Engineering Genetic Circuits: Modeling and Analysis from Coursera

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.

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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.

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.

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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

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

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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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Engineering Genetic Circuits

Modeling and Analysis

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