CSCE 459/859 – Genetically Engineered Systems
Time: MWF 2:30–3:20 p.m.
Location: BURN 201
Instructor Dr. Massimiliano Pierobon
Assistant Professor
104 Schorr Center
Department of Computer Science and Engineering
University of Nebraska-Lincoln
Lincoln, NE 68508
Tel: (402) 472-5021
Fax: (402) 472-7767
E-mail: pierobon@cse.unl.edu
Website of Class http://cse.unl.edu/~pierobon/teaching.html
Office Hours TBD or by appointment.
Description Introduction to the emerging field of synthetic biology, and its
interdisciplinary foundational concepts. This course will present
the technologies at the basis of synthetic biology, together with
the engineering concepts that underlie the design, modeling, and
realization of genetically engineered systems. The course will
survey examples of cutting edge applications, from the
production of biofuels to the design and implementation of
biosensors to detect harmful agents. A special emphasis will be
given to the International Genetically Engineered Machine
(iGEM) competition and its latest results in terms of research
and training. Ethical, legal, and societal aspects of this new
interdisciplinary field will be also discussed by glancing at
possible future scenarios.
Prerequisite A grade of "P" or "C" or better in CSCE 310, CSCE 310H,
CSCE 311, SOFT 260, SOFT 260H or RAIK 283H; STAT 380,
ECEN 305 or RAIK 270H. Completing CSCE/MATH 440/840,
MATH 432/832, MATH 439/839, and CSCE 471/871 prior to
taking this course is recommended. Exceptions can be granted
on a per-student basis by the instructor.
Graduate standing from Computer Science and Engineering,
Electrical Engineering, and Mathematics, or upon instructor
permission.
Most of the necessary concepts from physics, chemistry, and
biology, will be provided during the lectures. Student creativity,
passion, and open-minded attitude will be highly appreciated
and rewarded.
Required Textbook NO TEXTBOOK REQUIRED.
Main References:
Paul S Freemont, Richard I Kitney, et al.
“Synthetic Biology — A Primer”
Imperial College Press
Chris J. Myers
“Engineering Genetic Circuits”
Chapman and Hall/CRC Press
Uri Alon
“An Introduction to Systems Biology: Design Principles of
Biological Circuits”
Chapman and Hall/CRC Press
Lecture slides (PDF) will be available on the course’s
homepage.
A list of reference books and research papers will be given
throughout the semester.
Some of the research papers and reports will be distributed via
the course’s homepage.
HOMEWORKS and EXAMS will be based on what explained
during the lectures and supplemental reading materials.
Course Topics
0. Course Introduction
1. Molecular Biology Fundamentals
1.1 Information Storage in Biology
1.2 Information Flow in Biology
1.3 Control of Information Flow in Biology
1.4 The Cell: the Living Unit of Biology
1.5 Chemical Reactions: the Engine of Biology
1.6 Macromolecules: What Makes Up Biological Systems
2. Synthetic Biology Foundations
2.1 Enabling Technologies
2.2 Systematic Design
2.3 Standard DNA Assembly
2.4 Standard Measurements
2.5 Standard Part Characterization and Parts Registries
2.6 The BioCAD Concept
2.7 Information Exchange in Synthetic Biology
3. Introduction to Genetic Circuits
3.1 Networks in Biology
3.2 Genetic Circuits Basics
3.3 An Example of Biological Circuit
3.4 Genetic Circuit Models
3.5 Phage λ: A Simple Genetic Circuit
4. Genetic Circuit Modeling
4.1 Why is Mathematical Modeling Important?
4.2 Forward Engineering Approach
4.3 Differential Equation Analysis
4.4 Stochastic Analysis
4.5 Reaction-based Abstraction
4.6 Logical Abstraction
4.7 Learning Models
4.8 Model Repositories
5. Genetic Circuit Design
5.1 Standard Genetic Parts (and the PartsRegistry Protocol)
5.2 How to Design Genetic Constructs (Circuits) from Parts
5.3 Types of Genetic Constructs: Devices
5.4 Types of Genetic Constructs: Systems
6. Synthetic Biology and Society
6.1 Public Health and Environmental Risks
6.2 Biosecurity and Biohacking
6.3 The Ownership of Technology
6.4 “Playing God” and the Ethical Aspects
6.5 Public Value and New Global Inequality
Bonus Chapters:
7. Minimal Cells and Synthetic Life
8. Cutting Edge Applications
Course Organization There will be TWO exams, FOUR homeworks, and ONE
TEAM PROJECT assignment to be de.
Grade Distribution Homeworks: 20%
Exam 1: 20%
Exam 2: 20%
Project: 35%
In-class Participation: 5%
Final letter grades will be assigned tentatively based on the
following scale:
A+: ≥ 100 A: 97% to 100% A−: 94% to 96%
B+: 90% to 93% B: 87% to 89% B−: 84% to 86%
C+: 80% to 83% C: 77% to 79% C−: 74% to 76%
D+: 70% to 73% D: 67% to 69% D−: 64% to 66%
F: ≤ 63%
Homeworks Homework submissions will be through web handin
Late homework is penalized 10% per day, and no homework
will be accepted after the solution is posted online
Exams There will be TWO in-class exams.
Project There will be half-semester-long projects, focused on the
research of material from the available literature, analysis and
presentation to the class (at the end of the semester) of a
specific topic chosen from those introduced in the class. The
project will be assigned to students divided into teams
according to the class size.
459 Vs. 859 This course will not have major differences between the 459
and 859 versions in the delivery of the content. Instead, some
selected questions in the homeworks and exams will be
mandatory for 859 students, and optional for 459 students.
Academic Integrity All homework assignments, quizzes, exams, etc. must be your
own work. No direct collaboration with fellow students, past or
current, is allowed unless otherwise stated. The Computer
Science & Engineering department has an Academic Integrity
Policy:
http://cse.unl.edu/ugrad/resources/academic_integrity.php
All students enrolled in any computer science course are bound
by this policy. You are expected to read, understand, and follow
this policy. Violations will be dealt with on a case by case basis
and may result in a failing assignment or a failing grade for the
course itself.
Students with
Disabilities
Students with disabilities are encouraged to contact the
instructor for a confidential discussion of their individual needs
for academic accommodation. It is the policy of the University
of Nebraska-Lincoln to provide flexible and individualized
accommodations to students with documented disabilities that
may affect their ability to fully participate in course activities or
to meet course requirements. To receive accommodation
services, students must be registered with the Services for
Students with Disabilities (SSD) office, 232 Canfield
Administration, 472-3787 voice or TTY.
Suggestion Box The CSE Department has an anonymous suggestion box
(http://cse.unl.edu/department/suggestion.php) that you may use
to voice your concerns about any problems in the course or
department if you do not wish to be identified.
Stay Up-to-date It is CSE Department policy that all students in CSE courses are
expected to regularly check their email so they do not miss
important announcements.
CSE Resource
Student Center
The CSE Student Resource Center (Avery Hall 13A) is intended
to provide UNL Computer Science and Computer Engineering
majors who are new to the program with a set of resources that
will help them assimilate to college life and encourage them to
continue their study of Computer Science and Computer
Engineering (http://cse.unl.edu/src).
This syllabus will be updated and expanded as the semester progresses