User talk:Aporras1

The file has now been completed for input to GRNmap in class on Thursday. — Kdahlquist (talk) 23:39, 6 December 2017 (PST)

Antonio, I finished paring down the network. Here is the final file (renamed): 15-gene_44-edge_teamJASPAR_Sigmoid_estimation.xlsx. I posted this on your Week 15 journal page as well. — Kdahlquist (talk) 15:56, 6 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.
• 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.

1. 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.
2. You did not report the definitions of your 6 GO terms.
3. There was no interpretation of these GO terms in terms of cold shock or the deletion of the Zap1 transcription factor.
4. There was no summary paragraph. In particular, items 2-4 will be reported in your final project presentation and written report.
5. 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.
6. In your Acknowledgments section, you need to be explicit that you copied and modified the instructions from the Week 10 assignment.
7. 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.

— 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.

—Dondi (talk) 19:21, 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. Your computations and Excel file were correct--no corrections are needed there.
2. 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.
3. In the table in your PowerPoint slide, you switched the Bonferroni and B-H p value numbers; your notebook had them recorded correctly.
4. Good job with reporting and interpreting the Average Log Fold Changes and p values for NSR1 and CLN1.
5. 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?
6. 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.

— Kdahlquist (talk) 22:34, 16 November 2017 (PST)

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

Your team page hit the specifically-requested items listed in the Week 11 assignment, although Simon’s individual journal page link appears to be missing from the team template. 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, 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? (for example, Template:GRNsight Gene Page Project Links has already been created for you—won’t that be useful to have on your page as well?)

Note how these items are very similar to the content that can be seen on our own Main Page—this is not a coincidence.

—Dondi (talk) 00:10, 16 November 2017 (PST)

I want to add that links to the journal club presentations should be on the page (under Files) and that the annotated bibliography citations would be better organized in a single section. Antonio needs to sign his executive summary with his wiki signature. A consistent format for the executive summaries and reflections will improve the look and organization of the page.

— Kdahlquist (talk) 14:10, 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 its 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.

—Dondi (talk) 22:23, 20 November 2017 (PST)

Week 5 Feedback

(work in progress)

Shared Journal

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

—Dondi (talk) 19:22, 21 October 2017 (PDT)

Week 4 Feedback

Individual Journal

• You’ve gotten a lot of the “good habit” tasks down, but not all. For this week:
  • The individual journal was mostly on-time—35 edits’ worth!—with the last edit landing at 12:02am.
  • But on a positive note, all 35 listed edits had a summary entry—keep that up!
  • Your journal page still does not have a category—please put that in your template so that you don't have to worry about it again.
• Your lab notebook has some great detail, but remains quite easy to read and follow. This is great!
• Your references were as requested except that the Week 3 reference was not updated to Week 4.

Shared Journal

All questions and “good habit” points are fulfilled! And indeed the flip side of the Internet’s success is the danger and quality of our data. Vigilance for this can never let up.

Web Page

(both homework partners get the same feedback)

Most gene page requirements were fulfilled except:

• Filenames and title element weren’t customized to your chosen gene
• A separate gene summary paragraph was not seen
• The displayed Ensembl gene ID doesn't match the ID in the link
• The displayed UniProt ID is the taxon (organism) ID—note the link has a different value (plus there is a typo in the UniProt label)
• Acknowledgments and References should have had separate headings, plus Week 3 was not updated to Week 4

—Dondi (talk) 22:20, 2 October 2017 (PDT)

Week 3 Feedback

• Everything was turned in on time—good job! You fulfilled most of the “good habit/best practice” aspects of the assignment, with comments on 16 out of the 17 listed journal edits in the history.
• Your journal entry page does not have a category—just put this in your template so you don’t forget.
• You supplied an electronic notebook with this assignment, with a fine level of detail. Openness and reproducibility are the values that we are after here: 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?
  • Note that we’ll want you to integrate your notebook right with your journal page from this point on, instead of a separate page like you have here.
• Your hack-a-page work certainly fulfilled the instructions; if only Fox News’s biggest headlines were about domesticated teddy bear hamsters!
• You listed a good number of links for a variety of resource types, so that works out nicely.
• Your list of IDs was also of decent size, and in this case you took the most explicit ones, the element IDs. However, there were other kinds of IDs in the page and I was hoping you would catch those as well.
• Sorry to hear that you weren’t able to work out the “cleanup” commands. This might be good to follow-up on with your homework partner for this week, to make sure that you don’t miss out on the skills that the solution requires.
• Your shared journal entry and chosen quote actually speak to the heart of the “science” in “computer science”—limits. Theoretical computer science is very much about the limits of computation. As for how-to guidance, I’d say that office hours would be a great opportunity for getting that. I’ll be happy to review any of the technical content that you’ll see in the class.

—Dondi (talk) 15:46, 24 September 2017 (PDT)

Week 2 Feedback

• Thank you for turning in your assignment on time.
• You wrote something in the summary field for 32 of 38 saves (84%) in the period of review, which is very good. Remember we are aiming for 100%
• The number of total saves on your individual wiki page was 18, which is a good amount for this assignment.
• The link from your User page to the Week 2 assignment was missing, as was your category. Please make sure that these are included in your template and that you invoke the template on each journal entry, if you haven't made this change already.
• Your +1, +2, and +3 frame translations were correct.
• However, the -1, -2, and -3 frame translations were incorrect. It appears that you read them 3' to 5' instead of 5' to 3'. You either had to reverse the sequence or read it right to left to translate it correctly.
• Your determination of which frames contained ORFs was correct (but based on your mis-translation of the three minus frames).
• One other note: we do not label the ends of proteins 5' and 3', instead we label them N-ter and C-ter.
• Also, do not put the untranslated nucleotides at the end of the protein sequence. Since some nucleotides and amino acids share one-letter abbreviations, this is confusing.
• Finally, do not flip the orientation of the RNA "top" and "bottom" strands from what is given by the DNA sequence. Even though it is the RNA that is ultimately translated, we always refer to "top" and "bottom" with respect to DNA.
• I did not see an electronic lab notebook for this assignment. For this journal entry, the lab notebook would have explained how you arrived at your answers to the questions posed in the exercise.
• The technical language in articles from the primary literature is definitely a hurdle for students (and even for faculty from a different field), I'm glad you stuck with it. Like with other fields of endeavor, it is good to take a look at the primary source. Instead of just relying on your memory for terminology, you can always look something up online or in a text book or dictionary. I have to do that myself when I am reading something from a different field.

— Kdahlquist (talk) 23:40, 23 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:

• I don’t see an email from you regarding worries/concerns or additional information.
• You only went to two levels of depth with your headings; the instructions requested at least three levels.

None of these other items were found in your submission:

• Acknowledgments
• References

For your shared journal response, the following requested items were not seen:

• Link to shared response from user page
• Your answer to the first question after doing the readings. Unfortunately, it did not help that your answers were conflated into paragraph form, rather than a point-by-point Q&A. Implied answers were found to most of the questions, except for the first post-reading question.

Please make sure to check off all of the requested items in future assignments more thoroughly. The instructions asked for all of these to be included in your user page and/or shared journal response. Thank you!

—Dondi (talk) 21:42, 11 September 2017 (PDT)