ST590G:
|
Course prerequisite: ST 590A; competence in a programming language; basic knowledge of probability and statistics (ST 521 and 522 recommended)
Required text: Biological Sequence Analysis, by Durbin, Eddy, Krogh, and Mitchison Grading System: Your final grade will be as follows: 70% Programming Assignments 20% Oral Presentation 10% Participation and Attendance Syllabus (VERY tentative): Jan 10 - Jan 22: Random numbers and simulation Jan 24 - Jan 31: Pairwise alignment (Chapter 2) Feb 5 - Feb 14: Hidden Markov Models (Chapter 3) Feb 19 - Feb 28: Hidden Markov Models (Chapter 5) Mar 12 - Mar 21: Multiple Alignment (Chapter 6) Mar 26 - April 9: Phylogenetic Analysis (Chapters 7, 8) April 11 - April 25, May 4: Oral Presentations Communications: I may need to contact you with urgent information, such as an unexpected class cancellation. I will send any such notices by email, so please make sure your preferred email is registered with the university. Policy on Academic Integrity: The University policy on academic integrity is spelled out in Appendix L of the NCSU Code of Student Conduct. For a more though elaboration see the NCSU Office of Student Conduct website. For this course group work on homework is encouraged. However copying someone else's work and calling it your own is plagiarism, so the work you turn in should be your own. Violations of the Code of Student Conduct will be reported and severe penalties will be enforced. Students with Disabilities: Reasonable accommodations will be made for students with verifiable disabilities. In order to take advantage of available accommodations, students must register with Disability Services Office (DSO), 1900 Student Health Center, CB# 7509, 515-7653. Useful links: |
Course NEWS
4/9: Paper by Nick Goldman, discussed in class today. 4/4: Due date for Phylogeny assignment changed to 4/15. 4/2: Mistake in Tree 1 output example for Phylogeny assignment corrected. 3/28: Lots of new updates. Two new programming assignments: Phylogeny and your Personal Project; new critique assignments (due Wed April 4) and oral presentation dates. 3/12: Class 'replacement" on for March 26. Lior Pachter will be giving a bioinformatics seminar during our class period (4-5). I am cancelling class, with the expectation that you will attend this talk. I'll provide location information once I have it. Lior's web site 3/12: Material for Jeff Thorne's lectures: casp.pdf casp5andbaker.pdf databases2005R.pdf protstruct.pdf 3/7: Because of my stupidity with the due date, I have merged the two HMM pieces, which are due March 28. 2/22: Critique Assignments are posted. Due 2/28. 2/19: Test files for Assignments 1 and 2: - Simulation Test 1 - Simulation Test 2 - Simulation Test 3 - Reader Test 1 - Reader Test 2 2/5: Programming Assignment 3 is now posted. The due date has been changed to Feb 21. 2/5: Your first critique is due Feb 14. Please email a copy to both me and the student you are critiquing. BE POLITE AND CONSTRUCTIVE! 1/31: You should have received an email about documenting the installation/compilation of your programs. If not, please make sure you have the proper email registered with the university. 1/31: Student web pages and critique assignments will be linked from the Programming Assignments page here 1/24: As I mentioned in class, we are stuck with this room for now...more later. 1/24: I will grade the first two programming assignments as one, together. However, you MUST place a program on your web site (and email me the location) by the end of the day today. Document on your site what does/does not work right now, and update it before next week's due date. 1/11: I got a nice surprise today, and found out that Youfang Liu will be the TA for the course. She will help me test your programs as they are turned in. 1/11: Its not finalized, but it looks like we will be able to hold class in the BRC conference room. Programming Assignments 1. Data Reader/Writer Due 1/24 2. Data Simulator Due 1/31 3. Pairwise Alignment Due 2/21 4. HMM I Due 3/12 5. HMM II Due 3/28 6. Phylogeny Due 4/11 7. Your Project Due 4/25 |
||||||||||||||||||||||