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In Silico Simulation Of Biological Processes
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Book Synopsis 'In Silico' Simulation of Biological Processes by : Gregory R. Bock
Download or read book 'In Silico' Simulation of Biological Processes written by Gregory R. Bock and published by John Wiley & Sons. This book was released on 2003-07-07 with total page 270 pages. Available in PDF, EPUB and Kindle. Book excerpt: Over recent decades vast amounts of biological data have been accumulated. However, it is becoming increasingly difficult to apply traditional theoretical methods to the formulation of coherent pictures of cell and organ function because it is no longer possible for a human theorist to integrate all of the available information. Instead, computer technologies must now be used to perform this integration. This book brings together contributions from many different fields to summarize the current status of computer-assisted modelling of biological processes. The initial chapters deal with fundamental developments in hardware, software and mathematics that underlie current approaches to biological modelling. Next, different approaches to collating data on gene structure and function are presented. These databases form a vital resource for any investigator trying to construct an integrated picture of particular biological systems. Cell signalling systems form a particularly complicated aspect of all cellular function and are important both in the understanding of basic cellular processes and in selecting targets for drugs. Recent approaches to integrating data on cell signalling into computer models are covered. Further chapters build on these approaches to show how computerized models of intact cells can be developed. Finally, approaches to the computer modelling of whole organs such as the heart are presented. The role of computer modelling in drug design is the subject of the final chapter and is also touched on throughout the discussions.
Book Synopsis In Silico Systems Biology by : Maria Victoria Schneider
Download or read book In Silico Systems Biology written by Maria Victoria Schneider and published by Humana. This book was released on 2016-08-23 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Systems biology can now be considered an established and fundamental field in life sciences. It has moved from the identification of molecular 'parts lists' for living organisms towards synthesising information from different 'omics'-based approaches to generate and test new hypotheses about how biological systems work. In In Silico Systems Biology: Methods and Protocols, expert researchers in the field detail a practical set of chapters based often on actual materials used and develop for face-to-face training with examples and case studies. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, step-by-step workflows, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, In Silico Systems Biology: Methods and Protocols seeks to aid scientists in the further study of network biology and mathematical models of biological systems.
Book Synopsis In Silico Chemistry and Biology by : Girish Kumar Gupta
Download or read book In Silico Chemistry and Biology written by Girish Kumar Gupta and published by Walter de Gruyter GmbH & Co KG. This book was released on 2022-05-09 with total page 274 pages. Available in PDF, EPUB and Kindle. Book excerpt: In Silico Chemistry and Biology: Current and Future Prospects provides a compact overview on recent advances in this highly dynamic branch of chemistry. Various methods of protein modelling and computer-assisted drug design are presented, including fragment- and ligand-based approaches. Many successful practical applications of these techniques are demonstrated. The authors also look to the future and describe the main challenges of the field.
Book Synopsis In Silico Drug Discovery and Design by : Claudio N. Cavasotto
Download or read book In Silico Drug Discovery and Design written by Claudio N. Cavasotto and published by CRC Press. This book was released on 2015-08-06 with total page 558 pages. Available in PDF, EPUB and Kindle. Book excerpt: In Silico Drug Discovery and Design: Theory, Methods, Challenges, and Applications provides a comprehensive, unified, and in-depth overview of the current methodological strategies in computer-aided drug discovery and design. Its main aims are to introduce the theoretical framework and algorithms, discuss the range of validity, strengths and limita
Book Synopsis Computational Systems Biology by : Andres Kriete
Download or read book Computational Systems Biology written by Andres Kriete and published by Elsevier. This book was released on 2005-11-10 with total page 424 pages. Available in PDF, EPUB and Kindle. Book excerpt: Systems Biology is concerned with the quantitative study of complex biosystems at the molecular, cellular, tissue, and systems scales. Its focus is on the function of the system as a whole, rather than on individual parts. This exciting new arena applies mathematical modeling and engineering methods to the study of biological systems. This book is the first of its kind to focus on the newly emerging field of systems biology with an emphasis on computational approaches. The work covers new concepts, methods for information storage, mining and knowledge extraction, reverse engineering of gene and metabolic networks, as well as modelling and simulation of multi-cellular systems. Central themes include strategies for predicting biological properties and methods for elucidating structure-function relationships.
Download or read book In Silico written by Jason Sharpe and published by Morgan Kaufmann. This book was released on 2008-07-01 with total page 656 pages. Available in PDF, EPUB and Kindle. Book excerpt: In Silico introduces Maya programming into one of the most fascinating application areas of 3D graphics: biological visualization. In five building-block tutorials, this book prepares animators to work with visualization problems in cell biology. The book assumes no deep knowledge of cell biology or 3D graphics programming. An accompanying DVD-ROM includes code derived from the tutorials, the working Maya computer files, and sample animated movies. *Teaches artists and scientists to create realistic digital images of humans and nature with the popular CG program, Maya *This self-contained study guide includes background, foundations, and practice *Step-by-step example programs and end-result demonstrations help readers develop their own portfolios *Gorgeous four-color screen shots throughout
Download or read book Systems Biology written by Aleš Prokop and published by Springer Science & Business Media. This book was released on 2013-08-28 with total page 553 pages. Available in PDF, EPUB and Kindle. Book excerpt: Growth in the pharmaceutical market has slowed down – almost to a standstill. One reason is that governments and other payers are cutting costs in a faltering world economy. But a more fundamental problem is the failure of major companies to discover, develop and market new drugs. Major drugs losing patent protection or being withdrawn from the market are simply not being replaced by new therapies – the pharmaceutical market model is no longer functioning effectively and most pharmaceutical companies are failing to produce the innovation needed for success. This multi-authored new book looks at a vital strategy which can bring innovation to a market in need of new ideas and new products: Systems Biology (SB). Modeling is a significant task of systems biology. SB aims to develop and use efficient algorithms, data structures, visualization and communication tools to orchestrate the integration of large quantities of biological data with the goal of computer modeling. It involves the use of computer simulations of biological systems, such as the networks of metabolites comprise signal transduction pathways and gene regulatory networks to both analyze and visualize the complex connections of these cellular processes. SB involves a series of operational protocols used for performing research, namely a cycle composed of theoretical, analytic or computational modeling to propose specific testable hypotheses about a biological system, experimental validation, and then using the newly acquired quantitative description of cells or cell processes to refine the computational model or theory.
Book Synopsis Translational Systems Biology: Concepts and Practice for the Future of Biomedical Research by : Yoram Vodovotz
Download or read book Translational Systems Biology: Concepts and Practice for the Future of Biomedical Research written by Yoram Vodovotz and published by Academic Press. This book was released on 2017-11-13 with total page 178 pages. Available in PDF, EPUB and Kindle. Book excerpt: Are we satisfied with the rate of drug development? Are we happy with the drugs that come to market? Are we getting our money s worth in spending for basic biomedical research? In Translational Systems Biology, Drs. Yoram Vodovotz and Gary An address these questions by providing a foundational description the barriers facing biomedical research today and the immediate future, and how these barriers could be overcome through the adoption of a robust and scalable approach that will form the underpinning of biomedical research for the future. By using a combination of essays providing the intellectual basis of the Translational Dilemma and reports of examples in the study of inflammation, the content of Translational Systems Biology will remain relevant as technology and knowledge advances bring broad translational applicability to other diseases. Translational systems biology is an integrated, multi-scale, evidence-based approach that combines laboratory, clinical and computational methods with an explicit goal of developing effective means of control of biological processes for improving human health and rapid clinical application. This comprehensive approach to date has been utilized for in silico studies of sepsis, trauma, hemorrhage, and traumatic brain injury, acute liver failure, wound healing, and inflammation. Provides an explicit, reasoned, and systematic approach to dealing with the challenges of translational science across disciplines Establishes the case for including computational modeling at all stages of biomedical research and healthcare delivery, from early pre-clinical studies to long-term care, by clearly delineating efficiency and costs saving important to business investment Guides readers on how to communicate across domains and disciplines, particularly between biologists and computational researchers, to effectively develop multi- and trans-disciplinary research teams "
Book Synopsis Kinetic Modelling in Systems Biology by : Oleg Demin
Download or read book Kinetic Modelling in Systems Biology written by Oleg Demin and published by CRC Press. This book was released on 2008-10-24 with total page 360 pages. Available in PDF, EPUB and Kindle. Book excerpt: With more and more interest in how components of biological systems interact, it is important to understand the various aspects of systems biology. Kinetic Modelling in Systems Biology focuses on one of the main pillars in the future development of systems biology. It explores both the methods and applications of kinetic modeling in this emerging f
Book Synopsis Stochastic Models for In-silico Event-based Biological Network Simulation by : Preetam Ghosh
Download or read book Stochastic Models for In-silico Event-based Biological Network Simulation written by Preetam Ghosh and published by ProQuest. This book was released on 2007 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: The multi-scale biological system model is a new research direction to capture the dynamic measurements of complex biological systems. The current statistical thermodynamic models can not scale to this challenge due to the explosion of state-spaces of the system, where a biological organ may have billions of cells, each with millions of molecule types and each type may have a few million molecules. We seek to propose a phenomenological theory that will require a smaller number of state variables to address this multi-scaling problem. Discrete Markov statistical process is used to understand the system dynamics in the networking community for a long time. In this dissertation, we focus more specifically on a composite system by combining the state variables in the time-space domain as events, and determine the immediate dynamics between the events by using statistical analysis or simulation methods. In our approach the space-time behavior of the cell dynamics is captured by discrete state variables, where an event is a combined process of a large number of state transitions between a set of state variables. The execution time of these state transitions to manifest the event outcome is a random variable called event-holding time. The underlying assumption is that it will be possible to segregate the complete system state-space into a disjoint set of independent events and events can be executed simultaneously without any interaction once the execution conditions are satisfied (removal of resource bottleneck, collision). In this dissertation, we present the event-time models for some biological functions that will be incorporated in the discrete-event based stochastic simulator. In particular, we present analytical models for the molecular transport event in cells considering charged/non-charged macromolecules. We show, that molecular transport event completion time can be approximated by an exponential distribution. Next we present stochastic models for biochemical reactions in the cell (that can be extended to reactions occurring in the cell cytoplasm, membrane or nucleus). We show that the reaction completion time follows an exponential distribution when one of the reactant molecules enter the cell one at a time, whereas, it follows a gamma distribution when a batch of the reactant molecules enter the cell. We also present stochastic models for the protein-DNA binding and protein-ligand docking events and show that both these events have an exponentially distributed event completion time. We also validate each of the models presented in the dissertation with experimental findings reported in the literature. Finally, we present a markov chain based stochastic biochemical system simulator which can give us the dynamics of more complex events and can be used to improve the scalability of the discrete-event based stochastic simulator. We propose to successfully demonstrate this technique by modeling the complete dynamics of one Salmonella cell.
Book Synopsis Transactions on Computational Systems Biology VIII by : Corrado Priami
Download or read book Transactions on Computational Systems Biology VIII written by Corrado Priami and published by Springer. This book was released on 2007-10-28 with total page 108 pages. Available in PDF, EPUB and Kindle. Book excerpt: The LNCS journal Transactions on Computational Systems Biology is devoted to inter- and multidisciplinary research in the fields of computer science and life sciences. It supports a paradigmatic shift in the techniques from computer and information science to cope with the new challenges arising from the systems oriented point of view of biological phenomena. The six papers selected for this special issue cover a broad range of topics.
Book Synopsis Systems Biology in Psychiatric Research by : Felix Tretter
Download or read book Systems Biology in Psychiatric Research written by Felix Tretter and published by Wiley-Blackwell. This book was released on 2010-06-08 with total page 378 pages. Available in PDF, EPUB and Kindle. Book excerpt: This first book to provide a comprehensive overview of the recent progress made in this break-through approach includes expert contributions from a variety of disciplines. Particular focus is placed on high-throughput methods and the analysis of data thus obtained, as well as their use in silico experiments so as to gain an insight into the complex biological processes in neuronal systems. A must-have for everyone working in psychiatric research.
Book Synopsis Numerical Methods and Advanced Simulation in Biomechanics and Biological Processes by : Miguel Cerrolaza
Download or read book Numerical Methods and Advanced Simulation in Biomechanics and Biological Processes written by Miguel Cerrolaza and published by Academic Press. This book was released on 2017-10-17 with total page 454 pages. Available in PDF, EPUB and Kindle. Book excerpt: Numerical Methods and Advanced Simulation in Biomechanics and Biological Processes covers new and exciting modeling methods to help bioengineers tackle problems for which the Finite Element Method is not appropriate. The book covers a wide range of important subjects in the field of numerical methods applied to biomechanics, including bone biomechanics, tissue and cell mechanics, 3D printing, computer assisted surgery and fluid dynamics. Modeling strategies, technology and approaches are continuously evolving as the knowledge of biological processes increases. Both theory and applications are covered, making this an ideal book for researchers, students and R&D professionals. Provides non-conventional analysis methods for modeling Covers the Discrete Element Method (DEM), Particle Methods (PM), MessLess and MeshFree Methods (MLMF), Agent-Based Methods (ABM), Lattice-Boltzmann Methods (LBM) and Boundary Integral Methods (BIM) Includes contributions from several world renowned experts in their fields Compares pros and cons of each method to help you decide which method is most applicable to solving specific problems
Book Synopsis Molecular Kinetics in Condensed Phases by : Ron Elber
Download or read book Molecular Kinetics in Condensed Phases written by Ron Elber and published by John Wiley & Sons. This book was released on 2019-12-06 with total page 268 pages. Available in PDF, EPUB and Kindle. Book excerpt: A guide to the theoretical and computational toolkits for the modern study of molecular kinetics in condensed phases Molecular Kinetics in Condensed Phases: Theory, Simulation and Analysis puts the focus on the theory, algorithms, simulations methods and analysis of molecular kinetics in condensed phases. The authors – noted experts on the topic – offer a detailed and thorough description of modern theories and simulation methods to model molecular events. They highlight the rigorous stochastic modelling of molecular processes and the use of mathematical models to reproduce experimental observations, such as rate coefficients, mean first passage times and transition path times. The book’s exploration of simulations examines atomically detailed modelling of molecules in action and the connections of these simulations to theory and experiment. The authors also explore the applications that range from simple intuitive examples of one- and two-dimensional systems to complex solvated macromolecules. This important book: Offers an introduction to the topic that combines theory, simulation and analysis Presents a guide written by authors that are well-known and highly regarded leaders in their fields Contains detailed examples and explanation of how to conduct computer simulations of kinetics. A detailed study of a two-dimensional system and of a solvated peptide are discussed. Discusses modern developments in the field and explains their connection to the more traditional concepts in chemical dynamics Written for students and academic researchers in the fields of chemical kinetics, chemistry, computational statistical mechanics, biophysics and computational biology, Molecular Kinetics in Condensed Phases is the authoritative guide to the theoretical and computational toolkits for the study of molecular kinetics in condensed phases.
Book Synopsis Catalyzing Inquiry at the Interface of Computing and Biology by : National Research Council
Download or read book Catalyzing Inquiry at the Interface of Computing and Biology written by National Research Council and published by National Academies Press. This book was released on 2006-01-01 with total page 469 pages. Available in PDF, EPUB and Kindle. Book excerpt: Advances in computer science and technology and in biology over the last several years have opened up the possibility for computing to help answer fundamental questions in biology and for biology to help with new approaches to computing. Making the most of the research opportunities at the interface of computing and biology requires the active participation of people from both fields. While past attempts have been made in this direction, circumstances today appear to be much more favorable for progress. To help take advantage of these opportunities, this study was requested of the NRC by the National Science Foundation, the Department of Defense, the National Institutes of Health, and the Department of Energy. The report provides the basis for establishing cross-disciplinary collaboration between biology and computing including an analysis of potential impediments and strategies for overcoming them. The report also presents a wealth of examples that should encourage students in the biological sciences to look for ways to enable them to be more effective users of computing in their studies.
Book Synopsis Stochastic Processes, Multiscale Modeling, and Numerical Methods for Computational Cellular Biology by : David Holcman
Download or read book Stochastic Processes, Multiscale Modeling, and Numerical Methods for Computational Cellular Biology written by David Holcman and published by Springer. This book was released on 2017-10-04 with total page 377 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book focuses on the modeling and mathematical analysis of stochastic dynamical systems along with their simulations. The collected chapters will review fundamental and current topics and approaches to dynamical systems in cellular biology. This text aims to develop improved mathematical and computational methods with which to study biological processes. At the scale of a single cell, stochasticity becomes important due to low copy numbers of biological molecules, such as mRNA and proteins that take part in biochemical reactions driving cellular processes. When trying to describe such biological processes, the traditional deterministic models are often inadequate, precisely because of these low copy numbers. This book presents stochastic models, which are necessary to account for small particle numbers and extrinsic noise sources. The complexity of these models depend upon whether the biochemical reactions are diffusion-limited or reaction-limited. In the former case, one needs to adopt the framework of stochastic reaction-diffusion models, while in the latter, one can describe the processes by adopting the framework of Markov jump processes and stochastic differential equations. Stochastic Processes, Multiscale Modeling, and Numerical Methods for Computational Cellular Biology will appeal to graduate students and researchers in the fields of applied mathematics, biophysics, and cellular biology.
Book Synopsis Protein Folding in Silico by : Irena Roterman-Konieczna
Download or read book Protein Folding in Silico written by Irena Roterman-Konieczna and published by Elsevier. This book was released on 2012-10-04 with total page 240 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein folding is a process by which a protein structure assumes its functional shape of conformation, and has been the subject of research since the publication of the first software tool for protein structure prediction. Protein folding in silico approaches this issue by introducing an ab initio model that attempts to simulate as far as possible the folding process as it takes place in vivo, and attempts to construct a mechanistic model on the basis of the predictions made. The opening chapters discuss the early stage intermediate and late stage intermediate models, followed by a discussion of structural information that affects the interpretation of the folding process. The second half of the book covers a variety of topics including ligand binding site recognition, the "fuzzy oil drop" model and its use in simulation of the polypeptide chain, and misfolded proteins. The book ends with an overview of a number of other ab initio methods for protein structure predictions and some concluding remarks. Discusses a range of ab initio models for protein structure prediction Introduces a unique model based on experimental observations Describes various methods for the quantitative assessment of the presented models from the viewpoint of information theory
