MathematicalMembranesBayesianComplexityComputationalDynamicalBiomedicalPathwaysExperimentalSpatialOrganismSystem's responseQuantitativeMainstreamLaboratorySimulationsBiologyAbstractInterplayBiologistsFundamentalDefineDynamicsDataPaperProvideUnderstandingContextInteractionDevelopmentParametersMethodsOrderComplexStudiesAnalysisConcentrationsTimeResultsPhysicalMainBackgroundDetailsTaskComputer

- 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)
- 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)
- Biological models include the use of mathematical equations , computers , and other electronic equipment. (biology-online.org)
- Modelling biological systems is a significant task of systems biology and mathematical biology. (wikipedia.org)
- Creating a cellular model has been a particularly challenging task of systems biology and mathematical biology. (wikipedia.org)
- 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)
- These projects help students develop mathematical and computational skills needed to pursue quantitatively oriented biological problems. (utk.edu)
- Biomodeling may refer to: Mathematical Biology - the scientific discipline of building advanced mathematical models of biochemical systems thanks to advances in computer power and quantitative methods. (wikipedia.org)

- Ultrafast energy flow in model biological membranes. (uva.nl)
- This is a demonstration of how biological membranes can be understood using electrical models. (jove.com)

- 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)
- Automatic annotation of spatial expression patterns via sparse Bayesian factor models. (duke.edu)

- We design a method for dealing with model complexity, based on the analysis of dynamical models by means of Principal Process Analysis. (springer.com)
- 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)
- The enormous challenge posed by the complexity of biological systems represents a potential intellectual impasse to researchers and threatens to stall future progress in basic biology and healthcare. (ddw-online.com)
- However, at the more macroscopic scales at which these systems can be studied as 'biological' entities, the researcher is confronted with an enormous number of moving parts, a web of interactions of astronomical complexity, significant heterogeneity between the many 'copies' of the system and a degree of stochasticity that challenges any intuitive notion of how living systems function, let alone survive and thrive in hostile environments. (ddw-online.com)

- The models significantly reduce computational cost and, thereby, enhance the speed of simulation. (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)
- 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)
- 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)
- These grammar models are inferred and applied to efficiently solve various sequence analysis problems in computational biology, including multiple sequence alignment, fragment assembly, database redundancy removal, and structural prediction. (unl.edu)
- It is much more straightforward, for example, to capture in lines of computer code the orbit of a satellite or the load on a suspension bridge than it is to build a computational model of even the simplest and most well-studied of biological organisms. (ddw-online.com)

- Understanding the dynamical behaviour of biological systems is challenged by their large number of components and interactions. (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)

- Biomedical modeling - the process of building complex 3D models of body parts through a computer imaging process which allows for perfectly shaped acrylic or titanium inserts to be constructed to replace broken bones or other body parts. (wikipedia.org)

- 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)
- Studies in a wide variety of organisms have produced a general model for the induction of apoptosis in which multiple signaling pathways lead ultimately to activation of the caspase family of proteases. (duke.edu)

- 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)
- Behavior of this wastewater in continuous activated sludge systems is studied by model simulations based upon experimental results. (iwaponline.com)
- Capable of describing models that can be related to experimental data. (openwetware.org)

- 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)

- In this article, we review the properties of this organism as biological model and its biotechnological applications. (diva-portal.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)

- Early developments in biological modelling, driven largely by the convergence in systems biology of complementary approaches from other disciplines, hold the potential to forge a knowledge revolution in biology and to bring modelling into the mainstream of biological research in the way that it is in other fields. (ddw-online.com)

- 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)
- Driven by the rapid development of the technology available to scientists in the laboratory, the quantity, scope and resolution of biological data continues to grow at an accelerating pace. (ddw-online.com)

- 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)

- R esearchers in biology and the life sciences have yet to embrace modelling in the way that their peers in the fields of physics, chemistry and engineering have done. (ddw-online.com)

- In this work abstract grammars are used to model the primary and secondary structures present in biological data. (unl.edu)
- The use of this approach to develop algorithms for various sequence analysis tasks demonstrates the viability and versatility of using abstract grammars to model biological data. (unl.edu)

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

- Modelling can provide the kind of intellectual frameworks needed to transform data into knowledge, yet very few modelling methodologies currently exist that are applicable to the large, complex systems of interest to biologists. (ddw-online.com)
- This will require the development of modelling platforms that allow biological systems to be described using idioms familiar to biologists, that encourage experimentation and that leverage the connectivity of the internet for scientific collaboration and communication. (ddw-online.com)
- There are some very good reasons for this, not the least of which is that the systems of interest to biologists tend to be far more refractory to modelling than the systems that are studied in these other fields. (ddw-online.com)

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

- Model interpretations of the respirometric experiments are used to define the fate of slowly biodegradable COD. (iwaponline.com)

- 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)
- 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)

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

- This paper reviews the framework of the endogenous decay model and summarizes the necessary COD fractionation and the kinetic information to be incorporated in this model as applied to a meat processing effluent. (iwaponline.com)

- 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)

- The input is a paragraph describing a biological process, and the goal is to answer questions that require an understanding of the relations between entities and events in the process. (semanticscholar.org)

- This dissertation presents a continuum treatment of growth in biological tissue developed within the context of modern mixture theory. (umich.edu)
- Driving forces in a biological context are usually referred to as rhythms, pulses or clocks. (uleth.ca)
- The resulting context-free grammars are used to estimate structural pieces within biological sequences, which can in-turn be used as supplemental information to help guide various sequence analysis algorithms. (unl.edu)

- 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)
- 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 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 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)

- 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)

- A collection of models of biological parts that can be freely reused and composed with each other to produce more complex models. (openwetware.org)

- 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)
- 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)

- This concept is applied to solve several problems involving biological sequence analysis including multiple sequence alignment and phylogenetic clustering. (unl.edu)

- Allen L.J.: Some discrete-time SI, SIR, and SIS epidemic models. (springer.com)

- The results are used to construct a grammar based sequence distance metric which can be used to compare biological sequences by comparing their inferred grammars. (unl.edu)

- 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)

- The simplified models are easier to analyse, while retaining the main features of the original ones and their biological significance. (springer.com)

- Necessary Excel techniques and biological background will be provided. (utk.edu)

- Membrane computing is the task of modelling specifically a cell membrane. (wikipedia.org)

- 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)