# ECE 6760

Modeling and Analysis of Biological Networks

## Course description

With the sequencing of the human genome and the genomes of other organisms,
we now have a list of the parts that make up these biological systems.
Through the use of microarrays and other new technologies, we are also
beginning to get data on the functions of individual genes and how genes
interact with each other to perform complex biological functions. In the
functional genomic era, we will begin to take this vast amount of data, and
try to reason about how these genetic systems work. To accomplish this, a
systems biology perspective will need to be taken in which models and new,
efficient analysis techniques will need to be developed to reason about these
genetic networks. Engineers have had vast experience in modeling and analyzing
electronic circuits and systems. It is not difficult to develop a view of a
genetic network as a electronic circuit. Such a view was taken by McAdams and
Shapiro in their seminal paper in Science in 1995 with encouraging results.
Therefore, as in the sequencing of the human genome, collaborations between
engineers and systems biologists will be essential to the success of functional
genomics. In this new course, we will be reading papers on recent approaches
to the modeling and analysis of biological networks. The goal of this course is
to be useful to both engineers and computer scientists who wish to learn about
biological problems to which their models can be applied and to biologists and
bioengineers who would like to learn about models and analysis techniques that
can be used to study their systems of interest.
## Instructor

Instructor: Dr. Chris Myers
## Prerequisites

Students should either have some familiarity with genetics, cell biology,
molecular biology, or biochemistry OR modeling and analysis.
## Textbooks

One is being prepared by the instructor and will be available
here.
## Course Requirements

- Course participation - 10 percent
- Attend class and participate in class discussions.

- Homework - 40 percent
- Will learn how to use modeling and analysis tools.
- Use simple system for tutorial.
- Choose network to champion.
- Model/analyze your network with the tool.

- Project - 50 percent
- Model and analyze a biological network, or
- Design and implement an analysis tool.

## Meeting Times

Class |
3:40pm - 5:00pm |
TTh |
Dr. Myers |
EMCB 122 |

Office Hours |
noon - 1:00pm |
T |
Dr. Myers |
MEB 4112 |

Office Hours |
2:30pm - 3:30pm |
Th |
Dr. Myers |
MEB 4112 |

## Tentative Syllabus

All information here is tentative.
- Week 1: Brief Introduction to Biochemistry
- Week 2: Phage Lambda
- Weeks 3, 4, and 5: Stochastic Models
- Weeks 6, 7, and 8: Differential Equation Models
- Weeks 9, 10, and 11: Circuit Models
- Week 12: Bayesian Networks and Other Learning Methods
- Week 13: Flux Balance Analysis
- Week 14: Engineering Synthetic Gene Circuits
- Week 15: Project Presentations

## Suggested Models

## Related Web Pages