Harvard University, fas   
Fall 2003   


Biophysics 101

Genomics and Computational Biology

George Church, Ph.D. (HMS)






Info &








Times and Locations: The lectures will be offered Tuesdays at 12:00 noon to 2:00 PM at Harvard Medical School in the Cannon seminar room in Building C-1. A nearly identical lecture will be given at 5:30 PM to 7:30 PM in the Science Center Lecture Hall A room 113. Students are encouraged to attend at whichever location and time is convenient for lectures. The lecture video, lecture slides, articles, etc. will also be available on the course web sites: BIOL E101 will be cross-listed as Biophysics 101 and available to MIT students as HST 508. The course is also available on the Internet. See Distance Education. You will be assigned to a section based on your preferences from the questionnaire collected at the first lecture on Tue Sep 16 (preferred; or submitted online if necessary).

Section times and locations.
We hope to have video, audio and/or teleconference options for each type of section.

beginning the week of Sep 22

Tue 2:30-3:30pm ADV MEC 447 (HMS) -- Faisal
Tue 8:30-9:30pm BIO 53 Church St. Labs room L01 (Cambridge) – Tom
Tue 7:35-8:35pm CS Science Center 111 (Cambridge) -- J.
Wed 7:00-8:00pm CS MEC 333 (HMS) -- Griffin
Wed 6:30-7:30pm BIO Science Center 304 (Cambridge) -- Woodie
Wed 7:35-8:35pm BIO Science Center 304 (Cambridge) -- Chih Long

Thu 6:30-7:30pm ADV Science Center 110 (Cambridge) -- Lan

Thu 7:35-8:35pm CS Science Center 110 (Cambridge) -- Mike

Thu 7:00-8:00pm CS MEC 333 (HMS) -- Xiaoxia

Supplementary Section Times/rooms (beginning Sep 17)
Wed 17-Sep 7-9pm MEC 340 (HMS) – Perl/Excel (Griffin) -- Handout: MS-PPT | PDF
Thu 18-Sep 5:30-7:30pm Science Center 111 (Cambridge) -- Biology (Lan and Woodie) – Section Notes: MS-PPT-1, MS-PPT-2
Mon 22-Sep 5:30-7:30pm Science Center 111 (Cambridge) -- Biology (Lan and Woodie)
Wed 24-Sep 7:35-9:35pm Science Center 111 (Cambridge) – Perl/Excel (Tom)



George Church

George Church





Teaching fellows:

Lan Zhang

Head TF: Lan Zhang


Xiaoxia Lin

Xiaoxia Lin


Faisal Reza

Faisal Reza


Griffin Weber

Griffin Weber


Chih Long Liu

Chih Long Liu


J. Singh

J. Singh


Yipeng (Woodie) Zhao

Yipeng (Woodie) Zhao


Michael Jones

Michael Jones


Tom Patterson

Tom Patterson


Course organization: In addition to the lectures below there will be section discussion meetings at the days and times above. Students will participate in at least one of those sections and form problem-solving and project teams consisting of at least one biology expert and one math/computer/engineering expert (or two to four people knowledgeable in both disciplines). Separate section on the basics of programming and molecular biology will be available in the first few weeks to even out the expected wide variation in backgrounds. Grades will be based on five problem sets, one final project, and participation in discussion sections covering the problems and about one scientific article per week. Your time commitment will be about 4 hours for classes and 6 to 12 additional hours per week, depending on background.


Despite the large number of TFs, the sections may be crowded and hence may be limited to registered non-credit and for-credit students. Anyone registered who did not receive email should contact the TF for your favorite time/location. Distance students can participate in section via live phone conferencing during section meetings, plus section notes and videos available online.

Section Notes:



Oct. 2

Memory Storage, Recursion, Sequence Alignment

Oct. 2

Regular Expressions

Oct. 2

Mathematica programming techniques

Oct. 2

Perl for Bioinformatics - part 1

Oct. 2

Perl for Bioinformatics - part 2

Oct. 2

Perl for Bioinformatics - part 3

Oct. 9

Sequence Alignment (Joon)

Oct. 29

Bayesian Networks and Hidden Markov Models (Jon)

Nov. 5

Bayesian Networks (Gary)

Recommended Textbook References: see the Readings page

Course Discussion Forum



Please send comments to bphys101@fas.harvard.edu
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