Course Materials

The materials will be augmented by various instructors as the semester proceeds.

Assignments (reverse chronological order)

Due May 8 : Course projects. Each student will turn in a project report, with the other students as coauthors (see Grading). Presentation of the projects will occur in early May.

Due April 20 : Course project proposals. 3-5 pages. High quality.

Due April 20 : There will be no assignment from Prof. Knight, to allow focus on the course project.

Due April 17 : Assignment from Prof. Pollock.

Due April 5 : Assignment from Mr. McTavish.

Due March 29 : Assignment from Mr. Caporaso.

Due March 15: Student presentations on one of their completed programming assignments.

Due March 13 : Assignment from Prof. Goldberg

Due March 1 : Assignment from Prof. Kechris: Fit a mixture model using EM to a sequence generrated from a mixture of distributions. Make predictions.

Due Feb 27 : Assignment from Dr. Gu: Run PCLOUD, make figures to visualize output (preferably using R or PerlGD), and give a formal report.

Due Feb 20 : Assignment from Mr. Kim: Transform MATCH to DIST file to calculate distance distributions of pwm pairs; using DIST distributions, calculate empirical background distribution; provide a formal report. Extra credit: calculate significance of distance distributions different from the empirical background. Report p-values and selection of p-value threshold. Compare pairs satisfying the threshold to the pairs of known interaction.

Due Feb 15 : Assignment from Prof. Osguthorpe for predicting secondary structures using GOR. Brk files available here.

Due Jan 25: read up on extreme programming. Bone up on C/C++, PERL/CGI, HTML/Apache, PhP, R, PerlGD, Java, XML, MySQL, as necessary. Write 1-2 page plan of action for some basic analysis of gene or genomic information, based on exploration of web resources. Suggested topics to explore web resources:

• eukaryotic genomes
• phylogenetic organization, nomenclature (e.g., NCBI)
• gene locations and annotation
• regulatory regions and predictions
• acquire information on example gene families, e.g., COI, CYTB, beta-helix
• alignment; different programs; consider automation
• protein or RNA structures

Advice: Here are some "how to" pointers that will be useful to you during the class.

• write a project proposal
• present a paper
• provide context for a paper
• sample proposal outline
• sample report outline
• criteria for review of proposals

NIH Materials

• PHS 398 grant forms and instructions
• R03 program announcements
• General grant review criteria
• Peer review policy
• Federal regulations about NIH grants

JBI Materials

• Guide for authors and review criteria
• Scientific conduct editorial

Readings: In addition to the advice to scan the journals listed on the links page, here are some online conference proceedings for the last few years.

• ISMB 2006, 2005, 2004, 2003, 2002
• PSB 2007, 2006, 2005, 2004, 2003

rofs | Requirements | Syllabus | Course Materials | Course Links | Grading