Difference between revisions of "Week 10"

Revision as of 00:42, 3 November 2015

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

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 of Genomics Papers for your Species

For this assignment, you will be creating an annotated bibliography of genomics papers for your team's species.

• On your individual journal entry pages, you will keep an electronic lab notebook that details how you conducted your search, along with the results of your search.
• On your team page (see shared assignment below), you will combine your results with your teammates into one final, ranked bibliography. Specifically, you need to search the literature/biological databases for the following:
  1. The journal article which describes the results of the whole genome sequencing for your species. (Note that you will be giving a journal club presentation on this article for your Week 11 assignment.)
     • Use a keyword search for each of these 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?
     • 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?
     • Each of the references in your bibliography needs to have the following information (an example is given in another section below):
       • 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).)
       • The link to the abstract from PubMed.
       • The link to the full text of the article in PubMedCentral.
       • The link to the full text of the article (HTML format) from the publisher web site.
       • The link to the full PDF version of the article from the publisher web site.
       • 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”?
       • 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)
       • Is this article available in print or online only?
       • Has LMU paid a subscription or other fee for your access to this article?
  2. Use the genome sequencing article you found to perform a prospective search in the ISI Web of Science/Knowledge database.
     • Give an overview of the results of the search.
       • How many articles does this article cite?
       • How many articles cite this article?
       • Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced?
  3. Each person needs to find two potential journal articles that refer to public microarray data for your species than are different than what your teammates have found. Thus, each team should find 8 articles. If you cannot find all eight articles, please let the instructors know right away.
     • The experiments must be measuring gene expression aka transcriptional profiling or transcription profiling by array. Microarrays can also be used for other types of experiments, but these won't be suitable for analysis.
     • State which database you used (e.g., GoogleScholar, PubMed, ISI Web of Science/Knowledge). It may actually be easier to find the microarray data first and then find the corresponding journal article.
     • State what you used as search terms and what type of search terms they were.
     • Give an overview of the results of the search.
       • How many results did you get?
       • Give an assessment of how relevant the results were.
     • Record the full bibliographic citation of the relevant papers, formatted according to the Guidelines for Literature Citations in a Scientific Paper.
     • Create a link to the HTML version of the journal article on the publisher web site. Note that PubMed Central is not an actual publisher web site, but a secondary database of papers.
     • Download the PDF file of the journal article, upload it to the wiki and link to it from your team's home page. Note that you can only upload the PDF file to our wiki if there are no copyright restrictions on the article. If there are copyright restrictions, then you will need to provide a link to the download on the publisher site.
     • You must also link to the web site where the microarray data resides.
     • This instruction used to read: Download the microarray dataset file, upload it to the wiki, and link to it on your individual and team pages. However, for this week you do not need to download the data files, but simply link to the download page for the files as in the previous instruction. — Kdahlquist (talk) 10:36, 31 October 2013 (PDT)
       • Remeber, microarray data is not centrally located on the web. Some major sources are:
         • NCBI GEO
         • EBI ArrayExpress
         • Stanford Microarray Database
         • PUMAdb (Princeton Microarray Database)
         • In addition, microarray data can sometimes be found as supplementary information with a journal article or on an investigator's own web site.
       • For each of the microarray articles/datasets, answer the following:
         1. What experiment was performed? What was the "treatment" and what was the "control" in the experiment?
         2. Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each?
     • On your team wiki page, compile the list of citations, links, and answers to questions, ranking the papers one through six (or eight) in order of preference for using the dataset for your project. The instructors will review your results to make sure that the data are suitable for the project before you move forward with the analysis.

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.