Week 3

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This journal entry is due on Tuesday, September 19, at 12:01 AM PDT.

Overview

The purpose of this assignment is:

  1. To acquaint you with what goes on behind the scenes when you visit a web page.
  2. To give you some hands-on practice time with a command-line interface.
  3. To show you an example of how a manual task can be automated.
  4. To reinforce the material from the previous week.

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

Individual Journal Assignment

  • Store this journal entry as "username Week 3" (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.

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, Nicole Kalcic
  • Eddie Bachoura, Hayden Hinsch
  • Mary Balducci, Blair Hamilton
  • Dina Bashoura, Quinn Lanners
  • Arash Lari, Corinne Wong
  • John Lopez, Katie Wright
  • Antonio Porras, Simon Wroblewski
  • Emma Tyrnauer, Zachary Van Ysseldyk

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:

If you would like to do this work on your computer, you will need the following:

Recommended but not strictly required is a code-ready editor, which you may want to use to open an HTML file redirected from curl output; this includes but is not limited to:

The Seaver 120 computers have both of these applications already installed.

Hack-a-Page

  1. Visit any web page of your choice, with a decent mix of text and image content (LMU’s home page, for example)
  2. Using the web browser’s developer tools, “hack” the page in the following ways:
    • Modify some text content—make it pretty obvious that you modified the page and that it couldn’t possibly be actual content on the page
    • Modify an img element so that its src links to an image on this wiki (feel free to upload something new) or the web at large
  3. Take a screenshot of your “hacked” page with the developer tools open, showing the sections that you modified
  4. Take a screenshot of your “hacked” page without the developer tools open, for hours of fake news fun with friends and family
  5. The two screenshots comprise your deliverables for this part of the assignment; make sure to display them in your Week 3 submission page
    • Don’t forget to also document what you did in your electronic notebook page for this week

Be creative, funny, clever, satirical, entertaining…enjoy your newfound capabilities!

The Genetic Code, by Way of the Web

Now, let’s circle back around to biology. The ExPASy Translate Tool automates many of the activities that you performed on pencil and paper for Week 2. Try out a few sequences on it to get a feel for what it does.

For this portion of the assignment, we will go behind the scenes of this tool. As indicated in class, all web page activities are simply request-response cycles, with the web browser sending a request to a server on the Internet then displaying that server’s response. As you use the ExPASy translate tool, you are performing such a request-response cycle when you submit a DNA or RNA sequence.

You also saw in class that a web browser happens to be just one of many applications that can perform this request and response. Specifically, we covered how the curl command can do the exact same thing, except that it does not do any fancy code conversion or layout: you see the web server’s response purely at the data level—HTML thus far, and we will see other data formats later.

“DMing” the Server with curl

For this part of the assignment, you are asked to communicate with the ExPASy Translate Tool using curl then perform some command-line-based processing of the data that you receive (which, it should be noted, is exactly the same data that your web browser displays as a web page):

  1. Visit http://web.expasy.org/translate and open your web browser’s developer tools
  2. Invoke the Inspect command on the text area that is meant to receive your DNA or RNA sequence
  3. In the developer tools, you should see a textarea representing this entry field, and right above it, you should see an element that begins with form method="POST"
    • Take note of the action attribute on that element
  4. Enclosed within the form element are the textarea that you clicked on and two select elements
    • Take note of their name attributes and the data that they might hold
  5. These activities should lead you to infer the correct curl command that will perform the exact same translation request but outside the web browser
  6. Invoke the command and tweak it until you are sure that you are getting it right
    • You can compare the raw data that you receive to the Elements tab in the developer tools, to ensure that you’re getting the same thing
    • You might also want to watch the Network tab on your web browser, to see what happens when you interact with the page normally

Study the curl’ed Code

Once you have gotten the hang of issuing translation requests to ExPASy via curl, take a moment to study the responses of the server. You can study them either within the web browser using its developer tools, or you can capture a few curl responses as files (see, we said you’d need to know how to do this) so that you can open and study them in a code-savvy editor application, such as Atom or Microsoft Visual Studio Code. Both applications are free downloads and they are also pre-installed on the Seaver 120 lab computers. There are also other choices, but these are perhaps the most approachable and actively-developed ones at the moment.

If you are working within the bash on Ubuntu on Windows application, you will find the regular C: drive in the path /mnt/c/ within that environment.

Answer the following questions regarding what you see:

  1. Are there any links to other pages within the ExPASy translation server’s responses? List them and state where they go. (of course, if you aren’t sure, you can always go there with a web browser or curl)
  2. Are there any identifiers in the ExPASy translation server’s responses? List them and state what you think they identify.

Using the Command Line to Extract Just the Answers

Finally, we can move on to actually processing those responses semi-automatically.

  1. Get to know the ExPASy responses well, particularly the portions that are just boilerplate vs. the elements that actually have the data you want (i.e., the reading frame labels and sequences)
    Tip: For this portion, it becomes really useful for you to have some sample responses saved up and viewed on a code-savvy editor application. This is the best way to study the code and discern any patterns that you can use to perform this exercise.
  2. Develop a sequence of sed commands that will extract just this information from the full HTML web response
  3. Combine the curl command from the previous section with your sed sequence to form a full-blown compound command that, in a single invocation, will contact ExPASy, extract the relevant data, and display just this data on the command line

For example, if this sequence is submitted to ExPASy: 

cgatggtacatggagtccagtagccgtagtgatgagatcgatgagctagc

…for the output format=Verbose and genetic code=Standard, the result of your compound command should be: 

5'3' Frame 1
R W Y Met E S S S R S D E I D E L  
5'3' Frame 2
D G T W S P V A V V Met R S Met S Stop  
5'3' Frame 3
Met V H G V Q Stop P Stop Stop Stop D R Stop A S 
3'5' Frame 1
A S S S I S S L R L L D S Met Y H  
3'5' Frame 2
L A H R S H H Y G Y W T P C T I  
3'5' Frame 3
Stop L I D L I T T A T G L H V P S

Note that this is exactly what you would see in a web browser, but without any formatting or markup code. Yes, with the right commands, the computer will do all of the work for you!

Summary of Deliverables

Include the following on your Week 3 submission page:

  • The two screenshots of your “hacked” web page, with and without developer tools
  • The curl command that requests a translation at the command-line, raw-data level
  • Your answers to the two questions regarding the ExPASy translation server’s output
  • The sequence of commands that extracts “just the answers” from the raw-data response
  • The standard Acknowledgments and References sections as specified by the Week 1 assignment
  • Notes on your electronic notebook page for this week documenting how you worked through this exercise

You will notice that this week’s assignment involves a lot more process than product—in terms of size, the deliverables themselves will not be very long, but the process at getting to them is what comprises more of the work. This is exactly the kind of activity to document in your electronic notebook, especially because what you will be doing is not exactly easy to remember. Document what you do such that you can see yourself coming back to this later in the semester in order to replicate whatever you’ve accomplished this week.

Shared Journal Assignment

  • Store your journal entry in the shared Class Journal Week 3 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

This week focuses on the first two sections of this article: “The Man in the Taupe Blazer” and “Let’s Begin.”

Reflect

  1. Pull out a quote from the first two sections of “What is Code?” that you think directly relates to what you experienced in the individual portion of this assignment. Explain why this quote is particularly resonant for you.
  2. What do you think you need in order to grow more comfortable, confident, and effective with the command line and manipulating data at a “raw” level?
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