Week 10

This journal entry is due on Tuesday, November 10, at midnight PST. (Monday night/Tuesday morning)

This page is under construction.

Overview

• The purpose of this exercise is to create an annotated bibliography of papers related to the final research project.
• Two members of your team will present one of the primary research articles (genome or microarray paper) as a journal club presentation on Tuesday, November 17; the other two members of your team will present the other primary research article as a journal club presentation on Tuesday, November 24.
• You will also use these articles to write the Introduction and Discussion sections of your Final Project Report.

Individual Journal Assignment

• Store this journal entry as "username Week 10" (i.e., this is the text to place between the square brackets when you link to this page).
• Link from your user page to this Assignment page.
• Link to your journal entry from your user page.
• Link back from your journal entry to your user page.
• Don't forget to add the "Journal Entry" category to the end of your wiki page.
  • Note: you can easily fulfill all of these links by adding them to your template and then using your template on your journal entry.
• For your assignment this week, you will keep an electronic laboratory notebook on your individual journal entry page for this week. An electronic laboratory notebook records all the manipulations you perform on the data and the answers to the questions throughout the protocol. Like a paper lab notebook found in a wet lab, it should contain enough information so that you or someone else could reproduce what you did using only the information from the notebook.

Annotated Bibliography

1. Create a bibliography of a minimum of 4 citations to primary research articles.
   • A minimum of four articles should address the effect of cold shock on gene expression in budding yeast, Saccharomyces cerevisiae.

• A minimum of four should address the role of Hap4 in regulating gene expression in yeast. • Two articles for each of the above topics should have been published in the last three years. • Each of the 8 references in your bibliography needs to have the following information (an example is given at the end of the assignment handout): o The complete bibliographic reference in the APA style (see http://libguides.lmu.edu/content.php?pid=25618&sid=184708. You will be using one of three formats, “journal article from database (with DOI), journal article from database (no DOI) or journal article in print (no DOI).) o The link to the abstract from PubMed. o The link to the full text of the article in PubMedCentral. o The link to the full text of the article (HTML format) from the publisher web site. o The link to the full PDF version of the article from the publisher web site. o Who owns the rights to the article?  Does the journal own the copyright?  Do the authors own the copyright?  Do the authors own the rights under a Creative Commons license?  Is the article available “Open Access”? o What organization is the publisher of the article? What type of organization is it? (commercial, for-profit publisher, scientific society, respected open access organization like Public Library of Science or BioMedCentral, or predatory open access organization; see http://oaspa.org/membership/members/ for a list of members of the Open Access Scholarly Publishers Association) o Is this article available in print or online only? o Has LMU paid a subscription or other fee for your access to this article? 2. You must use these four databases/tools to find the references that you include in your bibliography: PubMed, GoogleScholar, Web of Science, Saccharomyces Genome Database (SGD). Answer the following questions as part of your assignment: a. Use a keyword search for the first three databases/tools and answer the following: PubMed • What original keyword(s) did you use? How many results did you get? • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search? Google Scholar • What original keyword(s) did you use? How many results did you get? • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search? Web of Science • What original keyword(s) did you use? How many results did you get? • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search? b. Use the advanced search functions for each of these three databases/tools and answer the following: PubMed • Which advanced search functions were most useful to narrow down the search? How many results did you get? Google Scholar • Which advanced search functions were most useful to narrow down the search? How many results did you get? Web of Science • Which advanced search functions were most useful to narrow down the search? How many results did you get? c. Perform a prospective search on the following three review articles in Web of Science and answer the following: • Aguilera, J., Randez-Gil, F., & Prieto, J.A. (2007). Cold Response in Saccharomyces cerevisiae: New Functions for Old Mechanisms. FEMS Microbiological Reviews, 31, 327–341. doi: 10.1111/j.1574-6976.2007.00066.x o How many articles does this article cite? o How many articles cite this article? • Al-Fageeh, M.B. & Smales, C.M. (2006). Control and Regulation of the Cellular Responses to Cold Shock: the Responses in Yeast and Mammalian Systems. Biochemical Journal, 397, 247–259. doi: 10.1042/BJ20060166 o How many articles does this article cite? o How many articles cite this article? • Thieringer, H.A., Jones, P.G.,& Inouye, M. (1998). Cold shock and adaptation. BioEssays, 20, 49–57. doi: 10.1002/(SICI)1521-1878(199801)20:1<49::AID-BIES8>3.0.CO;2-N o How many articles do each of these articles cite? o How many articles cite each of these articles? d. Using SGD, look up the gene, HAP4. • How many unique references are there in the SGD literature overview for this gene? • How many unique references are there in the SGD primary literature for this gene?

Team Journal Assignment

Team Membership

The project groups are:

1. Team 1
   • Coder:
   • Quality Assurance:
   • GenMAPP Users:
2. Team 2
   • Coder:
   • Quality Assurance:
   • GenMAPP Users:
3. Team 3
   • Coder:
   • Quality Assurance:
   • GenMAPP Users:
4. Team 4
   • Coder:
   • Quality Assurance:
   • GenMAPP Users:

Creating a Team Wiki Page

From this week on, your "Shared Journal Assignments" will become "Team Journal Assignments". For this week, some preliminary tasks are assigned to your team in preparation for your final projects.

• Name your team and create your team home page on the wiki.
  • The name of your team home page should simply be the team name.
  • This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to communicate with each other and with the instructors. Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.
  • Create a link to your team's page on the course Main page.
  • Create a category using your team name and use it on your team's main page and all pages you will create for the project.
  • Create a template for your team with useful information and links that you will use on all pages that you will create for the project.
• Choose one member of your team to be the Project Manager. Only one member of the team will serve in this role (no co-Project Managers). Record this information on the Group Project page and on your team's home page.