Download COEN691ACourseOutline010312

Department of Electrical & Computer Engineering and Department of Biology
Concordia University
BIOLOGICAL COMPUTIING & SYNTHETIC BIOLOGY
Winter 2011/12
>> Course Outline <<
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Course Instructors
Luc Varin, Ph.D. (Biology) & Nawwaf Kharma, Ph.D. (Computer Engineering)
Physical Offices: SP 501.05 (Loyola) & EV 5.171 (Downtown)
Office Hours: TBA
E-mail Addresses: [email protected] & [email protected]
Course Web Directory: www.ece.concordia.ca/~kharma/COEN691A
iGEM 2011 @ MIT: http://2011.igem.org/Main_Page
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Office Hours
We expect students to visit us during our respective office hours to discuss their progress, if nothing
else. Please do visit during office hours, but do not contact us at other times, except by e-mail or phone
for a quick question or to take an appointment.
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Brief Description & Objectives
This course is an interdisciplinary course with 2.5 class hours of lectures scheduled every week. This
course is, in essence, about designing computational machines that can be implemented in biological
media- mainly cells. Typically speaking, a computational functionality is required. A target
implementation platform (e.g. E. coli bacteria) is decided upon, and a network of interacting genes is
designed. That network, which is called a Gene Regulatory Network (GRN), is modeled using
available simulation software. If the simulation is satisfactory, then actual physical genes are
synthesized using recombinant DNA techniques, and then added to the genome of a cell. The result is
a cell (or, in some cases a sheet of cells) that implements, as part of its overall functionality, a
designed computational ability. The modified cell, as a whole, may be viewed as a biologicallyengineered robot with sensing (e.g. arsenic concentration), information processing and output
capabilities (e.g. fluorescence). Applications range widely, from environmental sensing to drug
delivery.
You will learn how to design your own GRN, and in a team of three, you will propose your design to the
instructors. In preparation for this, you will be given a 3-week crash course in Digital Computing and
Molecular Biology, followed by 10 research-paper-based lectures on the leading and latest works in
Synthetic Biology. The ultimate aim of the course is to empower and inspire inquisitive minds to want
to learn more and do research in Computational Synthetic Biology.
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Textbook & Papers
This course has no text book. All the slides used in the lectures will be made available to you, on-line.
Also, all of the research papers used for the latter part of the course will be available to you in PDF
format. You are expected to attend every lecture, participate in it, and make your own notes.
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Detailed Course Plan
Lecture Topics
For 3 weeks (3 lectures each)
I. Topics. The ECE (and CSE) students are required to attend the following lectures, given by
Dr. Luc Varin (LV):
01.
The Cell and its Genome (1 week)
02.
Transcription and Translation (1 week)
03.
Recombinant DNA Technology (1 week)
At the same time, the Biology students will are required attend the following lectures, by Dr.
Nawwaf Kharma (NK):
01.
Introduction to Digital Design (1 week)
02.
Introduction to Digital Design (1 week)
03.
Basic Programming Concepts (1 week)
For 10 weeks
Then, all students shall attend the following, given in collaboration by NK & LV (about half &
half):
04.
Modern Tools of Synthetic Biology (1 week)
05.
Synthetic Genomes and Metabolic Engineering (1 week)
06.
Inter-Cellular Signaling with Applications to Synthetic Biology (1 week)
07.
Interfacing cells with their environment (1 week)
08. Designing Cell-based Computational Devices: combinatorial components (1 week)
09. Designing Cell-based Computational Devices: sequential components (1 week)
10. Expanding Functionality via Inter-cellular Signaling & Midterm (1 week)
11. Design, Modeling & Simulation of Complete Gene Regulatory Networks (1 week)
12. Construction and Testing of Gene Regulatory Networks (1 week)
13. Landmark and Creative Applications of Synthetic Biology (1 week)
Project Work
A very important aspect of the course is the project. This project involves working in a team of three
(which must include at least 1 biology and 1 computer/electrical engineering student). The main
deliverable is a Project Proposal similar to those presented in international iGEM competitions. You
receive a bonus for creating a Poster for your project. You are not required to actually realize your
proposal as that would involve wet lab work, and is outside the scope of this course.
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Grades Breakdown
In terms of grading, the course will involve assessment via a Qualifying Exam (>.75  15%), a Midterm (in
week 10) worth 20%, and a Final Exam, which will be given during normal exams’ period (40%). if the Final
Exam grade (as a percentage) is greater than the midterm grade, then the final counts for both (i.e. 60%).
The 3-member team project is worth 20%. The project’s deliverables will consist of a written synthetic
biology Project Proposal and (for a bonus of 5%) a poster.
1. Qualifying Exam
2. Midterm Exam
3. Project Proposal
4. Final Exam
5. Potential Bonus
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