Genetic Design Automation: A Practical Approach for the Analysis, Verification and Synthesis of Genetic Logic Circuits 9783030523541, 9783030523558

Table of contents :
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