UNCONVENTIONAL COMPUTING I: DNA COMPUTING, CS 881b, Winter 2001

Announcements

• Deadline for submissions of the research paper: Friday, April 6, 2001, 5pm (file, paper copy, transparencies), MC 385.
• Details of submission.
• Class schedule: Thursdays, 1:00-3:00pm, MC 320
• How to print a .ps file

Course outline

Office hours

• Wednesday, 11:10am - 1:10 pm, MC 385, Lila Kari.

Invited speakers

• Greg Gloor , Dept. of Biochemistry, UWO
• Lars Konermann , Dept. of Chemistry, UWO
• Mark Perry , Dept. of Computer Science and Faculty of Law, UWO.
• Maurice Margenstern, Department of Computer Science, University of Metz, France.
• Mark Daley , Computer Science Dept, UWO.
• Rob Kitto, Faculty of Law, UWO

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.

Schedule

• January 4, Introduction. Lila Kari.
• January 11, Adleman's first experiment in DNA computing. Lila Kari. Suggested readings:
  • DNA computing: arrival of biological mathematics (first two sections)
    Fig.1 , Fig.2 , Fig.3 , Fig.4 , Fig.5 , Fig.6 , Fig.7
• January 18, Basic concepts used in DNA computing (nucleotides, DNA, proteins, amino-acids). Greg Gloor. Suggested readings:
  • Chapter 1 from "DNA Computing: new computing paradigms." G.Paun, G.Rozenberg, A.Salomaa, Springer Verlag 1998. CS I/O counter.
  • Copies of the slides. CS I/O counter.
  • Nucleic acid structure and function
  • A computer scientist's guide to molecular biology
• Wed., January 25, Potential bio-operations; molecular procedures (PCR, biotin-avidin purification, hybridization, etc.). Greg Gloor. Suggested readings:
  • From Readings of Jan.18: first two sections, and last 2 sections on implementation techniques and meta-thoughts.
  • Copies of the slides at the CS I/O counter.
  • Program (cgi)to predict the metling temperature of an oligonucleotide (updated).
• February 1, Cells do computations. . Lila Kari. Suggested readings:
  • Computational power of gene rearrangement (@AMS Press) .
  • Reversible molecular computation in ciliates (@Springer Verlag) .
• February 8. Recent trends in biological information processing. Lila Kari.
• February 15, Molecular expert systems , Rob Kitto. Circular insertions and deletions , Mark Daley. Suggested readings:
  • Circular insertions/deletions with applications to biomolecular computation (@IEEE CS Press)
  • Molecular expert systems
• February 22- Conference week.
• March 1, Implementing logic with proteins and DNA. Lars Konermann, Lila Kari. Readings:
  • Solving the Satisfiability Problem with DNA
• March 2, 3pm, MC 320 Distributed splicing systems. Maurice Margenstern
• March 15, 3pm, MC 320
  • Claire Wang, "DNA-based cryptography".
  • Cecilia Ionita, "DNA computing based on splicing: H-systems".
  • Shangqin Li, "Computing Boolean formulas with DNA".
  • Xuexin Li, "An analysis of the sticker-based system".
• March 22, 3pm, MC 320
  • Elena Losseva, "Error-free DNA encodings: an algebraic approach".
  • Amit Kumar, "Biomolecular optoelectronics".
  • Hue Tang, "Encoding information in DNA computing".
  • Songning Ding, "Comparision between surface-based and test-tube-based DNA computing".
• March 29, Ethical and legal implications of DNA computing. Mark Perry.
• April 5, 3pm, MC 320
  • Kathryn Ott, "Solving graph problems with DNA".
  • Rachel Bevan, "DNA computing with membranes".
  • Dong Liu, TBA.
  • Chris Power, "A DNA algorithm for a chess problem".

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