BCB 444/544 Fall 07 Oct04 HW544Extra #1 p 1 of 4
BCB 444/544
HW544 Extra #1
(20 pts)
_________________________________________
Due Mon Oct 1 by Noon (Task 1.1)
Due Mon Oct 8 by 5 PM (Task 1.2 & Task 2)
Name
(please send electronic copy to terrible@iastate.edu
or deliver hard copy to MBB 106 before Noon on due date)
Objectives:
1. To encourage you to begin planning your Team Semester Projects
2. To give you practice working with a small team to discuss a current research paper & evaluate it critically
Task #1: (10 pts total)
Begin planning your Team Semester Project
1.1 (5 pts) Get to know potential team members (other BCB 544 students in your class)
(this part only is due on or before noon on Mon Oct 1)
Type the following information into the Table below, and submit it in 2 ways:
1- Electronically (fill in & send this page as Word.doc attachment) to: terrible@iastate.edu
Name
Email address
Degree Program (BS, MS, PhD)
Department
Major Professor (if applicable)
"Biological" topics of interest to me:
"Computational" or "Statistical" topics of
interest to me:
Potential Team Project Ideas:
Other relevant information (e.g., I made
A+ in ComS 311; I own a 100-node cluster; I
do microarray research...)
ULR for my personal or research webpage
Optional, but nice if you have one
Photo (AccessPlus is fine)
Optional, but helpful!
By signing here, I give permission for this
information to be shared with other
members of my BCB 444/544 class (only)
BCB 444/544 Fall 07 Oct04 HW544Extra #1 p 2 of 4
1.2 (5 pts) Begin investigating potential team project topics
This assignment will be easier after you have seen the information above for your BCB 544 classmates, right?
Michael will collect and combine the above information and distribute it to all of you electronically on Tues, Oct 2
(so please submit the information requested in 1.1 ASAP & no later than Noon on Mon Oct 1) After reading the
information submitted by other students, you may see some "natural" overlaps between your interests & those of
your classmates. Because there are so few students in our class, we may need to help you form teams so that
every team will have both "biologists" and "computationalists," (this is negotiable). We imagine teams will have 2 or
3 members (this is also negotiable).
FYI: Examples of previous's BCB 544 projects are provided here:
2005: http://www.cs.iastate.edu/~cs544/project.htm
2006: http://www.public.iastate.edu/~f2007.com_s.544/project.htm
Please note that specific requirements for oral presentations & written reports may be slightly different this year
(and will be posted soon).
Keeping in mind the above comments, list 2 BCB 544 students with whom you think you would enjoy working
with on Team Project (no need to rank them!)
1.
2.
Briefly describe 3 project ideas you are considering (please do RANK THEM in order of your preference)
For each, be sure to mention:
a) Biological motivation/Question addressed
b) Some types of algorithms/software you'd like to develop or learn to use
c) Any other relevant information (i.e., Is this project related to work you've done before?
Is it almost the same as your project for another class? (this is probably OK with us),
Is this topic especially relevant to your own research or potential future research?)
Idea #1
Idea #2
Idea #3
BCB 444/544 Fall 07 Oct04 HW544Extra #1 p 3 of 4
Task # 2 - (10 pts)
The following paper was assigned as Required Reading for BCB 544 students:
Pollard KS, Salama SR, Lambert N, Lambot MA, Coppens S, Pedersen JS, Katzman S, King B, Onodera C, Siepel A,
Kern AD, Dehay C, Igel H, Ares M Jr, Vanderhaeghen P, Haussler D. (2006) An RNA gene expressed during cortical
development evolved rapidly in humans. Nature 443: 167-172.
http://www.nature.com/nature/journal/v443/n7108/abs/nature05113.html
doi:10.1038/nature05113
2.1 (5 pts)
After reading the paper (and without simply plagiarizing the abstract), in ~ 1 typed page,
briefly describe:
a) Biological motivation for and key question(s) addressed in this paper
b) Bioinformatic & experimental approaches used to address these questions
c) Results obtained & conclusions drawn, as presented by the authors
d) Significance of this work (according to the authors)
e) Do you agree with the authors' conclusions & their assessment of the significance of this work? Why or
why not?
BCB 444/544 Fall 07 Oct04 HW544Extra #1 p 4 of 4
2.2 (5 pts)
During lab on Thurs Oct 4 (if possible) meet with at least 1 or 2 other 544
students and prepare a JOINT answer to the following questions. You should discuss the answers,
perhaps divide the writing duties, & share the resulting answers. Each student should "cut & paste" the
same answers into his/her individual homework submission.
a) My name:
b) I worked with the following student(s) on these questions:
c) What part(s) of this paper did you find most difficult to understand? Be specific (refer to a specific figure
or section of text, etc.)
d) What part(s) did you find most interesting? Why?
e) Did you and your partner agree on these answers, or did you have different opinions? Explain.