CIS595: Homework 1
Assigned: January 24, 2005
Due: January 31, 2005 (in class)
Homework Policy
· All assignments are INDIVIDUAL! You may discuss the problems with your colleagues, but you must solve the homework by yourself. Please acknowledge all sources you use in the homework (papers, code or ideas from someone else).
· Assignments should be submitted in class on the day when they are due. No credit is given for assignments submitted at a later time, unless you have a medical problem.
Problems
Student Survey (answer the following questions)
· name
· grad/undergrad and year
· major/home department
· CS background
· biology background
· statistics background
· do you have personal access to a computer, printer, and the internet?
· will you be doing as much of the course as you can at home, work, or another off campus computer?
· why are you taking this course?
· what is your previous experience in the area of Bioinformatics?
Reading Assignment
Read “Molecular Biology for Computer Scientists” by L. Hunter (download from the course web page). Write a one-page summary (10 or 11pt font, single spaced) of major topics covered by this document. Also answer this: Was reading difficult? Did you learn something new?
Gaining Experience with PubMed
1. Search PubMed (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi) using “bioinformatics and review” keyword
o Provide the date of your search and give the total number of articles found
o Carry out the search using “bioinformatics” keyword and use the limit function to select only reviews within the publication type section
§ Click on limits
§ Toggle the tab window "Publication Types" for "Review"
§ Provide the date you did your search and give the total number of articles found with the search
o Compare the two searches. Do they give identical results? If not, examine the results and provide an explanation for the differences.
o MS Boguski has contributed significantly to the field of bioinformatics
§ Search for articles written by Boguski on bioinformatics (e.g., boguski ms AND bioinformatics)
§ How many articles are present?
§ Provide the complete reference to a paper he published in 1994.
2. Decapping enzyme is a eukaryotic enzyme that removes the cap of mRNAs and initiates mRNA degradation.
3. Search PubMed for decapping enzyme
4. Find the article which describes the isolation and characterization of yeast Dcp1p decapping enzyme
5. Provide the complete reference to that article
o Use the related articles link to illustrate neighboring in Entrez to identify related articles
o Provide the complete reference to the article by Haller AA and Sarnow P. published in August of 1997.
o View the free full-text article either at the Journal Site or PMC (PubMed Central)
6. For the article in #4
o Provide the number of papers published by the first author of the article
o Provide the complete reference to an article by the this author that is not on decapping or the decapping enzyme
GOOD LUCK!!!