Topic: Engineering Genetic Circuits

- Motivation
- Objectives
- Prerequisites
- Overview
- Reading
- Software
- Communication
- Grading
- Your Rights and Responsibilities

A hybrid system is a dynamic system that exhibits both continuous and discrete dynamic behavior, that is, a system that can both flow (as described by a differential equation) and jump (as described by a difference equation or a control graph). The continuous-discrete duality is a phenomenon that occurs naturally in many application areas such as real-time software, embedded systems, robotics, mechatronics, aeronautics, process control and biological systems. The course will cover the state-of-the-art modeling, design and analysis of hybrid systems. The main emphasis will be on biological systems, in particular on engineering genetic circuits.

By the end of this course the students will be provided with detailed knowledge and substantial
experience in the mathematical modeling, simulation and verification of hybrid systems, in particular of genetic circuits.

- Overview of the course
- An Engineer's Guide to Genetic Circuits
- Chemical reactions, Macromolecules, Genomes, Cells
- Genetic circuits, Viruses, Phage Lambda
- Learning Models
- Experimental methods, Experimental data, Cluster analysis
- Learning Bayesian networks, Learning causal networks, Design
- Differential Equations Analysis
- A classical kinetic model, Differential equations simulation
- Qualitative differential equations analysis, Spatial methods
- Stochastic Analysis
- A stochastic kinetic model, Chemical master equation, Gillespie's simulation algorithm
- Gibson/Bruck method, Relation to rate equations
- Reaction-Based Abstraction
- Irrelevant node elimination, Enzymatic approximations, Operator site reduction
- Statistical thermodynamic model, Dimerization reduction, Phage Lambda circuit
- Logical Abstraction
- Logical encoding, Piecewise models, Stochastic fininite-state machines
- Markov chain analysis, Qualitative logical models
- Genetic Circuit Design
- Assembly of genetic circuits, Combinational logic gates, PoPS Gates
- Sequential logic circuits, Future challenges

**Engineering Genetic Circuits**by C.J. Myers, Chapman & Hall, 2010, 278pp, ISBN 978-1-4200-8324-8.

Communication

**Special Needs**

If you have a physical, psychological, medical or learning disability that may impact on your ability to carry out assigned course work, you are urged to contact the staff in the Disabled

Student Services office (DSS), Room 133 Humanities, 632-6748/TDD. DSS will review your concerns and determine, with you, what accommodations are necessary and appropriate.

All information and documentation of disability is confidential.

**The Importance of Being Earnest**

Because a primary goal of the course is to teach professionalism, any academic dishonesty will be viewed as evidence that this goal has not been achieved. Any act of cheating will be treated with utmost seriousness.

You can discuss the course material with other students, but not the homework assignments themselves. In effect, you can discuss the problems but not the solutions. If you help another student with a homework, use examples that do not resemble those in the homework. Remember that there are many different ways to solve the same problem; even solutions with the same central idea can be formulated in many different ways. Therefore, suspiciously similar homework solutions will be considered as evidence of disallowed collaboration or copying.

In case you have any questions about whether an act of collaboration may constitute "cheating", please come and talk to the instructor beforehand to clarify the issue.

Copying an assignment from another student in this class or obtaining a solution from some other source will lead to an automatic F for this course and to a disciplinary action. Allowing another student to copy one's work will be treated as an act of academic dishonesty, leading to the same penalty as copying. You should learn how to protect your data. Failure to do so is also unprofessional and it may expose you to the danger that someone will copy your homework and will submit it as his or her own (see above). In this case, you may be given a score of 0 for the assignment in question (and the other party will get an F).

All cases of academic dishonesty will be reviewed by the Engineeing College's committee (CASA).

**Survival Tips**

Do not postpone working on assignments. Start working on programming assignments as soon as they are handed out. Do not wait till the day before the deadline. You will see that assignments take much more time when you work on them under pressure, than when you are more relaxed. Remember that no late submissions are allowed.

Do not postpone working on assignments! This cannot be understated. Despite the above warning, most students will end up working only around the deadline. Remember, the homeworks usually take more time that it initially appears. Furthermore, I expect both the TA and me to be swamped on the office hours before projects are due. So, you, being wiser than the rest, should start earlier and beat the rush!

Last updated on Feb 10, 2011 by Radu Grosu