University of Colorado Boulder - Engineering Genetic Circuits: Modeling and Analysis
- Offered byCoursera
Engineering Genetic Circuits: Modeling and Analysis at Coursera Overview
Duration | 24 hours |
Start from | Start Now |
Total fee | Free |
Mode of learning | Online |
Official Website | Explore Free Course  |
Credential | Certificate |
Engineering Genetic Circuits: Modeling and Analysis at Coursera Highlights
- Earn a certificate after completion of the course
- Assignment and quizzes
- Financial aid available
Engineering Genetic Circuits: Modeling and Analysis at Coursera Course details
- Design and analyze models of genetic circuits.
- Simulate genetic circuit models using ODE simulation methods.
- Simulate genetic circuit models using stochastic simulation methods.
- Utilize genetic technology mappers to select parts for genetic designs.
- 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.
Engineering Genetic Circuits: Modeling and Analysis at Coursera Curriculum
Genetic Circuit Models
Chemical Reaction Models
Laws of Thermodynamics
Law of Mass Action
Genetic Circuit Models
System Biology Markup Language
Overview
Project Management
Creating a Model
Species
Promoters
Compartments
Modules
Events
Event Examples
Unit Definitions
Model Editor
Constraints, Parameters, and Variables
Reactions
SBML Mathmatical Formulas
iBioSim Functions
Rules
Constraints
Model Editor Preferences
Engineering Genetic Circuits - Chapter 1 (Section 1.1)
Engineering Genetic Circuits - Chapter 1 (Section 1.7.4)
SBML Level 3: An Extensible Format for the Exchange and Reuse of Biological Models
iBioSim 3: A Tool for Model-Based Genetic Circuit Design
iBioSim Tutorial
iBioSim Demo Video
Chemical Reaction Model Basics
Genetic Circuit Models Using SMBL
Genetic Toggle Switch Model
Genetic Circuit Analysis (ODEs)
Overview
Classic Chemical Kinetic Model
ODE Model Example
Differential Equation Simulation
Euler's Method
Runge-Kutta Method
Adaptive Stepsize Control
Qualitative ODE Analysis
Saddle-Node Example
Transcritical Bifurcation Example
Pitchfork Bifurcation Example
Two-Dimentional ODE Model
Spatial Methods
Engineering Genetic Circuits Chapter 3 (Section 3.1)
Engineering Genetic Circuits Chapter 3 (Section 3.2)
Engineering Genetic Circuits Chapter 3 (Sections 3.3 and 3.4)
Chemical Kinetic Models
ODE Simulation Methods
Qualitative ODE Analysis
ODE Simulation Using iBioSim
Stochastic Analysis
Introduction
Stochastic Chemical Kinetic Model
Biomolecular Reaction Channel
Monomolecular Reactions
Trimolecular Reactions
Jump Markov Processes
Introduction
Derivation of Gillespie's Stochastic Simulation Algorithm
Implementation of Gillespie's SSA
Gillespie's SSA Examples
Gillespie's First Reaction Method
Gibson/Bruck's Improvements
Composition and Rejection
Tau Leaping
Explicit Tau-Leaping Simulation Algorithm
The Chemical Langevin Equation
The Reaction Rate Equation
Stochastic Petri Nets
Phage Lambda Model
Spatial Gillespie
Engineering Genetic Circuits Chapter 4 (Sections 4.1 and 4.2)
Engineering Genetic Circuits Chapter 4 (Section 4.3)
Engineering Genetic Circuits Chapter 4 (Sections 4.4 and 4.5)
Engineering Genetic Circuits Chapter 4 (Sections 4.6 to 4.9)
Stochastic Chemical Kinetics
Stochastic Simulation Methods
Alternative Stochastic Simulation Algorithms
Additional Stochastic Simulation Topics
Stochastic Simulation Using iBioSim
SSA Variations
Population-Based Models
The Hierarchical Stochastic Simulation Algorithm
Hierarchical Simulation Example
Runtime Comparison between hSSA and SSA
Array Package for Tracking Cellular Populations
Population of Repressilator Circuits Using Arrays
Population of Genetic Toggle Circuits Using Arrays
Motivation and Background
Important Sampling
Underlying Mathematics of the wSSA
The weighted stochastic simulation algorithm
Introduction and Motivation
Incremental Stochastic Simulation Algorithm
Marginal Probability Density Evolution
Mean Path
Median Path
Adaptive Time Step
Multiple Paths
Hierarchical Stochastic Simulation Algorithm for SBML Models of Genetic Circuits
Efficient Analysis of Systems Biology Markup Language Models of Cellular Populations using Arrays
An Efficient and Exact Stochastic Simulation Method to Analyze Rare Events in Biochemical Systems
Efficient Analysis Methods in Synthetic Biology
Hierarchical SSA (hSSA)
Weighted SSA (wSSA)
Incremental SSA (iSSA)
Genetic Circuit Technology Mapping
Introduction
Crosstalk
Signal Mismatch
Roadblocking
Genetic Context Effects
Automation and Computer Aided Design
Library Creation
Existing Technology Mapping
Overview of Cello
Genetic Gate Assignment
Impact of Gate Isolation and Gate and Gate Library
Cello Circuit Examples
Analysis of Circuit Failures
Overview of iBioSim's Technology Mapping
DAG Representation
Partitioning and Decomposition
Matching and Covering
Technology Mapping's Cost
Model Generation
Rule 30 Example
Sequential Genetic Circuits
Technology Mapping of Genetic Circuits: From Optimal to Fast Solutions
Genetic Circuit Design Automation
Directed Acyclic Graph-Based Technology Mapping of Genetic Circuit Models
Design of Asynchronous Genetic Circuits
Introduction to Genetic Technology Mapping
Cello's Technology Mapping
iBioSim's Technology Mapping
Verification of Genetic Circuit Designs
Engineering Genetic Circuits: Modeling and Analysis at Coursera Admission Process
Important Dates
Other courses offered by Coursera
Student Forum
Anything you would want to ask experts?
Engineering-Non CSElectrical EngineeringEngineering DesignEngineering Genetic Circuits: Modeling and Analysis