User talk:Mbalducc

Mary, I've made the GRNmap input file for use in class on Thursday: 17-genes_19-edges_team-hAPI_Sigmoid_estimation.xlsx. — Kdahlquist (talk) 00:37, 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. 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 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.
   • If there were issues with running the protocol, those need to be noted.
   • When you talk about saving files, please record the actual filename in your notebook for reference.
   • Be attentive to writing something in the summary field every time you make a change to the wiki.
2. While you reported the definitions of your 6 GO terms, you did not provide an interpretation with respect to cold shock or the deletion of the Cin5 transcription factor.
3. You included a summary paragraph, but your summary did not draw any conclusions about the data analysis you performed with respect to what is noted in number 2 above.
4. The gene list and GO list files were provided (make sure that they have the correct file extensions). 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.
5. The PowerPoint with the screenshots of the stem results was also not found. Without this, I was unable to really review your results. These screenshots will be included in your final presentation and report.
6. 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.
7. In your Acknowledgments section, you need to be explicit that you copied and modified the instructions from the Week 10 assignment.
8. 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) 23:29, 16 November 2017 (PST)

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

You covered some of the basics for your team page, but some specifically requested items were missing:

• You need to add a category with your team's name, i.e., "Page Desiigner".
• Please remove the category "Assignment" from your page/template.
• Arash's executive summary should provide a link to his Week 11 individual assignment page.

In addition, 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? You did include the Template:GRNsight Gene Page Project Links, but then redundantly added a separate list of guild links.
• Finally, having consistent formatting for the executive summaries and reflections will improve the look and organization of your page. Hayden and Arash should fix the formatting of their bullet points.

— Kdahlquist (talk) 13:54, 16 November 2017 (PST)

Week 9 Feedback

• The “good habit” aspects of your individual journal are almost fulfilled and on-time. An unusually low subset of the listed submissions in the page’s history have a summary, 9/24.
• The electronic notebook has good detail and is clear in its bulleted form.
• GRNsight testing is complete with clear feedback on the results.
• The final URL for the desired gene data is given correctly, along with the portions to substitute depending on the desired gene as well as the overall process for going from the gene symbol to the final gene data.

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) 18:29, 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 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 provided the formulas that were specific to your dataset. However, 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. At the top of the protocol, you recorded your strain, but did not record the number of replicates per timepoint.
4. You reported the Average Log Fold Changes and p values for NSR1 and 'HSF1, 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.
   • HSF1 also shows some largish Average Log Fold Changes. But more importantly, its Benjamini and Hochberg p value is ~0.02, which is significant. So, you can conclude that it is changing expression due to cold shock.
5. Your concluding paragraph is pretty good, but you need to include the interpretation of the p values of NSR1 and HSF1 as noted above. Also, you report 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) 16:57, 16 November 2017 (PST)

Week 7 Feedback

• The “good habit” aspects of your individual journal are mostly on point, except that the signature is missing from the acknowledgments section and the references are somewhat minimal—certainly more material was used in this assignment than just the instructions?
• Nearly all prior web page issues were addressed except:
  • Title tag was not modified to match gene.
  • The gene page does not have its own acknowledgments section (separate from the one in your individual journal page).
  • The gene page does not have its own references section (separate from the one in your individual journal page).
• Bootstrap grid layout and flex classes were seen, though used somewhat subtly and on small subsets of the page.
• 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. Good to see that the out-of-comfort exposure is looking just right for you. It is tricky to strike a balance between sufficient exposure to do something substantive alongside skipping some basics and practice in order to save time, but it's looking like the mix is generally OK for you except for the need for more practice.

—Dondi (talk) 22:43, 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) 19:00, 21 October 2017 (PDT)

Week 4 Feedback

Individual Journal

• Great work on your individual journal! All “good habit” items are addressed, it was submitted on time, you spaced your work out well (9 edits), and had summary entries for all of them.
• Your electronic notebook has sufficient detail and includes some very specific notes, giving it genuine individuality and keeping it from sounding like it could have been anyone else's process.

Shared Journal

• All questions and “good habit” points are fulfilled—once again, good job!
  • Note that the standard library you used here does have a name: Bootstrap
  • Indeed the flip side of widespread information availability is the loss of privacy and potential misinformation

Web Page

(both homework partners get the same feedback)

Most gene page requirements were fulfilled except:

• Your folder name and title element weren’t customized to your chosen gene, and the folder name wasn't all lowercase as specified
• Your link to the .zip file used File: rather than Media:; although this was not directly stipulated in the instructions, note that Media: leads to a download immediately, making it more convenient for the reader. If you want to accommodate readers who would like to see the file metadata, provide both links.
• A separate gene summary paragraph was not seen
• The content for gene function, differences, and reason for choosing the gene all work OK, but the choice of presentation is not ideal—controlling the “slideshow” isn’t obvious and this distracts from simply reading the information that you provided
• The image choice could have been better…stopping at just bread was somewhat generic, and not distinctive to your gene
• The web page was supposed to have its own Acknowledgments and References too

—Dondi (talk) 22:39, 2 October 2017 (PDT)

Week 2 Feedback

I see that Dr. Dionisio "lapped" me in providing feedback on Week 3 before I could record my feedback on Week 2 :) In any event, here is the feedback.

• Thank you for turning in your assignment on time.
• You wrote something in the summary field for 11 of 19 saves (58%) in the period of review. Remember we are aiming for 100%
• The number of total saves on your individual wiki page was 16, which is in the range of what was expected for this assignment.
• Your complementary DNA sequence was correct.
• Your +1, +2, frame translations were correct.
  • There was a missing "T" in the +3 frame.
• 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.
• 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.
• In your References section, you need to change the citation to the Week 2 assignment.
• For your shared journal, the link from your user page to the shared journal page was missing.
• I also can't really visualize a hypercube; it is something that we can't render in 2D or 3D, I think. The current table form emphasizes how the third nucleotide can be redundant and degenerate. I think the other representation would help to understand how the first or second amino acid could be mutated an change the translation to a related amino acid.

— Kdahlquist (talk) 23:07, 23 September 2017 (PDT)

Week 3 Feedback

• Everything was turned in on time—good job! You also fulfilled the “good habit/best practice” aspects of the assignment, including supplying comments for 16 out of the 17 listed journal edits.
• You supplied an electronic notebook with this assignment, with the kinds of details that support openness and reproducibility, the values that we are after here. Look to try to answer these questions: 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? In that spirit, one portion that could use more detail was the last portion, which you characterized as tricky. Digging into what made something tricky, or what you tried that didn’t work, can be just as helpful to readers of your notebook as talking about what did work.
• Your hack-a-page work certainly fulfilled the instructions, with a nice dash of humor (or is it satire?).
• Your list of links was quite thorough, and of course there are more where those came from.
• You correctly listed a subset of the IDs in the page, and in this case you took the most explicit ones, the element IDs. Note that there are other kinds of IDs in the page and I was hoping you would catch those as well—for example, each reading frame entry got its own ID.
• Your shared journal chosen quote is actually something I say a lot when I teach computer science courses—learning computer science takes away the “magic” that many people feel when faced with the wonders of technology. The hope, however, is that the knowledge behind the magic actually feels more fulfilling and empowering than the sense of magic itself.

—Dondi (talk) 22:53, 23 September 2017 (PDT)

Week 1 Feedback

• Thank you for completing the assignment on time.
• You completed all of the required content and skills except for the following list. You have the opportunity to make up the points you have lost on this assignment by completing the changes requested by the Week 3 journal deadline.
  • Please include Biological Databases and any other courses you are taking this semester in your list of upper division courses.
  • Please make an explicit statement about your career interests and goals.
  • You wrote something in the summary field for 13 of 24 saves, or 54%. We would like to see this approach 100%.
  • Please be careful to use the correct syntax for an internal wiki link versus an external one. Most of your internal links are formatted like external ones. While they do function as links, we would like you to please go back and correct the syntax so that you have practice in learning the MediaWiki syntax, including your name on the Main page.
  • You uploaded a file and linked to it on your page, but the name of the file is very generic “Resume.pdf” Someone else in the class could have uploaded a file with the same name and overwritten the file without your knowledge. Now is a good time to get into the habit of using more informative names for your files. Usually this includes your last name and the date, but could include the course, type of assignment, etc. This is especially important when you are posting or sending files via e-mail to another person.
  • You included a category on your page, but we would prefer you to use the category “Journal Entry” Please make this change, including it on your template, instead of on the User page itself.
  • Also, you did not put the link to the Shared Journal page from your User page. Please include this link on your template as well. For each week, you will need to include links to the actual assignment page, your individual journal page, and the shared journal page from your user page (as well as the category). If you get into the habit of including this on your template, you will only need to edit once and all the pages will reflect the change. You can also go ahead and make your template for the rest of the semester so you will always have this part of the assignment fulfilled.
• I answered your question on my User talk page.

— Kdahlquist (talk) 13:35, 12 September 2017 (PDT)