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Genetic Design Automation

Genetic Design Automation
Author: Hasan Baig
Publisher: Springer Nature
Total Pages: 171
Release: 2020-09-25
Genre: Technology & Engineering
ISBN: 3030523551
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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

Genetic Algorithms and Engineering Design
Author: Mitsuo Gen
Publisher: John Wiley & Sons
Total Pages: 436
Release: 1997-01-21
Genre: Technology & Engineering
ISBN: 9780471127413
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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

A Computational Framework for the Automated Design of Synthetic Genetic Circuits
Author: Linh Viet Huynh
Publisher:
Total Pages:
Release: 2016
Genre:
ISBN: 9781369616040
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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

Biodefense in the Age of Synthetic Biology
Author: National Academies of Sciences, Engineering, and Medicine
Publisher: National Academies Press
Total Pages: 189
Release: 2019-01-05
Genre: Technology & Engineering
ISBN: 0309465184
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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

Asynchronous Circuit Design
Author: Chris J. Myers
Publisher: John Wiley & Sons
Total Pages: 424
Release: 2004-04-05
Genre: Technology & Engineering
ISBN: 0471464120
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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.

Artificial Intelligence in Design ’96

Artificial Intelligence in Design ’96
Author: John S. Gero
Publisher: Springer Science & Business Media
Total Pages: 765
Release: 2012-12-06
Genre: Computers
ISBN: 9400902794
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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.

The Science and Applications of Synthetic and Systems Biology

The Science and Applications of Synthetic and Systems Biology
Author: Institute of Medicine
Publisher: National Academies Press
Total Pages: 570
Release: 2011-12-30
Genre: Science
ISBN: 0309219396
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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.

Engineering Genetic Circuits

Engineering Genetic Circuits
Author: Chris J. Myers
Publisher: CRC Press
Total Pages: 302
Release: 2016-04-19
Genre: Medical
ISBN: 1420083252
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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.

Biomolecular and Computational Frameworks for Genetic Circuit Design

Biomolecular and Computational Frameworks for Genetic Circuit Design
Author: Alec A. K. Nielsen
Publisher:
Total Pages: 322
Release: 2017
Genre:
ISBN:
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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.

Genetic Algorithms

Genetic Algorithms
Author: Kim-Fung Man
Publisher: Springer Science & Business Media
Total Pages: 346
Release: 2012-12-06
Genre: Mathematics
ISBN: 144710577X
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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.