Genetic Design Automation : A Practical Approach for the Analysis, Verification and Synthesis of Genetic Logic Circuits

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. Front Matter ....Pages i-xvi Front Matter ....Pages 1-1 Introduction (Hasan Baig, Jan Madsen)....Pages 3-10 Fundamentals of Molecular Biology and Genetic Circuits (Hasan Baig, Jan Madsen)....Pages 11-23 Front Matter ....Pages 25-25 Virtual Experimentation Using DVASim (Hasan Baig, Jan Madsen)....Pages 27-36 Genetic Circuits Timing Analysis (Hasan Baig, Jan Madsen)....Pages 37-60 Genetic Circuits Logic Analysis (Hasan Baig, Jan Madsen)....Pages 61-80 Technology Mapping of Genetic Circuits (Hasan Baig, Jan Madsen)....Pages 81-101 Front Matter ....Pages 103-103 Learn to Program Rapidly with Graphical Programming (Hasan Baig, Jan Madsen)....Pages 105-129 Project 1: Stochastic Simulations (Hasan Baig, Jan Madsen)....Pages 131-141 Project 2: Parsing the SBML File (Hasan Baig, Jan Madsen)....Pages 143-162 Back Matter ....Pages 163-164