User talk:Emmatyrnauer - Revision history

Kdahlquist: add link to GRNmap input file

2017-12-07T08:13:53Z

add link to GRNmap input file

Dondi: Add week 9 feedback.

2017-11-24T02:41:39Z

Add week 9 feedback.

Dondi: Add week 7 feedback.

2017-11-21T22:32:02Z

Add week 7 feedback.

Kdahlquist: /* Week 10 Feedback */ removed feedback that didn't belong

2017-11-17T07:50:00Z

‎Week 10 Feedback: removed feedback that didn't belong

Kdahlquist: added week 10 feedback

2017-11-17T07:49:01Z

added week 10 feedback

Kdahlquist: add week 11 team feedback

2017-11-16T21:59:43Z

add week 11 team feedback

Kdahlquist: /* Week 8 Feedback */ fixed bullet points

2017-11-15T20:05:15Z

‎Week 8 Feedback: fixed bullet points

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

2017-11-15T20:03:11Z

‎Week 8 Feedback: completed week 8 feedback

Kdahlquist: began Week 8 feedback

2017-11-15T19:57:59Z

began Week 8 feedback

Dondi: Add week 5 shared journal feedback.

2017-10-22T02:23:16Z

Add week 5 shared journal feedback.

← Older revision		Revision as of 08:13, 7 December 2017
Line 1:		Line 1:
		+	Emma, I've made the GRNmap input file based on your network for use in class on Thursday: [[Media:17-genes_39-edges_teamINT_Sigmoid_estimation.xlsx \| 17-genes_39-edges_teamINT_Sigmoid_estimation.xlsx]]. ''— [[User:Kdahlquist\|Kdahlquist]] ([[User talk:Kdahlquist\|talk]]) 00:13, 7 December 2017 (PST)''
		+
	== Week 10 Feedback ==		== Week 10 Feedback ==

← Older revision		Revision as of 02:41, 24 November 2017
Line 26:		Line 26:

	''— [[User:Kdahlquist\|Kdahlquist]] ([[User talk:Kdahlquist\|talk]]) 13:59, 16 November 2017 (PST)''		''— [[User:Kdahlquist\|Kdahlquist]] ([[User talk:Kdahlquist\|talk]]) 13:59, 16 November 2017 (PST)''
		+
		+	== Week 9 Feedback ==
		+
		+	* The “good habit” aspects of your individual journal are completely fulfilled and on-time. Thank you!
		+	* 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 almost complete but misses the last URL that delivers the full data for a single gene. After performing the needed '''esearch''' API calls, you want to make a final '''esummary''' API call in order to get the full dataset for the specific gene whose ID you were able to extract via '''esearch'''.
		+
		+	=== Shared Journal ===
		+	Questions and “good habit” aspects are all fulfilled, all on-time. Favorite pages are stated alongside the reasons for these preferences.
		+
		+	—[[User:Dondi\|Dondi]] ([[User talk:Dondi\|talk]]) 18:41, 23 November 2017 (PST)

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

← Older revision		Revision as of 22:32, 21 November 2017
Line 52:		Line 52:

	''— [[User:Kdahlquist\|Kdahlquist]] ([[User talk:Kdahlquist\|talk]]) 12:03, 15 November 2017 (PST)''		''— [[User:Kdahlquist\|Kdahlquist]] ([[User talk:Kdahlquist\|talk]]) 12:03, 15 November 2017 (PST)''
		+
		+	== Week 7 Feedback ==
		+
		+	* The “good habit” aspects of your individual journal are all on point. Your electronic notebook shows excellent detail, effectively narrated, and your references section thoughtfully includes the multiple sources you consulted for this assignment (although it appears to be missing the baseline reference for [[Week 7]]).
		+	* All prior web page issues were addressed—great to see that!
		+	* Bootstrap grid layout and flex classes were seen, though the latter was used somewhat subtly.
		+	* The use of collapse is noted as one of the requested “advanced Bootstrap” features.
		+	* The use of carousel is noted as the other “advanced Bootstrap” feature.
		+	* Both XML and JSON web API calls were adapted from the starter code as requested.
		+
		+	=== Shared Journal ===
		+	Questions and “good habit” aspects are fulfilled, all on-time. Yes, the coding can certainly be challenging and ideally would be given more practice time, but due to our time constraints we have to keep it in the "need-to-know/just-in-time" level. But that’s indeed why we have the mixed partners, so it’s good to hear that this helps you.
		+
		+	—[[User:Dondi\|Dondi]] ([[User talk:Dondi\|talk]]) 14:32, 21 November 2017 (PST)

	== Week 5 Feedback ==		== Week 5 Feedback ==

@@ Line 9: / Line 9: @@
 # While you reported the definitions of your 6 GO terms, you did not provide an interpretation with respect to cold shock.  Also, please include their GO IDs.
 # You included a summary paragraph, but your summary did not draw any conclusions about the data analysis you performed with respect to cold shock in yeast.
 # 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 as well as each of the GO term definitions, not just the general Gene Ontology site.

← Older revision		Revision as of 07:49, 17 November 2017
Line 1:		Line 1:
−	~~Talk~~ page of [[User:~~kwrigh35~~\|~~Katie Wright~~]].	+	== 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 and for providing all of the required links. You fulfilled all of the criteria for the assignment, except those things I note below. Because your B-H p value computations were incorrect in Week 8, you will need to redo the stem analysis. When you do, come back to edit this page and replace the results shown here with the new ones generated with the correct gene list. When you redo this, also pay attention to the feedback below, making the necessary changes. Your weekly electronic notebook for the project can then link to your Week 10 page, noting the corrections you made.
		+	# Your electronic notebook is insufficient.
		+	#* While I deemed it acceptable to copy and paste it from the assignment page, it needs to be '''''modified''''' as well. Your notebook needs to be in the ''past'' tense because it is something that you did. You do not need to include the "background" section here because it is not really part of anything that you did.
		+	#* If there were issues with running the protocol, those need to be noted.
		+	#* When you talk about saving or opening files, please record the actual filename in your notebook for reference at the point in the protocol where it is mentioned.
		+	# When you discussed why you chose the profile you did, you said the genes were down-regulated, but they are actually up-regulated in that profile.
		+	# While you reported the definitions of your 6 GO terms, you did not provide an interpretation with respect to cold shock. Also, please include their GO IDs.
		+	# You included a summary paragraph, but your summary did not draw any conclusions about the data analysis you performed with respect to cold shock in yeast.
		+	# You did not actually mention which profile you chose until the summary paragraph. This information is critical to your notebook. You reversed the number of genes that belonged to the profile versus expected. The profile you chose has a relatively small number of genes. It would be better to choose one of the profiles with at least 100 genes for the further analysis in the final project.
		+	# 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 as well as each of the GO term definitions, not just the general Gene Ontology site.
		+
		+	''— [[User:Kdahlquist\|Kdahlquist]] ([[User talk:Kdahlquist\|talk]]) 23:49, 16 November 2017 (PST)''

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

← Older revision		Revision as of 21:59, 16 November 2017
Line 1:		Line 1:
		+	Talk page of [[User:kwrigh35\|Katie Wright]].
		+
		+	== Week 11 Team Page Feedback (to address in Week 12) ==
		+
		+	You covered the basics requested in the assignment for your team page, but for [[Week 12]], let’s focus on the stated overall purpose of these pages: “This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to organize your work and communicate with each other and with the instructors. ''Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.''”
		+
		+	Considering that purpose (and hint), you will also want to include the following on your team page. Imagine yourselves in deep work mode, with your team page open in a window. What information, links, and resources will you want to have available on that page at all times? Here are a few items:
		+	* A projected schedule with due dates (both for milestones already defined in the guild pages and for internal accomplishments that your team determines) and meeting times. You can cross off these dates and times as your team makes progress using the <code>s</code> tag (<s>strikeout</s>).
		+	* Communication resources (e.g., additional channels like Slack; GitHub issues; the discussion “side” of various wiki pages; etc.) that your team can use to coordinate when not face-to-face
		+	* A section with links to uploaded files (including the journal club presentations), particularly for use by data analysts but really for any member of the team; this can also include a link to your GitHub branch and the project’s fork
		+	* Additional useful links—what links would be useful to always have there so that you can just click to visit them, minimizing typing? The links that currently exist on your template are a good start. If you do not want to actually use the [[Template:GRNsight Gene Page Project Links]], then you should add the other relevant links from that template to your own. Also, there is a weird line break in the link for Week 14.
		+	* Finally, having consistent formatting for the executive summaries and reflections will improve the look and organization of your page. Katie and Zach need to link to their Week 11 individual wiki pages and Emma, Blair, and Zach need to remove their individual templates from the page.
		+
		+	''— [[User:Kdahlquist\|Kdahlquist]] ([[User talk:Kdahlquist\|talk]]) 13:59, 16 November 2017 (PST)''
		+
	== Week 8 Feedback ==		== Week 8 Feedback ==

@@ Line 5: / Line 5: @@
 * 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.
-* You copied the methods from the [[Week 8]] page and made some changes to make them specific for what ''you'' did, but you needed to go further than you did with those changes.
+# You copied the methods from the [[Week 8]] page and made some changes to make them specific for what ''you'' did, but you needed to go further than you did with those changes.
-*# Since this is recording what you ''did'', the language should be in the ''past'' tense.
+#* Since this is recording what you ''did'', the language should be in the ''past'' tense.
-*# You replaced all ''STRAIN'' references with "wt", 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.
+#* You replaced all ''STRAIN'' references with "wt", 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.
-*# You have a typo for the number of genes that are p < 0.0001 in your PowerPoint slide.
+# You have a typo for the number of genes that are p < 0.0001 in your PowerPoint slide.
-*# When reporting the percent of genes that are changed, only give 1 or 2 decimal places instead of 4.
+# When reporting the percent of genes that are changed, only give 1 or 2 decimal places instead of 4.
-*# There is a mistake in the Benjamini-Hochberg p value computation.
+# There is a mistake in the Benjamini-Hochberg p value computation.
-*#* You need to sort the unadjusted p values smallest to largest before assigning their rank and applying the formula.  You just left them in the order of the Master Index, so all of the B-H p values will be wrong.
+#* You need to sort the unadjusted p values smallest to largest before assigning their rank and applying the formula.  You just left them in the order of the Master Index, so all of the B-H p values will be wrong.
-*#* You need to redo this computation.  Unfortunately, this also means that you will need to redo the stem clustering because it will have been based on the incorrect list of genes.
+#* You need to redo this computation.  Unfortunately, this also means that you will need to redo the stem clustering because it will have been based on the incorrect list of genes.
-*# You reported the Average Log Fold Changes and p values for ''NSR1'' and ''ADA2'', but your interpretation needs work.
+# You reported the Average Log Fold Changes and p values for ''NSR1'' and ''ADA2'', but your interpretation needs work.
-*#* The Average Log Fold Change at each time point tells us the ''magnitude'' of the gene expression change.  Since it is a log<sub>2</sub> value, anything with a Log Fold Change of 1 or above (or -1 or below) has at least a 2-fold difference in expression.  Which generally indicates a gene is changing expression
+#* The Average Log Fold Change at each time point tells us the ''magnitude'' of the gene expression change.  Since it is a log<sub>2</sub> value, anything with a Log Fold Change of 1 or above (or -1 or below) has at least a 2-fold difference in expression.  Which generally indicates a gene is changing expression
-*#* However, you also need to interpret the Log Fold Changes in terms of the ANOVA p value.  ''NSR1'' has a Bonferroni-corrected p value < 0.05, which means that is among the genes that are the most significantly changed in the dataset.
+#* However, you also need to interpret the Log Fold Changes in terms of the ANOVA p value.  ''NSR1'' has a Bonferroni-corrected p value < 0.05, which means that is among the genes that are the most significantly changed in the dataset.
-*#* ''ADA2'' also shows some largish Average Log Fold Changes.  But it has an unadjusted p value of ~0.008, which does not stay < 0.05 with either the Bonferroni and B-H corrections.  We have less confidence that ''ADA2'' is really changing its expression because of the p value.
+#* ''ADA2'' also shows some largish Average Log Fold Changes.  But it has an unadjusted p value of ~0.008, which does not stay < 0.05 with either the Bonferroni and B-H corrections.  We have less confidence that ''ADA2'' is really changing its expression because of the p value.
-*# Your summary paragraph is a good description of the flow of work for this week.  However, it should draw some more conclusions based on the table of p values and be corrected to interpret the expression of ''NSR1'' and ''ADA2'' above.
+# Your summary paragraph is a good description of the flow of work for this week.  However, it should draw some more conclusions based on the table of p values and be corrected to interpret the expression of ''NSR1'' and ''ADA2'' above.
-*#* In particular, do we know if genes are really changing expression, and how do we know it (hint: look at the percent of genes changed at each p value cut-off relative to the cut-off itself, e.g., p < 0.05 = 5%.)
+#* In particular, do we know if genes are really changing expression, and how do we know it (hint: look at the percent of genes changed at each p value cut-off relative to the cut-off itself, e.g., p < 0.05 = 5%.)
-*# You included your Acknowledgments and References.  However, you should have been more explicit in your Acknowledgments that you directly copied, then modified the Week 8 instructions.  You also needed to Acknowledge the source of the data.
+# You included your Acknowledgments and References.  However, you should have been more explicit in your Acknowledgments that you directly copied, then modified the Week 8 instructions.  You also needed to Acknowledge the source of the data.
 Please let me know if you have any questions.

← Older revision		Revision as of 19:57, 15 November 2017
Line 1:		Line 1:
		+	== 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.
		+	* You copied the methods from the [[Week 8]] page and made some changes to make them specific for what ''you'' did, but you needed to go further than you did with those changes.
		+	*# Since this is recording what you ''did'', the language should be in the ''past'' tense.
		+	*# You replaced all ''STRAIN'' references with "wt", 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.
		+	*# You have a typo for the number of genes that are p < 0.0001 in your PowerPoint slide.
		+	*# When reporting the percent of genes that are changed, only give 1 or 2 decimal places instead of 4.
		+	*# There is a mistake in the Benjamini-Hochberg p value computation.
		+	# You need to sort the unadjusted p values smallest to largest before assigning their rank and applying the formula. You just left them in the order of the Master Index, so all of the B-H p values will be wrong.
		+	# You need to redo this computation. Unfortunately, this also means that you will need to redo the stem clustering because it will have been based on the incorrect list of genes.
		+	*# You reported the Average Log Fold Changes and p values for ''NSR1'' and ''ADA2'', but your interpretation needs work.
		+	# The Average Log Fold Change at each time point tells us the ''magnitude'' of the gene expression change. Since it is a log<sub>2</sub> value, anything with a Log Fold Change of 1 or above (or -1 or below) has at least a 2-fold difference in expression. Which generally indicates a gene is changing expression
		+	# However, you also need to interpret the Log Fold Changes in terms of the ANOVA p value. ''NSR1'' has a Bonferroni-corrected p value < 0.05, which means that is among the genes that are the most significantly changed in the dataset.
		+	# ''ADA2'' also shows some largish Average Log Fold Changes. But it has an unadjusted p value of ~0.008, which does not stay < 0.05 with either the Bonferroni and B-H corrections. We have less confidence that ''ADA2'' is really changing its expression because of the p value.
		+
	== Week 5 Feedback ==		== Week 5 Feedback ==

← Older revision		Revision as of 02:23, 22 October 2017
Line 1:		Line 1:
		+	== Week 5 Feedback ==
		+
		+	(work in progress)
		+
		+	=== Shared Journal ===
		+	Questions and “good habit” aspects are all sufficiently fulfilled; thank you!
		+
		+	—[[User:Dondi\|Dondi]] ([[User talk:Dondi\|talk]]) 19:23, 21 October 2017 (PDT)
		+
	== Week 4 Partial Feedback ==		== Week 4 Partial Feedback ==