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Design and Analysis of Biomolecular Circuits
The book deals with engineering aspects of the two emerging and intertwined fields of synthetic and systems biology. Both fields hold promise to revolutionize the way molecular biology research is done, the way today’s drug discovery works and the way bio-engineering is done. Both fields stress the importance of building and characterizing small bio-molecular networks in order to synthesize incrementally and understand large complex networks inside living cells. Reminiscent of computer-aided design (CAD) of electronic circuits, abstraction is believed to be the key concept to achieve this goal. It allows hiding the overwhelming complexity of cellular processes by encapsulating network parts into abstract modules. This book provides a unique perspective on how concepts and methods from CAD of electronic circuits can be leveraged to overcome complexity barrier perceived in synthetic and systems biology.
Computational Methods in Systems Biology
This book constitutes the refereed proceedings of the 15th International Conference on Computational Methods in Systems Biology, CMSB 2017, held in Darmstadt, Germany, in September 2017. The 15 full papers, 4 tool papers and 4 posters presented together with 1 invited talk were carefully reviewed and selected from 41 regular paper submissions. Topics of interest include formalisms for modeling biological processes; models and their biological applications; frameworks for model verication, validation, analysis, and simulation of biological systems; high-performance computational systems biology and parallel implementations; model inference from experimental data; model integration from biological databases; multi-scale modeling and analysis methods; and computational approaches for synthetic biology.
Systems Biology Modelling and Analysis
Systems Biology Modelling and Analysis Describes important modelling and computational methods for systems biology research to enable practitioners to select and use the most suitable technique Systems Biology Modelling and Analysis provides an overview of state-of-the-art techniques and introduces related tools and practices to formalize models and automate reasoning for systems biology. The authors present and compare the main formal methods used in systems biology for modelling biological networks, including discussion of their advantages, drawbacks, and main applications. Each chapter includes an intuitive presentation of the specific formalism, a brief history of the formalism and of it...
A Systems Theoretic Approach to Systems and Synthetic Biology II: Analysis and Design of Cellular Systems
The 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...
Computational Methods in Systems Biology
This book constitutes the refereed proceedings of the 16th International Conference on Computational Methods in Systems Biology, CMSB 2018, held in BRNO, Czech Republic, in September 2018. The 15 full and 7 short papers presented together with 5 invited talks were carefully reviewed and selected from 46 submissions. Topics of interest include formalisms for modeling biological processes; models and their biological applications; frameworks for model verification, validation, analysis, and simulation of biological systems; high-performance computational systems biology; parameter and model inference from experimental data; automated parameter and model synthesis; model integration and biological databases; multi-scale modeling and analysis methods; design, analysis, and verification methods for synthetic biology; methods for biomolecular computing and engineered molecular devices. Chapters 3, 9 and 10 are available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.
Formal Methods. FM 2019 International Workshops
This book constitutes the refereed proceedings of the workshops which complemented the 23rd Symposium on Formal Methods, FM 2019, held in Porto, Portugal, in October 2019. This volume presents the papers that have been accepted for the following workshops: Third Workshop on Practical Formal Verification for Software Dependability, AFFORD 2019; 8th International Symposium From Data to Models and Back, DataMod 2019; First Formal Methods for Autonomous Systems Workshop, FMAS 2019; First Workshop on Formal Methods for Blockchains, FMBC 2019; 8th International Workshop on Formal Methods for Interactive Systems, FMIS 2019; First History of Formal Methods Workshop, HFM 2019; 8th International Workshop on Numerical and Symbolic Abstract Domains, NSAD 2019; 9th International Workshop on Open Community Approaches to Education, Research and Technology, OpenCERT 2019; 17th Overture Workshop, Overture 2019; 19th Refinement Workshop, Refine 2019; First International Workshop on Reversibility in Programming, Languages, and Automata, RPLA 2019; 10th International Workshop on Static Analysis and Systems Biology, SASB 2019; and the 10th Workshop on Tools for Automatic Program Analysis, TAPAS 2019.
Computational Methods in Systems Biology
This book constitutes the refereed proceedings of the 17th International Conference on Computational Methods in Systems Biology, CMSB 2019, held in Trieste, Italy, in September 2019. The 14 full papers, 7 tool papers and 11 posters were carefully reviewed and selected from 53 submissions. Topics of interest include formalisms for modeling biological processes; models and their biological applications; frameworks for model verification, validation, analysis, and simulation of biological systems; high-performance computational systems biology and parallel implementations; model inference from experimental data; model integration from biological databases; multi-scale modeling and analysis methods; computational approaches for synthetic biology; and case studies in systems and synthetic biology.
Computational Methods in Systems Biology
This book constitutes the proceedings of the 11th International Conference on Computational Methods in Systems Biology, CMSB 2013, held in Klosterneuburg, Austria, in September 2013. The 15 regular papers included in this volume were carefully reviewed and selected from 27 submissions. They deal with computational models for all levels, from molecular and cellular, to organs and entire organisms.
Working Together
Advances in the social sciences have emerged through a variety of research methods: field-based research, laboratory and field experiments, and agent-based models. However, which research method or approach is best suited to a particular inquiry is frequently debated and discussed. Working Together examines how different methods have promoted various theoretical developments related to collective action and the commons, and demonstrates the importance of cross-fertilization involving multimethod research across traditional boundaries. The authors look at why cross-fertilization is difficult to achieve, and they show ways to overcome these challenges through collaboration. The authors provide...
Handbook of Research on Computational Science and Engineering: Theory and Practice
By using computer simulations in research and development, computational science and engineering (CSE) allows empirical inquiry where traditional experimentation and methods of inquiry are difficult, inefficient, or prohibitively expensive. The Handbook of Research on Computational Science and Engineering: Theory and Practice is a reference for interested researchers and decision-makers who want a timely introduction to the possibilities in CSE to advance their ongoing research and applications or to discover new resources and cutting edge developments. Rather than reporting results obtained using CSE models, this comprehensive survey captures the architecture of the cross-disciplinary field, explores the long term implications of technology choices, alerts readers to the hurdles facing CSE, and identifies trends in future development.
