Genetic Design Automation

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Genetic Design Automation

Author : Hasan Baig
Publisher : Springer Nature
ISBN 13 : 3030523551
Total Pages : 171 pages
Book Rating : 4.0/5 (35 download)

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Book Synopsis Genetic Design Automation by : Hasan Baig

Download or read book Genetic Design Automation written by Hasan Baig and published by Springer Nature. This book was released on 2020-09-25 with total page 171 pages. Available in PDF, EPUB and Kindle. Book excerpt: This textbook introduces readers to the recent advances in the emerging field of genetic design automation (GDA). Starting with an introduction and the basic concepts of molecular biology, the authors provide an overview of various genetic design automation tools. The authors then present the DVASim tool (Dynamic Virtual Analyzer and Simulator) which is used for the analysis and verification of genetic logic circuits. This includes methods and algorithms for the timing and threshold value analyses of genetic logic circuits. Next, the book presents the GeneTech tool (A technology mapping tool for genetic circuits) and the methods developed for optimization, synthesis, and technology mapping of genetic circuits. Chapters are followed by exercises which give readers hands-on practice with the tools presented. The concepts and algorithms are thoroughly described, enabling readers to improve the tools or use them as a starting point to develop new tools. Both DVASim and GeneTech are available from the developer’s website, free of charge. This book is intended for a multidisciplinary audience of computer scientists, engineers and biologists. It provides enough background knowledge for computer scientists and engineers, who usually do not have any background in biology but are interested to get involved in this domain. This book not only presents an accessible basic introduction to molecular biology, it also includes software tools which allow users to perform laboratory experiments in a virtual in-silico environment. This helps newbies to get a quick start in understanding and developing genetic design automation tools. The third part of this book is particular useful for biologists who usually find it difficult to grasp programming and are reluctant to developing computer software. They are introduced to the graphical programming language, LabVIEW, from which they can start developing computer programs rapidly. Readers are further provided with small projects which will help them to start developing GDA tools.

Genetic Algorithms and Engineering Design

Author : Mitsuo Gen
Publisher : John Wiley & Sons
ISBN 13 : 9780471127413
Total Pages : 436 pages
Book Rating : 4.1/5 (274 download)

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Book Synopsis Genetic Algorithms and Engineering Design by : Mitsuo Gen

Download or read book Genetic Algorithms and Engineering Design written by Mitsuo Gen and published by John Wiley & Sons. This book was released on 1997-01-21 with total page 436 pages. Available in PDF, EPUB and Kindle. Book excerpt: The last few years have seen important advances in the use ofgenetic algorithms to address challenging optimization problems inindustrial engineering. Genetic Algorithms and Engineering Designis the only book to cover the most recent technologies and theirapplication to manufacturing, presenting a comprehensive and fullyup-to-date treatment of genetic algorithms in industrialengineering and operations research. Beginning with a tutorial on genetic algorithm fundamentals andtheir use in solving constrained and combinatorial optimizationproblems, the book applies these techniques to problems in specificareas--sequencing, scheduling and production plans, transportationand vehicle routing, facility layout, location-allocation, andmore. Each topic features a clearly written problem description,mathematical model, and summary of conventional heuristicalgorithms. All algorithms are explained in intuitive, rather thanhighly-technical, language and are reinforced with illustrativefigures and numerical examples. Written by two internationally acknowledged experts in the field,Genetic Algorithms and Engineering Design features originalmaterial on the foundation and application of genetic algorithms,and also standardizes the terms and symbols used in othersources--making this complex subject truly accessible to thebeginner as well as to the more advanced reader. Ideal for both self-study and classroom use, this self-containedreference provides indispensable state-of-the-art guidance toprofessionals and students working in industrial engineering,management science, operations research, computer science, andartificial intelligence. The only comprehensive, state-of-the-arttreatment available on the use of genetic algorithms in industrialengineering and operations research . . . Written by internationally recognized experts in the field ofgenetic algorithms and artificial intelligence, Genetic Algorithmsand Engineering Design provides total coverage of currenttechnologies and their application to manufacturing systems.Incorporating original material on the foundation and applicationof genetic algorithms, this unique resource also standardizes theterms and symbols used in other sources--making this complexsubject truly accessible to students as well as experiencedprofessionals. Designed for clarity and ease of use, thisself-contained reference: * Provides a comprehensive survey of selection strategies, penaltytechniques, and genetic operators used for constrained andcombinatorial optimization problems * Shows how to use genetic algorithms to make production schedules,solve facility/location problems, make transportation/vehiclerouting plans, enhance system reliability, and much more * Contains detailed numerical examples, plus more than 160auxiliary figures to make solution procedures transparent andunderstandable

A Computational Framework for the Automated Design of Synthetic Genetic Circuits

Author : Linh Viet Huynh
Publisher :
ISBN 13 : 9781369616040
Total Pages : pages
Book Rating : 4.6/5 (16 download)

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Book Synopsis A Computational Framework for the Automated Design of Synthetic Genetic Circuits by : Linh Viet Huynh

Download or read book A Computational Framework for the Automated Design of Synthetic Genetic Circuits written by Linh Viet Huynh and published by . This book was released on 2016 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Synthetic biology is an emerging research field with potential applications for a variety of disciplines from development of therapeutics, medicine to biofuel production and agriculture. In synthetic biology, we design a genetic circuit (i.e. a set of genetic parts and their interaction) encoded in the genetic material of a natural biological system to make this system exhibit novel functions. However, almost all genetic circuits were still designed by trial-and-error and tinkering approaches. Therefore, computational computer aided design (CAD) tools are essential for designing circuits faster, better and more reliably. Numerous CAD tools have been developed recently, however, there are still at least three challenges that prevent us building a CAD tool that is applicable for experimentalists: (i) How can we make a reliable circuit behavior prediction to guide the design work? (ii) How can we search for an optimal circuit from a huge circuit space due to the increase of both the number of genetic parts and the circuit complexity? (iii) How can we integrate all computational techniques into an unique tool that experimentalists can access? This dissertation proposed novel approaches to address these challenges. First, I proposed a novel parameter inference method to achieve more exact parameter values and thus we could provide a more reliable behavior prediction of a circuit. Second, I proposed two novel methods to search for circuits that behavior best approximated the desired one and the construction was simplest. Third, I introduced a computational framework that integrated both the work of simulating a circuit with inferred parameter values and optimizing the circuit design for a given user specification. Our CAD tool, SBROME, can utilize experimental data systematically to improve circuit behavior prediction, organize parts and their related parameter values in an unified database, and optimize circuit construction by reusing the old ones. In addition, an evaluation with a benchmark of 11 circuits and a curated dataset of experimental data (135 publications that contain 118 circuits and 165 genetic parts) also showed encouraging results. This dissertation contributes computational solutions that can help us move the field of synthetic biology closer to practical applications.

Biodefense in the Age of Synthetic Biology

Author : National Academies of Sciences, Engineering, and Medicine
Publisher : National Academies Press
ISBN 13 : 0309465184
Total Pages : 189 pages
Book Rating : 4.3/5 (94 download)

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Book Synopsis Biodefense in the Age of Synthetic Biology by : National Academies of Sciences, Engineering, and Medicine

Download or read book Biodefense in the Age of Synthetic Biology written by National Academies of Sciences, Engineering, and Medicine and published by National Academies Press. This book was released on 2019-01-05 with total page 189 pages. Available in PDF, EPUB and Kindle. Book excerpt: Scientific advances over the past several decades have accelerated the ability to engineer existing organisms and to potentially create novel ones not found in nature. Synthetic biology, which collectively refers to concepts, approaches, and tools that enable the modification or creation of biological organisms, is being pursued overwhelmingly for beneficial purposes ranging from reducing the burden of disease to improving agricultural yields to remediating pollution. Although the contributions synthetic biology can make in these and other areas hold great promise, it is also possible to imagine malicious uses that could threaten U.S. citizens and military personnel. Making informed decisions about how to address such concerns requires a realistic assessment of the capabilities that could be misused. Biodefense in the Age of Synthetic Biology explores and envisions potential misuses of synthetic biology. This report develops a framework to guide an assessment of the security concerns related to advances in synthetic biology, assesses the levels of concern warranted for such advances, and identifies options that could help mitigate those concerns.

Asynchronous Circuit Design

Author : Chris J. Myers
Publisher : John Wiley & Sons
ISBN 13 : 0471464120
Total Pages : 424 pages
Book Rating : 4.4/5 (714 download)

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Book Synopsis Asynchronous Circuit Design by : Chris J. Myers

Download or read book Asynchronous Circuit Design written by Chris J. Myers and published by John Wiley & Sons. This book was released on 2004-04-05 with total page 424 pages. Available in PDF, EPUB and Kindle. Book excerpt: With asynchronous circuit design becoming a powerful tool in thedevelopment of new digital systems, circuit designers are expectedto have asynchronous design skills and be able to leverage them toreduce power consumption and increase system speed. This book walksreaders through all of the different methodologies of asynchronouscircuit design, emphasizing practical techniques and real-worldapplications instead of theoretical simulation. The only guide ofits kind, it also features an ftp site complete with supportmaterials. Market: Electrical Engineers, Computer Scientists, DeviceDesigners, and Developers in industry. An Instructor Support FTP site is available from the Wileyeditorial department.

The Science and Applications of Synthetic and Systems Biology

Author : Institute of Medicine
Publisher : National Academies Press
ISBN 13 : 0309219396
Total Pages : 570 pages
Book Rating : 4.3/5 (92 download)

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Book Synopsis The Science and Applications of Synthetic and Systems Biology by : Institute of Medicine

Download or read book The Science and Applications of Synthetic and Systems Biology written by Institute of Medicine and published by National Academies Press. This book was released on 2011-12-30 with total page 570 pages. Available in PDF, EPUB and Kindle. Book excerpt: Many potential applications of synthetic and systems biology are relevant to the challenges associated with the detection, surveillance, and responses to emerging and re-emerging infectious diseases. On March 14 and 15, 2011, the Institute of Medicine's (IOM's) Forum on Microbial Threats convened a public workshop in Washington, DC, to explore the current state of the science of synthetic biology, including its dependency on systems biology; discussed the different approaches that scientists are taking to engineer, or reengineer, biological systems; and discussed how the tools and approaches of synthetic and systems biology were being applied to mitigate the risks associated with emerging infectious diseases. The Science and Applications of Synthetic and Systems Biology is organized into sections as a topic-by-topic distillation of the presentations and discussions that took place at the workshop. Its purpose is to present information from relevant experience, to delineate a range of pivotal issues and their respective challenges, and to offer differing perspectives on the topic as discussed and described by the workshop participants. This report also includes a collection of individually authored papers and commentary.

Artificial Intelligence in Design ’96

Author : John S. Gero
Publisher : Springer Science & Business Media
ISBN 13 : 9400902794
Total Pages : 765 pages
Book Rating : 4.4/5 (9 download)

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Book Synopsis Artificial Intelligence in Design ’96 by : John S. Gero

Download or read book Artificial Intelligence in Design ’96 written by John S. Gero and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 765 pages. Available in PDF, EPUB and Kindle. Book excerpt: Change is one of the most significant parameters in our society. Designers are amongst the primary change agents for any society. As a consequence design is an important research topic in engineering and architecture and related disciplines, since design is not only a means of change but is also one of the keystones to economic competitiveness and the fundamental precursor to manufacturing. The development of computational models founded on the artificial intelligence paradigm has provided an impetus for much of current design research -both computational and cognitive. These forms of design research have only been carried out in the last decade or so and in the temporal sense they are still immature. Notwithstanding this immaturity, noticeable advances have been made both in extending our understanding of design and in developing tools based on that understanding. Whilst many researchers in the field of artificial intelligence in design utilise ideas about how humans design as one source of concepts there is normally no attempt to model human designers. Rather the results of the research presented in this volume demonstrate approaches to increasing our understanding of design as a process.

Biomolecular and Computational Frameworks for Genetic Circuit Design

Author : Alec A. K. Nielsen
Publisher :
ISBN 13 :
Total Pages : 322 pages
Book Rating : 4.:/5 (988 download)

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Book Synopsis Biomolecular and Computational Frameworks for Genetic Circuit Design by : Alec A. K. Nielsen

Download or read book Biomolecular and Computational Frameworks for Genetic Circuit Design written by Alec A. K. Nielsen and published by . This book was released on 2017 with total page 322 pages. Available in PDF, EPUB and Kindle. Book excerpt: Living cells naturally use gene regulatory networks termed "genetic circuits" to exhibit complex behaviors such as signal processing, decision-making, and spatial organization. The ability to rationally engineer genetic circuits has applications in several biotechnology areas including therapeutics, agriculture, and materials. However, genetic circuit construction has traditionally been time- and labor-intensive; tuning regulator expression often requires manual trial-and-error, and the results frequently function incorrectly. To improve the reliability and pace of genetic circuit engineering, we have developed biomolecular and computational frameworks for designing genetic circuits. A scalable biomolecular platform is a prerequisite for genetic circuits design. In this thesis, we explore TetR-family repressors and the CRISPRi system as candidates. First, we applied 'part mining' to build a library of TetR-family repressors gleaned from prokaryotic genomes. A subset were used to build synthetic 'NOT gates' for use in genetic circuits. Second, we tested catalytically-inactive dCas9, which employs small guide RNAs (sgRNAs) to repress genetic loci via the programmability of RNA:DNA base pairing. To this end, we use dCas9 and synthetic sgRNAs to build transcriptional logic gates with high on-target repression and negligible cross-talk, and connected them to perform computation in living cells. We further demonstrate that a synthetic circuit can directly interface a native E. coli regulatory network. To accelerate the design of circuits that employ these biomolecular platforms, we created a software design tool called Cello, in which a user writes a high-level functional specification that is automatically compiled to a DNA sequence. Algorithms first construct a circuit diagram, then assign and connect genetic "gates", and simulate performance. Reliable circuit design requires the insulation of gates from genetic context, so that they function identically when used in different circuits. We used Cello to design the largest library of genetic circuits to date, where each DNA sequence was built as predicted by the software with no additional tuning. Across all circuits 92% of the output states functioned as predicted. Design automation simplifies the incorporation of genetic circuits into biotechnology projects that require decisionmaking, control, sensing, or spatial organization.

Engineering Genetic Circuits

Author : Chris J. Myers
Publisher : CRC Press
ISBN 13 : 1420083252
Total Pages : 302 pages
Book Rating : 4.4/5 (2 download)

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Book Synopsis Engineering Genetic Circuits by : Chris J. Myers

Download or read book Engineering Genetic Circuits written by Chris J. Myers and published by CRC Press. This book was released on 2016-04-19 with total page 302 pages. Available in PDF, EPUB and Kindle. Book excerpt: This text presents the modeling, analysis, and design methods for systems biology. It discusses how to examine experimental data to learn about mathematical models, develop efficient abstraction and simulation methods to analyze these models, and use analytical methods to design new circuits. The author reviews basic molecular biology and biochemistry principles, covers several methods for modeling and analyzing genetic circuits, and uses phage lambda as an example throughout to help illustrate the methods. He also explores the emerging area of synthetic biology. iBioSim software, lecture slides, and a password-protected solutions manual are available on the author's website.

Genetic Algorithms

Author : Kim-Fung Man
Publisher : Springer Science & Business Media
ISBN 13 : 144710577X
Total Pages : 346 pages
Book Rating : 4.4/5 (471 download)

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Book Synopsis Genetic Algorithms by : Kim-Fung Man

Download or read book Genetic Algorithms written by Kim-Fung Man and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 346 pages. Available in PDF, EPUB and Kindle. Book excerpt: This comprehensive book gives a overview of the latest discussions in the application of genetic algorithms to solve engineering problems. Featuring real-world applications and an accompanying disk, giving the reader the opportunity to use an interactive genetic algorithms demonstration program.

Automation in Proteomics and Genomics

Author : Gil Alterovitz
Publisher : John Wiley & Sons
ISBN 13 : 9780470741177
Total Pages : 340 pages
Book Rating : 4.7/5 (411 download)

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Book Synopsis Automation in Proteomics and Genomics by : Gil Alterovitz

Download or read book Automation in Proteomics and Genomics written by Gil Alterovitz and published by John Wiley & Sons. This book was released on 2009-03-16 with total page 340 pages. Available in PDF, EPUB and Kindle. Book excerpt: In the last decade DNA sequencing costs have decreased over a magnitude, largely because of increasing throughput by incremental advances in tools, technologies and process improvements. Further cost reductions in this and in related proteomics technologies are expected as a result of the development of new high-throughput techniques and the computational machinery needed to analyze data generated. Automation in Proteomics & Genomics: An Engineering Case-Based Approach describes the automation technology currently in the areas of analysis, design, and integration, as well as providing basic biology concepts behind proteomics and genomics. The book also discusses the current technological limitations that can be viewed as an emerging market rather than a research bottleneck. Topics covered include: molecular biology fundamentals: from ‘blueprint’ (DNA) to ‘task list’ (RNA) to ‘molecular machine’ (protein); proteomics methods and technologies; modelling protein networks and interactions analysis via automation: DNA sequencing; microarrays and other parallelization technologies; protein characterization and identification; protein interaction and gene regulatory networks design via automation: DNA synthesis; RNA by design; building protein libraries; synthetic networks integration: multiple modalities; computational and experimental methods; trends in automation for genomics and proteomics new enabling technologies and future applications Automation in Proteomics & Genomics: An Engineering Case-Based Approach is an essential guide to the current capabilities and challenges of high-throughput analysis of genes and proteins for bioinformaticians, engineers, chemists, and biologists interested in developing a cross-discipline problem-solving based approach to systems biology.

Computational Intelligence in Software Engineering

Author : Witold Pedrycz
Publisher : World Scientific
ISBN 13 : 9789810235031
Total Pages : 504 pages
Book Rating : 4.2/5 (35 download)

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Book Synopsis Computational Intelligence in Software Engineering by : Witold Pedrycz

Download or read book Computational Intelligence in Software Engineering written by Witold Pedrycz and published by World Scientific. This book was released on 1998 with total page 504 pages. Available in PDF, EPUB and Kindle. Book excerpt: This unique volume is the first publication on software engineering and computational intelligence (CI) viewed as a synergistic interplay of neurocomputing, granular computation (including fuzzy sets and rough sets), and evolutionary methods. It presents a unified view of CI in the context of software engineering. The book addresses a number of crucial issues: what is CI, what role does it play in software development, how are CI elements built into successive phases of the software life cycle, and what is the role played by CI in quantifying fundamental features of software artifacts? With contributions from leading researchers and practitioners, the book provides the reader with a wealth of new concepts and approaches, complete algorithms, in-depth case studies, and thought-provoking exercises. The topics coverage include neurocomputing, granular as well as evolutionary computing, object-oriented analysis and design in software engineering. There is also an extensive bibliography.

Genetic Algorithms for VLSI Design, Layout & Test Automation

Author : Pinaki Mazumder
Publisher : Prentice Hall
ISBN 13 : 9780130115669
Total Pages : 0 pages
Book Rating : 4.1/5 (156 download)

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Book Synopsis Genetic Algorithms for VLSI Design, Layout & Test Automation by : Pinaki Mazumder

Download or read book Genetic Algorithms for VLSI Design, Layout & Test Automation written by Pinaki Mazumder and published by Prentice Hall. This book was released on 1999 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides details about some of the EDA applications where GAs have been used. These applications include partitioning, automatic placement and routing, technology mapping for FPGAs, automatic test generation, and power estimation. One chapter is devoted to each of these topics. The objective is to provide examples where GAs have been successfull applied in the past so that the reader will be able to apply similar techniques in solving his/her own problems.

Neurocomputing for Design Automation

Author : Hyo Seon Park
Publisher : CRC Press
ISBN 13 : 9780849320927
Total Pages : 242 pages
Book Rating : 4.3/5 (29 download)

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Book Synopsis Neurocomputing for Design Automation by : Hyo Seon Park

Download or read book Neurocomputing for Design Automation written by Hyo Seon Park and published by CRC Press. This book was released on 1998-05-22 with total page 242 pages. Available in PDF, EPUB and Kindle. Book excerpt: Neurocomputing for Design Automation provides innovative design theories and computational models with two broad objectives: automation and optimization. This singular book: Presents an introduction to the automation and optimization of engineering design of complex engineering systems using neural network computing Outlines new computational models and paradigms for automating the complex process of design for unique engineering systems, such as steel highrise building structures Applies design theories and models to the solution of structural design problems Integrates three computing paradigms: mathematical optimization, neural network computing, and parallel processing The applications described are general enough to be applied directly or by extension to other engineering design problems, such as aerospace or mechanical design. Also, the computational models are shown to be stable and robust - particularly suitable for design automation of large systems, such as a 144-story steel super-highrise building structure with more than 20,000 members. The book provides an exceptional framework for the automation and optimization of engineering design, focusing on a new computing paradigm - neural networks computing. It presents the automation of complex systems at a new and higher level never achieved before.

Cell-Free Synthetic Biology

Author : Jian Li
Publisher : Frontiers Media SA
ISBN 13 : 2889740803
Total Pages : 205 pages
Book Rating : 4.8/5 (897 download)

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Book Synopsis Cell-Free Synthetic Biology by : Jian Li

Download or read book Cell-Free Synthetic Biology written by Jian Li and published by Frontiers Media SA. This book was released on 2022-01-13 with total page 205 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Biomimicry for Optimization, Control, and Automation

Author : Kevin M. Passino
Publisher : Springer Science & Business Media
ISBN 13 : 1846280699
Total Pages : 934 pages
Book Rating : 4.8/5 (462 download)

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Book Synopsis Biomimicry for Optimization, Control, and Automation by : Kevin M. Passino

Download or read book Biomimicry for Optimization, Control, and Automation written by Kevin M. Passino and published by Springer Science & Business Media. This book was released on 2005-09-08 with total page 934 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biomimicry uses our scienti?c understanding of biological systems to exploit ideas from nature in order to construct some technology. In this book, we focus onhowtousebiomimicryof the functionaloperationofthe “hardwareandso- ware” of biological systems for the development of optimization algorithms and feedbackcontrolsystemsthatextendourcapabilitiestoimplementsophisticated levels of automation. The primary focus is not on the modeling, emulation, or analysis of some biological system. The focus is on using “bio-inspiration” to inject new ideas, techniques, and perspective into the engineering of complex automation systems. There are many biological processes that, at some level of abstraction, can berepresentedasoptimizationprocesses,manyofwhichhaveasa basicpurpose automatic control, decision making, or automation. For instance, at the level of everyday experience, we can view the actions of a human operator of some process (e. g. , the driver of a car) as being a series of the best choices he or she makes in trying to achieve some goal (staying on the road); emulation of this decision-making process amounts to modeling a type of biological optimization and decision-making process, and implementation of the resulting algorithm results in “human mimicry” for automation. There are clearer examples of - ological optimization processes that are used for control and automation when you consider nonhuman biological or behavioral processes, or the (internal) - ology of the human and not the resulting external behavioral characteristics (like driving a car). For instance, there are homeostasis processes where, for instance, temperature is regulated in the human body.

Synthetic Biology

Author : Daniel G. Gibson
Publisher : Perspectives Cshl
ISBN 13 : 9781621821182
Total Pages : 0 pages
Book Rating : 4.8/5 (211 download)

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Book Synopsis Synthetic Biology by : Daniel G. Gibson

Download or read book Synthetic Biology written by Daniel G. Gibson and published by Perspectives Cshl. This book was released on 2017 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Synthetic biology involves the rational design and construction of biological components and systemsfrom genetic elements and metabolic pathways to entirely new organisms. Progress in this field has been rapid, and it promises to significantly expand our capabilities in biotechnology, medicine, and agriculture. Written and edited by experts in the field, this collection from Cold Spring Harbor Perspectives in Biology examines the tools and techniques employed by synthetic biologists, how these may be used to develop new drugs, diagnostic approaches, food sources, and clean energy, and what the field of synthetic biology has taught us about natural living systems. The contributors discuss advances in DNA synthesis and assembly, genome editing (e.g., CRISPR/Cas9), and artificial genetic systems. Progress in designing complex genetic switches and circuits, expanding the genetic code, modifying cellular organization, producing proteins using cell-free systems, and developing biodesign automation tools is also covered. The authors also explore ways to produce new organisms and products that have particular attributesfor example, microbial "molecular factories," synthetic organs and tissues, and plants with novel traits. This volume is an essential resource for molecular, cell, and systems biologists who seek to engineer living systems for human benefit.