Harvard University, fas   
Fall 2003   


Biophysics 101

Genomics and Computational Biology

George Church, Ph.D. (HMS)






Info &








News/Event Info




Mon 24-Nov-03


Schedule for final presentations is now up online here.

Fri 7-Nov-03


An advanced optimization software is now available for use for the final projects. If your project involves the development and solution of large-scale optimization models (for example, flux balance analysis (FBA)), see here for details.

Tue 4-Nov-03


The template perl program for the clustering problem in PS4 has been updated with a revised version (as of Nov 4th, 3:50pm). However, if you have already downloaded the program and started working on it, you simply need to make the following two changes on the old version:

a. Change the command line processing to:
my ($input_file, $cluster_number, $method, $out_file) = @ARGV;
die("Usage: clustering.pl [INPUT_FILE] [CLUSTER_NUMBER] [CLUSTERING_METHOD: s or c] [OUTPUT_FILE]\n")
unless ($#ARGV == 3 && ($method eq "s" || $method eq "c"));

b. For the subroutine that updates the distance matrix, one more argument, the clustering method, should be added.

Fri 24-Oct-03


A version of the Section 5 notes with answers has been posted on the "Lectures" page. The original Section 5 notes have been updated, with one corrected slide and two new slides. All new/corrected slides have a purple background.

Final project idea submissions have been posted for a portion of the class. Click through the link near the top of the "Projects" page to access this year's final project idea submissions.

Wed 15-Oct-03


PS3 is up on the course website. Please start early (the perl part is a bit challenging) and seek help from your TF if needed.

The course videos will soon be password protected. Please see instructions on the “Lectures” page about how to access them.

Mon 6-Oct-03


PS2 has just been updated on the course website. Here’s a list of changes:

  1. The original matrix provided in 1.2.2 was incorrect (thanks to those who pointed it out). It has been replaced with a new matrix in the updated pset2 on the course website. Please answer question 1.2.2 and 1.2.3 according to the new matrix.
  2. In question 1.2.7, there was a typo: “Based on what you get in 1.2.4” should really be “Based on what you get in 1.2.6”.
  3. In question 1.2.3 and 1.2.7, it’s now stated explicitly that you need to list all of the best alignment(s). Originally it was implied. 1 point was moved from 1.2.7 to 1.2.3.
  4. In question 1.3.2, tblastn was missing from the list of BLAST tools. Now it’s added.

Sun 5-Oct-03


Notes for this coming week’s section is now posted on the “lectures” page.

Thu 2-Oct-03


PS1 answer key is now posted on the “problem sets” page.

Thu 25-Sep-03


PS1 has just been updated on the course website -- an alternative problem is added for the Excel bonus part of PS1 (so the old Excel bonus is called Bonus A and the newly added problem is called Bonus B). Please note that you only need to do ONE of them to get the bonus points, so you don’t need to worry about it if you’ve already done the bonus problem. But if you haven’t done it yet, we highly recommend you to do Bonus B because it’s more biologically relevant.

Tue 23-Sep-03


Students who haven’t received emails from their TFs please email bphys101@fas.harvard.edu ASAP with your accurate contact info.

Notes for the BIO introductory section is now posted online.

Last year’s problem sets are posted online for your reference.

Thu 18-Sep-03


Problem set policy has just been updated. Please read carefully about how to submit your problem set. Also notes for the first Perl/Excel introductory section is now posted online.

Wed 17-Sep-03


Course video for the first lecture is now online. You’ll need the RealPlayer from www.real.com to watch it.

Tue 16-Sep-03


Problem set 1 is now posted online. It’s due on Sep. 30th.

Wed 10-Sep-03


For this year’s course, we will be using Excel instead of Mathematica for an easier learning curve. An introduction to Excel will be included in our extra sections.






Please send comments to bphys101@fas.harvard.edu
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