Week 3 - Revision history

Dondi: Fix an incorrect outline level.

2017-09-16T22:01:45Z

Fix an incorrect outline level.

Dondi: Late-breaking details and clarifications.

2017-09-15T05:36:49Z

Late-breaking details and clarifications.

Dondi: All done.

2017-09-11T05:48:03Z

All done.

Dondi: /* Homework Partners */ Set Week 3 pairings.

2017-09-11T00:05:44Z

‎Homework Partners: Set Week 3 pairings.

Dondi: /* Summary of Deliverables */ Some wordsmithing.

2017-09-10T23:52:44Z

‎Summary of Deliverables: Some wordsmithing.

Dondi: /* Shared Journal Assignment */ Transcribe week 3 shared instructions.

2017-09-10T23:51:59Z

‎Shared Journal Assignment: Transcribe week 3 shared instructions.

Dondi: Finish up individual instructions.

2017-09-10T23:49:26Z

Finish up individual instructions.

Dondi: /* The Genetic Code, by Way of the Web */ Fix mistyped wiki link markup.

2017-09-10T23:15:31Z

‎The Genetic Code, by Way of the Web: Fix mistyped wiki link markup.

Dondi: /* = Using the Command Line to Extract Just the Answers */ Markup fix.

2017-09-10T22:43:44Z

‎= Using the Command Line to Extract Just the Answers: Markup fix.

Dondi: Even more Week 3 instructions.

2017-09-10T22:43:03Z

Even more Week 3 instructions.

@@ Line 134: / Line 134: @@
 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 ====
+=== Summary of Deliverables ===
 Include the following on your Week 3 submission page:

@@ Line 40: / Line 40: @@
 * Antonio Porras, Simon Wroblewski
 * Emma Tyrnauer, Zachary Van Ysseldyk
 === Hack-a-Page ===
@@ Line 46: / Line 66: @@
 # 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 <code>img</code> element so that its <code>src</code> links to an image on this wiki (feel free to upload something new)
+#* Modify an <code>img</code> element so that its <code>src</code> links to an image on this wiki (feel free to upload something new) or the web at large
 # Take a screenshot of your “hacked” page with the developer tools open, showing the sections that you modified
 # Take a screenshot of your “hacked” page ''without'' the developer tools open, for hours of fake news fun with friends and family
@@ Line 80: / Line 100: @@
 Once you have gotten the hang of issuing translation requests to ExPASy via <code>curl</code>, 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 <code>curl</code> 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 [https://atom.io Atom] or [https://code.visualstudio.com 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.
 Answer the following questions regarding what you see:

@@ Line 1: / Line 1: @@
 '''This journal entry is due on Tuesday, September 19, at 12:01 AM PDT.'''
 == Overview ==
@@ Line 16: / Line 14: @@
 * [http://dondi.lmu.build/share/intro/wheres-my-stuff.pdf Where's my Stuff?]
 * [[Introduction to the Command Line]]
-* http://explainshell.com/ —lets you type in a command and will display a visual explanation of what it does (to the best of its ability)
+* [[Dynamic Text Processing]]
 == Individual Journal Assignment ==
@@ Line 25: / Line 25: @@
 * 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.'''''
+**'''''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.

@@ Line 32: / Line 32: @@
 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 [[Week_1#Acknowledgments | Acknowledgments section]] of your journal assignment.  Homework partners for this week are:
-{{Under Construction}}
+* Eddie Azinge, Nicole Kalcic
 === Hack-a-Page ===

@@ Line 112: / Line 112: @@
 * 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 indicated in the [[Week 1]] assignment
+* 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

← Older revision		Revision as of 23:51, 10 September 2017
Line 119:		Line 119:
	== Shared Journal Assignment ==		== Shared Journal Assignment ==

−	~~{{Under Construction}}~~	+	* 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 (<code><nowiki>~~~~</nowiki></code>).
		+	* Add the "Journal Entry" and "Shared" categories to the end of the wiki page (if someone has not already done so).
		+
		+	=== Read ===
		+
		+	* [http://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/ Ford, Paul. “What is Code?” ''Business Week'', June 11, 2015.] This is a ''long'' article—but quite worthwhile. If you can read it in one sitting, go right ahead; we will focus on specific parts at various points in the semester.
		+
		+	This week focuses on the first two sections of this article: “The Man in the Taupe Blazer” and “Let’s Begin.”
		+
		+	=== Reflect ===
		+
		+	# Pull out a quote from the first two sections of [http://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/ “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.
		+	# 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?
		+
		+	[[Category:Assignment]]

@@ Line 69: / Line 69: @@
 #* 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
 ==== Using the Command Line to Extract Just the Answers ====
-{{Under Construction}}
+Finally, we can move on to actually ''processing'' those responses semi-automatically.
 Include the following on your Week 3 submission page:
 * The <code>curl</code> command that requests a translation at the command-line, raw-data level
 * The sequence of commands that extracts “just the answers” from the raw-data response
 * The standard ''Acknowledgments'' and ''References'' sections as indicated in the [[Week 1]] assignment
 * Notes on your electronic notebook page for this week documenting how you worked through this exercise
-Unless you do this kind of thing everyday, ''you are almost certain to engage in some trial-and-error'' plus will need to look up some web resources as well as consult with your homework partner—'''this is exactly the kind of activity to document in your electronic notebook'''.
+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 ==
 {{Under Construction}}

@@ Line 49: / Line 49: @@
 === The Genetic Code, by Way of the Web ===
-Now, let’s circle back around to biology. The [ExPASy Translate Tool http://web.expasy.org/translate/] 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.
+Now, let’s circle back around to biology. The [http://web.expasy.org/translate/ 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.

@@ Line 7: / Line 7: @@
 The purpose of this assignment is:
 # To give you some hands-on practice time with a command-line interface.
 # To show you an example of how a manual task can be automated.
@@ Line 30: / Line 31: @@
 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 [[Week_1#Acknowledgments | Acknowledgments section]] of your journal assignment.  Homework partners for this week are:
 {{Under Construction}}