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.
Download or read book In Silico Systems Biology written by Maria Victoria Schneider and published by Humana Press. This book was released on 2013-05-29 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.
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.
Download or read book An Algorithm and VLSI Architecture for a Stochastic Particle based Biological Simulator written by Laurier Boulianne and published by . This book was released on 2010 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
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.
Download or read book Modeling and Simulation of Biological Processes written by and published by . This book was released on 2011 with total page 99 pages. Available in PDF, EPUB and Kindle. Book excerpt:
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.
Download or read book Simulation of Biological Processes by Analog and Digital Computers written by Liang-tseng Fan and published by . This book was released on 1970 with total page 120 pages. Available in PDF, EPUB and Kindle. Book excerpt:
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
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 "
Download or read book A Discrete Event Based Stochastic Simulation Approach for Studying the Dynamics of Biological Networks written by Samik Ghosh and published by . This book was released on 2007 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: With increasing availability of data resources on the molecular parts of a living cell, biologists are focussing on holistic understanding of cellular mechanisms and the emergent dynamics arising out of their complex interactions. Comprehending the fine-grained signal specificity, gene regulation and feedback mechanisms of molecular interactions at a network level forms a central theme of systems biology. With the speed and sophistication of computational methods, in silico modeling and simulation techniques have become a powerful tool for biologists challenged with understanding the system complexity of biological networks. Numerical simulation of classical chemical kinetics (CCK), agent-based simulations of biological processes, and linear optimization models of metabolic networks, have been applied to the study of cellular behaviors with varying degrees of success. The spatio-temporal scales of cellular processes, coupled with the knowledge gap and complexity of biological networks limit the application of existing computational techniques. In this dissertation, we present a network-centric modeling and simulation approach to systematically study the stochastic dynamics of cellular processes at a molecular level. The central theme of our approach revolves around abstracting a complex biological process as a collection of discrete, interacting molecular entities driven in time by a set of discrete biological events (bioEvents). We develop the discrete-event based simulation engine, called iSimBioSys, together with an integrated database of biological pathways, which captures the temporal dynamics of the molecules through stochastic interactions of different bioEvents. With an illustrative case study of signal transduction networks in bacterial cells, we highlight the efficiency of a discrete event based approach in capturing high-level system dynamics of a biological process, particularly in reproducing the switching effect of the PhoPQ pathway in Salmonella cells as reported in experimental work. Next, we build a detailed stochastic model for the fundamental process of gene expression in prokaryotic cells and study the biological events of transcription and translation using the proposed simulation framework. Our results identify the role of transcriptional and translation machinery in controlling the burstiness of protein generation. We extend our simulator to incorporate a hybrid algorithm which combines stochastic models of signalling and regulatory events with a flow-based model for metabolic networks. In order to validate the efficacy of the hybrid simulation approach, we develop an integrated database of signaling and metabolic networks in the bacterial cell Escherechia Coli. The hybrid simulation recreates experimentally observed regulation of metabolic flux distributions in the network while providing new insights into the mechanism of regulation.
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 569 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.
Download or read book Theoretical and in Silico Modeling of Biological Systems written by Bogdan Barz and published by . This book was released on 2009 with total page 96 pages. Available in PDF, EPUB and Kindle. Book excerpt: This thesis describes four distinct studies (involving a variety of concepts and methods from the physical sciences) of complex biological systems and processes that cover a wide range of time and length scales (extending from the molecular to the multi-cellular level), namely: 1) identification of near-native structures from a large set of in silico predicted structures for a given target protein by probing the stability of the structures against simulated heating using Molecular Dynamics (MD) simulations; 2) all atom MD simulation study of protein-cell membrane interactions designed to elucidate the relation between the conformational structure of the GP41 fusion peptide of HIV-1 virus and the density of the lipid membrane; 3) calculation of the potential of mean force for water transport through single wall carbon nanotubes from nonequilibrium MD simulations; and 4) development and application of a novel computational method, referred to as the cellular particle dynamics (CPD) method, for the simulation of the dynamics of multicellular systems.
Download or read book The Simulation of Biological Processes written by Donald Clem Young and published by . This book was released on 1962 with total page 488 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Tutorial for Modeling and Simulation of Biological Processes written by Michel Kana and published by . This book was released on 2010 with total page 145 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Computational Systems Biology written by Andres Kriete and published by Academic Press. This book was released on 2013-11-26 with total page 549 pages. Available in PDF, EPUB and Kindle. Book excerpt: This comprehensively revised second edition of Computational Systems Biology discusses the experimental and theoretical foundations of the function of biological systems at the molecular, cellular or organismal level over temporal and spatial scales, as systems biology advances to provide clinical solutions to complex medical problems. In particular the work focuses on the engineering of biological systems and network modeling. Logical information flow aids understanding of basic building blocks of life through disease phenotypes Evolved principles gives insight into underlying organizational principles of biological organizations, and systems processes, governing functions such as adaptation or response patterns Coverage of technical tools and systems helps researchers to understand and resolve specific systems biology problems using advanced computation Multi-scale modeling on disparate scales aids researchers understanding of dependencies and constraints of spatio-temporal relationships fundamental to biological organization and function.
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 651 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
