Difference between revisions of "Malverso Week 10"

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(added questions to answer for annotated bibliography)
(→‎Microarray Papers: added more questions to answer)
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*Has LMU paid a subscription or other fee for your access to this article?
 
*Has LMU paid a subscription or other fee for your access to this article?
  
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*you must also link to the web site where the microarray data resides.
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*What experiment was performed? What was the "treatment" and what was the "control" in the experiment?
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*Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each?
  
 
===Citation Style===
 
===Citation Style===

Revision as of 04:17, 9 November 2015

Annotated Bibliography

  • We must rank the microarrray papers. Dr.Dahlquist will pick which one is suitable for us to use. There should be at least four papers. If we can not find at least four, we should talk to Dr.Dahlquist.
  • Electronic lab notebook should include our search process.
  • Individual page should include my own annotated bibliography (genome sequence paper and one or twp microarray papers).
  • Group page should have one genome sequence paper and ranked list of the microarray papers.

Papers to Include

  1. Find genome sequence paper. Find the canonical one! This may require searching around or consulting with Dr.Dahlquist.
  2. Find microarray data papers. We are likely to find something different than the authors found even though they have already analyzed it. It is still important, however, to figure out what information has already been found out by others.

Genome Paper

Heidelberg, J. F., Paulsen, I. T., Nelson, K. E., Gaidos, E. J., Nelson, W. C., Read, T. D., ... & Fraser, C. M. (2002). Genome sequence of the dissimilatory metal ion–reducing bacterium Shewanella oneidensis. Nature biotechnology, 20(11), 1118-1123.

  • 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?

Microarray Papers

  • 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?
  • you must also link to the web site where the microarray data resides.
  • What experiment was performed? What was the "treatment" and what was the "control" in the experiment?
  • Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each?

Citation Style

Use APA style for this bibliography. Or the style of the PeerJ - which has a downloadable citation style for the zotero program.

  • make sue to translate the citation into wiki text.

Search Journal

Genome Paper

  • Went to Pubmed and used general keyword search with the term: shewanella oneidensis genome
  • There were 185 results, which is a lot. So we decided to do advanced search instead.
  • I searched shewanella oneidensis genome[Title/Abstract] which gave me only 3 results.
  • By clicking on a result and copy and pasting its title into Google Scholar, I am able to easily cite the source I choose.
  • I used the search term "Shewanella oneidensis genome" in Google Scholar. I got 7970 results.
  • Although this is a huge number, the first result looked promising because it was an article published by nature, and also was cited 580 times.
  • Using this same search term in Web of Science, I got 441 results.
  • I was able to get the number of results down to 262 by refining the results to only articles.
  • Web of Science does allow me to see who cited the article and also what articles are referenced within that article.
  • Our group decided that one of our results looked very promising because it was published in Nature Biotechnology and was cited 580 times.
  • Here is the citation for the article of our choice, which was found at this link :

Heidelberg, J. F., Paulsen, I. T., Nelson, K. E., Gaidos, E. J., Nelson, W. C., Read, T. D., ... & Fraser, C. M. (2002). Genome sequence of the dissimilatory metal ion–reducing bacterium Shewanella oneidensis. Nature biotechnology, 20(11), 1118-1123.

Microarray Papers

  • Then I searched using Array Express
    • I clicked browse.
    • then I filtered by organisms > shewanella oneidensis and experiment types RNA assay and Array assay.
    • I got 20 experiments as results.
    • I looked for transcription profiling by array (all of my results fell under this category)
    • I made sure my articles of choice had a decent number of assays.
  • When I click on one of the results, what I will eventually want is the sample and data relationship file. The raw data file is where we want to find the gene Id's.
  • I looked for citations to get to the paper that corresponds to that data set.


Team Page

Heavy Metal HaterZ

Assignments

Individual Journal Entries

Shared Journal Entries

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