2nd course in the Engineering Genetic Circuits Specialization

Instructor: Chris Myers, PhD, Professor

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 modulle 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.

Learning Outcomes

  • Construct chemical reaction models of genetic circuits using iBioSim.
  • Learn the basics of chemical kinetic models.
  • Learn techniques for the qualitative analysis of ODEs.
  • Understand Gillespie's Stochastic Simulation Algorithm (SSA).
  • Exposed to additional advanced stochastic analysis topics.
  • Learn about incremental SSA (iSSA) algorithms that allow the determination of typical behaviors.
  • Learn about genetic constraints that can be checked with model-guided technology mapping procedures.
  • Learn about existing genetic circuit technology mapping tools, such as Cello, iBioSim, and others.
  • Learn how model generation approaches can be used to validate the designs produced by technology mapping tools.

Syllabus

Duration: 6.5 hours

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.

Duration: 4.5 hours

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.

Duration: 6 hours

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.

Duration: 4 hours

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.

Duration: 4.5 hours

This module presents various ways that modeling can be utilized in genetic circuit design to select parts for optimal performance.

Duration: 24 hours 

This module contains materials for the final project. Submit the final project to demonstrate mastery of the material presented in this course.

Grading

Assignment
Percentage of Grade

Chemical Reaction Model Basics

1%

Genetic Circuit Models using SBML

1%

Genetic Toggle Switch Model

6%

Chemical Kinetic Models

1%

ODE Simulation Using iBioSim

5%

ODE Simulation Methods

10%

Qualitative ODE Analysis

1%

Stochastic Chemical Kinetics

1%

Stochastic Simulation Using iBioSim

5%

Stochastic Simulation Methods

10%

Alternative Stochastic Simulation Algorithms

1%

Additional Stochastic Simulation Topics

1%

Hierarchical SSA (hSSA)

1%

Weighted SSA (wSSA)

1%

Incremental SSA (iSSA)

1%

Introduction to Genetic Technology Mapping

1%

Cello's Technology Mapping

1%

iBioSim's Technology Mapping

1%

Verification of Genetic Circuit Designs

1%

Final Genetic Circuit Model Project

50%

Letter Grade Rubric

Letter Grade 
Minimum Percentage

A

93%

A-

90%

B+

86%

B

83%

B-

80%

C+

76%

C

73%

C-

70%

D+

66%

D

60%

F

0%