computers are critical to analysis and modelling of these data. (wikipedia.org)
- Medical Product Safety Evaluation: Biological Models and Statistical Methods presents cutting-edge biological models and statistical methods that are tailored to specific objectives and data types for safety analysis and benefit-risk assessment. (target.com)

**order**- A fractional complex transformation was applied to turn the fractional biological models into an equivalent integer order ordinary differential equation. (aimsciences.org)
- We observed that introducing fractional order to the biological models changes the nature of the solution. (aimsciences.org)
- The computerized text-mining algorithms are used to convert free grammar of human language into a set of formalized relationships between biological concepts in order to use this wealth of information. (eurekaselect.com)
- 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)

**unified theory**- 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)

**parameters**- 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)

**physical**- Systems that require a driving force of some kind are very common in physical and biological settings. (uleth.ca)
- To store, curate and support models related to physical Biobricks . (openwetware.org)

**insights**- Modeling biological systems can provide key insights for scientists an. (bio-medicine.org)

**membranes**- 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)

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

**laboratory**- 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)

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

**computer**- 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)

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

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

**research**- Chickens (Gallus gallus domesticus) and their eggs have been used extensively as research models throughout the history of biology. (wikipedia.org)
- It has both theoretical and practical applications in biological, biomedical and biotechnology research. (wikipedia.org)

**complexity**- 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)

**details**- 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)

**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)