7.89/CSB.100  Topics in Comp & Sys Biology

Hi all,

Thanks to those who have completed the MIT subject evaluation and/or the feedback form!

For those who haven't yet, please complete both of these – should take no more than about 5-10 min each.  On the feedback form, it's ok to leave some questions blank if you don't have strong feelings about them.  I'd really like to have everyone's opinions represented.  Many thanks and good luck on finals!

Cheers,

Chris

Dear students,

I am very interested in hearing what you think of this course – what you learned the most from, what you liked most/least, what you'd like to see changed.  Every year I carefully read feedback from students and adjust the content of the course - topics, papers, etc., as needed.
This feedback takes two forms:

1) The official MIT subject evaluations that other students can see at http://web.mit.edu/subjectevaluation/

2) Your answers to a specific set of questions that help me evaluate and adjust course content.

I have posted these questions as a one page Word doc on the course web site under Week 11.
If you could download this and either hand write or type your comments and bring to
class, that would be great.
The questions are straightforward but might take a few minutes if you need to refresh your memory of the titles of particular papers, etc.  If you don't have time before class, you can also drop them in the box outside my office later tomorrow or Monday.

I need all students to complete both of these evaluations so that everyone's opinion is considered.

THANK YOU FOR A GREAT SEMESTER AND THANKS IN ADVANCE FOR YOUR FEEDBACK ON THE COURSE.

See you all tomorrow.

Cheers,

Chris

Hi All,
For the last week of the course, we will read some papers that are representative of "Big Biology" / consortium-style science, as well as commentary on these projects.
Paper 1 is a computational paper analyzing data from the 1000 Genomes Project.  Please read it carefully and we will discuss in moderate depth.  It contains some population-genetic concepts that are important but may not be familiar (e.g., "derived allele frequency"), so BE SURE TO LEARN THEM.
Paper 2 is the main paper from "Phase 2" of the ENCODE Project, a landmark project that also generated its share of controversy.  It is way too long and complex to read in depth, so I am just asking that you read pages 57-61 (through Fig 1) and any text/methods/etc. necessary to understand Fig 4 (which is not trivial).   We will primarily discuss Figs 1 and 4.
Read the rest of the paper if you like.
Please also read the background paper by W. Ford Doolittle, which is his perspective on the definitions of words like 'function' and 'regulation' that were at the heart of some of the controversy, which we will discuss briefly.
Looking forward to the discussion.
Cheers,
Chris

Hi all,

I hope everyone had a good Thanksgiving.
Just a reminder that we're all reading the Elowitz and Chau et al papers,
plus each of you is reading an additional paper and writing a short essay about
it, due in hardcopy at start of class (last writing assignment of the semester!).
In class, we will spend approx 40 min on Elowitz, 60 min on Chau because it's
more complicated, and the remainder of time discussing synthetic biology in
general, and to set this up I'll ask each of you to summarize the additional paper
you read in about two sentences.  Should be a fun class.

Cheers,

C

Hi all,
Hope you had a relaxing week with no class Friday and have located the papers
for this week, when we'll have another guest instructor, Prof Gene-Wei Li.
Prof Gehring mentioned to me that she was disappointed that no one looked
up ChIP-Exo, an important method used in the papers discussed her week.
As a reminder, you are responsible for doing whatever it takes to understand
all methods used in the papers as well as you can.
Again this week there are some methods that may be unfamiliar, so please
be sure to do your homework and look up any unfamiliar methods before class.
FYI, there will be one more writing assignment, related to synthetic biology,
but it will be fairly short.
Cheers,
Chris