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Biological Computing: At the Crossroads of Engineering and Science >> Content Detail


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Assignments



Assignments

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



Writing Assignments


About a third of the way into the course you will have to write an abstract to a previously published paper (you will receive the paper without the abstract). Along with the abstract you will have to turn in a short paragraph discussing whether the paper you were given was a scientific or an engineering paper.

About two thirds of the way into the course you will have to turn in a short (3-4 page) paper describing somewhat in detail one of the techniques or methods we encountered in the class readings. Include a short section discussing the differences in the uses and usefulness of the technique for scientific and engineering applications. The first draft of the paper will be due two weeks before the assignment due date. I will edit that draft to give you a chance to improve it for the final submission.

Example of published paper with a removed abstract section. (PDF - 2.0 MB)#



Oral Presentations


Several times through the semester, you will be asked to give a short formal introduction to one of the papers discussed in class that day. Your introduction should include what you think the main point of the paper was, what you thought was particularly interesting about the paper, and any part or idea in the paper that deserves scrutiny, if any. These should be low-stress assignments, as they are designed to help you improve your formal speaking skills in preparation for final presentations.

At the end of the semester, you will be required to present a published paper as your own. The topic and the paper itself can be a follow-up on anything discussed in class or a completely independent topic related to the overall theme of the seminar. The presentation must include an introduction that briefly reviews relevant literature, a hypothesis or a model, a set of experiments to test the hypothesis or validate the model, experimental results, and interpretations of these results. Your presentation should highlight scientific and engineering aspects of the paper. The format of the presentation should follow the format of the paper.



Student Work


The example student work in the table below is included courtesy of the students named and used with their permission.


STUDENTsWRITING ASSIGNMENT 1WRITING ASSIGNMENT 2oral presentations
Anonymous(PDF)#Bioluminescence: Science and Engineering Applications (PDF)#

Engebrecht, J., K. Nealson, and M. Silverman. "Bacterial bioluminescence: isolation and genetic analysis of functions from Vibrio fischeri." Cell 32, no. 3 (March 1983): 773-81.

Weiss, Ron, and Thomas F. Knight. "Engineered Communications for Microbial Robotics." In DNA 2000, Lecture Notes in Computer Science. (DNA Computing: 6th International Workshop on DNA-Based Computers, Leiden, The Netherlands, June 13-17, 2000.) Edited by A. Condon. Vol. 2054. Berlin, Germany: Springer-Verlag GmbH, 2001, pp. 1-16. ISSN: 03029743.		Yan, H., S. H. Park, G. Finkelstein, J. H. Reif, and T. H. LaBean. "DNA-templated self-assembly of protein arrays and highly conductive nanowires." Science 301, no. 5641 (September 26, 2003): 1882-4.
Anonymous(PDF)#The Development of Genetic Circuitry (PDF)#

Engebrecht, J., K. Nealson, and M. Silverman. "Bacterial bioluminescence: isolation and genetic analysis of functions from Vibrio fischeri." Cell 32, no 3 (March 1983): 773-81.

Weiss, Ron, and Thomas F. Knight. "Engineered Communications for Microbial Robotics." In DNA 2000, Lecture Notes in Computer Science. (DNA Computing: 6th International Workshop on DNA-Based Computers, Leiden, The Netherlands, June 13-17, 2000.) Edited by A. Condon. Vol. 2054. Berlin, Germany: Springer-Verlag GmbH, 2001, pp. 1-16. ISSN: 03029743.

Yokobayashi, Y., R. Weiss R, and A. H. Arnold. "Directed Evolution of a Genetic Circuit." Proc Natl Acad Sci U.S.A. 99, no. 26 (December 2002): 16587-91.		Ramachandra, M., A. Rahman, A. Zou, M. Vaillancourt, J. A. Howe, D. Antelman, B. Sugarman, G. W. Demers, H. Engler, D. Johnson, and P. Shabram. "Re-engineering adenovirus regulatory pathways to enhance oncolytic specificity and efficacy." Nat Biotechnol 19, no. 11 (November 2001): 1035-41.
Anonymous(PDF)#Polymerase Chain Reaction (PDF - 1.1 MB)#

Augusten, L., R. A. Bowen, and M. Rouge, Contributors. "Thermostable DNA Polymerases." In Biotechnology and Genetic Engineering. Colorado State University: Colorado, December 1999.

Don, R. H., P. T. Cox, B. J. Wainright, K. Baker, and J. S. Mattick. "Touchdown PCR to circimvent spurious priming during gene amplification." Nucleic Acid Research 19, no. 14 (April 1999): 4008.

"Polymerase Chain Reaction." Wikipedia (April 2005).

"Taq DNA Polymerase with ThermoPol Buffer." New England Biolabs, Inc.

"Touchdown PCR." Wikipedia (March 2005).		Basu, S., Y. Gerchman, C. H. Collins, F. H. Arnold, and R. Weiss. "A synthetic multicellular system for programmed pattern formation." Nature 434, no. 7037 (April 28, 2005): 1130-4.
Anonymous(PDF)#The Magic of Magnetism (PDF)#

Adleman, L. M. "Molecular computation of solutions to combinatorial problems." Science 266, no. 5187 (November 11, 1994): 1021-4.		(PDF)

Yu, L. S., J. Uknalis, and S. I. Tu. "Immunomagnetic separation methods for the isolation of Campylobacter jejuni from ground poultry meats." J Immunol Methods 256, no. 1-2 (October 1, 2001): 11-8.
Mark Garcia(PDF)#(PDF)#

Weiss, Ron, and Thomas F. Knight. "Engineered Communications for Microbial Robotics." In DNA 2000, Lecture Notes in Computer Science. (DNA Computing: 6th International Workshop on DNA-Based Computers, Leiden, The Netherlands, June 13-17, 2000.) Edited by A. Condon. Vol. 2054. Berlin, Germany: Springer-Verlag GmbH, 2001, pp. 1-16. ISSN: 03029743.		(PDF)

Rothemund, P. W. "Using lateral capillary forces to compute by self-assembly." Proc Natl Acad Sci U.S.A. 3, no. 97 (February 1, 2000): 984-9.
Erin Mathewson(PDF)#Formation of DNA Nanotubes to Produce Nanowires (PDF)#

Liu, D., S. H. Park, J. H. Reif, and T. H. LaBean. "DNA nanotubes self-assembled from triple-crossover tiles as templates for conductive nanowires." Proc Natl Acad Sci U.S.A. 101, no 6 (January 6, 2004): 717-722.		(PDF)

Kobayashi, H., M. Kaern, M. Araki, K. Chung, T. S. Gardner, C. R. Cantor, and J. J. Collins. "Programmable cells: interfacing natural and engineered gene networks." Proc Natl Acad Sci U.S.A. 22, no 101 (June 1, 2004): 8414-9. Epub May 24, 2004.
Kate Stafford(PDF)#Microbial Signaling Systems: Methods and Applications (PDF - 1.1 MB)#

Weiss, Ron, and Thomas F. Knight. "Engineered Communications for Microbial Robotics." In DNA 2000, Lecture Notes in Computer Science. (DNA Computing: 6th International Workshop on DNA-Based Computers, Leiden, The Netherlands, June 13-17, 2000.) Edited by A. Condon. Vol. 2054. Berlin, Germany: Springer-Verlag GmbH, 2001, pp. 1-16. ISSN: 03029743.		(PDF)

Kuhlman, B., G. Dantas, G. C. Ireton, G. Varani, B. L. Stoddard, and D. Baker. "Design of a novel globular protein fold with atomic-level accuracy." Science 302, no. 5649 (November 21, 2003): 1364-8.

 








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