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Systems Genetics
by Klaus Schughart Robert W. WilliamsThis volume focuses on the use of system genetic methods and the use of murine models to study the role of gene variants and environmental factors on human health and disease--what is now often called personalized or precision health care. The protocols in this book will help readers analyze genetic causes of heritable variation across a wide range of systems and traits using rodent models. The chapters in this book are separated into three sections that cover: 1) resources for systems genetics; 2) tools for analysis and integration in systems genetics; and 3) systems genetics use cases. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and tools, step-by-step, readily reproducible protocols, and tips on troubleshooting and avoiding known pitfalls. Practical and thorough, Systems Genetics: Methods and Protocols is a valuable resource for anyone who is interested in this diverse field.
Systems Immunology: An Introduction to Modeling Methods for Scientists (Foundations of Biochemistry and Biophysics)
by Jayajit Das Ciriyam Jayaprakash"Taken together, the body of information contained in this book provides readers with a bird’s-eye view of different aspects of exciting work at the convergence of disciplines that will ultimately lead to a future where we understand how immunity is regulated, and how we can harness this knowledge toward practical ends that reduce human suffering. I commend the editors for putting this volume together." –Arup K. Chakraborty, Robert T. Haslam Professor of Chemical Engineering, and Professor of Physics, Chemistry, and Biological Engineering, Massachusetts Institute of Technology, Cambridge, USA New experimental techniques in immunology have produced large and complex data sets that require quantitative modeling for analysis. This book provides a complete overview of computational immunology, from basic concepts to mathematical modeling at the single molecule, cellular, organism, and population levels. It showcases modern mechanistic models and their use in making predictions, designing experiments, and elucidating underlying biochemical processes. It begins with an introduction to data analysis, approximations, and assumptions used in model building. Core chapters address models and methods for studying immune responses, with fundamental concepts clearly defined. Readers from immunology, quantitative biology, and applied physics will benefit from the following: Fundamental principles of computational immunology and modern quantitative methods for studying immune response at the single molecule, cellular, organism, and population levels. An overview of basic concepts in modeling and data analysis. Coverage of topics where mechanistic modeling has contributed substantially to current understanding. Discussion of genetic diversity of the immune system, cell signaling in the immune system, immune response at the cell population scale, and ecology of host-pathogen interactions.
Systems-Level Modelling of Microbial Communities: Theory and Practice (Focus Computational Biology Series)
by Aarthi Ravikrishnan Karthik RamanSystems-Level Modelling of Microbial Communities: Theory and Practice introduces various aspects of modelling microbial communities and presents a detailed overview of the computational methods which have been developed in this area. This book is aimed at researchers in the field of computational/systems biology as well as biologists/experimentalists studying microbial communities, who are keen on embracing the concepts of computational modelling. The primary focus of this book is on methods for modelling interactions between micro-organisms in a community, with special emphasis on constraint-based and network-based modelling techniques. A brief overview of population- and agent-based modelling is also presented. Lastly, it covers the experimental methods to understand microbial communities, and provides an outlook on how the field may evolve in the coming years.
Systems Medicine: Physiological Circuits and the Dynamics of Disease (Chapman & Hall/CRC Computational Biology Series)
by Uri AlonWhy do we get certain diseases, whereas other diseases do not exist? In this book, Alon, one of the founders of systems biology, builds a foundation for systems medicine. Starting from basic laws, the book derives why physiological circuits are built the way they are. The circuits have fragilities that explain specific diseases and offer new strategies to treat them. By the end, the reader will be able to use simple and powerful mathematical models to describe physiological circuits. The book explores, in three parts, hormone circuits, immune circuits, and aging and age-related disease. It culminates in a periodic table of diseases. Alon writes in a style accessible to a broad range of readers - undergraduates, graduates, or researchers from computational or biological backgrounds. The level of math is friendly and the math can even be bypassed altogether. For instructors and readers who want to go deeper, the book includes dozens of exercises that have been rigorously tested in the classroom
Systems Medicine (Methods in Molecular Biology #2486)
by Jane P. F. Bai Junguk HurThis volume explores the latest technological advances and covers all facets of systems medicine with respect to precision medicine. The chapters in this book are organized into four parts. Part One highlights the recent achievements in proteomics for biomarkers identification, integration of omics and phenotypic data for precision medicine, and medicine-guided treatment of drug-induced Stevens-Johnson syndrome. Part Two covers systems-based computational approaches for pharmaceutical research and drug development, the principle of optimizing systemic exposure of drugs, and Animal Rule for drug repurposing. Part Three looks at computational tools and methodologies of network biology, quantitative systems toxicology, and modeling and stimulating patient response variabilities. Part Four talks about how systems medicine can address unmet medical and health needs, and identify educational needs. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.Cutting-edge and thorough, Systems Medicine: Methods and Protocols is a valuable resource for the scientific community that will help researchers work together toward the further advancement of achieving the goal of promoting global health.Chapter 8 is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com
Systems Metabolic Engineering
by Hal S. AlperWith the ultimate goal of systematically and robustly defining the specific perturbations necessary to alter a cellular phenotype, systems metabolic engineering has the potential to lead to a complete cell model capable of simulating cell and metabolic function as well as predicting phenotypic response to changes in media, gene knockouts/overexpressions, or the incorporation of heterologous pathways. In Systems Metabolic Engineering: Methods and Protocols, experts in the field describe the methodologies and approaches in the area of systems metabolic engineering and provide a step-by-step guide for their implementation. Four major tenants of this approach are addressed, including modeling and simulation, multiplexed genome engineering, 'omics technologies, and large data-set incorporation and synthesis, all elucidated through the use of model host organisms. Written in the highly successful Methods in Molecular BiologyTM series format, chapters include introductions on their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Comprehensive and cutting-edge, Systems Metabolic Engineering: Methods and Protocols serves as an ideal guide for metabolic engineers, molecular biologists, and microbiologists aiming to implement the most recent approaches available in the field.
Systems Metabolic Engineering
by Christoph Wittmann Sang Yup LeeSystems Metabolic Engineering is changing the way microbial cell factories are designed and optimized for industrial production. Integrating systems biology and biotechnology with new concepts from synthetic biology enables the global analysis and engineering of microorganisms and bioprocesses at super efficiency and versatility otherwise not accessible. Without doubt, systems metabolic engineering is a major driver towards bio-based production of chemicals, materials and fuels from renewables and thus one of the core technologies of global green growth. In this book, Christoph Wittmann and Sang-Yup Lee have assembled the world leaders on systems metabolic engineering and cover the full story - from genomes and networks via discovery and design to industrial implementation practises. This book is a comprehensive resource for students and researchers from academia and industry interested in systems metabolic engineering. It provides us with the fundaments to targeted engineering of microbial cells for sustainable bio-production and stimulates those who are interested to enter this exiting research field.
Systems Modeling
by Mukhtar AhmedAchieving food security and economic developmental objectives in the face of climate change and rapid population growth requires systems modelling approaches, for example in the design of sustainable agriculture farming systems. Such approaches increase our understanding of system responses to different soil and climatic conditions, and provide insights into the effects of various variable climate change scenarios, providing valuable information for decision-makers. Further, in the agricultural sector, systems modelling can help optimise crop management and adaptation measures to boost productivity under variable climatic conditions. Presenting key outcomes from crop models used in agricultural systems this book is a valuable resource for professionals interested in using modelling approaches to manage the growth and improve the quality of various crops.
Systems Neuroscience (Advances in Neurobiology #41)
by Albert Cheung-Hoi Yu Kai Gao Jiangshan ZhanThe new edition of this popular book brings together experts in the field of Systems Neuroscience to present an overview of the area. Topics covered include how different neural circuits analyze sensory information, form perceptions of the external world, make decisions, and execute movements; how nerve cells behave when connected together to form neural networks; the relationship between molecular and cellular approaches to understanding brain structure and function; the study of high-level mental functions; and studying brain pathologies and disease. Among the topics covered in the new edition are artificial intelligence-assisted computational neuroscience for deciphering neural networks, spatial transcriptomics single cell sequencing, and exome/whole genome sequencing for understanding brain disorders in human genetics. The best way to study the brain, the most complex organ in the body composed of 100 billion neurons with trillions of interconnections, is with a systems biology approach.
Systems Neuroscience (Advances in Neurobiology #21)
by Albert Cheung-Hoi Yu Lina LiThis edition of Advances in Neurobiology brings together experts in the emerging field of Systems Neuroscience to present an overview of this area of research. Topics covered include: how different neural circuits analyze sensory information, form perceptions of the external world, make decisions, and execute movements; how nerve cells behave when connected together to form neural networks; the relationship between molecular and cellular approaches to understanding brain structure and function; the study of high-level mental functions; and studying brain pathologies and diseases with Systems Neuroscience. A hierarchy of biological complexity arises from the genome, transcriptome, proteome, organelles, cells, synapses, circuits, brain regions, the whole brain, and behaviour. The best way to study the brain, the most complex organ in the body composed of 100 billion cells with trillions of interconnections, is with a Systems Biology approach. Systems biology is an inter-disciplinary field that focuses on complex interactions within biological systems to reveal 'emergent properties' - properties of cells and groups of cells functioning as a system whose actual and theoretical description is only possible using Systems Biology techniques.
Systems of Life: Biopolitics, Economics, and Literature on the Cusp of Modernity (Forms of Living)
by Richard A. Barney and Warren MontagSystems of Life offers a wide-ranging revaluation of the emergence of biopolitics in Europe from the mid– eighteenth to the mid–nineteenth century. In staging an encounter among literature, political economy, and the still emergent sciences of life in that historical moment, the essays collected here reopen the question of how concepts of animal, vegetable, and human life, among other biological registers, had an impact on the Enlightenment project of thinking politics and economics as a joint enterprise. The volume’s contributors consider politics, economics, and the biological as distinct, semi-autonomous spheres whose various combinations required inventive, sometimes incomplete, acts of conceptual mediation, philosophical negotiation, disciplinary intervention, or aesthetic representation.
Systems Orthodontics: From Clinical Reasoning to Computation, and Back (Understanding Complex Systems)
by Pietro Auconi Guido Caldarelli Antonella PolimeniThis book marks one of the first applications of the Medicine Network discipline to an everyday scenario. It explores situations where patients, often in adolescence, grapple with the decision of whether to commence a treatment, seeking insights into the more plausible future scenarios. Additionally, the specific feedback from biological systems in the human body serves as a potent metaphor for addressing various challenges in the field of Complex Systems. In recent times, systems thinking and complexity theory have yielded substantial conceptual advancements across various research domains. In the context of orthodontics, these approaches offer a more comprehensive understanding in contrast to the traditional mechanistic approach, which primarily focuses on the analysis of applied forces. Systems thinking directs attention to the interaction among dentoskeletal components, where the behavior of one element can influence others. The amalgamation of multiple elements leads to entities with properties distinct from those of individual components. The increasing complexity of orthodontic reality beyond clinical or radiological observations necessitates the development of new theories. Complexity theory has demonstrated that emergent properties in biological systems can be discerned through appropriate computational models, as opposed to the analytical study of individual components. The central metaphor for the interactive craniofacial system during growth is portrayed by the facial topology revealed through network analysis, facilitating a systemic reevaluation of traditional orthodontic theories. This book delineates the novel insights derived from the clinical-computational approach, applicable for a prognostic and early interception perspective in managing dentofacial dysmorphoses. Its objective is to captivate practitioners and persuade them of the practical utility of these innovative approaches.
Systems, Patterns and Data Engineering with Geometric Calculi (SEMA SIMAI Springer Series #13)
by Sebastià Xambó-DescampsThe intention of this collection agrees with the purposes of the homonymous mini-symposium (MS) at ICIAM-2019, which were to overview the essentials of geometric calculus (GC) formalism, to report on state-of-the-art applications showcasing its advantages and to explore the bearing of GC in novel approaches to deep learning. The first three contributions, which correspond to lectures at the MS, offer perspectives on recent advances in the application GC in the areas of robotics, molecular geometry, and medical imaging. The next three, especially invited, hone the expressiveness of GC in orientation measurements under different metrics, the treatment of contact elements, and the investigation of efficient computational methodologies. The last two, which also correspond to lectures at the MS, deal with two aspects of deep learning: a presentation of a concrete quaternionic convolutional neural network layer for image classification that features contrast invariance and a general overview of automatic learning aimed at steering the development of neural networks whose units process elements of a suitable algebra, such as a geometric algebra. The book fits, broadly speaking, within the realm of mathematical engineering, and consequently, it is intended for a wide spectrum of research profiles. In particular, it should bring inspiration and guidance to those looking for materials and problems that bridge GC with applications of great current interest, including the auspicious field of GC-based deep neural networks.
Systems Practice: How to Act
by Ray IsonIt is now accepted that humans are changing the climate of the Earth and this is the most compelling amongst a long litany of reasons as to why, collectively, we have to change our ways of thinking and acting. Most people now recognise that we have to be capable of adapting quickly as new and uncertain circumstances emerge: this capability will need to exist at personal, group, community, regional, national and international levels, all at the same time. Systems Practice is structured into four parts. Part I introduces the societal need to move towards a more systemic and adaptive governance against the backdrop of human-induced climate change. Part II unpacks what is involved in systems practice by means of a juggler metaphor; examining situations where systems thinking offers useful understanding and opportunities for change. Part III identifies the main factors that constrain the uptake of systems practice and makes the case for innovation in practice by means of systemic inquiry, systemic action research and systemic intervention. The book concludes with Part IV, which critically examines how systems practice is, or might be, utilised at different levels from the personal to the societal. The development of our capabilities to think and act systemically is an urgent priority and Systems Practice aims to show how to do systems thinking and translate that thinking into praxis (theory informed practical action) which will be welcomed by those managing in situations of complexity and uncertainty across all domains of professional and personal concern.
Systems Research I: Essays in Honor of Yasuhiko Takahara on Systems Theory and Modeling (Translational Systems Sciences #26)
by Kyoichi Kijima Junichi Iijima Ryo Sato Hiroshi Deguchi Bumpei NakanoThis book is in honor of Yasuhiko Takahara, a first-class researcher who has been active for some 50 years at the global level in systems research. Researchers and practitioners from Japan and other countries who have been influenced by Takahara have come together from far and wide to contribute their major research masterpieces in the field of systems research in the broadest sense.While the roots of Takahara’s systems research are in general systems theory and systems control theory, he developed his research and teaching in diverse directions such as management information science, engineering, social simulation, and systems thinking. As a result, many of the researchers and practitioners he supervised or influenced have established their own positions and are now active around the world in a wide range of systems research.Volume I is a collection of their masterpieces or representative works in the field of systems theory and modeling.
Systems Research II: Essays in Honor of Yasuhiko Takahara on Systems Management Theory and Practice (Translational Systems Sciences #27)
by Kyoichi Kijima Junichi Iijima Ryo Sato Hiroshi Deguchi Bumpei NakanoThis book is in honor of Yasuhiko Takahara, a first-class researcher who has been active for some 50 years at the global level in systems research. Researchers and practitioners from Japan and other countries who have been influenced by Takahara have come together from far and wide to contribute their major research masterpieces in the field of systems research in the broadest sense.While the roots of Takahara’s systems research are in general systems theory and systems control theory, he developed his research and teaching in diverse directions such as management information science, engineering, social simulation, and systems thinking. As a result, many of the researchers and practitioners he supervised or influenced have established their own positions and are now active around the world in a wide range of systems research.Volume II is a collection of their masterpieces or representative works in the fields of systems management theory and practice.
Systems Science Level 4
by Cheryl Chiapperino Macki Jones Sheri Leasure Lisa WoodA science book set for Christian educators and schools worldwide. Topics covered include: life science: stability, physical sciences, earth & space: balance and human body wellness.
Systems Science: Theory, Analysis, Modeling, and Design
by George E. MobusThis book describes a comprehensive approach to applying systems science formally to the deep analysis of a wide variety of complex systems. Detailed ‘how-to’ examples of the three phases (analysis-modeling-design) of systems science are applied to systems of various types (machines, organic (e.g. ecosystem), and supra-organic (e.g. business organizations and government). The complexity of the global system has reached proportions that seriously challenge our abilities to understand the consequences of our use of technology, modification of natural ecosystems, or even how to govern ourselves. For this reason, complex mathematics is eschewed when simpler structures will suffice, allowing the widest possible audience to apply and benefit from the available tools and concepts of systems science in their own work. The book shows, in detail, how to functionally and structurally deconstruct complex systems using a fundamental language of systems. It shows how to capture the discovered details in a structured knowledge base from which abstract models can be derived for simulation. The knowledge base is also shown to be a basis for generating system design specifications for human-built artifacts, or policy recommendations/policy mechanisms for socio-economic-ecological systems management. The book builds on principles and methods found in the authors’ textbook Principles of Systems Science (co-authored with Michael Kalton), but without prerequisites. It will appeal to a broad audience that deals with complex systems every day, from design engineers to economic and ecological systems managers and policymakers.
A Systems Theoretic Approach to Systems and Synthetic Biology I: Models And System Characterizations
by Vishwesh V. Kulkarni Guy-Bart Stan Karthik RamanThe complexity of biological systems has intrigued scientists from many disciplines and has given birth to the highly influential field of systems biology wherein a wide array of mathematical techniques, such as flux balance analysis, and technology platforms, such as next generation sequencing, is used to understand, elucidate, and predict the functions of complex biological systems. More recently, the field of synthetic biology, i. e. , de novo engineering of biological systems, has emerged. Scientists from various fields are focusing on how to render this engineering process more predictable, reliable, scalable, affordable, and easy. Systems and control theory is a branch of engineering and applied sciences that rigorously deals with the complexities and uncertainties of interconnected systems with the objective of characterising fundamental systemic properties such as stability, robustness, communication capacity, and other performance metrics. Systems and control theory also strives to offer concepts and methods that facilitate the design of systems with rigorous guarantees on these properties. Over the last 100 years, it has made stellar theoretical and technological contributions in diverse fields such as aerospace, telecommunication, storage, automotive, power systems, and others. Can it have, or evolve to have, a similar impact in biology? The chapters in this book demonstrate that, indeed, systems and control theoretic concepts and techniques can have a significant impact in systems and synthetic biology. Volume I provides a panoramic view that illustrates the potential of such mathematical methods in systems and synthetic biology. Recent advances in systems and synthetic biology have clearly demonstrated the benefits of a rigorous and systematic approach rooted in the principles of systems and control theory - not only does it lead to exciting insights and discoveries but it also reduces the inordinately lengthy trial-and-error process of wet-lab experimentation, thereby facilitating significant savings in human and financial resources. In Volume I, some of the leading researchers in the field of systems and synthetic biology demonstrate how systems and control theoretic concepts and techniques can be useful, or should evolve to be useful, in order to understand how biological systems function. As the eminent computer scientist Donald Knuth put it, "biology easily has 500 years of exciting problems to work on". This edited book presents but a small fraction of those for the benefit of (1) systems and control theorists interested in molecular and cellular biology and (2) biologists interested in rigorous modelling, analysis and control of biological systems.
A Systems Theoretic Approach to Systems and Synthetic Biology II: Analysis And Design Of Cellular Systems
by Vishwesh V. Kulkarni Guy-Bart Stan Karthik RamanThe complexity of biological systems has intrigued scientists from many disciplines and has given birth to the highly influential field of systems biology wherein a wide array of mathematical techniques, such as flux balance analysis, and technology platforms, such as next generation sequencing, is used to understand, elucidate, and predict the functions of complex biological systems. More recently, the field of synthetic biology, i. e. , de novo engineering of biological systems, has emerged. Scientists from various fields are focusing on how to render this engineering process more predictable, reliable, scalable, affordable, and easy. Systems and control theory is a branch of engineering and applied sciences that rigorously deals with the complexities and uncertainties of interconnected systems with the objective of characterising fundamental systemic properties such as stability, robustness, communication capacity, and other performance metrics. Systems and control theory also strives to offer concepts and methods that facilitate the design of systems with rigorous guarantees on these properties. Over the last 100 years, it has made stellar theoretical and technological contributions in diverse fields such as aerospace, telecommunication, storage, automotive, power systems, and others. Can it have, or evolve to have, a similar impact in biology? The chapters in this book demonstrate that, indeed, systems and control theoretic concepts and techniques can have a significant impact in systems and synthetic biology. Volume II contains chapters contributed by leading researchers in the field of systems and synthetic biology that concern modeling physiological processes and bottom-up constructions of scalable biological systems. The modeling problems include characterisation and synthesis of memory, understanding how homoeostasis is maintained in the face of shocks and relatively gradual perturbations, understanding the functioning and robustness of biological clocks such as those at the core of circadian rhythms, and understanding how the cell cycles can be regulated, among others. Some of the bottom-up construction problems investigated in Volume II are as follows: How should biomacromolecules, platforms, and scalable architectures be chosen and synthesised in order to build programmable de novo biological systems? What are the types of constrained optimisation problems encountered in this process and how can these be solved efficiently? As the eminent computer scientist Donald Knuth put it, "biology easily has 500 years of exciting problems to work on". This edited book presents but a small fraction of those for the benefit of (1) systems and control theorists interested in molecular and cellular biology and (2) biologists interested in rigorous modelling, analysis and control of biological systems.
Systems Theory and PDEs: Open Problems, Recent Results, and New Directions (Trends in Mathematics)
by Felix L. Schwenninger Marcus WaurickThis volume presents recent advances and open problems in the cross section of infinite-dimensional systems theory and the modern treatment of PDEs. Chapters are based on talks and problem sessions from the first “Workshop on Systems Theory and PDEs” (WOSTAP), held at TU Bergakademie Freiberg in July 2022. The main topics covered include: Differential algebraic equations Port-Hamiltonian systems in both finite and infinite dimensions Highly nonlinear equations related to elasticity/plasticity Modeling of thermo-piezo-electromagnetism
Systems Theory for Engineering Practice: Insights from Physics
by Maosheng Zheng Jie YuThis book presents cognition of the universality of systems theory thinking by using some ordinary physical phenomena and their methods in study, of which the involved treatments are consistent with the viewpoint of systems theory. It contains the collective actions of classical vibration of many bodies and wave, the extreme value problem in natural world, status of electrons in atom-molecule and metals, Ising model in phase transition and elementary excitation in solid, multi-objective optimization in a system, description of effective media approximation, certainty in uncertain phenomena, all these reflect the cooperative/synergetic effects, wholeness of group actions, “unity of opposites” inside a system, and collective phenomena in a system completely. The relevant methodologies for systems theory are organic combination and synergism of both “reductionism” and “holism” instead of “confrontation” or “separation” of them, which could be used in dealing with analogous problems in systems science and engineering fields in response to the idiom of “stones from other hills being good for polishing this jade” and “comprehend by analogy”, so as to promote the transformation of wisdom to productivity. The authors wish this work could play its role as a paving stone to serve the research and application of systems theory. This book can be used as a textbook for postgraduate and advanced undergraduate students in relevant majors, and a reference book for scientists and practitioners in related fields.
Systems Theory for Pragmatic Schooling: Toward Principles of Democratic Education
by Craig A. CunninghamWriting for educators and education leaders, Cunningham shows that combining a philosophy of pragmatism with thinking about education as systems can illuminate challenges in contemporary schooling and provide practical solutions for creating a democratic education.
Systems Thinkers
by Karen Shipp Magnus RamageThis book presents a biographical history of the field of systems thinking, by examining the life and work of thirty of its major thinkers. It discusses each thinker's key contributions, the way this contribution was expressed in practice and the relationship between their life and ideas. This discussion is supported by an extract from the thinker's own writing, to give a flavour of their work and to give readers a sense of which thinkers are most relevant to their own interests.
Systems Thinking: Managing Chaos And Complexity: A Platform For Designing Business Architecture
by Jamshid GharajedaghiSystems Thinking, Third Edition combines systems theory and interactive design to provide an operational methodology for defining problems and designing solutions in an environment increasingly characterized by chaos and complexity. This new edition has been updated to include all new chapters on self-organizing systems as well as holistic, operational, and design thinking. <p><p> The book covers recent crises in financial systems and job markets, the housing bubble, and environment, assessing their impact on systems thinking. A companion website is available at interactdesign.com. <p> This volume is ideal for senior executives as well as for chief information/operating officers and other executives charged with systems management and process improvement. It may also be a helpful resource for IT/MBA students and academics.