DNA COMPUTING, CS 9562B/4462B, Winter 2008-2009

Students in this course are eligible for the 500 dollar

University of Western Ontario BIOCOMPUTING STUDENT AWARD

Announcements

Class schedule: Wednesday 9:30am-10:30am, Friday 9:30am-11:30am, MC320.
How to print a .ps file

Course Outline

Presentations, papers, assignments

Assignments will be evaluated for completeness (cover all the main points of the lectures), clarity, style and elegance.
Paper and Presentations DOs and DON'Ts
Presentations schedule: see lecture schedule

Office hours

Wednesday, 10:30am-11:30am, MC 385, Lila Kari.

Textbook

"Theoretical and Experimental DNA Computation", Martyn Amos

Assignments

Each assignment will consist of a 1000-1500 word paper that summarizes, in your own words, the lectures (including student presentations) that were presented in the weeks preceding the week the assignment is due (more details in the course outline). The assignments are due in the course locker (TBA). The penalty for late assignments is 10% for each day late.

Lecture Schedule (tentative)

Fri., Jan. 9, Adleman's first experiment in DNA computing. Prof. Lila Kari. Suggested readings:
- Section 1, Section 5.4 from the textbook.
- DNA computing: arrival of biological mathematics (first two sections)
  Fig.1 , Fig.2 , Fig.3 , Fig.4 , Fig.5 , Fig.6 , Fig.7
Fri., Jan. 16, Basic concepts used in DNA computing (nucleotides, DNA, proteins, amino-acids) Prof. Kathleen Hill. Suggested readings:
- Lecture Notes ppt
- (pdf file 2008)
- Chapter 1 from the textbook.
- Chapter 1 from "DNA Computing: new computing paradigms." G.Paun, G.Rozenberg, A.Salomaa, Springer Verlag 1998. CS I/O counter.
- Nucleic acid structure and function
- A computer scientist's guide to molecular biology
Fri., Jan. 23, Potential bio-operations; molecular procedures (PCR, biotin-avidin purification, hybridization, etc.). Prof. Kathleen Hill.
Lecture Notes 1
Lecture Notes 2
Recombinant DNA
PCR
Gel Electrophoresis
Blotting
Suggested readings:
- From Readings for Jan. 9 (Article: first two sections, and last 2 sections on implementation techniques and meta-thoughts).
Fri., Jan 30, Cells do computations. . Prof. Lila Kari. Suggested readings:
- Computational power of gene rearrangement (@AMS Press) .
- Reversible molecular computation in ciliates (@Springer Verlag) .
Fri. Feb. 6 The surprisingly succinct sequence sorcery of stichotrichous ciliates. Prof.Mark Daley. Suggested reading.
- Chapter 6 from textbook
- Lecture Notes
Fri., Feb 13 Encoding information in DNA Shinnosuke Seki
- Lecture Notes.
Fri. Feb. 20 Reading Week
Fri. Feb. 27 Nanocomputation by self-assembly Prof. Lila Kari. Suggested readings:
- Lecture notes
- Section 3.4, Section 5.9.5 from textbook
Fri, March 6, Natural Computing Lila Kari
Fri, March 13, DNA automata, Turing machines and molecular computers Arif Raza
Fri., March 20, DNA Algorithms for 3-SAT Sardar Anisul Haque. Scanned examples. Read in the order: page 2 (example of 3-SAT), page 1 (encoding by Lipton's method), page 3 (encoding by the new proposed method).
Fri., March 27, DNA memory and DNA information Israt Jarin. DNA Computing by self-assembly: Theory and experiments. Mohammed Ashraf Ali
Fri., April 3, DNA nanomachines Jenna Cameron

Some DNA computing Web resources

A few useful materials on molecular biology

G.Paun, G.Rozenberg, A.Salomaa. DNA Computing .Springer Verlag, 1999.
K.Drlica. Understanding DNA and gene cloning: a guide for the curious , 3rd edition, John Wiley and Sons, 1997.
C.R.Calladine, H.R.Drew. Understanding DNA: the molecule and how it works. Academic Press, 1999.
P.C.Turner et al. Instant Notes in Molecular Biology Bios Scientific Publishers. 1997.

Presentations homepage: TBA