Week 6 - Revision history

Kdahlquist: removed under construction banner

2019-10-03T18:48:18Z

removed under construction banner

Kdahlquist: /* Introduction to DNA Microarrays */ comment out microarray animation because not working

2019-10-03T18:45:41Z

‎Introduction to DNA Microarrays: comment out microarray animation because not working

Kdahlquist: /* Homework Partners */ add homework partners

2019-10-03T18:43:59Z

‎Homework Partners: add homework partners

Kdahlquist: /* View */ add link to data sharing slides

2019-10-03T01:14:15Z

‎View: add link to data sharing slides

Kdahlquist: /* Shared Journal Assignment */ add in shared reflectgion

2019-10-03T01:10:42Z

‎Shared Journal Assignment: add in shared reflectgion

Kdahlquist: /* Background */ remove section

2019-10-03T01:09:31Z

‎Background: remove section

Kdahlquist: /* Electronic Lab Notebook */ paste in from OWW

2019-10-03T01:09:15Z

‎Electronic Lab Notebook: paste in from OWW

Kdahlquist: /* Electronic Lab Notebook */ abbreviated lab notebook guidelines

2019-10-03T01:08:09Z

‎Electronic Lab Notebook: abbreviated lab notebook guidelines

Kdahlquist: /* Overview */ add purpose

2019-10-03T01:04:35Z

‎Overview: add purpose

Kdahlquist: stubbed out assignment by copying from week 2

2019-10-03T01:03:32Z

stubbed out assignment by copying from week 2

New page

{{Under Construction}}

'''This journal entry is due on Thursday, October 10, at 12:01am Pacific time.'''

== Overview ==

The purpose of this assignment is:
#

== 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).
* Create the following set of links. '''''(HINT: These links should all be in your personal template that you created for the [[Week 1 | 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.
** Don't forget to 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:

* TBA
=== Background ===

=== Electronic Lab Notebook ===

* [http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004385 Schnell, S. (2015). Ten Simple Rules for a Computational Biologist’s Laboratory Notebook. PLoS Comput Biol, 11(9), e1004385. DOI: 10.1371/journal.pcbi.1004385]

Complete your electronic notebook for your assigned part of the Molecular Genetics Explorer project 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.
** 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 in the protocol, 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?

==== Data and Files ====

* Files left on the Desktop or My Documents or Downloads folders on the Seaver 120 computers will be deleted upon restart of the computers. Files stored on the <code>T:</code> drive will be saved. However, it is not a good idea to trust that they will be there when you next use the computer.
* Thus, it is a critical skill for data and computer literacy to back-up your data and files in at least '''two''' ways:
** [[Special:Upload | Upload the files to this wiki.]]
** Upload the files to [https://auth.lmu.edu/cas/login?entityId=box.net&service=https://auth.lmu.edu:443/idp/Authn/Cas Box].
** Back them up on your personal flash drive.
* References to data and files should be made within the methods and results section of your notebook, listed above.
* 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.

==== 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 ==

* 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 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 ===

=== Reflect ===

[[Category:Assignment]]

← Older revision		Revision as of 18:48, 3 October 2019
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−	~~{{Under Construction}}~~
−
	'''This journal entry is due on Thursday, October 10, at 12:01am Pacific time.'''		'''This journal entry is due on Thursday, October 10, at 12:01am Pacific time.'''

@@ Line 60: / Line 60: @@
 * [http://www.ncbi.nlm.nih.gov/books/NBK26818/#A1633 Alberts ''et al''. (2002) ''Molecular Biology of the Cell'', Ch. 8: Microarrays]
-* [http://www.bio.davidson.edu/courses/genomics/chip/chip.html Microarray animation]
+<!--* [http://www.bio.davidson.edu/courses/genomics/chip/chip.html Microarray animation]-->
 * Brown, P.O. & Botstein, D. (1999) [http://www.nature.com/ng/journal/v21/n1s/full/ng0199supp_33.html Exploring the new world of the genome with DNA microarrays] ''Nature Genetics''  21: 33-37.
 * Campbell, A.M. and Heyer, L.J. (2003), “Chapter 4:  Basic Research with DNA Microarrays”, in ''Discovering Genomics, Proteomics, and Bioinformatics'', Cold Spring Harbor Laboratory Press, pp. 107-124. ([http://brightspace.lmu.edu Available on Brightspace])

@@ Line 82: / Line 82: @@
 * Add the "Journal Entry" and "Shared" categories to the end of the wiki page (if someone has not already done so).
-=== View ===
+=== View & Read ===
 * Watch the video [https://www.youtube.com/watch?v=eV9dcAGaVU8 "Deception at Duke" from CBS ''60 Minutes''].
 === Reflection ===

← Older revision		Revision as of 01:09, 3 October 2019
Line 25:		Line 25:

	* TBA		* TBA
−	~~=== Background ===~~
−
−
−
	=== Electronic Lab Notebook ===		=== Electronic Lab Notebook ===

@@ Line 51: / Line 51: @@
 #* 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 ==

@@ Line 24: / Line 24: @@
 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:
-* TBA
+* Aby and Joey
 === Electronic Lab Notebook ===

@@ Line 31: / Line 31: @@
 === Electronic Lab Notebook ===
-* [http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004385 Schnell, S. (2015). Ten Simple Rules for a Computational Biologist’s Laboratory Notebook. PLoS Comput Biol, 11(9), e1004385. DOI: 10.1371/journal.pcbi.1004385]
+Because of the nature of the assignment this week, you will have four sections of the electronic notebook:
-Complete your electronic notebook for your assigned part of the Molecular Genetics Explorer project on your individual journal page.  Your notebook entry should contain:
+# The '''purpose''':  what is the purpose of this assignment?
-* The '''purpose''':  what was the purpose of your investigations?
+# Answers to the questions posed in the assignment.
-* Your '''methods''': what did you actually do?  Give a step by step account.
+# The '''Acknowledgments''' section.
-** There should be enough detail provided so that you or another person could re-do it based solely on your notebook.
+#* 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:
-** You may copy protocol instructions on your page and modify them as to what '''''you''''' actually did, as long as you provide appropriate attribution.
+#** 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.
-** Take advantage of the electronic nature of the notebook by providing screenshots, links to web pages, links to data, etc.
+#* 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.
-* Your '''results''': the answers to the questions in the protocol, plus any other results you gathered.
+#* 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.
-** Usually it makes sense to embed your answers to the questions/results in the "methods" in the order in which you obtained them.
+#* If you need to reference '''''content''''', include the formal citation in your References section (see below).
-* A '''scientific conclusion''':  what was your main finding for today's project?  Did you fulfill the purpose?  Why or why not?
+#* 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."'''''
-==== Data and Files ====
+#* Sign your Acknowledgments section with your wiki signature.
+# The '''References''' section. In this section, you need to provide properly formatted citations to any '''''content''''' that was not entirely of your own devising.
-* Files left on the Desktop or My Documents or Downloads folders on the Seaver 120 computers will be deleted upon restart of the computers.  Files stored on the <code>T:</code> drive will be saved.  However, it is not a good idea to trust that they will be there when you next use the computer.
+#* Do not include citations/references to sources that you did not use.
-* Thus, it is a critical skill for data and computer literacy to back-up your data and files in at least '''two''' ways:
+#* You should include a reference to this week's assignment page.
-** [[Special:Upload | Upload the files to this wiki.]]
+#* The references should be formatted according to the [https://owl.purdue.edu/owl/research_and_citation/using_research/documents/20180719CitationChart.pdf APA guidelines].
-** Upload the files to [https://auth.lmu.edu/cas/login?entityId=box.net&service=https://auth.lmu.edu:443/idp/Authn/Cas Box].
+#* 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.
-** Back them up on your personal flash drive.
+#* 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
-* References to data and files should be made within the methods and results section of your notebook, listed above.
+#* 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 ==

← Older revision		Revision as of 01:04, 3 October 2019
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	The purpose of this assignment is:		The purpose of this assignment is:
−	#

		+	# To learn about how DNA microarray experiments work.
		+	# To reason through some DNA microarray analysis problems.
		+	# To discuss a case where standards of research ethics were violated.

	== Individual Journal Assignment ==		== Individual Journal Assignment ==