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Reviews
1. Systems Biology: Constraint-based Reconstruction and Analysis
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Systems Biology Constraint Based Reconstruction and AnalysisDescription
Recent technological advances have enabled comprehensive determination of the molecular composition of living cells. The chemical interactions between many of these molecules are known, giving rise to genome-scale reconstructed biochemical reaction networks underlying cellular functions. Mathematical descriptions of the totality of these chemical interactions lead to genome-scale models that allow the computation of physiological functions. Reflecting these recent developments, this textbook explains how such quantitative and computable genotype-phenotype relationships are built using a genome-wide basis of information about the gene portfolio of a target organism. It describes how biological knowledge is assembled to reconstruct biochemical reaction networks, the formulation of computational models of biological functions, and how these models can be used to address key biological questions and enable predictive biology. Developed through extensive classroom use, the book is designed to provide students with a solid conceptual framework and an invaluable set of modeling tools and computational approaches.2. Mathematical Modeling in Systems Biology: An Introduction (MIT Press)
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An introduction to the mathematical concepts and techniques needed for the construction and analysis of models in molecular systems biology.
Systems techniques are integral to current research in molecular cell biology, and system-level investigations are often accompanied by mathematical models. These models serve as working hypotheses: they help us to understand and predict the behavior of complex systems. This book offers an introduction to mathematical concepts and techniques needed for the construction and interpretation of models in molecular systems biology. It is accessible to upper-level undergraduate or graduate students in life science or engineering who have some familiarity with calculus, and will be a useful reference for researchers at all levels.
The first four chapters cover the basics of mathematical modeling in molecular systems biology. The last four chapters address specific biological domains, treating modeling of metabolic networks, of signal transduction pathways, of gene regulatory networks, and of electrophysiology and neuronal action potentials. Chapters 3--8 end with optional sections that address more specialized modeling topics. Exercises, solvable with pen-and-paper calculations, appear throughout the text to encourage interaction with the mathematical techniques. More involved end-of-chapter problem sets require computational software. Appendixes provide a review of basic concepts of molecular biology, additional mathematical background material, and tutorials for two computational software packages (XPPAUT and MATLAB) that can be used for model simulation and analysis.
3. Thinking in Systems: A Primer
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Ships from VermontDescription
In the years following her role as the lead author of the international bestseller, Limits to Growththe first book to show the consequences of unchecked growth on a finite planet Donella Meadows remained a pioneer of environmental and social analysis until her untimely death in 2001.
Thinking in Systems, is a concise and crucial book offering insight for problem solving on scales ranging from the personal to the global. Edited by the Sustainability Institutes Diana Wright, this essential primer brings systems thinking out of the realm of computers and equations and into the tangible world, showing readers how to develop the systems-thinking skills that thought leaders across the globe consider critical for 21st-century life.
Some of the biggest problems facing the worldwar, hunger, poverty, and environmental degradationare essentially system failures. They cannot be solved by fixing one piece in isolation from the others, because even seemingly minor details have enormous power to undermine the best efforts of too-narrow thinking.
While readers will learn the conceptual tools and methods of systems thinking, the heart of the book is grander than methodology. Donella Meadows was known as much for nurturing positive outcomes as she was for delving into the science behind global dilemmas. She reminds readers to pay attention to what is important, not just what is quantifiable, to stay humble, and to stay a learner.
In a world growing ever more complicated, crowded, and interdependent, Thinking in Systems helps readers avoid confusion and helplessness, the first step toward finding proactive and effective solutions.
4. An Introduction to Systems Biology: Design Principles of Biological Circuits (Chapman & Hall/CRC Mathematical and Computational Biology)
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Chapman Hall CRCDescription
Thorough and accessible, this book presents the design principles of biological systems, and highlights the recurring circuit elements that make up biological networks. It provides a simple mathematical framework which can be used to understand and even design biological circuits. The textavoids specialist terms, focusing instead on several well-studied biological systems that concisely demonstrate key principles.An Introduction to Systems Biology: Design Principles of Biological Circuits builds a solid foundation for the intuitive understanding of general principles. It encourages the reader to ask why a system is designed in a particular way and then proceeds to answer with simplified models.
5. A First Course in Systems Biology
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A First Course in Systems Biology is an introduction for advanced undergraduate and graduate students to the growing field of systems biology. Its main focus is the development of computational models and their applications to diverse biological systems. The book begins with the fundamentals of modeling, then reviews features of the molecular inventories that bring biological systems to life and discusses case studies that represent some of the frontiers in systems biology and synthetic biology. In this way, it provides the reader with a comprehensive background and access to methods for executing standard systems biology tasks, understanding the modern literature, and launching into specialized courses or projects that address biological questions using theoretical and computational means.
New topics in this edition include: default modules for model design, limit cycles and chaos, parameter estimation in Excel, model representations of gene regulation through transcription factors, derivation of the Michaelis-Menten rate law from the original conceptual model, different types of inhibition, hysteresis, a model of differentiation, system adaptation to persistent signals, nonlinear nullclines, PBPK models, and elementary modes.
The format is a combination of instructional text and references to primary literature, complemented by sets of small-scale exercises that enable hands-on experience, and large-scale, often open-ended questions for further reflection.
6. Systems Biology: A Textbook
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This advanced textbook is tailored for an introductory course in Systems Biology and is well-suited for biologists as well as engineers and computer scientists.
It comes with student-friendly reading lists and a companion website featuring a short exam prep version of the book and educational modeling programs. The text is written in an easily accessible style and includes numerous worked examples and study questions in each chapter. For this edition, a section on medical systems biology has been included.