Introduction to Computational Biology

A Tour in 45 Pieces.

Spanning Systems & Synthetic Biology, Biophysics & Bioinformatics.

Modalities.

The following is a list of teaching modalities. "One surprize per lecture."

=Lab. =Homework. =Exam. =Group activity. =Project. =Film.

=Advance prep needed.

1. HACKING Slideshow: molecular hacking. Transposons and viruses.
2. HELLO Roll Call: 20-30 words from everyone. What's compbio to you? (Instructors too!)
3. HELLOWIKI Wiki page creation. Mugshot thumbnail upload. Roll Call Page. Unix Lab.
4. DOGMA Slideshow/film: information, genetic code, central dogma.
5. STRUCTURE1 Protein Structure Visualization. Primary==>quaternary structure.
6. PERL1 Perl lecture/lab. Strings & scalars, conditionals, loops.
7. PERL2 References/pointers, paged memory, machine code, buffer overflows.
8. DATABASES Assigned group presentations on File formats & Databases.
9. PERL3 Perl lecture/lab. Arrays, References & Anonymous Arrays.
10. TOPTRUMPS Top Pfams / find-interaction-partners game, e.g. DIP (H.pylori? c.f. Falush et al) (or venomics)
11. INFORMATION Chalktalk/slides: Information content & entropy. Codes & compression.
12. PERL4 Perl lecture/lab. Subroutines.
13. HIDING Codebreaking Exercise: Steganography.
14. FINDING Codebreaking Exercise: Sliding-window entropy scan.
15. PERL5 Perl lecture/lab. Patterns & Regular Expressions.
16. STEGANOGRAPHY Presentation of cryptanalysis techniques.
17. REVIEW1 Review of Molecular Database Basics, Perl Basics, Entropy Basics.
18. MIDTERM1 Midterm exam #1.
19. PROJECT1 Overview of project: Phylometagenomics
20. DICE (MacKay book) Dice experiments: Bayes' Theorem & loaded dice.
21. TRAFFIC Codebreaking: Traffic Analysis. Pairwise homology detection.
22. SUBSTITUTION Chalktalk/slides: Theory of pairwise substitution matrices.
23. ALIGNMENT Everyone helps fill Smith-Waterman DP matrix(ces).
24. COMPLEXITY Algorithmic complexity. Binary chops & trees; sorts. Multiple sequence alignments.
25. EVOLUTION Molecular Evolution: the Jukes-Cantor model.
26. PHYLOGENY Phylogeny by UPGMA.
27. ONTOLOGY Ontologies. The GO. Reactome. GALEN. OWL. More...
28. PERL6 Perl lecture/lab. Hashes. GO/Reactome gene associations.
29. PROJECT2 Presentations on assigned protein domains & pathways for project.
30. REVIEW2 Using Perl to run Unix tools. Review of Bayes, alignment, phylogeny.
31. MIDTERM2 Midterm exam #2.
32. GUEST1 Guest lecture on systems biology.
33. GUEST2 Guest lecture on synthetic biology.
34. LATTICE1 Biophysics simulation: Brownian motion & diffusion-limited aggregation.
35. TOUR JGI tour.
36. GUEST3 Guest lecture on biophysics.
37. GUEST4 Guest lecture on bioinformatics software libraries.
38. PROJECT3 Presentations of initial project results.
39. ETHICS Discussion: ethics of synthetic biology.
40. LATTICE2 Biophysics simulation: Protein folding on a discrete lattice.
41. STRUCTURE2 Slideshow: RNA structure. DNA & RNA motifs. Approx statistics thereof.
42. STRUCTURE3 Biophysics: Thermodynamic RNA folding & structure visualization.
43. DESIGN Paper review: computational DNA design.
44. REVIEW3 Review of class content.
45. FINAL Final exam.
46. PROJECT4 Final project presentations.
47. MOVIE Movie: GATTACA

Other ideas:

1. Bio blog review.
2. Automating workflow with "make".
3. Simulations of immune system dynamics.
4. Drug-target docking. ()
5. Information & inference in neuro-engineering. ()
6. CoreWars

Each of the above needs at least one page of notes (incl. overview paragraph: didactic goals, pedagogical modalities, key examples, daily surprise, blah blah blah). The prepared slideshows/lectures typically will need more. Homework exercises, project specs, midterms, etc., will also need more.

At least 1 in 6 classes to be guest lectures.

At least two 1-week periods to be alternate instructors (TA, grads).

Try and think of some more unusual & interesting group activities.

Set up "Teaching" web with "Fall 2007" subweb.

Use Blackboard.

Assessment

A mix of the following:

• Homework assignments
• Project
• Participation in group discussions & presentations
• Examinations

PRIZES for codebreaking exercises, midterms, presentations, best project (mug, coaster, stationery, Top Trumps deck, cheater dice, T-shirt, molecular modeling kit...)

Points to hit in homework & classroom exercises

• FBI homicide statistics
• Derivation of Student's t distribution, (will be very hard, but at least introduces the concepts)

Reader

Need to prepare a reader for the class.

• Published papers
  • All of those referenced above, and then some...
• Book chapters
  • O'Reilly Perl books
  • Durbin book
  • MacKay book
  • Protein lattice simulations?
  • Algorithms?
  • Phylogeny?
  • More?

TA Duties

1. Review all wiki pages prior to class. Clear solutions etc.
2. Book largest Etcheverry lab. Set up class account. Register students' user accounts.
3. Ensure all practicals are set up in advance, and run smoothly on the day.
4. Help grade class presentations & group activity.
5. Grade & provide model solutions for homeworks.
6. Grade & provide model solutions for midterm exams.
7. Teach at least 3 lectures.
8. Be prepared to teach any lecture, or run most activities.