Johnllopez Week 7

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Correcting Previous Errors

The first step to completing this week's assignment was to appropriately respond to all of the comments made about the previous upload of my page. The comments addressed were the following:

  • Your folder and HTML file names weren’t customized to your chosen gene, and the folder name wasn't all lowercase as specified
  • The HTML filename ended with two .htmls (index.html.html)—keep an eye out for file extensions; this is why we recommend that they be made visible at all times
  • A separate gene summary paragraph was not seen
  • The Ensembl gene ID was the same as the SGD ID—it shouldn’t be
  • The Ensembl link does not go where it should (in fact it appears to be an error page)
  • For the DNA and protein sequences, note that they appear better with a so-called "fixed-width" font—these are the ones where every letter has the same width
  • Your gene function, site differences, and reason for choosing your gene all work out; one small note: in gene function, where you reference baker’s yeast’s formal species name, the formatting convention should be italics (i.e., S. cerevisiae)
  • The Week 4 assignment reference is missing from the References list on the gene page—note it’s still applicable to the page itself, not just your journal

These steps were addressed in the following order:

  • I changed the .html docunment and folder names to meet the specification.
  • My partner, Dina Bashoura provided the summary paragraph which I would incorporate later into the page.
  • I provided a fixed-width font for the DNA and Protein Sequences.
  • I corrected the Ensembl gen ID and he Ensembl link.
  • I added italics over S. cerevisiae.
  • I added the week 4 assignment reference.

Adding to the Page

Fortunately this part of the assignment did not need much work. Because the page already had the "table" and "card" features integrated, the only things that needed to be added were the "gridbox" and "flexbox" portions.

I learned how to do this by visiting the following pages: 

https://getbootstrap.com/docs/4.0/utilities/flex/
https://getbootstrap.com/docs/4.0/layout/grid/

I decided to organize the page into two columns. The first column would be where the original accordion of cards would be. The second column would contain 3 flexbox cards. The first card would be the summary that I missed. The second and third cards would display the data pulled from the other pages.

Using Ajax

Despite the fact that I missed class on Thursday, I was able to follow the assignment page to learn how to link the page to the XML of UniProt and the JSON of NCBI. I merely copied and pasted the script, renamed it,, put it into my page, updated the JSON page, and copied and pasted the boxes of UniProt and NCBI on to my page. 

http://localhost:3474/ajax-starter.html

I put the two boxes into cards of my flexbox column, and I changed the JQuery links when you click the button to direct the data to flow from NCBI's and UniProt's pages on ADH1. Thus, my page was finished.

The Final Product

Here is the finished file.

Acknowledgements and References

Acknowledgements

I worked with my partner Dina Bashoura on the project. After discussing what we had to do on Tuesday, I spent Monday making all of the necessary modifications to the page. She provided the summary paragraph and gave me some assistance in what I had to do. While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.

Johnllopez616 (talk) 21:25, 16 October 2017 (PDT)

References

*Emw. (2009, December 15). Protein ADH5 PDB 1m6h. Retrieved from https://upload.wikimedia.org/wikipedia/commons/a/a5/Protein_ADH5_PDB_1m6h.png
*ADH1. Saccharomyces Genome Database. Retrieved September 24, 2017, from https://www.yeastgenome.org/locus/S000005446#interaction
*ADH1 alcohol dehydrogenase ADH1 [Saccharomyces cerevisiae S288C] – Gene'. NCBI. Retrieved September 24, 2017, from https://www.ncbi.nlm.nih.gov/gene/854068#genomic-context
*Transcript: ADH1. Ensembl. Retrieved September 24, 2017, from https://www.ensembl.org/Saccharomyces_cerevisiae/Transcript/Summary?db=core%3Bg 
*Alcohol dehydrogenase 1. UniProt. Retrieved September 24, 2017, from http://www.uniprot.org/uniprot/P00330
*Using "Collapse". Bootstrap. Retrieved September 24, 2017, from  https://getbootstrap.com/docs/4.0/components/collapse/
*Using "Navbar". Bootstrap. Retrieved September 24, 2017, from https://v4-alpha.getbootstrap.com/components/navbar/
*Using "Tables". Bootstrap. Retrieved September 24, 2017, from  http://getbootstrap.com/docs/4.0/content/tables/
*Flex'. Bootstrap. Retrieved October 16, 2017, from https://getbootstrap.com/docs/4.0/utilities/flex/
*Grid System. Bootstrap. Retrieved October 16, 2017, from https://getbootstrap.com/docs/4.0/layout/grid/
*LMU BioDB 2017. (2017). Week 7. Retrieved September 24, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_7

Individual Journal Entries and Assignments

Class Assignments

Class Weekly Journal Entries / Project Weekly Journal Entries

My Page

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