User talk:Dbashour

Dina, here is the new input file: 15-genes 32-edges team-hAPI Sigmoid estimation.xlsx. I ran it on one of the computers in Seaver 120 in the back row. I left a note with your name on it there. The files will be on the T: drive in a folder called "Dina". I reduced the size of the network for the input file because it was too big. You will need to view it in GRNsight again. — Kdahlquist (talk) 10:58, 9 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. 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. You forgot to invoke your template on the page, so you were missing the link to the assignment page and your category. The link to your user page was only present in your signature.
2. 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.
   • The name of your PowerPoint file was very generic and did not specify your initials or the strain you worked with.
3. 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 Gln3 transcription factor.
4. There was no summary paragraph. In particular, items 3-5 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 as well as the GO term definitions. Please use the full APA format for citations in your references section.

— Kdahlquist (talk) 22:55, 16 November 2017 (PST)

Week 9 Feedback

• The “good habit” aspects of your individual journal are completely fulfilled and on-time. Great!
• 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 possibility that the data/Gene web service request might return more than one result (e.g., BRO1). In this case, since you know that you are working with SGD, you will want to pick the entry whose primaryIdentifier property looks like an SGD ID (that is, S#########).

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) 19:01, 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. In the table in your PowerPoint slide, you switched the Bonferroni and B-H p value numbers; your notebook had them recorded correctly.
3. 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 "dGLN3", 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.
   • When the instructions say "repeat for all timepoints" you also need to provide the formulas for those because the cell references will change.
4. At the top of your notebook, you did not record your strain, nor the number of replicates per timepoint.
5. The number of replacements of "NA" was also not recorded.
6. You reported the Average Log Fold Changes and p values for NSR1 and ADH1, 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. In your dataset, NSR1 has an unadjusted p value < 0.05, but is no longer significant with the corrections. This means that we have some confidence that is is really changing in this experiment, but not as much as some other genes.
   • None of the ADH1 p values are < 0.05, so the Average Log Fold Changes you see are likely just noise.
   • Also note that p values are between 0 and 1, which is why we use the "IF" statement to clear that up. For both genes, you should just report 1 for the Bonferroni p value.
7. Your concluding paragraph is not sufficient. You need to summarize the purpose of this analysis, what you did, and your main results, both in terms of the numbers of genes significant and the specific NSR1 and ADH1 values., but you need to include the interpretation of the p values of NSR1 and HSF1 as noted above.
8. Instead of having a separate section to report the answers to the questions, it would be better to just answer them at the point in which they appear in the protocol.
9. This entire wiki page is your electronic notebook. The extra section you wrote, more properly belongs in the Acknowledgments section where you describe how you and Zach worked together.
10. Finally, you also 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) 21:29, 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 the team template Template:Gene hAPI is somewhat underpopulated—continue reading to get further ideas on what can go there.

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) 00:20, 16 November 2017 (PST)

I also want to note that Eddie did not sign his executive summary/reflection with his wiki signature. The citations in you annotated bibliography should also be added to your team page.

— Kdahlquist (talk) 14:06, 16 November 2017 (PST)

Week 7 Feedback

• The “good habit” aspects of your individual journal are all on point. Be careful with the formatting of the references section: you have a leading space on each line, which results in that fixed-width format. Not sure if that was your intent. Your electronic notebook shows a moderate level of detail.
• All prior web page issues were addressed except that the “Week 7” reference entry is still listed with the title “Week 4.”
• 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 a fixed nav is noted as the other “advanced Bootstrap” feature.
• The XML API call was not adapted correctly: the request was supposed to have been adopted to show information about your gene specifically (ADH1).
• The JSON API adaptation was not seen.

Shared Journal

Questions and “good habit” aspects are fulfilled, all on-time. The far-from-comfort-zone observation on computer science is noted; I agree with your sentiment that no knowledge is wasted knowledge in this regard. For you, although you are unlikely to write computer code in the future, the hope is that you walk away from this class with enough good exposure to coding that it influences how you think and approach problems, computer-related or not. This is where your exposure to programming and code might make you tackle a problem with greater rigor or precision.

—Dondi (talk) 23:05, 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

• You’ve gotten a lot of the “good habit” tasks down, but not all. For this week:
  • Punctuality took a hit, with 3 out of 7 listed edits coming after 12:01am, the last one being at 2:43pm
  • On the bright side, 7 edits is a good number for this size journal, and you added summary entries to all of them
• Your lab notebook has very good detail, written in chronological log style, with a good focus on content acquisition

Shared Journal

• All questions and “good habit” points are fulfilled—good job here!
  • 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 stealing of information

Web Page

(both homework partners get the same feedback)

Most gene page requirements were fulfilled except:

• Your folder and HTML file names weren’t customized to your chosen gene, and the folder name wasn't all lowercase as specified
• The HTML filename ended with two .htmls (index.html.html)—keep an eye out for file extensions; this is why we recommend that they be made visible at all times
• A separate gene summary paragraph was not seen
• The Ensembl gene ID was the same as the SGD ID—it shouldn’t be
• The Ensembl link does not go where it should (in fact it appears to be an error page)
• For the DNA and protein sequences, note that they appear better with a so-called "fixed-width" font—these are the ones where every letter has the same width
• Your gene function, site differences, and reason for choosing your gene all work out; one small note: in gene function, where you reference baker’s yeast’s formal species name, the formatting convention should be italics (i.e., S. cerevisiae)
• The Week 4 assignment reference is missing from the References list on the gene page—note it’s still applicable to the page itself, not just your journal

Nice image pick! Protein images are always very interesting.

—Dondi (talk) 23:19, 2 October 2017 (PDT)

Week 2 Feedback

I see that Dr. Dionisio "lapped" me in terms of providing feedback on the Week 3 Assignment before I added my feedback on Week 2 :) It looks like you addressed some of the issues I list below in your Week 2 journal entry, but here is the feedback anyway.

• Thank you for turning in your assignment on time.
• You wrote something in the summary field for 13 of 27 saves (48%) in the period of review. Remember we are aiming for 100%
• However, the number of total saves on your individual wiki page is quite small (only 4). We are encouraging you to save your work in smaller "chunks"; a range of 10-20 saves is what would have been expected for this assignment.
• Technically, you should have given the complementary DNA sequence, as requested. Instead, you converted the T's to U's to make an RNA sequence. Be careful to follow the directions and give what is asked for.
  • Also, there appeared to be a spell check problem--"complementary" was given as "contemporary".
• 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.
• 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.
• Your Acknowledgments section is missing your wiki signature.
• In your References section, you need to change the citation to the Week 2 assignment.
• I also note that the links to and from your User page to the journal entry and assignment are formatted as external links. Please be sure to follow the correct syntax for internal wiki links versus external links. Please remove the "Journal entries" category and just keep the "Journal Entry" category.
• My apologies for not getting to discussing "transcriptomes" and "proteomes" in class. We will be picking up those topics in the next week or two. In brief, a transcriptome refers to all of the mRNAs found in a cell at a given time and a protein refers to all of the proteins in a cell at a particular time. The difference is looking at one mRNA or proteina, versus all of them.

— Kdahlquist (talk) 23:32, 23 September 2017 (PDT)

Week 3 Feedback

• Everything was turned in on time—thank you! You also fulfilled the “good habit/best practice” aspects of the assignment, including supplying comments for all 13 of the listed journal edits.
• You supplied an electronic notebook with this assignment, and it provided some good details in the spirit of openness and reproducibility, the values that we are after here. Keep it up, and always keep these questions in mind when journaling: 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, with your hacked headline fitting with the background image quite nicely!
• Your list of links was quite thorough, including the cgi-bin links for the reading frames, which I was hoping that students would catch. However…
• …I was also hoping that the values after seqdna in those links would be recognized by students as IDs. You listed element IDs, which are technically correct, but as noted above, there were other IDs on this page beyond those kinds.
• There were a couple of small glitches in your acknowledgments and references: first, the signature should follow your statement about your work in the acknowledgments; in this journal page it appears after the references. And speaking of the references, the assignment reference still says “Week 1” rather than “Week 3.”
• Your shared journal’s chosen quote reflects an unfortunate tendency in computer science, which is the proliferation of jargon. I agree with your sentiments. Here’s hoping that we produce better-trained practitioners who will put more thought into the names that they choose!

—Dondi (talk) 23:02, 23 September 2017 (PDT)

Week 1 Feedback

• You completed most of your assignment on time, but we note that you did make some changes after the deadline, including your shared journal assignment and posting questions to myself and Dr. Dionisio’s talk pages.
• 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.
  • You included your off-campus residence address on the page to fulfill the requirement for a “snail mail” address. However, to protect your privacy, we suggest that you replace this with the “1 LMU Drive…” general campus address.
  • You wrote something in the summary field for 10 of 13 saves, or 77%. We would like to see this approach 100%.
  • Please create a new wiki page (your Week 2 or Week 3 individual journal page will now fulfill this requirement).
  • 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.
  • Please provide a link to an external website on your User page. This could be to the LMU home page or to some other organization you wish to highlight, for example.
  • You organized your page using the three levels of headers, ==, ===, and ====, but you need to be careful to use them “in order” in outline form. For example, use === only underneath ==, don’t skip from == to ====.
  • One of the idiosyncrasies of using a numbered list in MediaWiki is that you cannot skip lines in between each line that begins with a “#” because it will restart the numbering from “1” again. Please go back and remove the lines in between, so that the numbered lines appear correctly. You can also make sub-lists by using “**”, “#*”, or “#*”, or “##”. Just make sure that you don’t skip lines in between.
  • You created a link to a file you intended to provide on your page, but the file itself was never uploaded to the wiki. Just like with images, it is a two-step process to upload the file and then to link to it on your page.
  • Please use the category “Journal Entry” instead of the one you used, including it on your template.
  • In a comment, you said you used Eddie Bachoura's page as inspiration. You actually need to say this visibly in your Acknowledgments section; this is the type of thing that we mean needs to go in this section.
• I answered your question on my User talk page.

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