Assignments

Spring 2009

Starting with Problem Set 5, all sets will be due on Tuesdays at 4:00 PM. Homework should be turned into the Bi1 closet.

Problem Set 1 (Due Tuesday, April 7 @ 5 PM)

• PDF
• Solutions (PDF)

Problem Set 2 (Due Tuesday, April 14 @ 12 PM)

• ZIP archive containing all PS2 files
• PS2 PDF
• BR.fasta
• Bacteriorhodopsin.pse
• DNAprotein.pse
• PyMOL tutorial PDF
• Electronic figure submission guidelines (optional)
  
  
• Solutions (PDF)

Problem Set 3 (Due Tuesday, April 21 @ 12 PM)

• PDF
• Solutions (PDF)

Problem Set 4 (Due Tuesday, April 28 @ 12 PM)

• PDF (Note: if you have trouble viewing the Greek characters in this PDF file, please open it with Adobe Acrobat).
• Supplemental PCR reading:
  • IDT tutorial: "The polymerase chain reaction" (PDF, Caltech only)
  • IDT tutorial: "A basic PCR protocol" (PDF, Caltech only)
• Solutions (PDF)

Midterm (Due Monday, May 4 @ 5 PM)

• PDF
• Midterm Resources Page
• Glossary (PDF)
• Statistics:
  • Average: 285.8 out of 330 (or 86.6%)
  • Standard deviation: 32.2
• Solutions (PDF)

Problem Set 5 (Due Tuesday, May 12 @ 4 PM)

• PDF
• Solutions (PDF)
  

Problem Set 6 (Due Tuesday, May 19 @ 4 PM)

• PDF
• Solutions (PDF)

Problem Set 7 (Due Tuesday, May 26 @ 4 PM)

• ZIP archive containing all PS7 files
• PS7 PDF
• HLA.pdb
• PyMOL tutorial PDF
• Solutions (PDF)

Problem Set 8 (Due Tuesday, June 2 @ 4 PM)

• ZIP archive containing all PS8 files
• PS8 PDF
• RSV p60 src.txt
• src proteins.txt
• Solutions (PDF)

Final (Due Thursday, June 11 @ 4 PM)

• PDF
• Final Resources Page
• Glossary (PDF)

Extra Credit Opportunities

• CROI Lectures & Questions (PDF)
  For this assignment, you are asked to watch webcast lectures from the Conference on Retroviruses and Opportunistic Infections (CROI) and then answer several related questions. Responses should be submitted to Alex Webster (awebster@caltech.edu) by June 10.
  
  
• Darwin Seminars - Thursday, May 14
  For extra credit, attend the one or more of the Darwin seminars on Thursday, May 14 and do a short write up on what you have heard. If you attend a talk at the seminar and write a brief (~200 word) summary, you will get an extra section point. The Jesse Bloom talk "The Molecular Underpinnings of Virus Evolution" and the Francis Arnold talk "On Beyond Nature: Protein Evolution in the Laboratory" are each worth 1.5 section points. Please turn this in by 5PM on Thursday, May 21 by email to Damien. You may earn a total of 3 section points for the Darwin talks. A schedule of the symposium is available here (PDF).
  
  
• Folding@home - extra credit (PDF)
  Donate your spare computing cycles to a distributed computing project that aims to "to understand protein folding, misfolding, and related diseases" -- and earn extra credit in Bi1.
  
  
• Write your own Bi1 question - Extra credit (PDF)
  Write a Bi1 homework question to earn extra credit. If we end up using the problem, you may earn even more credit.
  
  
• Engineering Immunity - extra credit (PDF)
  Propose your own cure for HIV for extra credit!
  • Click here to read an article from the Tech about a student who did this extra credit assignment last year and has turned it into an ongoing research project (PDF, Caltech only)
  • Gates Foundation: Call for proposals, Fall 2009.