Difference between revisions of "Week 9"

Revision as of 02:14, 24 October 2017

This journal entry is due on Tuesday, October 31, at 12:01 AM PDT. 🎃

Objectives

The purpose of this assignment is:

• to learn how to work with and explore a web service API more deeply
• to lay additional groundwork for the semester’s research project
  • spending some hands-on time with GRNsight
  • looking at the “favorite gene” pages created by the class

Individual Journal Assignment

• Store this journal entry as "username Week 9" (i.e., this is the text to place between the square brackets when you link to this page).
• Invoke your template on your journal entry page so that you:
  • Link from your journal entry page to this Assignment page.
  • Link from your journal entry to your user page.
  • Add the "Journal Entry" category to the end of your wiki page.
• Because you have invoked your template on your user page, you should also have a:
  • Link from your user page to this Assignment page.
  • Link to your journal entry from your user page.
• Include both the Acknowledgments and References section as specified by the Week 1 assignment.
• For your assignment this week, the electronic laboratory notebook you will keep on your individual wiki page retains a crucial role. Because most of this week’s activities are exploratory, it is imperative that these explorations are recorded in sufficient detail so that:
  • You do not lose important information that you will need later on.
  • You do not unnecessarily repeat something that you already tried this week.
  • Readers can get a clear idea of what you tried and didn’t try, what worked and didn’t work.

Homework Partners

Homework partners for this week are listed below. The particular web service API and GRNsight functional area that you and your partner will work on are also indicated below. You are expected to consult with your partner, sharing your domain expertise, in order to complete the assignment. However, each partner must submit his or her own work as the individual journal entry (direct copying 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.

• Eddie Azinge, Corinne Wong (tbd; D-Pad Control)
• Eddie Bachoura, Katie Wright (tbd; Viewport Size)
• Mary Balducci, Quinn Lanners (tbd; Edge Weights + Gray Threshold)
• Dina Bashoura, Simon Wroblewski (tbd; Edge Weights + Normalization)
• Blair Hamilton, Emma Tyrnauer (tbd; Gray Threshold + Zoom)
• Hayden Hinsch, John Lopez (tbd; Normalization + Zoom)
• Nicole Kalcic, Arash Lari (tbd; Restrict Viewport + Edge Weights)
• Antonio Porras, Zach Van Ysseldyk (tbd; Restrict Viewport + Zoom)

Web Service API Exploration

Hands-On with GRNsight

Each homework pair has been assigned one subset of the GRNsight client-side testing protocol for the current beta version of GRNsight. Follow this protocol and report the results of your tests in the electronic journal. Homework partners have one testing subset each so that you can talk to each other about the requested tests, but the testing itself should still be done and reported individually, in the spirit of seeking reproducible results.

1. Each feature is to be tested in combination will all three formats that GRNsight can read (Excel Workbook, SIF, GraphML). This is already specified in the testing document. Choose one file for each of these formats from this website for use in your tests and specify them in your electronic notebook. In order to have a basis for comparison, homework partners should use the same test files for their individual test sequences.
2. Each test specifies a sequence of actions to perform, followed by their expected results. Use the latter to determine whether GRNsight passed a particular test. Report the result of each test in your electronic notebook.
   • The version of GRNsight that you are testing is a beta version, so results that diverge from the expected ones are certainly possible.
   • If the observed result is the same as the expected result, indicate that GRNsight passed that particular test.
   • If the observed result is not the same as the expected result, indicate that GRNsight failed that particular test and document what was different. For many tests, a screenshot will be the most effective way to document this difference, so do not hesitate to supply one.
3. As always, make sure to document and acknowledge your interactions with your homework partner in the Acknowledgments section of your individual journal.

Shared Journal Assignment

• Store your journal entry in the shared Class Journal Week 9 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).

Review

Look at the gene pages that the class has collectively created via the Week 4 and Week 7 assignments:

• ACT1
• ADA2
• ADH1
• ASP1
• BRO1
• CLN1
• HSF1
• SPT15

Decide

On the shared journal page:

1. Identify two (2) gene pages that you particularly like.
2. State what you like about each gene page.
   • Format these as separate answers, for a total of three distinct responses in this week’s shared journal.