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Author: James M. Bower
Publisher: MIT Press
Published: 2001
Total Pages: 386
ISBN-13: 9780262524230
DOWNLOAD EBOOKHow new modeling techniques can be used to explore functionally relevant molecular and cellular relationships.
Author: James M. Bower
Publisher:
Published: 2001
Total Pages:
ISBN-13:
DOWNLOAD EBOOKAuthor: James M. Bower
Publisher:
Published: 2004
Total Pages: 336
ISBN-13: 9788180520518
DOWNLOAD EBOOKAuthor: Ivan V. Maly
Publisher: Humana Press
Published: 2009-03-26
Total Pages: 500
ISBN-13: 9781934115640
DOWNLOAD EBOOKThe rapidly developing methods of systems biology can help investigators in various areas of modern biomedical research to make inference and predictions from their data that intuition alone would not discern. Many of these methods, however, are commonly perceived as esoteric and inaccessible to biomedical researchers: Even evaluating their applicability to the problem at hand seems to require from the biologist a broad kno- edge of mathematics or engineering. This book is written by scientists who do possess such knowledge, who have successfully applied it to biological problems in various c- texts, and who found that their experience can be crystallized in a form very similar to a typical biological laboratory protocol. Learning a new laboratory procedure may at first appear formidable, and the int- ested researchers may be unsure whether their problem falls within the area of applicability of the new technique. The researchers will rely on the experience of others who have condensed it into a methods paper, with the theory behind the method, its step-by-step implementation, and the pitfalls explained thoroughly and from the practical angle. It is the intention of the authors of this book to make the methods of systems biology widely understood by biomedical researchers by explaining them in the same proven format of a protocol article.
Author: Corrado Priami
Publisher: Springer Science & Business Media
Published: 2003-02-07
Total Pages: 224
ISBN-13: 3540006052
DOWNLOAD EBOOKRovereto,December2002 CorradoPriami ProgrammeCommitteeofCMSB 2003 CorradoPriami(Chair),UniversityofTrento(Italy), CharlesAu?ray,CNRS,Villejuif(France), CosimaBaldari,Universit`adiSiena(Italy), AlexanderBockmayr,Universit ́eHenriPoincar ́e(France), LucaCardelli,MicrosoftResearchCambridge(UK), VincentDanos,Universit ́eParisVII(France), PierpaoloDegano,Universitad ` iPisa(Italy), Francois ̧ Fages,INRIA,Rocquencourt(France), DrabløsFinn,NorwegianUniversityofScienceandTechnology,Trondheim(N- way), MonikaHeiner,BrandenburgUniversityofTechnologyatCottbus(Germany), InaKoch,UniversityofAppliedSciencesBerlin,(Germany), JohnE.
Author: Ina Koch
Publisher: Springer Science & Business Media
Published: 2010-10-21
Total Pages: 378
ISBN-13: 1849964742
DOWNLOAD EBOOKThe emerging, multi-disciplinary field of systems biology is devoted to the study of the relationships between various parts of a biological system, and computer modeling plays a vital role in the drive to understand the processes of life from an holistic viewpoint. Advancements in experimental technologies in biology and medicine have generated an enormous amount of biological data on the dependencies and interactions of many different molecular cell processes, fueling the development of numerous computational methods for exploring this data. The mathematical formalism of Petri net theory is able to encompass many of these techniques. This essential text/reference presents a comprehensive overview of cutting-edge research in applications of Petri nets in systems biology, with contributions from an international selection of experts. Those unfamiliar with the field are also provided with a general introduction to systems biology, the foundations of biochemistry, and the basics of Petri net theory. Further chapters address Petri net modeling techniques for building and analyzing biological models, as well as network prediction approaches, before reviewing the applications to networks of different biological classification. Topics and features: investigates the modular, qualitative modeling of regulatory networks using Petri nets, and examines an Hybrid Functional Petri net simulation case study; contains a glossary of the concepts and notation used in the book, in addition to exercises at the end of each chapter; covers the topological analysis of metabolic and regulatory networks, the analysis of models of signaling networks, and the prediction of network structure; provides a biological case study on the conversion of logical networks into Petri nets; discusses discrete modeling, stochastic modeling, fuzzy modeling, dynamic pathway modeling, genetic regulatory network modeling, and quantitative analysis techniques; includes a Foreword by Professor Jens Reich, Professor of Bioinformatics at Humboldt University and Max Delbrück Center for Molecular Medicine in Berlin. This unique guide to the modeling of biochemical systems using Petri net concepts will be of real utility to researchers and students of computational biology, systems biology, bioinformatics, computer science, and biochemistry.
Author:
Publisher: Academic Press
Published: 2009-12-03
Total Pages: 712
ISBN-13: 9780123750235
DOWNLOAD EBOOKThe combination of faster, more advanced computers and more quantitatively oriented biomedical researchers has recently yielded new and more precise methods for the analysis of biomedical data. These better analyses have enhanced the conclusions that can be drawn from biomedical data, and they have changed the way that experiments are designed and performed. This volume, along with previous and forthcoming Computer Methods volumes for the Methods in Enzymology serial, aims to inform biomedical researchers about recent applications of modern data analysis and simulation methods as applied to biomedical research. * Presents step-by-step computer methods and discusses the techniques in detail to enable their implementation in solving a wide range of problems * Informs biomedical researchers of the modern data analysis methods that have developed alongside computer hardware *Presents methods at the "nuts and bolts" level to identify and resolve a problem and analyze what the results mean
Author: Andreas Wagner
Publisher: Princeton University Press
Published: 2007-07-22
Total Pages: 383
ISBN-13: 0691134049
DOWNLOAD EBOOKAll living things are remarkably complex, yet their DNA is unstable, undergoing countless random mutations over generations. Despite this instability, most animals do not grow two heads or die, plants continue to thrive, and bacteria continue to divide. Robustness and Evolvability in Living Systems tackles this perplexing paradox. The book explores why genetic changes do not cause organisms to fail catastrophically and how evolution shapes organisms' robustness. Andreas Wagner looks at this problem from the ground up, starting with the alphabet of DNA, the genetic code, RNA, and protein molecules, moving on to genetic networks and embryonic development, and working his way up to whole organisms. He then develops an evolutionary explanation for robustness. Wagner shows how evolution by natural selection preferentially finds and favors robust solutions to the problems organisms face in surviving and reproducing. Such robustness, he argues, also enhances the potential for future evolutionary innovation. Wagner also argues that robustness has less to do with organisms having plenty of spare parts (the redundancy theory that has been popular) and more to do with the reality that mutations can change organisms in ways that do not substantively affect their fitness. Unparalleled in its field, this book offers the most detailed analysis available of all facets of robustness within organisms. It will appeal not only to biologists but also to engineers interested in the design of robust systems and to social scientists concerned with robustness in human communities and populations.
Author: Bruce R. Donald
Publisher: MIT Press
Published: 2023-08-15
Total Pages: 497
ISBN-13: 0262548798
DOWNLOAD EBOOKAn overview of algorithms important to computational structural biology that addresses such topics as NMR and design and analysis of proteins.Using the tools of information technology to understand the molecular machinery of the cell offers both challenges and opportunities to computational scientists. Over the past decade, novel algorithms have been developed both for analyzing biological data and for synthetic biology problems such as protein engineering. This book explains the algorithmic foundations and computational approaches underlying areas of structural biology including NMR (nuclear magnetic resonance); X-ray crystallography; and the design and analysis of proteins, peptides, and small molecules. Each chapter offers a concise overview of important concepts, focusing on a key topic in the field. Four chapters offer a short course in algorithmic and computational issues related to NMR structural biology, giving the reader a useful toolkit with which to approach the fascinating yet thorny computational problems in this area. A recurrent theme is understanding the interplay between biophysical experiments and computational algorithms. The text emphasizes the mathematical foundations of structural biology while maintaining a balance between algorithms and a nuanced understanding of experimental data. Three emerging areas, particularly fertile ground for research students, are highlighted: NMR methodology, design of proteins and other molecules, and the modeling of protein flexibility. The next generation of computational structural biologists will need training in geometric algorithms, provably good approximation algorithms, scientific computation, and an array of techniques for handling noise and uncertainty in combinatorial geometry and computational biophysics. This book is an essential guide for young scientists on their way to research success in this exciting field.
Author: Leah Edelstein-Keshet
Publisher: SIAM
Published: 1988-01-01
Total Pages: 629
ISBN-13: 9780898719147
DOWNLOAD EBOOKMathematical Models in Biology is an introductory book for readers interested in biological applications of mathematics and modeling in biology. A favorite in the mathematical biology community, it shows how relatively simple mathematics can be applied to a variety of models to draw interesting conclusions. Connections are made between diverse biological examples linked by common mathematical themes. A variety of discrete and continuous ordinary and partial differential equation models are explored. Although great advances have taken place in many of the topics covered, the simple lessons contained in this book are still important and informative. Audience: the book does not assume too much background knowledge--essentially some calculus and high-school algebra. It was originally written with third- and fourth-year undergraduate mathematical-biology majors in mind; however, it was picked up by beginning graduate students as well as researchers in math (and some in biology) who wanted to learn about this field.
