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Author : Philippe Tracqui
Publisher :
ISBN 13 :
Total Pages : 293 pages
Book Rating : 4.:/5 (592 download)
Download or read book Modelling and Simulation of Biological Processes in the Context of Genomics written by Philippe Tracqui and published by . This book was released on 2002 with total page 293 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : François Kepes
Publisher :
ISBN 13 :
Total Pages : 293 pages
Book Rating : 4.:/5 (493 download)
Download or read book Modelling and Simulation of Biological Processes in the Context of Genomics written by François Kepes and published by . This book was released on 2002 with total page 293 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Patrick Amar (Informaticien).)
Publisher :
ISBN 13 : 9782847040371
Total Pages : 209 pages
Book Rating : 4.0/5 (43 download)
Download or read book Proceedings of the Evry Spring School on Modelling and Simulation of Biological Processes in the Context of Genomics written by Patrick Amar (Informaticien).) and published by . This book was released on 2004 with total page 209 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author :
Publisher :
ISBN 13 : 9782847040364
Total Pages : 269 pages
Book Rating : 4.0/5 (43 download)
Download or read book Proceedings of the Dieppe Spring School on Modelling and Simulation of Biological Processes in the Context of Genomics written by and published by . This book was released on 2003 with total page 269 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Nikolay Kolchanov
Publisher : Springer Science & Business Media
ISBN 13 : 0387294554
Total Pages : 545 pages
Book Rating : 4.3/5 (872 download)
Download or read book Bioinformatics of Genome Regulation and Structure II written by Nikolay Kolchanov and published by Springer Science & Business Media. This book was released on 2006-06-15 with total page 545 pages. Available in PDF, EPUB and Kindle. Book excerpt: The last 15 years in development of biology were marked with accumulation of unprecedentedly huge arrays of experimental data. The information was amassed with exclusively high rates due to the advent of highly efficient experimental technologies that provided for high throughput genomic sequencing; of functional genomics technologies allowing investigation of expression dynamics of large groups of genes using expression DNA chips; of proteomics methods giving the possibility to analyze protein compositions of cells, tissues, and organs, assess the dynamics of the cell proteome, and reconstruct the networks of protein-protein interactions; and of metabolomics, in particular, high resolution mass spectrometry study of cell metabolites, and distribution of metabolic fluxes in the cells with a concurrent investigation of the dynamics of thousands metabolites in an individual cell. Analysis, comprehension, and use of the tremendous volumes of experimental data reflecting the intricate processes underlying the functioning of molecular genetic systems are unfeasible in principle without the systems approach and involvement of the state-of-the-art information and computer technologies and efficient mathematical methods for data analysis and simulation of biological systems and processes. The need in solving these problems initiated the birth of a new science— postgenomic bioinformatics or systems biology in silico.
Author : Parimal Pal Chaudhuri
Publisher : Springer
ISBN 13 : 9811316392
Total Pages : 335 pages
Book Rating : 4.8/5 (113 download)
Download or read book A New Kind of Computational Biology written by Parimal Pal Chaudhuri and published by Springer. This book was released on 2018-09-26 with total page 335 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book reflects more than three decades of research on Cellular Automata (CA), and nearly a decade of work on the application of CA to model biological strings, which forms the foundation of 'A New Kind of Computational Biology' pioneered by the start-up, CARLBio. After a brief introduction on Cellular Automata (CA) theory and functional biology, it reports on the modeling of basic biological strings with CA, starting with the basic nucleotides leading to codon and anti-codon CA models. It derives a more involved CA model of DNA, RNA, the entire translation process for amino acid formation and the evolution of protein to its unique structure and function. In subsequent chapters the interaction of Proteins with other bio-molecules is also modeled. The only prior knowledge assumed necessary is an undergraduate knowledge of computer programming and biology. The book adopts a hands-on, “do-it-yourself” approach to enable readers to apply the method provided to derive the CA rules and comprehend how these are related to the physical ‘rules’ observed in biology. In a single framework, the authors have presented two branches of science – Computation and Biology. Instead of rigorous molecular dynamics modeling, which the authors describe as a Bottoms-Up model, or relying on the Top-Down new age Artificial Intelligence (AI) and Machine Language (ML) that depends on extensive availability of quality data, this book takes the best from both the Top-Down and Bottoms-up approaches and establishes how the behavior of complex molecules is represented in CA. The CA rules are derived from the basic knowledge of molecular interaction and construction observed in biological world but mapped to a few subset of known results to derive and predict results. This book is useful for students, researchers and industry practitioners who want to explore modeling and simulation of the physical world complex systems from a different perspective. It raises the inevitable the question – ‘Are life and the universe nothing but a collection of continuous systems processing information’.
Author : Raquell M. Holmes
Publisher : John Wiley & Sons
ISBN 13 : 9780470139349
Total Pages : 224 pages
Book Rating : 4.1/5 (393 download)
Download or read book A Cell Biologist's Guide to Modeling and Bioinformatics written by Raquell M. Holmes and published by John Wiley & Sons. This book was released on 2008-02-13 with total page 224 pages. Available in PDF, EPUB and Kindle. Book excerpt: A step-by-step guide to using computational tools to solve problems in cell biology Combining expert discussion with examples that can be reproduced by the reader, A Cell Biologist's Guide to Modeling and Bioinformatics introduces an array of informatics tools that are available for analyzing biological data and modeling cellular processes. You learn to fully leverage public databases and create your own computational models. All that you need is a working knowledge of algebra and cellular biology; the author provides all the other tools you need to understand the necessary statistical and mathematical methods. Coverage is divided into two main categories: Molecular sequence database chapters are dedicated to gaining an understanding of tools and strategies—including queries, alignment methods, and statistical significance measures—needed to improve searches for sequence similarity, protein families, and putative functional domains. Discussions of sequence alignments and biological database searching focus on publicly available resources used for background research and the characterization of novel gene products. Modeling chapters take you through all the steps involved in creating a computational model for such basic research areas as cell cycle, calcium dynamics, and glycolysis. Each chapter introduces a new simulation tooland is based on published research. The combination creates a rich context for ongoing skill and knowledge development in modeling biological research systems. Students and professional cell biologists can develop the basic skills needed to learn computational cell biology. This unique text, with its step-by-step instruction, enables you to test and develop your new bioinformatics and modeling skills. References are provided to help you take advantage of more advanced techniques, technologies, and training.
Author : National Research Council
Publisher : National Academies Press
ISBN 13 : 0309180716
Total Pages : 102 pages
Book Rating : 4.3/5 (91 download)
Download or read book Review of the Department of Energy's Genomics: GTL Program written by National Research Council and published by National Academies Press. This book was released on 2006-04-19 with total page 102 pages. Available in PDF, EPUB and Kindle. Book excerpt: The U.S. Department of Energy (DOE) promotes scientific and technological innovation to advance the national, economic, and energy security of the United States. Recognizing the potential of microorganisms to offer new energy alternatives and remediate environmental contamination, DOE initiated the Genomes to Life program, now called Genomics: GTL, in 2000. The program aims to develop a predictive understanding of microbial systems that can be used to engineer systems for bioenergy production and environmental remediation, and to understand carbon cycling and sequestration. This report provides an evaluation of the program and its infrastructure plan. Overall, the report finds that GTL's research has resulted in and promises to deliver many more scientific advancements that contribute to the achievement of DOE's goals. However, the DOE's current plan for building four independent facilities for protein production, molecular imaging, proteome analysis, and systems biology sequentially may not be the most cost-effective, efficient, and scientifically optimal way to provide this infrastructure. As an alternative, the report suggests constructing up to four institute-like facilities, each of which integrates the capabilities of all four of the originally planned facility types and focuses on one or two of DOE's mission goals. The alternative infrastructure plan could have an especially high ratio of scientific benefit to cost because the need for technology will be directly tied to the biology goals of the program.
Author : Avner Friedman
Publisher : Springer
ISBN 13 : 3319083147
Total Pages : 152 pages
Book Rating : 4.3/5 (19 download)
Download or read book Mathematical Modeling of Biological Processes written by Avner Friedman and published by Springer. This book was released on 2014-09-19 with total page 152 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book on mathematical modeling of biological processes includes a wide selection of biological topics that demonstrate the power of mathematics and computational codes in setting up biological processes with a rigorous and predictive framework. Topics include: enzyme dynamics, spread of disease, harvesting bacteria, competition among live species, neuronal oscillations, transport of neurofilaments in axon, cancer and cancer therapy, and granulomas. Complete with a description of the biological background and biological question that requires the use of mathematics, this book is developed for graduate students and advanced undergraduate students with only basic knowledge of ordinary differential equations and partial differential equations; background in biology is not required. Students will gain knowledge on how to program with MATLAB without previous programming experience and how to use codes in order to test biological hypothesis.
Author : Edenilson Brandl
Publisher : Edenilson Brandl
ISBN 13 :
Total Pages : 267 pages
Book Rating : 4./5 ( download)
Download or read book Genomic Biointelligence written by Edenilson Brandl and published by Edenilson Brandl. This book was released on with total page 267 pages. Available in PDF, EPUB and Kindle. Book excerpt: It is with great enthusiasm that I present to you the book "Genomic Biointelligence". This book is a fascinating journey through the ever-evolving world of genomics and artificial intelligence, exploring their intersection and the role of the genomic biointelligence within this context. Genomics has revolutionized our understanding of the genetic code and brought with it a vast volume of data that challenges our ability to analyze and interpret. On the other hand, artificial intelligence has emerged as a powerful tool to deal with this complexity and extract valuable information from genomic data. Within the pages of this book, you will be guided on a comprehensive journey through key topics related to the application of artificial intelligence in genomics. From the history and evolution of artificial intelligence in genomics research to the latest applications in diagnostics, drug discovery, precision medicine and disease research, each chapter presents an important aspect of this rapidly expanding field. You will learn about genetic algorithms and their application in genomics, mathematical modeling of genomic regulatory networks, the use of neural networks in predicting protein structures, and much more. We will also discuss the challenges and limitations of using artificial intelligence in genomics, as well as ethical issues and the importance of data privacy. In addition, we will highlight the fundamental role of the genomic biointelligencist, a multidisciplinary professional who combines knowledge in genomics, artificial intelligence, bioinformatics and other related areas. The genomic biointelligence plays a crucial role in applying artificial intelligence to advance genomic research, discover new treatments, develop personalized therapies, and drive precision medicine. As we progress through this book, you will be invited to explore recent advances and the exciting possibilities that arise from the combination of genomics and artificial intelligence. Through practical examples, case studies and in-depth discussions, we hope to provide you with a solid understanding of the concepts and applications of this rapidly expanding field. Finally, I would like to express my gratitude to all the experts and researchers who contributed their unique knowledge and insights to this book. Their efforts and dedication are instrumental in advancing the field of genomics and artificial intelligence. I hope you will find this book a valuable source of information and inspiration. May it arouse your curiosity, stimulate discussions and motivate you to further explore the frontiers of knowledge in the field of genomics and artificial intelligence.
Author : Daniel Machado
Publisher : Frontiers Media SA
ISBN 13 : 2889197549
Total Pages : 117 pages
Book Rating : 4.8/5 (891 download)
Download or read book Current Challenges in Modeling Cellular Metabolism written by Daniel Machado and published by Frontiers Media SA. This book was released on 2016-01-21 with total page 117 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mathematical and computational models play an essential role in understanding the cellular metabolism. They are used as platforms to integrate current knowledge on a biological system and to systematically test and predict the effect of manipulations to such systems. The recent advances in genome sequencing techniques have facilitated the reconstruction of genome-scale metabolic networks for a wide variety of organisms from microbes to human cells. These models have been successfully used in multiple biotechnological applications. Despite these advancements, modeling cellular metabolism still presents many challenges. The aim of this Research Topic is not only to expose and consolidate the state-of-the-art in metabolic modeling approaches, but also to push this frontier beyond the current edge through the introduction of innovative solutions. The articles presented in this e-book address some of the main challenges in the field, including the integration of different modeling formalisms, the integration of heterogeneous data sources into metabolic models, explicit representation of other biological processes during phenotype simulation, and standardization efforts in the representation of metabolic models and simulation results.
Author : Russell Schwartz
Publisher : MIT Press
ISBN 13 : 0262303396
Total Pages : 403 pages
Book Rating : 4.2/5 (623 download)
Download or read book Biological Modeling and Simulation written by Russell Schwartz and published by MIT Press. This book was released on 2008-07-25 with total page 403 pages. Available in PDF, EPUB and Kindle. Book excerpt: A practice-oriented survey of techniques for computational modeling and simulation suitable for a broad range of biological problems. There are many excellent computational biology resources now available for learning about methods that have been developed to address specific biological systems, but comparatively little attention has been paid to training aspiring computational biologists to handle new and unanticipated problems. This text is intended to fill that gap by teaching students how to reason about developing formal mathematical models of biological systems that are amenable to computational analysis. It collects in one place a selection of broadly useful models, algorithms, and theoretical analysis tools normally found scattered among many other disciplines. It thereby gives the aspiring student a bag of tricks that will serve him or her well in modeling problems drawn from numerous subfields of biology. These techniques are taught from the perspective of what the practitioner needs to know to use them effectively, supplemented with references for further reading on more advanced use of each method covered. The text, which grew out of a class taught at Carnegie Mellon University, covers models for optimization, simulation and sampling, and parameter tuning. These topics provide a general framework for learning how to formulate mathematical models of biological systems, what techniques are available to work with these models, and how to fit the models to particular systems. Their application is illustrated by many examples drawn from a variety of biological disciplines and several extended case studies that show how the methods described have been applied to real problems in biology.
Author : Hamid Bolouri
Publisher : Imperial College Press
ISBN 13 : 1848162200
Total Pages : 341 pages
Book Rating : 4.8/5 (481 download)
Download or read book Computational Modeling of Gene Regulatory Networks written by Hamid Bolouri and published by Imperial College Press. This book was released on 2008 with total page 341 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book serves as an introduction to the myriad computational approaches to gene regulatory modeling and analysis, and is written specifically with experimental biologists in mind. Mathematical jargon is avoided and explanations are given in intuitive terms. In cases where equations are unavoidable, they are derived from first principles or, at the very least, an intuitive description is provided. Extensive examples and a large number of model descriptions are provided for use in both classroom exercises as well as self-guided exploration and learning. As such, the book is ideal for self-learning and also as the basis of a semester-long course for undergraduate and graduate students in molecular biology, bioengineering, genome sciences, or systems biology.
Author : Liesbet Geris
Publisher : Springer
ISBN 13 : 3319212966
Total Pages : 471 pages
Book Rating : 4.3/5 (192 download)
Download or read book Uncertainty in Biology written by Liesbet Geris and published by Springer. This book was released on 2015-10-26 with total page 471 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computational modeling allows to reduce, refine and replace animal experimentation as well as to translate findings obtained in these experiments to the human background. However these biomedical problems are inherently complex with a myriad of influencing factors, which strongly complicates the model building and validation process. This book wants to address four main issues related to the building and validation of computational models of biomedical processes: 1. Modeling establishment under uncertainty 2. Model selection and parameter fitting 3. Sensitivity analysis and model adaptation 4. Model predictions under uncertainty In each of the abovementioned areas, the book discusses a number of key-techniques by means of a general theoretical description followed by one or more practical examples. This book is intended for graduate students and researchers active in the field of computational modeling of biomedical processes who seek to acquaint themselves with the different ways in which to study the parameter space of their model as well as its overall behavior.
Author : Ilya Shmulevich
Publisher : Princeton University Press
ISBN 13 : 1400865263
Total Pages : 314 pages
Book Rating : 4.4/5 (8 download)
Download or read book Genomic Signal Processing written by Ilya Shmulevich and published by Princeton University Press. This book was released on 2014-09-08 with total page 314 pages. Available in PDF, EPUB and Kindle. Book excerpt: Genomic signal processing (GSP) can be defined as the analysis, processing, and use of genomic signals to gain biological knowledge, and the translation of that knowledge into systems-based applications that can be used to diagnose and treat genetic diseases. Situated at the crossroads of engineering, biology, mathematics, statistics, and computer science, GSP requires the development of both nonlinear dynamical models that adequately represent genomic regulation, and diagnostic and therapeutic tools based on these models. This book facilitates these developments by providing rigorous mathematical definitions and propositions for the main elements of GSP and by paying attention to the validity of models relative to the data. Ilya Shmulevich and Edward Dougherty cover real-world situations and explain their mathematical modeling in relation to systems biology and systems medicine. Genomic Signal Processing makes a major contribution to computational biology, systems biology, and translational genomics by providing a self-contained explanation of the fundamental mathematical issues facing researchers in four areas: classification, clustering, network modeling, and network intervention.
Author : National Research Council
Publisher : National Academies Press
ISBN 13 : 030909612X
Total Pages : 469 pages
Book Rating : 4.3/5 (9 download)
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.
Author : Samuli Niiranen
Publisher : Springer Science & Business Media
ISBN 13 : 3642196217
Total Pages : 234 pages
Book Rating : 4.6/5 (421 download)
Download or read book Information Processing and Biological Systems written by Samuli Niiranen and published by Springer Science & Business Media. This book was released on 2011-03-10 with total page 234 pages. Available in PDF, EPUB and Kindle. Book excerpt: Living beings require constant information processing for survival. In cells, information is being processed and propagated at various levels, from the gene regulatory network to chemical pathways, to the interaction with the environment. How this is achieved and how information is coded is still poorly understood. For example, what a cell interprets as information in the temporal level of an mRNA and what is interpreted as noise remains an open question. Recently, information theoretical methods and other tools, developed in the context of engineering and natural sciences, have been applied to study diverse biological processes. This book covers the latest findings on how information is processed in various biological processes, ranging from information processing and propagation in gene regulatory networks to information processing in natural language. An overview is presented of the state-of-the-art in information processing in biological systems and the opinion of current leaders in this research field on future research directions.
