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Engineering Genetic Circuits: Design

Engineering Genetic Circuits: Design

This course is part of Engineering Genetic Circuits Specialization

Instructors: Chris Myers

5,129 already enrolled

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5 modules

Gain insight into a topic and learn the fundamentals.

38 reviews

Beginner level

Recommended experience

Flexible schedule

2 weeks at 10 hours a week

Learn at your own pace

Build toward a degree

Learn more

5 modules

Gain insight into a topic and learn the fundamentals.

38 reviews

Beginner level

Recommended experience

Flexible schedule

2 weeks at 10 hours a week

Learn at your own pace

Build toward a degree

Learn more

What you'll learn

Identify the different types of cells, their components, and structure.
Discover the underlying structure of devices and their connection to genetic parts.
Contrast different experimental techniques used in genetic construction.
Evaluate the different principles used in genetic circuit design.

Skills you'll gain

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Assessments

10 assignments

Taught in English

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This course is part of the Engineering Genetic Circuits Specialization

When you enroll in this course, you'll also be enrolled in this Specialization.

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Gain a foundational understanding of a subject or tool
Develop job-relevant skills with hands-on projects
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There are 5 modules in this course

This course gives an introduction to the biology and biochemistry necessary to understand genetic circuits. It starts by providing an engineering viewpoint on genetic circuit design and a review of cells and their structure. The second module introduces genetic parts and the importance of standards followed by a discussion of genetic devices used within circuit design. The last two modules cover experimental techniques and construction methods and principles applied during the design process.  

Module details

This week gives a brief introduction to the biology and biochemistry necessary to understand genetic circuits. The material covered is only a basic overview, since it is usually the topic of whole courses. It should, however, give the grounding necessary to begin studying the modeling, analysis, and design of genetic circuits.

What's included

8 videos5 readings3 assignments

8 videosTotal 119 minutes

What is Systems Biology?10 minutes
The Phage Lambda Example14 minutes
What is Synthetic Biology?9 minutes
A Brief History of Synthetic Biology23 minutes
Cells and Viruses16 minutes
Macromolecules18 minutes
Genomes12 minutes
Genetic Circuits16 minutes

5 readingsTotal 66 minutes

Course Updates and Accessibility Support1 minute
Non-Credit Students: Welcome and Where to Find Help10 minutes
Adventures in Synthetic Biology10 minutes
A Brief History of Synthetic Biology30 minutes
Engineering Genetic Circuits - Chapter 1 (Section 1.1 to 1.6)15 minutes

3 assignmentsTotal 55 minutes

Instructions on accessing reading materials5 minutes
Brief Introduction to Biochemistry20 minutes
Introduction to Synthetic Biology30 minutes

This week highlights the importance of standards in synthetic biology as an engineering discipline. Furthermore, the week introduces genetic parts - the basic building used to construct genetic circuits.

What's included

17 videos10 readings3 assignments

17 videosTotal 121 minutes

Sequence Ontology6 minutes
SBOL Visual8 minutes
Standard Parts3 minutes
Data Repositories19 minutes
FASTA and GenBank Standards5 minutes
SBOL Data Model Overview3 minutes
SBOL Data Model Details20 minutes
SBOL Data Model Advanced Elements6 minutes
Conversion of iGEM dataset4 minutes
Comparison of Data Standards2 minutes
Promoters10 minutes
Operator Sites21 minutes
Ribosome Binding Sites4 minutes
Protein Coding Regions2 minutes
Terminators2 minutes
SynBioHub Tutorial3 minutes
Excel2SBOL Tutorial3 minutes

10 readingsTotal 265 minutes

Sequence Ontology30 minutes
SBOL Visual15 minutes
SynBioHub15 minutes
SBOLme15 minutes
JBEI ICE30 minutes
SBOL Version 130 minutes
SBOL Version 230 minutes
SBOL Version 330 minutes
Engineering Genetic Circuits - Chapter 1 (Section 1.7)10 minutes
Common Genetic Parts60 minutes

3 assignmentsTotal 45 minutes

Resources15 minutes
SBOL Data Model15 minutes
Genetic Part Selection15 minutes

This week introduces genetic devices, the aggregation of multiple genetic parts. Basic rules for composing, as well as different types of devices, are introduced, as well.

What's included

11 videos2 readings2 assignments1 peer review

11 videosTotal 74 minutes

Basic Rules of Devices8 minutes
Types of Devices10 minutes
Biological Logic Gates3 minutes
Genetic Inverter and Oscillator7 minutes
Basic Biological Logic Gates6 minutes
Chemical Inducer and One Gene Logic Gates4 minutes
Sequential Logic Circuits5 minutes
Genetic Toggle Switch6 minutes
Genetic Muller C-Element12 minutes
Genetic Circuit Design Challenges7 minutes
SBOLCanvas Tutorial8 minutes

2 readingsTotal 20 minutes

Engineering Genetic Circuits - Chapter 7 (Sections 7.1 to 7.3)10 minutes
Engineering Genetic Circuits - Chapter 7 (Sections 7.4 to 7.5)10 minutes

2 assignmentsTotal 25 minutes

Basic device rules15 minutes
Genetic Logic Identification10 minutes

1 peer reviewTotal 60 minutes

Genetic Device Design60 minutes

This week introduces techniques used to construct a genetic circuit. This includes commonly used methods like polymerase chain reaction for cloning and DNA assembly methods. Finally, construction methods to assemble different genetic parts are presented.

What's included

7 videos7 readings1 assignment1 peer review

7 videosTotal 39 minutes

Gene Cloning and Polymerase Chain Reaction6 minutes
Vectors and Plasmids3 minutes
DNA Assembly methods1 minute
BioBrick Standard Assembly11 minutes
Golden Gate Assembly7 minutes
End Homology Methods4 minutes
DNA Synthesis6 minutes

7 readingsTotal 109 minutes

PCR Demonstration4 minutes
Molecular Cloning30 minutes
Polymerase Chain Reaction30 minutes
BioBrick Standard Assembly10 minutes
Golden Gate Assembly20 minutes
Gibson Assembly10 minutes
SBOLDesigner and Benching Tutorial5 minutes

1 assignmentTotal 15 minutes

Experimental Techniques15 minutes

1 peer reviewTotal 60 minutes

Genetic Construction Planning60 minutes

This week introduces practical challenges in realizing genetic circuit designs.

What's included

5 videos2 readings1 assignment

5 videosTotal 43 minutes

Introduction9 minutes
Failure Modes13 minutes
Context Issues7 minutes
Alternative Genetic Circuit Design Styles10 minutes
The Road Ahead4 minutes

2 readingsTotal 60 minutes

Principles of Genetic Circuit Design30 minutes
Computational Synthetic Biology: Progress and the Road Ahead30 minutes

1 assignmentTotal 15 minutes

Potential Genetic Design Problems15 minutes

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Build toward a degree

This course is part of the following degree program(s) offered by University of Colorado Boulder. If you are admitted and enroll, your completed coursework may count toward your degree learning and your progress can transfer with you.¹