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Held: Thursday, 5 November 2009
We ground our understanding of structure prediction by implementing the
standard Chou-Fasman algorithm.
- Don't forget the Medical Informatics talk at 4:30 today in 3821. Refreshements at 4:15 in the CS Loungue.
- Don't forget the Destination ImagiNation Fun Run/Walk this weekend!
- Look ahead to the Rights and the Environment symposium next week.
- Today's programming project will be your next homework assignment.
- We anticipate returning your exams next Tuesday. (Sorry for the delay.)
- Next reading from the literature: Krings et al. 1997. (It's on P'Web)
- Discussion: Picking independent projects.
- Programming project: 7.5: Chou-Fasman.
- The last quarter or so of the semester is devoted to independent projects.
- What is an independent project?
- A group of students (mixed Bio/Non-bio) design and explore a problem
- What do we mean by
- Identify and gather an appropriate set of data
- Identify and use existing tools to explore those data
- Build at least one program that will aid in your analysis
- Write a paper that summarizes your results
- What kinds of projects might you do?
- You could extend one of the algorithms we discussed in class
- Implement your own version of BLAST
- Produce a new data set for and improved implementation of Chou-Fasman
- Implement the Kellis algorithm and use it on a different set of data
- You could delve more deeply into data sets from one of our papers
- Thursday, 12 November: Turn in project proposals
- Tuesday, 17 November: Turn in peer reviews of project proposals
- Thursday, 19 November: Short (five minute) overviews of propoals for visitor
- Tuesday, 24 November, In-class time for working on projects
- Thursday, 26 November, Thanksgiving
- Tuesday, 1 December, In-class time for working on projects
- Thursday, 3 December, Presentations (about fifteen minutes per group)
- This programming project is also a homework assignment.
- Finish implementing Chou-Fasman.
- Analyze its efficacy on three proteins of your choice. (Should be
proteins with a known structure.)
- Find out how people make it better, and describe those improvements