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Chris Myers
This course gives an introduction to how to create genetic circuit models. These models leverage chemical reactions represented using the Systems Biology Markup Language (SBML). The second module introduces methods to simulate these models using ordinary differential equation (ODE) methods. The third module teach stochastic simulation methods. The fourth module introduces several variations of the stochastic simulation algorithm. Finally, the fifth module introduces genetic technology method that leverage computational analysis for selecting parts and verifying their performance.
Read more
This course gives an introduction to how to create genetic circuit models. These models leverage chemical reactions represented using the Systems Biology Markup Language (SBML). The second module introduces methods to simulate these models using ordinary differential equation (ODE) methods. The third module teach stochastic simulation methods. The fourth module introduces several variations of the stochastic simulation algorithm. Finally, the fifth module introduces genetic technology method that leverage computational analysis for selecting parts and verifying their performance.
Read more
This course gives an introduction to how to create genetic circuit models. These models leverage chemical reactions represented using the Systems Biology Markup Language (SBML). The second module introduces methods to simulate these models using ordinary differential equation (ODE) methods. The third module teach stochastic simulation methods. The fourth module introduces several variations of the stochastic simulation algorithm. Finally, the fifth module introduces genetic technology method that leverage computational analysis for selecting parts and verifying their performance.
This course can also be taken for academic credit as ECEA 5935, part of CU Boulder’s Master of Science in Electrical Engineering.
Register for this course and see more details by visiting:
OpenCourser.com/course/ks8rsm/engineering
What's inside
Syllabus
Genetic Circuit Models
This week will describe the basics of modeling biological systems using chemical reactions, how these models can be represented using the Systems Biology Markup Language (SBML) standard, and how these models can be constructed using software tools such as iBioSim.
Read more
Syllabus
Genetic Circuit Models
This week will describe the basics of modeling biological systems using chemical reactions, how these models can be represented using the Systems Biology Markup Language (SBML) standard, and how these models can be constructed using software tools such as iBioSim.
Read more
Genetic Circuit Analysis (ODEs)
This module will introduce the theory and methods for the analysis of genetic circuit models using ordinary differential equations (ODEs). In particular, it will describe the classical chemical kinetic model, numerical methods for ODE simulation of these models, and techniques to analyze these ODE models qualitatively.
Stochastic Analysis
This module will introduce stochastic analysis methods for genetic circuits. In particular, it will introduce the stochastic chemical kinetics model, Gillespie's Stochastic Simulation Algorithm (SSA) to analyze these models, and various alternative stochastic analysis methods. Finally, the module will conclude with some additional topics: the Chemical Langevin Equation, stochastic Petri nets, the phage lambda model, and spatial Gillespie methods.
SSA Variations
This module presents several variations on the SSA algorithm to solve particular analysis problems. In particular, the hierarchical SSA (hSSA) methods enable the analysis of large models, the weighted SSA (wSSA) methods allow for the analysis of rare events, and the incremental SSA (iSSA) methods enable the determination of typical behaviors.
Genetic Circuit Technology Mapping
This module presents various ways that modeling can be utilized in genetic circuit design to select parts for optimal performance.
Good to know
Good to know
Know what's good ,
what to watch for , and
possible dealbreakers
Modules 1-3 cover core genetic circuit modeling and analysis
Module 4 covers variations of stochastic simulations
Provides a high-level view of genetic circuit technology
Teaches foundational concepts in genetic modeling using SBML
Covers advanced topics such as hSSA, wSSA, iSSA methods
Introduces computational analysis for part selection and performance verification
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Activities
Be better prepared
before
your course. Deepen your understanding
during
and
after
it. Supplement your coursework and achieve mastery of the topics covered
in Engineering Genetic Circuits: Modeling and Analysis with these
activities:
Summarize key concepts and examples
Show steps
Enhance your understanding and retention by creating a concise summary of key concepts and examples covered in the course materials.
Show steps
-
Review lecture notes, textbook chapters, and other course resources
-
Identify and extract the most important concepts and examples
-
Summarize these concepts and examples in a clear and concise format
Review basic molecular biology concepts
Show steps
Revisit the basics of molecular biology to strengthen your foundation for understanding genetic circuit models.
Browse courses on
Molecular Biology
Show steps
-
Review the structure and function of DNA and RNA
-
Understand the processes of transcription and translation
-
Review the basics of gene regulation
Review general chemistry concepts
Show steps
Revisit general chemistry concepts to ensure a strong foundation for the more advanced topics covered in this course.
Browse courses on
General Chemistry
Show steps
-
Review your notes and textbooks from previous chemistry courses.
-
Take practice quizzes or exams to test your understanding.
-
Attend a refresher course or workshop on general chemistry.
Ten other activities
Expand to see all activities and additional details
Show all 13 activities
Follow tutorials on SBML
Show steps
Strengthen your understanding of SBML by completing guided tutorials that provide practical examples of its use.
Show steps
-
Find online tutorials or documentation on SBML
-
Work through the tutorials, creating and editing SBML models
-
Explore the SBML specification to understand the syntax and semantics
Organize and review course notes and assignments
Show steps
Maximize your learning by organizing and reviewing your course materials regularly.
Show steps
-
Create a designated folder or notebook for course notes and assignments.
-
File and organize your materials in a logical and accessible manner.
-
Review your materials periodically to reinforce your understanding.
-
Annotate and highlight key concepts and ideas.
Connect with experts in genetic circuit modeling
Show steps
Expand your knowledge by seeking guidance from experts in genetic circuit modeling, gaining insights and perspectives beyond the scope of the course.
Show steps
-
Identify potential mentors through professional networks, conferences, or research publications
-
Reach out to mentors and express your interest in learning from their expertise
-
Establish regular communication and ask specific questions
Follow online tutorials on genetic circuit simulation
Show steps
Supplement your understanding by following guided tutorials that provide hands-on experience with genetic circuit simulation.
Browse courses on
Simulation Methods
Show steps
-
Search for online tutorials on genetic circuit simulation.
-
Select tutorials that cover topics relevant to your interests.
-
Follow the tutorial instructions and complete the exercises.
-
Review the concepts and techniques presented in the tutorials.
Solve problems on genetic circuit analysis
Show steps
Reinforce your understanding of genetic circuit analysis by practicing problem-solving and applying the concepts covered in the course.
Show steps
-
Find practice problems or create your own
-
Apply the concepts of ODE modeling and stochastic simulation to solve the problems
-
Check your solutions against provided answers or discuss them with peers
Participate in study sessions with classmates
Show steps
Enhance your understanding by discussing concepts, solving problems, and sharing insights with peers.
Show steps
-
Identify a group of classmates with similar interests and goals.
-
Establish a regular schedule for study sessions.
-
Review the course material together.
-
Discuss and work through challenging concepts.
-
Share notes and resources.
Develop a study guide for complex ODE methods
Show steps
Deepen your understanding of complex ODE methods by creating a comprehensive study guide.
Browse courses on
Ordinary Differential Equations
Show steps
-
Identify key concepts and formulas related to complex ODE methods.
-
Gather relevant resources such as textbooks, lecture notes, and online materials.
-
Organize and summarize the information in a logical and cohesive manner.
-
Review and revise your study guide regularly to reinforce your learning.
-
Use your study guide to prepare for exams and assignments.
Solve stochastic analysis problems
Show steps
Enhance your problem-solving abilities in stochastic analysis by solving practice problems.
Show steps
-
Review the concepts and techniques of stochastic analysis.
-
Find practice problems and exercises online or in textbooks.
-
Attempt to solve the problems independently.
-
Check your solutions and learn from your mistakes.
Create a presentation on a genetic circuit design
Show steps
Solidify your understanding of genetic circuit design by creating a presentation that demonstrates your ability to apply the principles learned in the course.
Browse courses on
Genetic Circuit Design
Show steps
-
Choose a genetic circuit design problem
-
Research and understand the design principles involved
-
Create a presentation that explains the design, implementation, and expected outcomes
-
Practice presenting your work effectively
Build a genetic circuit model for a simple biological system
Show steps
Apply your knowledge to a practical project by constructing a genetic circuit model for a simple biological system, simulating its behavior, and analyzing the results.
Show steps
-
Define a simple biological system and identify the relevant genetic components
-
Construct a genetic circuit model using an appropriate software tool
-
Simulate the model to predict the behavior of the biological system
-
Analyze the simulation results and draw conclusions about the system's dynamics
Summarize key concepts and examples
Show steps
Enhance your understanding and retention by creating a concise summary of key concepts and examples covered in the course materials.
Show steps
Show steps
Show steps
- Review lecture notes, textbook chapters, and other course resources
- Identify and extract the most important concepts and examples
- Summarize these concepts and examples in a clear and concise format
Review basic molecular biology concepts
Show steps
Revisit the basics of molecular biology to strengthen your foundation for understanding genetic circuit models.
Browse courses on
Molecular Biology
Show steps
Show steps
Show steps
- Review the structure and function of DNA and RNA
- Understand the processes of transcription and translation
- Review the basics of gene regulation
Review general chemistry concepts
Show steps
Revisit general chemistry concepts to ensure a strong foundation for the more advanced topics covered in this course.
Browse courses on
General Chemistry
Show steps
Show steps
Show steps
- Review your notes and textbooks from previous chemistry courses.
- Take practice quizzes or exams to test your understanding.
- Attend a refresher course or workshop on general chemistry.
Ten other activities
Expand to see all activities and additional details
Show all 13 activities
Follow tutorials on SBML
Show steps
Strengthen your understanding of SBML by completing guided tutorials that provide practical examples of its use.
Show steps
Show steps
Show steps
- Find online tutorials or documentation on SBML
- Work through the tutorials, creating and editing SBML models
- Explore the SBML specification to understand the syntax and semantics
Organize and review course notes and assignments
Show steps
Maximize your learning by organizing and reviewing your course materials regularly.
Show steps
Show steps
Show steps
- Create a designated folder or notebook for course notes and assignments.
- File and organize your materials in a logical and accessible manner.
- Review your materials periodically to reinforce your understanding.
- Annotate and highlight key concepts and ideas.
Connect with experts in genetic circuit modeling
Show steps
Expand your knowledge by seeking guidance from experts in genetic circuit modeling, gaining insights and perspectives beyond the scope of the course.
Show steps
Show steps
Show steps
- Identify potential mentors through professional networks, conferences, or research publications
- Reach out to mentors and express your interest in learning from their expertise
- Establish regular communication and ask specific questions
Follow online tutorials on genetic circuit simulation
Show steps
Supplement your understanding by following guided tutorials that provide hands-on experience with genetic circuit simulation.
Browse courses on
Simulation Methods
Show steps
Show steps
Show steps
- Search for online tutorials on genetic circuit simulation.
- Select tutorials that cover topics relevant to your interests.
- Follow the tutorial instructions and complete the exercises.
- Review the concepts and techniques presented in the tutorials.
Solve problems on genetic circuit analysis
Show steps
Reinforce your understanding of genetic circuit analysis by practicing problem-solving and applying the concepts covered in the course.
Show steps
Show steps
Show steps
- Find practice problems or create your own
- Apply the concepts of ODE modeling and stochastic simulation to solve the problems
- Check your solutions against provided answers or discuss them with peers
Participate in study sessions with classmates
Show steps
Enhance your understanding by discussing concepts, solving problems, and sharing insights with peers.
Show steps
Show steps
Show steps
- Identify a group of classmates with similar interests and goals.
- Establish a regular schedule for study sessions.
- Review the course material together.
- Discuss and work through challenging concepts.
- Share notes and resources.
Develop a study guide for complex ODE methods
Show steps
Deepen your understanding of complex ODE methods by creating a comprehensive study guide.
Browse courses on
Ordinary Differential Equations
Show steps
Show steps
Show steps
- Identify key concepts and formulas related to complex ODE methods.
- Gather relevant resources such as textbooks, lecture notes, and online materials.
- Organize and summarize the information in a logical and cohesive manner.
- Review and revise your study guide regularly to reinforce your learning.
- Use your study guide to prepare for exams and assignments.
Solve stochastic analysis problems
Show steps
Enhance your problem-solving abilities in stochastic analysis by solving practice problems.
Show steps
Show steps
Show steps
- Review the concepts and techniques of stochastic analysis.
- Find practice problems and exercises online or in textbooks.
- Attempt to solve the problems independently.
- Check your solutions and learn from your mistakes.
Create a presentation on a genetic circuit design
Show steps
Solidify your understanding of genetic circuit design by creating a presentation that demonstrates your ability to apply the principles learned in the course.
Browse courses on
Genetic Circuit Design
Show steps
Show steps
Show steps
- Choose a genetic circuit design problem
- Research and understand the design principles involved
- Create a presentation that explains the design, implementation, and expected outcomes
- Practice presenting your work effectively
Build a genetic circuit model for a simple biological system
Show steps
Apply your knowledge to a practical project by constructing a genetic circuit model for a simple biological system, simulating its behavior, and analyzing the results.
Show steps
Show steps
Show steps
- Define a simple biological system and identify the relevant genetic components
- Construct a genetic circuit model using an appropriate software tool
- Simulate the model to predict the behavior of the biological system
- Analyze the simulation results and draw conclusions about the system's dynamics
Career center
Learners who complete Engineering Genetic Circuits: Modeling and Analysis will develop knowledge and skills
that may be useful to these careers:
Systems Biologist
Systems Biologist
Aspiring Systems Biologists, who study complex biological systems using mathematical and computational models, may find this course highly relevant. The training in this course will provide you with a deep understanding of genetic circuit modeling and analysis, which forms the foundation of systems biology approaches to studying biological systems.
Computational Biologist
Computational Biologist
Individuals interested in careers as Computational Biologists, where they will use computational tools and techniques to study biological systems, may be interested in this course. The training you will receive will help you develop the skills you need to use computational models to analyze and simulate biological systems, which can advance our understanding of these systems and develop new treatments for diseases.
Bioinformatics Scientist
Bioinformatics Scientist
The training in engineering genetic circuits you will receive from this course can help you prepare for a career as a Bioinformatics Scientist, where you will conduct research and develop new techniques for storing, retrieving, organizing, and analyzing biological data. Your expertise in analyzing genetic circuits will give you the skills to analyze large datasets and identify patterns that can help advance our understanding of biological systems.
Research Scientist
Research Scientist
For individuals pursuing a career as a Research Scientist, where you will conduct research in various scientific fields, this course may be beneficial. Your training in this course can help you build a foundation in genetic circuit analysis and modeling, which can be applied to a wide range of research areas in biology and medicine.
Molecular Biologist
Molecular Biologist
Those interested in pursuing a career as a Molecular Biologist, where you will study the structure and function of molecules, may find this course helpful. Your training in this course can aid you in understanding the molecular basis of genetic circuits and how they function within biological systems.
Statistician
Statistician
This course may be beneficial for individuals pursuing a career as a Statistician, particularly in the field of biostatistics. The training in this course will equip you with skills to analyze and interpret biological data, which is essential for advancing our understanding of biological systems and developing new treatments for diseases.
Geneticist
Geneticist
For those interested in a career as a Geneticist, where you will study genes and heredity and diagnose and treat genetic disorders, this course may be useful. The training you will receive in this course can help you develop the foundational knowledge of genetic circuits that can aid your work in this field.
Technical Writer
Technical Writer
Individuals interested in pursuing a career as a Technical Writer, who create technical documentation and materials, may find this course helpful. The training in this course will provide you with a deeper understanding of genetic circuits and their applications, enabling you to write more effectively about these topics for various technical audiences.
Software Engineer
Software Engineer
This course may be of interest to individuals pursuing a career as a Software Engineer, where you will design, develop, and maintain software systems. The training in this course can help you develop the analytical and problem-solving skills needed to succeed in software development, particularly in the field of bioinformatics.
Healthcare Data Analyst
Healthcare Data Analyst
This course may be of interest to those pursuing a career as a Healthcare Data Analyst, where you will use data to improve patient care and outcomes. The skills you gain in this course will help you develop the analytical skills needed to analyze and interpret healthcare data, which can lead to advancements in patient care.
Physician
Physician
This course may be helpful for those interested in a career as a Physician, where you will diagnose and treat medical conditions. Your training in this course can help you develop a foundational knowledge of genetic circuits and their role in disease, which can aid in diagnosis and treatment planning.
Biomedical Engineer
Biomedical Engineer
If you are interested in a career as a Biomedical Engineer, where you will design and develop medical devices and equipment, then this course may be helpful. Your training in this course can help you understand the biological systems that medical devices interact with, enabling you to design more effective and efficient devices.
Data Analyst
Data Analyst
This course may be useful for those interested in a career as a Data Analyst, where you will collect, analyze, and interpret data to identify trends and patterns. The skills you gain in this course can help you develop the analytical skills you need to succeed in this role, particularly in the field of bioinformatics.
Pharmacist
Pharmacist
Individuals interested in a career as a Pharmacist, where they will dispense medications and provide patient care, may find this course useful. The training you will receive in this course can help you develop a better understanding of the molecular basis of genetic circuits, which can be beneficial for understanding drug interactions and their effects on biological systems.
Science Writer
Science Writer
This course may be useful for aspiring Science Writers, who communicate complex scientific concepts to the public. The course can provide a deeper understanding of genetic circuits and their significance, allowing you to write more accurately and engagingly about these topics for various audiences.
For more career information including salaries, visit:
OpenCourser.com/course/ks8rsm/engineering
Reading list
We've selected six books
that we think will supplement your
learning. Use these to
develop background knowledge, enrich your coursework, and gain a
deeper understanding of the topics covered in
Engineering Genetic Circuits: Modeling and Analysis.
Provides a detailed overview of engineering genetic circuits, including chapters on modeling and analysis.
This lab manual provides detailed instructions for designing, building, and testing genetic circuits.
Save
Provides a rigorous mathematical treatment of biological systems modeling, including chapters on genetic circuit modeling and analysis.
Provides a comprehensive overview of systems biology, including chapters on genetic circuit modeling and analysis.
Provides an overview of bioinformatics and systems biology, including chapters on genetic circuit modeling and analysis.
Save
Provides an overview of statistical methods for systems biology, including chapters on genetic circuit modeling and analysis.
For more information about how these books relate to this course, visit:
OpenCourser.com/course/ks8rsm/engineering
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Effort
5 weeks, 4-6 hours/week
Level
Intermediate
Via
Coursera
Institution
University of Colorado Boulder
Instructor
Chris Myers
Language
English
Good to know
Modules 1-3 cover core genetic circuit modeling and analysis
Module 4 covers variations of stochastic simulations
Provides a high-level view of genetic circuit technology
Teaches foundational concepts in genetic modeling using SBML
Covers advanced topics such as hSSA, wSSA, iSSA methods
Introduces computational analysis for part selection and performance verification
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