Below is the class schedule. A few notes:
- All regular meetings are in the Annenberg Auditorium (room 105). This includes the evening exercises, when students work together under the guidance of the course staff.
- The lessons are labeled with the initials of their primary author/presenter from the course staff.
- There will be a special pre-bootcamp session on Sunday night from 8-9 pm in 328 Sherman Fairchild Library for students who are unable to complete Lesson 0.
- The schedule is pretty stable, but may have some minor changes.
Sunday, September 13
- 8-9 pm
- Lesson 0 (JB/SS): Configuring your computer
Monday, September 14
- 9 am - noon
- Lesson session 1
- Lesson 1 (JB): Welcome and Hello, world.
- Lesson 2 (AM): Basic command line skills (command_line_tutorial.zip)
- Lesson 3 (JB): Variables, operators, and types
- Lesson 4 (JB): More operators and conditionals
- noon-1 pm
- Lunch
- 1-4 pm
- Lesson session 2
- Lesson 5 (JB): Lists and tuples
- Lesson 6 (JB): Iteration
- Lesson 7 (JB): Introduction to functions
- Lesson 8 (JB): String methods
- 4:15-5:15 pm
- Faculty lecture: Niles Pierce, Engineering Programmable Molecular Instruments
- 5:15-7 pm
- Dinner
- 7-10 pm
- Exercise 1
Tuesday, September 15
- 9 am - noon
- Lesson session 3
- Lesson 9 (JB): Review of exercise 1
- Lesson 10 (JB): Introduction to object-oriented programming
- Lesson 11 (JB): Dictionaries (hash tables)
- Lesson 12 (JB): Packages and modules
- noon-1 pm
- Lunch
- 1-4 pm
- Lesson session 4
- Lesson 13 (JB): File I/O (1OLG.pdb)
- Lesson 14 (JB): Exceptions and error handling
- Lesson 15 (JB): Testing and test-driven development
- Lesson 16 (AM): Regular expressions (towels.txt, genbank_seq.txt, aligned.fasta)
- 4:15-5:15 pm
- Faculty lecture: Michael Elowitz, Dynamics and Design Logic of Cellular Systems
- 5:15-7 pm
- Dinner
- 7-10 pm
- Exercise 2 (salmonella_sp1_region.fna)
Wednesday, September 16
- 9 am - noon
- Lesson session 5
- Lesson 17 (JB): Review of exercise 2
- Lesson 18 (AM): More command line skills
- Lesson 19 (JB): Introduction to scripting (leica_tiffs.zip)
- Lesson 20 (JB): Introduction to NumPy and the SciPy stack
- noon-1 pm
- Lunch
- 1-4 pm
- Lesson session 6
- Lesson 21 (JB): NumPy arrays and operations with them (xa_high_food.csv, xa_low_food.csv)
- Lesson 22 (JB): Introduction to Matplotlib (xa_high_food.csv, xa_low_food.csv)
- Lesson 23 (JB): Random number generation
- Lesson 24 (JB): Monte Carlo simulation
- 4:15-5:15 pm
- Faculty lecture: Paul Sternberg, Small Worm, Big Data
- 5:15-7 pm
- Dinner
- 7-10 pm
- Exercise 3
Thursday, September 17
- 9 am - 11:20 am
- Lesson session 7
- Lesson 25 (JB): Review of exercise 3
- Lesson 26 (JB): Python style (PEP 8)
- Lesson 27 (JB): Version control with Git
- 11:20 am-12:20 pm
- Lunch
- 12:20-4 pm
- Lesson session 8
- Lesson 28 (JB): Case study: Computing the Luria-Delbrück distribution
- Lesson 29 (JB): Introduction to Pandas (xa_high_food.csv, xa_low_food.csv)
- Lesson 30 (JB): Case study: extracting data of interest from frog tongue adhesion (frog_tongue_adhesion.csv)
- Lesson 31 (SS): Introduction to BioPython
- Lesson 32 (SS): Case study: scripting BLAST searches
- 4:15-5:15 pm
- Faculty lecture: Mary Kennedy, A Set of Tools for Understanding Biochemical Networks: Computational Reconstitution of Cellular Functions
- 5:15-7 pm
- Dinner
- 7-10 pm
- Exercise 4 (grant.zip)
Friday, September 18
- 9 am - noon
- Lesson session 9
- Lesson 33 (JB/SS): Review of exercise 4
- Lesson 34 (JB): Introduction to image processing (ecoli_images.zip)
- Lesson 35 (JB): Case study: Basic image quantification (HG104_images.zip)
- Lesson 36 (JB): Performing regressions (bcd_gradient.csv)
- noon-1 pm
- Lunch
- 1-1:40 pm
- Lesson session 10a
- Lesson 37 (JB): Algorithmic complexity: Finding the longest common subsequence
- 1:45-2:45 pm
- Faculty lecture: Mitch Guttman, lncRNAs: Function and Mechanism in Controlling Cellular Identity
- 3:55 - 5:15 pm
- Lesson session 10b
- Lesson 38 (MG): Efficient genomic queries
- Lessons 39 and 40 (MG): Quantifiying gene expression (slides)
- 5:15-7 pm
- Dinner
- 7-10 pm
- Exercise 5 (bacterial_growth.zip)