Synthetic Biology and iGEM: Techniques, Development and Safety Concerns: An Omics Big-data Mining Perspective

Preface
About the Book
Contents
About the Editors
Chapter 1: Introduction to Synthetic Biology
	1.1 The History and Importance of Synthetic Biology
		1.1.1 Timeline for the Development of Synthetic Biology (Fig. 1.1)
	1.2 Synthetic Biology Techniques
		1.2.1 DNA and Gene Synthesis
		1.2.2 Sequencing
		1.2.3 Microfluidics
		1.2.4 Modularity
		1.2.5 Modeling
		1.2.6 Synthetic Transcription Factors
	1.3 Synthetic Biology Applications
		1.3.1 Biological Computers
		1.3.2 Biosensors
		1.3.3 Cell Transformation
		1.3.4 Designed Proteins
		1.3.5 Designed Nucleic Acid Systems
		1.3.6 Space Exploration
		1.3.7 Synthetic Life
		1.3.8 Drug Delivery Platforms
	1.4 The Synthetic Biology Frontiers
		1.4.1 Gene Editing
		1.4.2 Genome Engineering
		1.4.3 De Novo Protein Design
		1.4.4 Synthesis of Unnatural Materials
		1.4.5 Design of the Gene Circuit
		1.4.6 Directed Evolution
		1.4.7 Cell Factory/Therapy
		1.4.8 Big Data-Assisted Biological Design
		1.4.9 Education of Synthetic Biology
		1.4.10 Synthetic Biology Community
	1.5 The Future Challenges for Synthetic Biology
		1.5.1 Automation and Industrialization
		1.5.2 Deep Learning for DNA Design
		1.5.3 Designing with Whole-Cell Simulations
		1.5.4 Biosensing: Detecting Anything, Anywhere
		1.5.5 Real-Time Precise Control of Evolution
		1.5.6 Cellular Communities and Multicellularity
		1.5.7 Custom and Dynamic Synthetic Genomes
		1.5.8 Artificial Cells
		1.5.9 Materials with DNA-Encoded Properties
		1.5.10 Engineered Organisms for Sustainability Goals
	1.6 Synthetic Biology Case Studies
	References
Chapter 2: iGEM: The Competition on Synthetic Biology
	2.1 iGEM´s History and Current Status
	2.2 iGEM and Synthetic Biology Research
	2.3 iGEM´s Representative Projects
		2.3.1 iGEM Project by HUST-China 2021
		2.3.2 iGEM Project by HUST-China 2019
		2.3.3 iGEM Project by HUST-China 2018
		2.3.4 iGEM Project by XMU-China 2020
	2.4 iGEM Needs a Great Leap Forward
	2.5 iGEM: Bright Futures Toward Better Synthetic Biology
	References
Chapter 3: Synthetic Biology-Related Multiomics Data Integration and Data Mining Techniques
	3.1 Introduction to Multiomics
	3.2 Timeline of Omics Development
	3.3 Databases and Tools for Omics Studies
	3.4 Multiomics Applications
	3.5 Future Perspectives
	References
Chapter 4: Synthetic Biology: Technical Issues
	4.1 Introduction and Background
	4.2 DNA Synthesis and Assembly
		4.2.1 DNA Synthesis
		4.2.2 Biobricks and Standardization
		4.2.3 Homologous Recombination
			Different Models of Homologous Recombination
			Application of Homologous Recombination: Gene Knockout
		4.2.4 Golden Gate and Gibson Assembly
			Golden Gate
			Gibson Assembly
		4.2.5 Transformation-Associated Recombination (TAR)
	4.3 Gene-Editing Technology
		4.3.1 Cre-loxP and Conditional Editing
		4.3.2 ZFN and TALEN
		4.3.3 CRISPR/Cas
		4.3.4 MAGE/CAGE
			CAGE
			Integrated Application of MAGE and CAGE in Evolutionary
	4.4 Directed Evolution and Artificial Design
		4.4.1 Directed Evolution: PACE and RAGE
		4.4.2 Artificial Design Tools
	4.5 Chassis
		4.5.1 From Microorganisms to Cells
		4.5.2 Animals and Plants
		4.5.3 Cell-Free System
	References
Chapter 5: Synthetic Biology: Development Issues
	5.1 Challenges Faced by Synthetic Biology
		5.1.1 Predictability
			Data Collection
			Tools and Technology of Biological Design
		5.1.2 Competitiveness of Supply Chains
		5.1.3 Accessibility
	5.2 The Lack of a Standard Platform to Evaluate the Effectiveness of the Synthetic System
		5.2.1 Systems Modeling, Standards, and Metrology
	5.3 iGEM´s Issues
		5.3.1 iGEM: Is It for Elites or Commons?
	References
Chapter 6: Synthetic Biology: Safety Issues
	6.1 Biosafety Issues
		6.1.1 The ``Creation´´ of Life
		6.1.2 Biosafety
		6.1.3 Biosecurity
	6.2 Design Principles for Safety Control
		6.2.1 Potential Risks of Synthetic Biology
		6.2.2 Biosafety Concerns
		6.2.3 Ethical Concerns
	6.3 Code of Action for Safety Control
		6.3.1 Code of Conduct for Scientists
		6.3.2 Nationwide Governance
		6.3.3 Efforts by International Societies
	References
Chapter 7: Synthetic Biology: Data Resources, Web Services, and Visualizations
	7.1 iGEM Registry
		7.1.1 iGEM Registry Overview
		7.1.2 Catalog
		7.1.3 Repository
		7.1.4 Assembly
	7.2 Literature Resources
		7.2.1 PubMed Database (an Important Source of Literature Download)
		7.2.2 NCBI Bookshelf
		7.2.3 BLAST
		7.2.4 Blast-Type Selection
		7.2.5 Result Analysis
	7.3 Tools
		7.3.1 ENTREZ Search System
			EMBL-EBI Database
		7.3.2 Service
			Data Retrieval
			Protein Function Analysis
			Sequence Similarity Analysis
			Multiple Sequence Alignment
			Double Sequence Alignment
		7.3.3 Phylogenetic Analysis
		7.3.4 Sequence Format Conversion
		7.3.5 Sequence Statistics
		7.3.6 Sequence of Translation
	7.4 Databases
		7.4.1 GenBank
			GenBank Overview
		7.4.2 DDBJ
			DDBJ Overview
			Database
			Data Retrieval
			Data Analysis
		7.4.3 UniProt
			UniProt Overview
			Database
			UniParc
			UniProtKB
			UniRef
			Proteomes
		7.4.4 OpenWetWare
			OpenWetWare Overview
			Reference Materials
	References
Chapter 8: Synthetic Biology: Case Studies
	8.1 iGEM Project by HUST-China 2021
	8.2 iGEM Project by HUST-China 2019
	8.3 iGEM Project by HUST-China 2018
	8.4 iGEM Project by HUST-China 2017
	8.5 iGEM Project by XMU-China 2020
	8.6 iGEM Project by TUDelft 2017
	8.7 iGEM Project by TJUSLS China 2016
	8.8 iGEM Project by SCAU-China 2016
	8.9 iGEM Project by SJTU-Software 2019
	References
Chapter 9: Concluding Remarks
	References
Appendix
	Databases for Synthetic Biology
	Software for Synthetic Biology