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.
Author(s): Hasan Baig, Jan Madsen
Year: 2020
Language: English
Pages: 164
City: Cham
Preface
Contents
Acronyms
Part I Introduction
1 Introduction
1.1 Why Computations in Cells?
1.2 State-of-the-Art
1.3 Motivation
1.4 Scope of This Book
1.4.1 Virtual Experimentation
1.4.2 Timing and Threshold Analysis
1.4.3 Automatic Logic Validation
1.4.4 Effortless Circuit Designing
1.5 Book Organization
1.6 Resources
1.7 Conventions Used in This Book
References
2 Fundamentals of Molecular Biology and Genetic Circuits
2.1 Central Dogma of Molecular Biology
2.2 Example Genetic Circuit: Lac Operon
2.2.1 Genetic Logic in lac operon
2.2.2 The Standard SBOL Representation of lac operon
2.3 Standards
2.4 Genetic Design Automation (GDA) Tools
2.4.1 Sequence Editing Tools
2.4.2 Biochemical Modeling and Design Composition Tools
2.4.3 Genetic Mapping Tools
References
Part II Virtual Experimentation and Technology Mapping of Genetic Circuits
3 Virtual Experimentation Using DVASim
3.1 Motivation
3.2 Experimental Approach
3.2.1 SBML Support
3.2.2 Virtual Instrumentation
3.2.3 Virtual Experimentation
3.2.4 Logic Verification and Timing Analysis
3.3 Summary
Problems
References
4 Genetic Circuits Timing Analysis
4.1 Methodology
4.1.1 Preliminary Analysis of Threshold Value
4.1.2 Preliminary Analysis of Propagation Delay
4.1.3 D-VASim Plug-in for Threshold Value and Propagation Delay Analyses
4.1.3.1 Illustrative Explanation of the Algorithm
4.2 Experimentation by Simulation
4.2.1 Effects of Varying kd on the Threshold Values and Propagation Delays
4.2.2 Effects of Varying Threshold Values on the Propagation Delays
4.2.3 Effects of Varying Threshold Values on the % Output Consistency at High kd
4.2.4 Other Parameters Effecting the Threshold Values
4.2.5 Intermediate Propagation Delays
4.2.6 Experimentation on the SBML Model of Real Genetic Circuit
4.3 Summary
Problems
References
5 Genetic Circuits Logic Analysis
5.1 Methodology
5.1.1 Overview
5.1.2 Input Combinations Analysis
5.1.3 Variation Analysis and Boolean Expression Construction
5.2 Experimentation by Simulation
5.2.1 Analysis of the SBOL-SBML Converted Genetic Circuit Models
5.2.2 Logic Analysis and Verification
5.2.3 Effects of Varying Threshold Value on Circuit's Behavior
5.2.4 Performance Analysis
5.3 Summary
Problems
References
6 Technology Mapping of Genetic Circuits
6.1 Introduction and Motivation
6.2 Methodology
6.2.1 Logic Optimization
6.2.2 Logic Synthesis
6.2.3 Genetic Technology Mapping
6.3 GeneTech Interface
6.4 Experimentation by Simulation
6.5 Summary
Problems
References
Part III GDA Tool Development: A Quick Project-Oriented Approach
7 Learn to Program Rapidly with Graphical Programming
7.1 Getting Familiar with LabVIEW Interface
7.2 First LabVIEW Program
7.2.1 Creating Controls and Indicators
7.2.2 Building Graphical Logic
7.2.2.1 Conditional Logic: Case Structures
7.2.2.2 Continuous Iteration Using While Loops
7.3 Second LabVIEW Program
7.3.1 Reading a File in LabVIEW
7.3.2 Arrays and For Loops
7.3.3 Sequence Structures
7.3.4 Creating a SubVI
7.3.4.1 Creating an Icon of SubVI
7.3.5 Putting It Altogether
7.4 Other Important Structures
7.4.1 Formula Node
7.4.2 Event Structure
7.5 Summary
Problems
8 Project 1: Stochastic Simulations
8.1 Gillespie's Stochastic Simulation Algorithm
8.2 Implementation
8.3 Discussion
8.4 Challenge
8.5 Summary
9 Project 2: Parsing the SBML File
9.1 SBML Parsing
9.1.1 Extraction of Species Data
9.1.2 Extraction of Parameters Data
9.1.3 Extraction of Reactions Data
9.2 Challenge
9.3 Summary
Index
