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Endy, Andrew, 20.180 Biological Engineering Programming, Spring 2006. (Massachusetts Institute of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed 07 Jul, 2010). License: Creative Commons BY-NC-SA
Excerpt from the comic "Adventures in Synthetic Biology". (Image by Drew Endy, Isadora Deese, MIT Synthetic Biology Working Group, and Chuck Wadey.)
Course Highlights
This course features a full set of assignments and a selection of lecture notes.
Course Description
In this course problems from biological engineering are used to develop structured computer programming skills and explore the theory and practice of complex systems design and construction.
The official course Web site can be viewed at: BE.180 Biological Engineering Programming.
Technical Requirements
Special software is required to use some of the files in this course: .dict.
Syllabus
Overview
Welcome to 20.180, MIT Biological Engineering's programming course! For many of you this will be the first time learning to program computers; others may already be programming gurus. Regardless of your background, upon completing 20.180 you'll have learned how to solve complex biological engineering problems using computational approaches. You'll also discover the rudiments of how to program DNA, the genetic material that runs inside all living organisms. Along the way, you'll be exposed to powerful ideas that underlie all of modern engineering. We hope that you have a great experience with the course!
Assignments and Exams
We expect that all assignments will be turned in by 5pm on the day they are due. You may discuss assignments with your classmates but we expect that you will submit your own work. Late assignments will be assigned a grade of zero (your lowest assignment grade will be dropped from your final grade). A family crisis or severe illness requiring attention from the infirmary and prohibiting you from all your coursework are acceptable reasons for missing an exam; every effort will be made to accommodate you in these exceptional circumstances.
Grading
Course grading.
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ACTIVITIES
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PERCENTAGES
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Exam 1
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20%
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Exam 2
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20%
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Class Participation
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10%
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Programming Assignments
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50%
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Calendar
Course calendar.
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SES #
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TOPICS
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KEY DATES
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1
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Biological Engineering and Programming DNA
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2
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Abstraction: From DNA to Parts
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3
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Abstraction: From Parts to Devices
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Assignment 1 out
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4
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Device Modeling and Simplification
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5
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Guest Lecture: Tom Knight
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Assignment 1 due
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6
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Guest Lecture: Gerry Sussman
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7
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Device Analysis
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Assignment 2 out
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8
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Device Composition
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9
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Decomposition of Complex Problems
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Assignment 2 due
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10
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Devices, Revisited
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11
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Genetic Devices and Device Modeling
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12
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Discussion and Review
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Exam 1
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13
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Sequence Optimization
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14
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DNA Detection and Identification
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Assignment 3 out
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15
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Space and Time Systems
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16
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Programming Space and Time Systems
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Assignment 3 due
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17
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Programming Space and Time Systems (cont.)
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18
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Growing Point Language
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Assignment 4 out
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19
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"Crop Circle" Language
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20
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Semester Review
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Assignment 4 due
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Exam 2
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21
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Course Evaluation and Wrap-Up
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