Difference between revisions of "Week 10"

Latest revision as of 22:47, 16 December 2015

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

Overview

The two main objectives of this week's exercise is to:

1. Create your team's home page, select your species, and select your Project Manager.
2. Create an annotated bibliography of papers from which you will derive data for your final research project. This is the second Assignment in the course that specifically addresses the requirements to fulfill the Information Literacy flag for the course.
   • 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.

Grading for this assignment

• Your individual journal entry for this week is worth a total of 15 points (instead of 10).
• Your team journal entry for this week is worth a total of 10 points (instead of 3). Each member of the team will receive the same grade for the team journal entry.

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.

Note that each person will complete an individual annotated bibliography. Information from each team member's bibliography will then be compiled on your team's page. This will require coordination among the team members so that both the individual and team assignment will be completed by the journal deadline.

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 the Writing LibGuide) 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 the list of) (Open Access Scholarly Publishers Association Members) here.
       • Is this article available in print or online only?
       • Has LMU paid a subscription or other fee for your access to this article?
         • A list of the journals LMU pays for access to can be found here.
  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 1-2 potential journal articles that refer to public/published microarray data for your species than are different than what your teammates have found. Thus, each team should find 4-8 articles. If you cannot find a minimum of four 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.
       • A minimum of three biological replicates need to have been performed for each condition measured (so that we can do statistical analysis of the data).
       • The experiment performed is a competitive hybridization (also known as a "two-color" or "two-channel") experiment where one sample was labeled with the Cy3 dye and the other sample was labeled with the Cy5 dye (i.e., not an "Affymetrix" chip).
       • The control sample needs to be derived from mRNA and not genomic DNA.
       • The gene IDs used on in the data files must match the gene IDs that are cross-referenced by UniProt (Dr. Dahlquist can help with this one).
     • We recommend that you begin by searching for the data, and then by finding the journal article related to the data. State which database you used to find the data and 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.
     • For each article, please provide all of the same information that you provided for the genome article above.
     • In addition, you must also link to the web site where the microarray data resides.
       • 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?
       • Remember, microarray data is not centrally located on the web. Some major sources are:
         • EBI ArrayExpress (recommended)
           • Click on the link to "Browse ArrayExpress"
           • Use the drop down "Filter Search Results" to filter datasets by your organism, by "RNA assay" and "Array assay" to narrow your search.
         • NCBI GEO
         • 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.
     • On your team wiki page, compile the list of citations, links, and answers to questions, ranking the papers one through 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.

Sample Bibliographic Entry

For example, see the bibliographic entry for Schade et al. (2004) below which is available both in print and online:

Schade, B., Jansen, G., Whiteway, M., Entian, K.D., & Thomas, D.Y. (2004). Cold Adaptation in Budding Yeast. Molecular Biology of the Cell, 15, 5492-5502. doi: 10.1091/mbc.E04-03-0167

• PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/15483057
• PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC532028/
• Publisher Full Text (HTML): http://www.molbiolcell.org/content/15/12/5492.long
• Publisher Full Text (PDF): http://www.molbiolcell.org/content/15/12/5492.full.pdf+html
• Copyright: 2004 by the American Society for Cell Biology (information found on PDF version of article); article is not Open Access, but is freely available 2 months after publication
• Publisher: American Society for Cell Biology (scientific society)
• Availability: in print and online
• Did LMU pay a fee for this article: no

Team Journal Assignment

Team Membership

The project groups are:

1. Heavy Metal HaterZ (a.k.a. Team 1 a.k.a the best team) - Shewanella oneidensis
   • Coder: Mary Alverson
   • Quality Assurance: Josh Kuroda
   • GenMAPP Users: Ron Legaspi & Emily Simso
2. Class Whoopers - Bordetella pertussis
   • Coder: Nicole Anguiano
   • Quality Assurance: Brandon Klein
   • GenMAPP Users: Lena Olufson & Mahrad Saeedi
3. GÉNialOMICS - Burkholderia cenocepacia
   • Coder: Anu Varshneya (Project Manager)
   • Quality Assurance: Brandon Litvak
   • GenMAPP Users: Veronica Pacheco & Kevin Wyllie
4. Oregon Trail Survivors - Shigella flexneri
   • Coder: Jake Woodlee
   • Quality Assurance: Trixie Roque
   • GenMAPP Users: Erich Yanoschik & Kristen Zebrowski

• 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.

Selecting Your Team's Species

Each team will choose from among the species shown below:

• Burkholderia cenocepacia
• Bordetella pertussis
• Shewanella oneidensis
• Shigella flexneri

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 to kickstart 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. Also use the category "Group Projects" on your team's pages.
  • 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.
• On your team wiki page, compile a single annotated bibliography for your group (including the bibliographic citations, links, and answers to questions about the papers) with the genome paper from your species and the microarray papers ranked one through 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.