User talk:Aporras1 - Revision history

Kdahlquist: note that file is now complete for GRNmap

2017-12-07T07:39:57Z

note that file is now complete for GRNmap

Kdahlquist: note about file pared down and uploaded to Week 15 page

2017-12-06T23:56:39Z

note about file pared down and uploaded to Week 15 page

Dondi: Add week 9 feedback.

2017-11-24T03:21:11Z

Add week 9 feedback.

Dondi: /* Week 7 Feedback */ Punctuation.

2017-11-21T06:45:20Z

‎Week 7 Feedback: Punctuation.

Dondi: Move week 7 to appear below week 8 feedback.

2017-11-21T06:25:37Z

Move week 7 to appear below week 8 feedback.

Dondi: Add week 7 feedback.

2017-11-21T06:23:39Z

Add week 7 feedback.

Kdahlquist: /* Week 10 Feedback */ note to reference GO

2017-11-17T06:46:46Z

‎Week 10 Feedback: note to reference GO

Kdahlquist: add signature to week 8 feedback

2017-11-17T06:34:49Z

add signature to week 8 feedback

Kdahlquist: provided Week 10 feedback

2017-11-17T06:34:01Z

provided Week 10 feedback

Kdahlquist: /* Week 8 Feedback */ gave week 8 feedback

2017-11-17T06:01:02Z

‎Week 8 Feedback: gave week 8 feedback

← Older revision		Revision as of 07:39, 7 December 2017
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		+	The file has now been completed for input to GRNmap in class on Thursday. ''— [[User:Kdahlquist\|Kdahlquist]] ([[User talk:Kdahlquist\|talk]]) 23:39, 6 December 2017 (PST)''
		+
	Antonio, I finished paring down the network. Here is the final file (renamed): [[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx \| 15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]]. I posted this on your Week 15 journal page as well. ''— [[User:Kdahlquist\|Kdahlquist]] ([[User talk:Kdahlquist\|talk]]) 15:56, 6 December 2017 (PST)''		Antonio, I finished paring down the network. Here is the final file (renamed): [[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx \| 15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]]. I posted this on your Week 15 journal page as well. ''— [[User:Kdahlquist\|Kdahlquist]] ([[User talk:Kdahlquist\|talk]]) 15:56, 6 December 2017 (PST)''

← Older revision		Revision as of 23:56, 6 December 2017
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		+	Antonio, I finished paring down the network. Here is the final file (renamed): [[Media:15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx \| 15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx]]. I posted this on your Week 15 journal page as well. ''— [[User:Kdahlquist\|Kdahlquist]] ([[User talk:Kdahlquist\|talk]]) 15:56, 6 December 2017 (PST)''
		+
	== Week 10 Feedback ==		== Week 10 Feedback ==

← Older revision		Revision as of 03:21, 24 November 2017
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	''— [[User:Kdahlquist\|Kdahlquist]] ([[User talk:Kdahlquist\|talk]]) 22:34, 16 November 2017 (PST)''		''— [[User:Kdahlquist\|Kdahlquist]] ([[User talk:Kdahlquist\|talk]]) 22:34, 16 November 2017 (PST)''
		+
		+	== Week 9 Feedback ==
		+
		+	* The “good habit” aspects of your individual journal are on-time, and completely fulfilled. Great work!
		+	* The electronic notebook has decent detail and is well-integrated with the GRNsight testing and API exploration results.
		+	* GRNsight testing is complete with clear feedback on the results.
		+	* The overall process for going from the gene symbol to the final gene data, with the necessary substitutions, is completely and correctly specified.
		+
		+	=== Shared Journal ===
		+	Questions and “good habit” aspects are all on-time, and mostly fulfilled (your shared entry does not have a wiki signature). Favorite pages are stated alongside the reasons for these preferences.
		+
		+	—[[User:Dondi\|Dondi]] ([[User talk:Dondi\|talk]]) 19:21, 23 November 2017 (PST)

	== Week 8 Feedback ==		== Week 8 Feedback ==

@@ Line 57: / Line 57: @@
 * The “good habit” aspects of your individual journal are all on point; the electronic notebook shows excellent detail and our reference list is quite thorough.
 * Nearly all prior web page issues were addressed except:
-** Title tag was not modified to match gene
+** Title tag was not modified to match gene.
-** Although the UniProt ID was fixed, its label wasn’t: the UniProt ID is not a ''taxonomic'' ID
+** Although the UniProt ID was fixed, its label wasn’t: the UniProt ID is not a ''taxonomic'' ID.
-* Bootstrap grid layout and flex classes were seen, though used somewhat subtly
+* Bootstrap grid layout and flex classes were seen, though used somewhat subtly.
-* The use of collapse is noted as one of the requested “advanced Bootstrap” features
+* The use of collapse is noted as one of the requested “advanced Bootstrap” features.
-* The use of card is noted as the other “advanced Bootstrap” feature, though it’s usage does not really maximize its potential
+* The use of card is noted as the other “advanced Bootstrap” feature, though its usage does not really maximize its potential.
-* The XML and JSON API calls were adapted correctly
+* The XML and JSON API calls were adapted correctly.
 === Shared Journal ===

@@ Line 16: / Line 16: @@
 ''&mdash; [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 22:34, 16 November 2017 (PST)''
 == Week 8 Feedback ==
@@ Line 68: / Line 52: @@
 ''&mdash; [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 14:10, 16 November 2017 (PST)''
 == Week 5 Feedback ==

← Older revision		Revision as of 06:23, 21 November 2017
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	''— [[User:Kdahlquist\|Kdahlquist]] ([[User talk:Kdahlquist\|talk]]) 22:34, 16 November 2017 (PST)''		''— [[User:Kdahlquist\|Kdahlquist]] ([[User talk:Kdahlquist\|talk]]) 22:34, 16 November 2017 (PST)''
		+
		+	== Week 7 Feedback ==
		+
		+	* The “good habit” aspects of your individual journal are all on point; the electronic notebook shows excellent detail and our reference list is quite thorough.
		+	* Nearly all prior web page issues were addressed except:
		+	** Title tag was not modified to match gene
		+	** Although the UniProt ID was fixed, its label wasn’t: the UniProt ID is not a ''taxonomic'' ID
		+	* Bootstrap grid layout and flex classes were seen, though used somewhat subtly
		+	* The use of collapse is noted as one of the requested “advanced Bootstrap” features
		+	* The use of card is noted as the other “advanced Bootstrap” feature, though it’s usage does not really maximize its potential
		+	* The XML and JSON API calls were adapted correctly
		+
		+	=== Shared Journal ===
		+	Questions and “good habit” aspects are fulfilled, all on-time. Your comment about the computer science exposure being too far too fast is a side effect of the "just in time" learning structure of the class. It does result in a lighter treatment of certain topics and that's what I think you’re feeling. Basics coverage would have been great but it would have cost additional time. It’s a tradeoff that we’ve made consciously, but of course if you’re interested in additional details, feel free to come to office hours to talk about these things.
		+
		+	—[[User:Dondi\|Dondi]] ([[User talk:Dondi\|talk]]) 22:23, 20 November 2017 (PST)

	== Week 8 Feedback ==		== Week 8 Feedback ==

@@ Line 13: / Line 13: @@
 # The PowerPoint file with screenshots and the gene list and GO list files were provided.  However, you did not provide the updated Excel workbook with the "stem" worksheet, nor the .txt file used as input for stem.  In the interests of reproducible research, these files must be provided.
 # In your Acknowledgments section, you need to be explicit that you copied and modified the instructions from the Week 10 assignment.
-# In your References section, you need to cite the stem software that you used.
+# In your References section, you need to cite the stem software that you used.  Eventually when you look up the GO term definitions, you will need to cite those pages as well.
 ''&mdash; [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 22:34, 16 November 2017 (PST)''

@@ Line 33: / Line 33: @@
 # Your concluding paragraph is very good.  My only note is that you need to explain why you are reporting the percent of genes changing at different cut-off levels; why is that important?
 # Finally, you need to be more specific in your Acknowledgments section that you copied and modified the [[Week 8]] assignment page.  Please also acknowledge the source of the data.
 == Week 11 Team Page Feedback (to address in Week 12) ==

← Older revision		Revision as of 06:34, 17 November 2017
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		+	== Week 10 Feedback ==
		+
		+	I have reviewed your Week 10 individual journal assignment so that you can move forward with the final project.
		+
		+	* Thank you for submitting the assignment on time.
		+	* All required links were present on the page.
		+
		+	You fulfilled all of the criteria for the assignment, except those things I note below. You will need to make corrections to these before moving forward with the project. Please go ahead and fix them on your Week 10 page. Your weekly electronic notebook for the project can then link to your Week 10 page, just noting the corrections you made.
		+	# Your electronic notebook is basically complete. One note is that when you talk about saving files, please record the actual filename in your notebook for reference.
		+	# You did not report the definitions of your 6 GO terms.
		+	# There was no interpretation of these GO terms in terms of cold shock or the deletion of the Zap1 transcription factor.
		+	# There was no summary paragraph. In particular, items 2-4 will be reported in your final project presentation and written report.
		+	# The PowerPoint file with screenshots and the gene list and GO list files were provided. However, you did not provide the updated Excel workbook with the "stem" worksheet, nor the .txt file used as input for stem. In the interests of reproducible research, these files must be provided.
		+	# In your Acknowledgments section, you need to be explicit that you copied and modified the instructions from the Week 10 assignment.
		+	# In your References section, you need to cite the stem software that you used.
		+
		+	''— [[User:Kdahlquist\|Kdahlquist]] ([[User talk:Kdahlquist\|talk]]) 22:34, 16 November 2017 (PST)''
		+
	== Week 8 Feedback ==		== Week 8 Feedback ==

← Older revision		Revision as of 06:01, 17 November 2017
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	== Week 8 Feedback ==		== Week 8 Feedback ==
		+
		+	I have reviewed your Week 8 individual journal assignment so that you can move forward with the final project.
		+
		+	* Thank you for submitting the assignment on time.
		+	* All required links were present on the page.
		+
		+	You fulfilled all of the criteria for the assignment, except those things I note below. You will need to make corrections to these before moving forward with the project. Please go ahead and fix them on your Week 8 page. Your weekly electronic notebook for the project can then link to your Week 8 page, just noting the corrections you made.
		+	# Your computations and Excel file were correct--no corrections are needed there.
		+	# You copied the methods from the Week 8 page and made changes to make them specific for what you did, but you needed to go further than you did with those changes.
		+	#* Good work changing the instructions to the past tense. Make sure that this is followed through for the entire protocol.
		+	#* You replaced all STRAIN references with "dZAP1", but you should have actually provided the exact formulas that you used in Excel as well. The formulas are written in a general form to apply to the whole class; you need to provide the exact formula with cell references. In addition, when the instructions said to "repeat" for other timepoints, you did not provide the formulas for the other timepoints. This is necessary because the cell references change.
		+	# In the table in your PowerPoint slide, you switched the Bonferroni and B-H p value numbers; your notebook had them recorded correctly.
		+	# Good job with reporting and interpreting the Average Log Fold Changes and p values for ''NSR1'' and ''CLN1''.
		+	# Your concluding paragraph is very good. My only note is that you need to explain why you are reporting the percent of genes changing at different cut-off levels; why is that important?
		+	# Finally, you need to be more specific in your Acknowledgments section that you copied and modified the [[Week 8]] assignment page. Please also acknowledge the source of the data.

	== Week 11 Team Page Feedback (to address in Week 12) ==		== Week 11 Team Page Feedback (to address in Week 12) ==