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
Syllabus
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% |