Week 4

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This journal entry is due on Tuesday, September 26, at 12:01 AM PDT.

Overview

The purpose of this assignment is:

  1. To have you build a web page in code from first principles, with solely the help of one popular web authoring toolkit, Bootstrap.
  2. To acquaint you with the information that is typically documented, gathered, or collected regarding a gene.
  3. To give you additional practice time with editing and managing files.

Resources

These resources will be of direct help in completing the assignment:

Grading

For this assignment, points will be assigned as follows:

  • 10 points for your individual journal entry.
  • 3 points for your shared journal entry.
  • 10 points for the web page deliverable.

Each partner will receive the same number of points for the shared web page. The individual journal entry and shared journal entry will be graded on an individual basis.

Individual Journal Assignment

  • Store this journal entry as "username Week 4" (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 wiki page. 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.
    • To be clear, on your individual wiki page, you will document your individual process in your electronic lab notebook.
    • From this week onward, please use the individual journal page for your electronic lab notebook instead of a separate notebook page.
    • The deliverable, your gene's web page, will be shared. One web page per pair of students, linked to from your individual pages.

Homework Partners

For most weeks in the semester, you will be assigned a "homework partner" from a complementary discipline. You will be expected to consult with your partner, sharing your domain expertise, in order to complete the assignment. However, unless otherwise stated, each partner must submit his or her own work as the individual journal entry (direct copies of each other's work is not allowed). You must give the details of the interaction with your partner in the Acknowledgments section of your journal assignment. Homework partners for this week are:

  • Eddie Azinge, Antonio Porras CLN1
  • Eddie Bachoura, Nicole Kalcic ACT1
  • Mary Balducci, Arash Lari HSF1
  • Dina Bashoura, John Lopez "Our favorite Gene: ADH 1"
  • Blair Hamilton, Katie Wright Our favorite Gene: ASP1
  • Hayden Hinsch, Zach Van Ysseldyk BRO1
  • Quinn Lanners, Emma Tyrnauer - ADA2
  • Corinne Wong, Simon Wroblewski - SPT15

Software Requirements for this Assignment

The computers in Seaver 120 are already set up for this assignment, and do not require any setup for you to do this week’s work:

  • Google Chrome with Developer Tools for viewing your work in progress
  • A code-ready editor for editing your work in progress; this includes but is not limited to:
  • A file compression/decompression utility that can compress/decompress .zip files. Many operating systems also have this functionality built-in; the Seaver 120 computers also have 7-Zip installed.

If you would like to do this work on your computer, you will need the same applications as listed above. All applications are available for both Windows and macOS. Each operating system also capable of handling .zip files out of the box.

  • Note that opening a compressed file to view the contents is not the same as decompressing it. Files may not work properly if they are not decompressed.

“My Favorite Gene”

With your homework partner, author a web page using direct HTML code and Bootstrap that displays the relevant information for a “favorite gene.” (OK, so maybe you don’t really have a favorite gene—but it makes for a fun assignment title)

Method

  1. Prepare your files
    1. Download the starter files that have been uploaded to this wiki.
    2. Unzip the file using 7zip or an equivalent utility. You should get a folder called bootstrap-starter.
    3. Rename the folder to your chosen gene (see below). Keep the name in lowercase and separate words with hyphens (like bootstrap-starter itself). This is a naming convention that is typically used for files that are intended to be served from a website.
    4. Rename the starter-page.html file within the folder to that of your chosen gene with a file extension of .html. Use the same naming convention as the containing folder.
    5. Delete the grnsight-screenshot.png file.
  2. Work on your page—this is not strictly sequential; it will consist of some combination of:
    • Edit pre-existing HTML (such as the title) to customize its content for your gene.
    • Browse the Bootstrap website for presentation styles or formats that appeal to you. Copy and paste the sample HTML into your page and edit/customize as needed.
    • Download any applicable images to your working folder and use img tags to display them on your page.
    • Keep your HTML file open in a web browser and refresh it every time you make an edit, in order to see how it looks.
  3. Compress your folder into a .zip file and upload it to the wiki.
  4. Homework partners are to collaborate on one “favorite gene” page together, but still submit individual journal entry pages with their own acknowledgments and references sections. The individual journal entry pages would then link to the same uploaded .zip file.

Things to Try

For this assignment, we are focused primarily on simplicity and content. However, you are free to experiment with various Bootstrap features if you find them interesting and would like to use them in your page. Using a Bootstrap feature is fairly straightforward:

  1. Locate the sample code for the feature.
  2. Copy the sample code into your HTML file.
  3. Customize the sample code to suit your content.

Features of interest, with corresponding links:

Note, this aspect is optional. If it feels overwhelming, then just stick to the basics and focus on the information about your chosen gene, specified below.

Content

For this exercise (and the rest of the semester), we will focus on budding yeast (a.k.a. Baker's yeast, Brewer's yeast, Saccharomyces cerevisiae) as a model organism. A model organism is used for research because it has some property that makes it easy to study the phenomenon of interest. Budding yeast is a simple, single-celled eukaryote that shares fundamental properties with human cells, yet is much easier to study. A lot of foundational work in understanding cancer, for example, was performed in yeast.

For the Week 4 exercise, you will select your favorite yeast gene to highlight.

  1. To choose your gene, visit the Saccharomyces Genome Database (SGD), a model organism database that aims to be a one-stop shop for yeast data.
    • You can search for a gene or protein in the search field or browse the resources at the site through the various tabs. If you do not already have a gene in mind that you want to find, the curators at SGD maintain a blog to highlight interesting research. Browse through the Research Spotlights or Yeast and Human Disease categories for inspiration.
    • You may not use the same gene as another group. Gene choices are first-come, first-served. To claim your gene, edit this page, listing the gene you have chosen next to the names of you and your homework partners.
  2. Once you have identified your gene, you will look it up in four different databases and create a summary of what you have learned about your gene on your own web page. The four databases are:
    • SGD itself
    • NCBI Gene Database
    • Ensembl
    • UniProt
    • The summary should be one paragraph about the function of your gene based on what you have read in each of the four databases. This is one paragraph that synthesizes information, not one paragraph per database.
  3. Provide the following additional information about your gene on your web page:
    1. What is the standard name, systematic name, and name description for your gene (from SGD)?
    2. What is the gene ID (identifier) for your gene in all four databases (SGD, NCBI Gene, Ensembl, UniProt)?
      • Provide hyperlinks to the specific pages for your gene in each of the above databases.
    3. What is the DNA sequence of your gene?
    4. What is the protein sequence corresponding to your gene?
    5. What is the function of your gene?
    6. What was different about the information provided about your gene in each of the parent databases?
      • Were there differences in content, the information or data itself?
      • Were there differences in presentation of the information?
    7. Why did you choose your particular gene? i.e., why is it interesting to you and your partner?
    8. Include an image related to your gene (be careful that you do not violate any copyright restrictions!)
      • Please make the image something scientific (not like the random images seen on the SGD blog posts).
      • If a 3D structure of the protein your gene encodes is available, you can choose to embed a rotating image of the structure on your page using the FirstGlance in Jmol software. This is optional, a different static image would be OK, too.
    9. Include Acknowledgments and References sections on your web page (in addition to the ones in your wiki journal pages).
      • You need to cite the specific database page from which you derived your information for each of the questions.
      • When answering the free-form questions, be sure to paraphrase.

Summary of Deliverables

Your Week 4 submission page should include:

  • An uploaded .zip file of the folder containing the favorite gene page and any images used by your page, one per homework partner pair
  • Individually, your electronic notebook recording how you went about working on this assignment, with the requisite Acknowledgment and References sections as specified by the Week 1 assignment.

Note again that you are to work on the favorite gene page in pairs, with both of your journal entry pages linking to the same final upload. The rest of the content—electronic notebook, acknowledgments, references—remain individual.

Shared Journal Assignment

  • Store your journal entry in the shared Class Journal Week 4 page. If this page does not exist yet, go ahead and create it (congratulations on getting in first 👏🏼)
  • Link to your journal entry from your user page.
  • Link back from the journal entry to your user page.
    • NOTE: You can easily fulfill the links part of these instructions by adding them to your template and using the template on your user page.
  • Sign your portion of the journal with the standard wiki signature shortcut (~~~~).
  • Add the "Journal Entry" and "Shared" categories to the end of the wiki page (if someone has not already done so).

Read/Watch

  • What is Code Parts 3 and 4: “Why are Programmers So Intense About Languages?” and “Why are Coders Angry?” (are you?)
  • Official award citation to Sir Tim Berners-Lee, the 2016 Turing Award winner
  • Weaving the Web: A profile and video to commemorate Sir Tim Berners-Lee’s award
  • Tim Berners-Lee et al, The World-Wide Web (1994), Communications of the ACM, Volume 37, Issue 8, pp. 76–82.

Reflect

  1. Based on these readings:
    • Did you code in a language for this assignment?
    • Did you use a standard library?
    • Do you understand what Paul Ford meant about coders being “angry?”
  2. How similar or different do you think Tim Berners-Lee’s original vision for The World-Wide Web is from today’s web? State ways where you think today’s web is better, and today’s web is worse.
  3. Out of the four databases you accessed for this assignment (SGD itself, NCBI Gene Database, Ensembl, UniProt), which did you like the best, and why? Which did you like the least, and why? (Refer back to the question about differences in content or presentation that you noted on your gene's web page.)
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