Difference between revisions of "Week 6"

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'''This journal entry is due on Thursday, February 22, at 12:01am Pacific time.'''
 
'''This journal entry is due on Thursday, February 22, at 12:01am Pacific time.'''
  
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* To become familiar with a relational database using the Microsoft Access software
 
* To become familiar with a relational database using the Microsoft Access software
 +
* To manage files in the Windows operating system
 
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* To experience a real-world example of how raw data sets can be distributed and formatted
 
* To experience a real-world example of how raw data sets can be distributed and formatted
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** Also, be sure to use the syntax '''<nowiki>[[Media:filename | visible label]]</nowiki>''' to create the link, ''not'' '''<nowiki>[[File:filename]]</nowiki>'''.
 
** Also, be sure to use the syntax '''<nowiki>[[Media:filename | visible label]]</nowiki>''' to create the link, ''not'' '''<nowiki>[[File:filename]]</nowiki>'''.
  
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=== Preliminary Tasks ===
 
=== Preliminary Tasks ===
  
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*# Click the OK button.
 
*# 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.
 
* 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 ====
 
==== Setting the Download Options for FireFox and Chrome ====
  
−
* For Mozilla FireFox (122.0.1 or higher)
+
* For '''Mozilla FireFox''' (122.0.1 or higher)
 
** For this class we want to set the default download folder to "Desktop" and have Firefox ask each time a file is downloaded
 
** For this class we want to set the default download folder to "Desktop" and have Firefox ask each time a file is downloaded
 
*** Go to the Settings menu, General.
 
*** Go to the Settings menu, General.
−
*** First, under the Files and Applications > Downloads section, next to "Save files to" click the "Browse" button, select the T: drive, and click the OK button.
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*** First, under the Files and Applications > Downloads section, next to "Save files to" click the "Browse" button, select the Desktop, and click the OK button.
−
*** Second, click the radio button next to "Always ask me where to save files"
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*** Second, check the box next to "Always ask you where to save files"
−
* For Google Chrome (Version 44.0.2403.157 m or higher)
+
* For '''Google Chrome''' (Version 121.0.6167.162 or higher)
 +
** For this class we want to set the default download folder to "Desktop" and have Chrome ask each time a file is downloaded
 
** Options set to default downloads to Desktop and to ask each time a file is downloaded
 
** 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"
+
*** Go to Settings page, click on the "Downloads" menu item on the left hand side.
−
*** First, under the "Downloads" section, click the "Change..." button, select the T: drive, and click the OK button.
+
*** First, under the "Location" section, click the "Change" button, select the Desktop, and click the OK button.
−
*** Second, check the box next to "Ask where to save each file before downloading"
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*** Second, move the slider "Ask where to save each file before downloading" to the right to turn it on.
−
 
 
−
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 [http://www.7-zip.org/ 7-zip Download page].)  To compress a single file or a group of files, do the following:
 
−
*# Select all of the files you want to zip together by clicking and dragging or control-clicking on the filenames.
 
−
*# Right-click on your selection.  In the context menu that appears, select the menu option: 7-Zip > Add to archive
 
−
*# 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).
 
−
*# Select "zip" as the Archive format.
 
−
*# 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.
 
−
-->
 
  
−
<!--
+
==== Decompressing Files in Windows ====
−
=== 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
+
* Files with the .zip extension are compressed files that need to be decompressed before using them.
 +
* Right-click on the file icon to open the context menu.
 +
** Select "Extract all".
 +
** Click the "Extract" button.
  
−
The site includes both a link to the downloadable files (compressed in .zip format) and the schema (“entity relationship diagram”) for those files.
+
=== Electronic Lab Notebook ===
  
−
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:
+
Because of the nature of the assignment this week, you will have four sections of the electronic notebook:
  
−
# Download and decompress the files.
+
# The '''purpose''':  what is the purpose of this assignment?
−
# Import the data files into a Microsoft Access database you will create.
+
# A ''brief'' '''methods/results''' section that summarizes what you did for the tutorial. Upload your completion certificate here.
−
# Configure the fields in your tables to match the schema provided by the FDA (keys, datatypes).
+
# A '''conclusion''' section that mirrors your purpose.
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# Set the relationships between your tables to match the schema provided by the FDA.
+
# The '''Acknowledgments''' section.
−
# Answer the questions below.
+
#* 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.
−
 
+
#* Acknowledge anyone else you worked with who was not your assigned partner.  This could be Dr. Dahlquist, other students in the class, or even other students or faculty outside of the class.
−
<!--
+
#* If you copied <code>wiki syntax</code> 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.   
−
 
+
#* If you need to reference '''''content''''', include the formal citation in your References section (see below).
−
=== Electronic Lab Notebook and Questions to Answer ===
+
#* You '''must''' also include this statement:   
−
 
+
#** '''''"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."'''''
−
Complete your electronic notebook  on your individual journal page. Your notebook entry should contain:
+
#* Sign your Acknowledgments section with your wiki signature.
−
* The '''purpose''':  what was the purpose of your investigations?
+
# The '''References''' section. In this section, you need to provide properly formatted citations to any '''''content''''' that was not entirely of your own devising.   
−
* Your '''methods''': what did you actually do?  Give a step by step account for Tasks 1-4 listed above.
+
#* Do not include citations/references to sources that you did not use.
−
** There should be enough detail provided so that you or another person could re-do it based solely on your notebook.
+
#* You should include a reference to this week's assignment page.
−
** You may copy protocol instructions on your page and modify them as to what '''''you''''' actually did, as long as you provide appropriate attribution.
+
#* The references should be formatted according to the [https://owl.purdue.edu/owl/research_and_citation/using_research/documents/20180719CitationChart.pdf APA guidelines].
−
** Take advantage of the electronic nature of the notebook by providing screenshots, links to web pages, links to data, etc.
+
#* For more detailed guidelines, please see the document [[Media:BIOL367_Spring2024_GuidelinesforLiteratureCitations.pdf | Guidelines for Literature Citations in a Scientific Paper]] that you were given on the first day of class.
−
* Your '''results''': the answers to the questions below, plus any other results you gathered.
+
#* Cite the appropriate weekly Assignment page.  For example, the citation for the [[Week 1]] Assignment page is: LMU BioDB 2024. (2024). Week 1. Retrieved August 27, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_1
−
** Usually it makes sense to embed your answers to the questions/results in the "methods" in the order in which you obtained them.
+
#* Even if you have nothing else to cite, the References section must be present and include the citation to the appropriate weekly assignment page.
−
* A '''scientific conclusion''':  what was your main finding for today's project?  Did you fulfill the purpose?  Why or why not?
 
−
 
 
−
'''[https://support.office.com/en-us/article/access-sql-basic-concepts-vocabulary-and-syntax-444d0303-cde1-424e-9a74-e8dc3e460671 Access SQL: basic concepts, vocabulary, and syntax]'''
 
−
 
 
−
For your electronic lab notebook this week, do the following:
 
−
# Upload your zipped Microsoft Access FDA database to the wiki and link to it on your individual journal page.
 
−
# 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.
 
−
-->
 
−
 
 
−
<!--
 
−
''For the questions below, supply (a) the answer to the question and (b) the query that you used to answer the question.''
 
−
# What are the names of the drug products that are administered in the ''form'' <code>INJECTABLE;INTRAVENOUS, SUBCUTANEOUS</code>?
 
−
# What are the names of the drug products whose active ingredient (''activeingred'') is <code>ATROPINE</code>?
 
−
# In what ''form''s and ''dosage''s can the drug product named <code>BENADRYL</code> be administered?
 
−
# Which drug products have a name ''ending'' in <code>ESTROL</code>?
 
−
# Produce a table listing all of the known values for the ''therapeutic_potential'' column in the ''application'' table and how many ''application'' records there are of each. (''Side note:'' The ''therapeutic_potential'' codes are explained in the ''ReviewClass_Lookup.txt'' file, in case you’re interested.)
 
−
# Produce a table listing all of the known values for the ''chemical_type'' column in the ''application'' table and how many ''application'' records there are of each. (''Side note:'' The ''chemical_type'' codes are explained in the ''ChemTypeLookup.txt'' file, in case you’re interested.)
 
−
# What are the names of the drug products that are sponsored (''sponsor applicant'' column) by <code>MERCK</code>?
 
−
# Which ''sponsor applicant'' companies have the text <code>LABS</code> in their names and have products whose active ingredients (''activeingred'') include ''both'' <code>ASPIRIN</code> and <code>CAFFEINE</code>?
 
−
# Also answer, would you have been able to answer these questions using the web interface that the FDA provides to this database ([https://www.accessdata.fda.gov/scripts/cder/daf/index.cfm Drugs@FDA?])
 
−
-->
 
−
 
 
−
<!--
 
−
==== 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. 
 
−
# 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.
 
−
# 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.
 
−
# If you copied <code>wiki syntax</code> 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.   
 
−
# 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).
 
−
# 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."'''''
 
−
# 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 [https://owl.purdue.edu/owl/research_and_citation/using_research/documents/20180719CitationChart.pdf APA guidelines].
 
−
* For more detailed guidelines, please see the document [[Media:BIOL367_Fall2019_GuidelinesforLiteratureCitations.pdf | 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 ==
 
== Shared Journal Assignment ==
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# What are the advantages of using a database, like Microsoft Access, instead of a spreadsheet program, like Microsoft Excel, when managing your data?
 
# What are the advantages of using a database, like Microsoft Access, instead of a spreadsheet program, like Microsoft Excel, when managing your data?
 
# Which part of the tutorial made the most sense to you?
 
# Which part of the tutorial made the most sense to you?
−
# Which part of the tutorial do you feel least confident about?  What would you like to know more about?
+
# Which part of the tutorial do you feel least confident about?   
 +
# What would you like to know more about?
 
# The blog post mentions a "fraught relationship about data, privacy, and how private companies operate in public spaces."   
 
# The blog post mentions a "fraught relationship about data, privacy, and how private companies operate in public spaces."   
 
#* What is this fraught relationship?   
 
#* What is this fraught relationship?   

Latest revision as of 15:06, 15 February 2024

This journal entry is due on Thursday, February 22, at 12:01am Pacific time.

Overview

The purpose of this assignment is:

  • To become familiar with a relational database using the Microsoft Access software
  • To manage files in the Windows operating system

Individual Journal Assignment

  • Store this journal entry as "username Week 6" (i.e., this is the text to place between the square brackets when you link to this page).
  • Invoke your personal template that you created for the Week 1 Assignment on your individual journal entry page. Your template should provide the following set of navigation links:
    • Link to your user page.
    • Links to the weekly Assignment pages.
    • Links to your weekly Individual Journal entry pages.
    • Links to the weekly Class Journal pages.
    • The category "Journal Entry".

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:

  • Hailey & Charlotte
  • Katie & Natalija
  • Dean & Andrew

LinkedIn Learning Tutorial for Microsoft Access

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

  • To access the LinkedIn Learning tutorial, do the following:
    • Go to LinkedIn Learning portal.
    • Enter your LMU lion email address, and click continue
    • You will be prompted to enter your LMU username and password on an LMU Authentication page.
  • Complete the course called Learning Access for Office 365 by Adam Wilbert. It is 1 hour and 7 minutes long. Be sure that you are selecting the right course because there are several for Microsoft Access. It is best if you follow along doing the exercises. The files needed are downloadable from the tutorial.
    • We will have time in class on Tuesday, February 20 to work on this, but you are welcome to get started before that.
      • Please bring headphones/ear buds to class on Tuesday, if possible so that you can listen to the tutorial video at your own pace.
    • Microsoft Access is not available on computers running MacOS. It is available on the Windows computers in Seaver 120. There are also 22 computers running Windows in the Hannon Libray Information Commons that have Microsoft Access installed.
  • 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 6 of you uploading similar files.
    • Also, be sure to use the syntax [[Media:filename | visible label]] to create the link, not [[File:filename]].

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:
    Folder Options window
    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 (122.0.1 or higher)
    • For this class we want to set the default download folder to "Desktop" and have Firefox ask each time a file is downloaded
      • Go to the Settings menu, General.
      • First, under the Files and Applications > Downloads section, next to "Save files to" click the "Browse" button, select the Desktop, and click the OK button.
      • Second, check the box next to "Always ask you where to save files"
  • For Google Chrome (Version 121.0.6167.162 or higher)
    • For this class we want to set the default download folder to "Desktop" and have Chrome ask each time a file is downloaded
    • Options set to default downloads to Desktop and to ask each time a file is downloaded
      • Go to Settings page, click on the "Downloads" menu item on the left hand side.
      • First, under the "Location" section, click the "Change" button, select the Desktop, and click the OK button.
      • Second, move the slider "Ask where to save each file before downloading" to the right to turn it on.

Decompressing Files in Windows

  • Files with the .zip extension are compressed files that need to be decompressed before using them.
  • Right-click on the file icon to open the context menu.
    • Select "Extract all".
    • Click the "Extract" button.

Electronic Lab Notebook

Because of the nature of the assignment this week, you will have four sections of the electronic notebook:

  1. The purpose: what is the purpose of this assignment?
  2. A brief methods/results section that summarizes what you did for the tutorial. Upload your completion certificate here.
  3. A conclusion section that mirrors your purpose.
  4. The Acknowledgments section.
    • 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.
    • Acknowledge anyone else you worked with who was not your assigned partner. This could be Dr. Dahlquist, other students in the class, or even other students or faculty outside of the class.
    • 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.
    • If you need to reference content, include the formal citation in your References section (see below).
    • You must also include this statement:
      • "Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
    • Sign your Acknowledgments section with your wiki signature.
  5. The References section. In this section, you need to provide properly formatted citations to any content that was not entirely of your own devising.
    • Do not include citations/references to sources that you did not use.
    • You should include a reference to this week's assignment page.
    • 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 2024. (2024). Week 1. Retrieved August 27, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/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 6 page. If this page does not exist yet, go ahead and create it (congratulations on getting in first :) )
  • Link to the Class Journal page from your user page (should be part of your template).
  • Link back from the Class Journal page to 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

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. Which part of the tutorial made the most sense to you?
  3. Which part of the tutorial do you feel least confident about?
  4. What would you like to know more about?
  5. 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?
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