User talk:Emmatyrnauer

Emma, I've made the GRNmap input file based on your network for use in class on Thursday: 17-genes_39-edges_teamINT_Sigmoid_estimation.xlsx. — Kdahlquist (talk) 00:13, 7 December 2017 (PST)

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.

1. 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.
2. 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.
3. 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.
4. 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.
5. In your Acknowledgments section, you need to be explicit that you copied and modified the instructions from the Week 10 assignment.
6. 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.

— Kdahlquist (talk) 23:49, 16 November 2017 (PST)

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 s tag (strikeout).
• 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.

— 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.

—Dondi (talk) 18:41, 23 November 2017 (PST)

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.

1. 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.
2. You have a typo for the number of genes that are p < 0.0001 in your PowerPoint slide.
3. When reporting the percent of genes that are changed, only give 1 or 2 decimal places instead of 4.
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.
5. 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 log₂ 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.
6. 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%.)
7. 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.

— 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.

—Dondi (talk) 14:32, 21 November 2017 (PST)

Week 5 Feedback

(work in progress)

Shared Journal

Questions and “good habit” aspects are all sufficiently fulfilled; thank you!

—Dondi (talk) 19:23, 21 October 2017 (PDT)

Week 4 Partial Feedback

I am posting partial feedback on your Week 4 assignment, with respect to your favorite gene page because the Week 7 assignment will build on that.

• Your favorite gene page had all of the required syntax and content except as follows:
  • Your folder name and name for your HTML file was based on your last names instead of the gene standard name as requested in the assignment.
  • Your folder name and HTML filename should have been all lowercase letters.
  • You provided the image in the folder, but did not delete the grnsight-screenshot.html which was not used in your page.
  • Thank you for providing the in-text citations and references in APA format. However, because we have the power of HTML, it would have been nice to have URLs in the references provided as actual hyperlinks.
  • I did not see an actual summary paragraph about your gene.
• Aesthetics of the layout were not part of this assignment, but I want to note that as you revise this page, most of the text is flush with the left side of the browser window without any buffering "white space", making it a little difficult to read.
• Typically DNA and protein sequences are given in a "monospaced" or "fixed width" font, such as Courier, so the letters line up, which is what you saw on the parent databases.
• The carousel option for your reviews of the individual databases was a nice touch. However, since the length of the content for each "slide" is different, the page "jumps" when the slide is advanced. It might also be nice to either set the view time for each slide to be longer or disable the auto-advance because I didn't have enough time to read each slide.
• Otherwise, a clean-looking page with nice section breaks!

— Kdahlquist (talk) 12:40, 10 October 2017 (PDT)

More Week 4 Feedback

• I want to note that you submitted both your individual and shared journal entries on time.
• Don't forget to invoke your template on your individual journal entry page--you were missing the link back to your User page because of it.
• Your electronic lab notebook had a moderate level of detail about what you did, but could have included some of the results as well, gene data and some examples of code that you used for your web page.
• You made a total of 21 edits to the wiki in the window of review and wrote something in the summary field 100% of the time--keep up the good work!
• You had a complete list of references in APA format, but since this is a wiki, please make the URLs hyperlinks!

— Kdahlquist (talk) 16:00, 13 October 2017 (PDT)

Week 3 Feedback

• Everything was turned in on time—good job! You fulfilled all of the “good habit/best practice” aspects of the assignment, supplying comments for all 18 of the listed journal edits.
• You supplied an electronic notebook with this assignment, separated into a Notebook subheading for each section; the subheadings are a good idea and the content is in the right direction, supportive of the openness and reproducibility values that we are after here. Keep on doing this; note that a piece of information or action that you took is worth journaling if it helps inform either of these question: can someone reading your notebook get a clear understanding of what you did for this assignment? Do they have enough information to replicate the results that you posted on your journal page?
• Your hack-a-page work certainly fulfilled the instructions…I’m pleasantly surprised that you didn’t encounter any issues with a Facebook image (note how I wouldn’t have known this if you hadn’t indicated as much in your notebook!). Sometimes they limit linkable items from their feeds; good that you weren’t bitten by that here.
• You identified a sufficient number and variety of links correctly, including the cgi-bin action that does the actual transcription/translation. This appears not only as an action but also in bona fide a href links, and that ties in to the ID question…
• I was hoping that the values after seqdna in the cgi-bin links would be recognized by students as IDs. You listed the action by itself, which is technically correct, but a finer grain was also present. Further, pre_text and method="POST" are not IDs in the same sense that they are used in the assigned reading, particularly McMurry et al. IDs closer to the spirit of that reading would have been better.
• For the curl/sed exercise, I was hoping that students would notice the output option that can be provided along with pre_text. This option controls how the amino acids are displayed. Supplying output=Verbose to the curl command would have obviated the need for the sed commands that “spell out” the amino acid letters. Looking for additional options like this can sometimes save us a lot of work.
• Your shared journal’s chosen quote captures one of the biggest adjustments that people need to make when learning to work with computers—detail and specificity are indeed paramount in computing, beyond what we are used to in other endeavors. We all have frustrating moments when we realize that a lot of time might have been lost due to a single punctuation mark. It sounds like you aren’t deterred—don’t be! Indeed it is by continued exposure that you will gain the foundation you mentioned to increasingly make good use of the functions that are available to you on the command line.

—Dondi (talk) 17:22, 24 September 2017 (PDT)

Week 2 Feedback

• Your turned in most of your assignment on time, but you changed 5' and 3' to N-ter and C-ter after the deadline.
• You wrote something in the summary field for 13 of 15 saves (87%) in the period of review, which is very good. Remember, we are aiming for 100%.
• The number of total saves to your Week 2 journal entry before the deadline was 10, which is just within the range for this assignment.
• You were missing the Category "Journal Entry", please add it to your template and invoke your template on future journal entries.
• You were also missing a link back to your User page, except in your wiki signature in the Acknowledgments. Please add this to your template if you have not already and invoke your template in future assignments.
• Your complementary DNA sequence was correct.
• Your translations were correct, except that you substituted a G for the second W in the -1 frame.
• Your determination of which frames contained ORFs was correct.
• One note I will make is that you reversed your labeling of the +1, +2, and +3 strands with -1, -2, and -3. It is the convention to call the top 5' to 3' DNA strand the (+) frames and the bottom 3' to 5' DNA strand the (-) frames. That is because we normally report gene sequences in the 5' to 3' direction, left to right, and the top-strand would be considered the "mRNA-like" strand because it is in that orientation.
• I did not find any electronic lab notebook for this assignment. In this case, the lab notebook would have explained how you arrived at your answers to the questions posed in the exercise. Please be sure to keep your electronic lab notebook for future assignments.
• Not only do experimental descriptions use technical language, they presuppose familiarity with the procedures that those new to the field do not have. We assign this because, like with other fields of endeavor, it is good to take a look at the primary source. I can try to answer any specific questions you have, if you like.

— Kdahlquist (talk) 17:14, 21 September 2017 (PDT)

Week 1 Feedback

Thank you for submitting your work on time. Your Week 1 work has been reviewed, and the following points of improvement have been identified. Other than these items, your wiki skills and deliverables checked out OK:

• 20 edits were made to your user page—a good, gradual pace—but only around five of those had a summary message. Please make it a habit to provide a summary, no matter how small the change might be.
• There is a difference between internal wiki links (double bracket) and external links (single bracket). The link on the main page to your user page is written out as if it were an external link, but it is more compact if written as an internal one.
• Commented-out content (<!-- -->) was not seen in your submission.
• You created a template correctly, but it is not used.

For your shared journal response, a link to the shared response from your user page was not seen. Thank you for answering the questions!

—Dondi (talk) 21:48, 11 September 2017 (PDT)