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20.180 Biological Engineering Programming

Spring 2006

Two comic book panels featuring a researcher and her young assistant.

Excerpt from the comic "Adventures in Synthetic Biology". (Image byDrew Endy, Isadora Deese, MIT Synthetic Biology Working Group, andChuck 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


ACTIVITIESPERCENTAGES
Exam 120%
Exam 220%
Class Participation10%
Programming Assignments50%




Calendar

SES #TOPICSKEY DATES
1Biological Engineering and Programming DNA
2Abstraction: From DNA to Parts
3Abstraction: From Parts to DevicesAssignment 1 out
4Device Modeling and Simplification
5Guest Lecture: Tom KnightAssignment 1 due
6Guest Lecture: Gerry Sussman
7Device AnalysisAssignment 2 out
8Device Composition
9Decomposition of Complex ProblemsAssignment 2 due
10Devices, Revisited
11Genetic Devices and Device Modeling
12Discussion and Review
Exam 1
13Sequence Optimization
14DNA Detection and IdentificationAssignment 3 out
15Space and Time Systems
16Programming Space and Time SystemsAssignment 3 due
17Programming Space and Time Systems (cont.)
18Growing Point LanguageAssignment 4 out
19"Crop Circle" Language
20Semester ReviewAssignment 4 due
Exam 2
21Course Evaluation and Wrap-Up




Lecture Notes

This section contains documents created from scanned original files, which are inaccessible to screen reader software. A "#" symbol is used to denote such documents.


SES #TOPICSREFERENCES
1Biological Engineering and Programming DNA (PDF)
2Abstraction: From DNA to Parts
3Abstraction: From Parts to Devices
4Device Modeling and Simplification
5Guest Lecture: Tom Knight
6Guest Lecture: Gerry Sussman
7Device Analysis
8Device Composition
9Decomposition of Complex Problems
10Devices, Revisited
11Genetic Devices and Device Modeling (PDF)Comic (PDF - 1.5 MB)#

First Order Decay (PDF)

Second Order Binding (PDF)
12Discussion and Review
Exam 1
13Sequence Optimization
14DNA Detection and Identification
15Space and Time Systems
16Programming Space and Time Systems
17Programming Space and Time Systems (cont.)
18Growing Point Language
19"Crop Circle" Language
20Semester Review
Exam 2
21Course Evaluation and Wrap-Up




Assignments

Special software is required to use some of the files in this section: .dict.


ASSIGNMENTSSUPPLEMENTAL FILESSOLUTIONS
Assignment 1 (PDF)Additional Information (PDF)

Parts.txt (TXT)
Solutions and Comments (PDF)

Code (Q1q2code.txt) (TXT)

Test file (Q1tester.txt) (TXT)
Assignment 2 (PDF)Additional Information (PDF)

parts.dict (DICT)

map.dict (DICT)
Code (Pset2code.txt) (TXT)
Assignment 3 (PDF)Additional Information (PDF)

GeneticCode.dict (DICT)

Protein.txt (TXT)

NC_003418.txt (TXT)
Solutions (PDF)

Code (Spencers_4.txt) (TXT)
Assignment 4 (PDF - 3.0 MB)




Exams

Exam 1

Exam 1 Solutions (PDF)



Exam 2

Exam 2 Review Questions (PDF)

Exam 2 Solutions (PDF)





Study Materials

Introduction to Python Tutorial (PDF)

Unix and Python Tutorial for 20.180 (PDF) (Courtesy of Sampsa Hautaniemi, Sabrina Spencer, and Laura Sontag. Used with permission.)

Programming Tutorial (PDF)




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