Week 4

This journal entry is due on Thursday, September 26, at 12:01am Pacific time.

Note that there is an interim deadline of Tuesday, September 24, at 2:00pm Pacific time to complete the LinkedIn Learning tutorial and upload your completion certificate to your individual journal page.

Overview

The purpose of this assignment is:

• To gain experience working directly with a relational database using the Microsoft Access software
• To experience a real-world example of how raw data sets can be distributed and formatted
• To get some practice with database queries using the graphical interface of MS Access

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).
• Create the following set of links. (HINT: These links should all be in your personal template that you created for the Week 1 Assignment; you should then simply invoke your template on each new journal entry.)
  • Link to your journal entry from your user page.
  • Link back from your journal entry to your user page.
  • Link to this assignment from your journal entry.
  • Add the "Journal Entry" category to the end of your wiki page.

Homework Partners

You will work in groups of two for this week's assignment. Please sit next to your partner in class. You will be expected to consult with your partner, 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). Homework partners for this week are:

• Aby and Michael
• Christina and David
• DeLisa and Naomi
• Emma and Iliana
• Ivy and Jonar
• Joey and Marcus
• Kaitlyn and Mihir

LinkedIn Learning Tutorial for MS Access

LMU provides free accounts to LinkedIn Learning (formerly Lynda.com). You will take advantage of this resource by using the tutorial for learning Microsoft Access, the database software we will use in this class.

• This page explains how to access LinkedIn Learning using your LMU credentials.
• Complete the tutorial called "Learning Access 2016" by Adam Wilbert (Released on May 4, 2016). It is 1 hour and 6 minutes long. Be sure that you are selecting the right tutorial because there are several for MS Access.
• When you are finished, download the certificate of completion, upload it to this wiki and link to it on your individual journal page. Be sure to change the filename so that it is specific to you (e.g., add your last name or username to the filename) because there will be 14 of you uploading similar files.

Preliminary Tasks

Turning on File Extensions in Windows 10

• The Windows 10 operating systems defaults to hiding file extensions. To turn them back on, do the following:
  
  1. Go to the Search menu (circle icon) "File Explorer Options" in the search field. Select the result.
  2. When the File Explorer Options window appears, click on the View tab.
  3. Uncheck the box for "Hide extensions for known file types".
  4. Click the OK button.
• The computers in Seaver 120 are are set to erase all custom user settings and restore the defaults once they have been restarted, so if you have done this previously, you might have to do it again.

Setting the Download Options for FireFox and Chrome

• For Mozilla FireFox (40.0.2 or higher)
  • Options set to default downloads to Desktop and to ask each time a file is downloaded
    • Go to the Options menu, General options
    • First, under the "Downloads" section, next to "Save files to" click the "Browse" button, select the T: drive, and click the OK button.
    • Second, click the radio button next to "Always ask me where to save files"
• For Google Chrome (Version 44.0.2403.157 m or higher)
  • Options set to default downloads to Desktop and to ask each time a file is downloaded
    • Go to Settings page, click on link to "Show advanced settings"
    • First, under the "Downloads" section, click the "Change..." button, select the T: drive, and click the OK button.
    • Second, check the box next to "Ask where to save each file before downloading"

Note that for the computers in Seaver 120, anything saved to the Desktop, My Documents, Downloads, or any other folder will be deleted when the computers are restarted. To make sure that your work will still be available to you, save your files to the T: drive. ("T" stands for the "thawspace" of the Deep Freeze software that manages the deletions.)

Compressing and Decompressing Files with 7-Zip

• The 7-Zip file compression software has been installed on the computers in Seaver 120. (If you want to install this software on your own computer, go to the 7-zip Download page.) To compress a single file or a group of files, do the following:
  1. Select all of the files you want to zip together by clicking and dragging or control-clicking on the filenames.
  2. Right-click on your selection. In the context menu that appears, select the menu option: 7-Zip > Add to archive
  3. Make sure there is a meaningful filename in the field under the word "Archive:". If not, change it to something that is. Typically you will want to include your name or initials, a short descriptor of what the file contains, and the date in year-month-day format (yyyy-mm-dd).
  4. Select "zip" as the Archive format.
  5. You do not need to change any of the other defaults. Click OK. The zip file will appear in the same folder as the files you compressed.
• To decompress files with 7-zip, right click on the file icon. From the context menu that appears, select 7-zip > Extract Here.
  • Note that Windows Explorer will allow you to view the contents of a zipped archive without actually decompressing them. It may even seem like you can open them or otherwise manipulate them. However, issues will arise from doing this, most commonly, not being able to save your changes. Always make sure that you decompress (unzip) the files before using them.

The FDA Drug Database

The United States Food and Drug Administration (FDA) provides, as a matter of public record, the full data set for its approved drugs at this website: http://www.fda.gov/Drugs/InformationOnDrugs/ucm079750.htm

The site includes both a link to the downloadable files (compressed in .zip format) and the schema (“entity relationship diagram”) for those files.

Using these files, what you have learned in the LinkedIn Learning tutorial, and additional information found in this wiki and on the aforementioned FDA website, do the following:

1. Download and decompress the files.
2. Import the data files into a Microsoft Access database you will create.
3. Configure the fields in your tables to match the schema provided by the FDA (keys, datatypes).
4. Set the relationships between your tables to match the schema provided by the FDA.
5. Answer the questions below.

Electronic Lab Notebook and Questions to Answer

Complete your electronic notebook on your individual journal page. Your notebook entry should contain:

• The purpose: what was the purpose of your investigations?
• Your methods: what did you actually do? Give a step by step account for Tasks 1-4 listed above.
  • There should be enough detail provided so that you or another person could re-do it based solely on your notebook.
  • You may copy protocol instructions on your page and modify them as to what you actually did, as long as you provide appropriate attribution.
  • Take advantage of the electronic nature of the notebook by providing screenshots, links to web pages, links to data, etc.
• Your results: the answers to the questions below, plus any other results you gathered.
  • Usually it makes sense to embed your answers to the questions/results in the "methods" in the order in which you obtained them.
• A scientific conclusion: what was your main finding for today's project? Did you fulfill the purpose? Why or why not?

Access SQL: basic concepts, vocabulary, and syntax

For your electronic lab notebook this week, do the following:

1. Upload your zipped Microsoft Access FDA database to the wiki and link to it on your individual journal page.
2. Write up the methods you used to create the database, load the tables, and write your first query.

We will work with this database for a future assignment in the class.

Data and Files

• References to data and files should be made within the methods and results section of your notebook.
• In addition to these inline links, create a "Data and Files" section of your notebook to make a list of the files generated in this exercise. In particular, you will need to zip and upload a compressed version of your MS Access FDA drug database. Make sure that your filename contains your last name or username to distinguish it from databases created by other students in the class.

Acknowledgments

In this section, you need to acknowledge anyone who assisted you with your assignment, either in person, electronically, or even anonymously without their knowledge.

1. You must acknowledge your homework partner or team members with whom you worked, giving details of the nature of the collaboration. You should include when and how you met and what content you worked on together. An appropriate statement could be (but is not limited to) the following:
   • I worked with my homework partner (give name and link name to their user page) in class. We met face-to-face one time outside of class. We texted/e-mailed/chatted online three times. We worked on the <details> portion of the assignment together.
2. Acknowledge anyone else you worked with who was not your assigned partner. This could be Dr. Dahlquist (for example, via office hours), the TA, other students in the class, or even other students or faculty outside of the class.
3. If you copied wiki syntax or a particular style from another wiki page, acknowledge that here. Provide the user name of the original page, if possible, and provide a link to the page from which you copied the syntax or style.
4. If you need to reference content (such as the methods of a protocol), that belongs in the References section where you will give a include a formal APA-formatted citation (see below).
5. You must also include this statement unless otherwise noted:
   • "Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
6. Sign your Acknowledgments section with your wiki signature.

References

• In this section, you need to provide properly formatted citations to any content that was not entirely of your own devising. This includes, but is not limited to:
  • methods
  • data
  • facts
  • images
  • documents, including the scientific literature
• Do not include extraneous references that you do not cite or use on your page.
• The references in this section should be accompanied by in text citations on your page that refer to these references.
• The references should be formatted according to the APA guidelines.
• For more detailed guidelines, please see the document Guidelines for Literature Citations in a Scientific Paper that you were given on the first day of class.
• Cite the appropriate weekly Assignment page. For example, the citation for the Week 1 Assignment page is: LMU BioDB 2019. (2019). Week 1. Retrieved August 27, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_1
• Even if you have nothing else to cite, the References section must be present and include the citation to the appropriate weekly assignment page.

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

• Blog post by LMU librarian Aisha Conner-Gaten, Lynda Becomes LinkedIn Learning, posted on August 1, 2019.
• Return to “What is Code?”, now looking at these sections within Section 5, “The Time You Attended the E-mail Address Validation Meeting:”

5.1 What is the Relationship Between Code and Data?

5.2 Where Does Data Live?

5.3 The Language of White Collars

Reflect

1. What are the advantages of using a database, like Microsoft Access, instead of a spreadsheet program, like Microsoft Excel, when managing your data?
2. The blog post mentions a "fraught relationship about data, privacy, and how private companies operate in public spaces."
   • What is this fraught relationship?
   • How do you feel about it? I.e., where do you stand on the trade-off between the "ease of use" you receive as a user and giving up your private data to companies who will use it to turn a profit?
   • What are the social justice issues involved?
3. Based on what you have seen of the FDA database, do you feel that you have a better understanding of how the data mentioned in section 5.1 of What is Code?—Spotify music, Fitbit exercise tracking, Twitter tweets, IRS tax returns, etc.—might look when stored on a computer?