User talk:Kwyllie

Week 12 Feedback

• I am posting feedback on your compiled raw data here and will post a comment on Veronica's talk page to refer her to this page.
• Kudos for working ahead, but there are some intermediate steps you need to take before moving on to the statistics calculations.
• Your chip has each gene spotted in quadruplicate. These are considered technical replicates and they should be averaged before doing any further analysis.
  • I have separated the quadrupliate spots and compiled them in columns next to each other in this file: Raw_compiled_data_KD20151124.xls. I started another file because the previous one was getting too large.
  • You need to average the technical replicates for each sample first.
  • Then you need to average the averages for biofilm and for tobramycin. (It doesn't make sense to average biofilm and tobramycin together since they are separate treatments).
  • Because your reference sample is genomic DNA and not RNA, you need to then take the ratio of the averages for the biofilm and tobramycin samples to get the ratio of tobramycin to control (tobramycin over biofilm). Because the numbers are in log space, you will subtract the biofilm average from the tobramycin average to get this number.
  • You will conduct a two-sample t test comparing the 5 biofilm samples to the 3 tobramycin samples using the TTEST function in Excel, not the equation we did for Vibrio. It will directly compute the p value.
  • Then you can compute the Bonferroni and Benjamini and Hochberg corrected p values like you did in the Vibrio exercise.
• Let me know if you have any questions.

— Kdahlquist (talk) 17:08, 24 November 2015 (PST)

Week 6 Feedback

I’ve chosen to issue partial feedback sooner than complete feedback later, in case it will help you address issues with Week 8.

Best Practices

• Individual and shared work were both submitted on time.
• Requisite links to and from the user page as well as page categories are all present.
• Electronic notebook was maintained.
• Work was submitted in appropriate frequencies with corresponding summaries.
• This amounts to a “best practices” perfect score. Good work, keep it up!

Database Exercises

Work in progress.

—Dondi (talk) 16:43, 25 October 2015 (PDT)

Week 4 Feedback

• Work was submitted on time, with 12 minutes to spare.
• Almost all good-habit items are fulfilled:
  • All expected links were noted.
  • ...but you forgot to include the Journal Entry category on your individual journal page.
  • Electronic notebook content was seen.
  • Summaries were consistently provided over a good number of edits.
• For the exercises, the following issues were seen; all others were correct:
  • You were off by one nucleotide on the transcription start site.
  • The given code for “tagging” the terminator had a typo—three consecutive periods (...) somehow became ellipses (…) in your submission.
  • Your mRNA strand reflected the off-by-one error, plus you did not convert the ts to us.
  • The amino acid command and result were correct, but your electronic notebook for this section showed a significant drop in detail as compared to the previous answers.
• Shared responses were provided and they came in on time.

—Dondi (talk) 23:40, 4 October 2015 (PDT)

Week 3 Feedback

• Work was submitted on time, with just over a couple hours to spare. This wiggle room is good to maintain in case you experience unexpected delays.
• All good-habit items are fulfilled:
  • All expected links and categories were noted, but the links to the assignment and class journal are incorrect. Make sure that you are using the internal link notation ([[ ]]) for those.
  • You phased your work well and you consistently supplied a change summary with all but the file uploads. Make sure to include summaries with those also—don’t assume that the filenames will explain what they are when someone looks at your contribution history.
  • You accompanied your work with electronic notes and processes.
• All exercises were performed or answered correctly:
  • For the complement, you did not need to reverse the sequence, but I can understand why you thought this would be needed.
  • Your annotated screenshots were very useful! That was certainly going above and beyond the expectation of the assignment, but they contributed very strongly to the presentation of your answers.
• Thank you for your shared responses. Your writing voice struck me as very personal and distinctive. I’m glad to hear that the computer pace has been OK for you; we definitely want to make sure that the material accommodates both first-timers and experienced coders. And yes, I am of the mindset that the robot apocalypse is not as close as some people might think, precisely because I know how dumb computers can still be :)

—Dondi (talk) 18:42, 26 September 2015 (PDT)

Week 2 Feedback

• Although, the Week 2 scores have not yet been posted, I want to give you feedback on the assignment that you can incorporate to your your Week 3 submission.
• First, thank you for submitting your assignment on time.
• Your translations are correct; although it would have been better for completeness to go ahead and translate the rest of the sequence after the stop codon, in this case.
• Your electronic notebook for this assignment was good, keep up the good work! I'm assuming that doing research with me has taught you some good habits. :)
• You wrote something in the Summary field for 42/43 contributions between the Week 1 and Week 2 deadlines, keep up the good work!
• For each week's assignment, you will need to create links from your User page to that week's assignment and to your individual and shared journal entries, as well as a link back from your individual journal entry and to the category "Journal Entry". You completed all of these for this assignment, but you did them on an "ad hoc" basis. Ideally, you should create all of these links on your template and then just simply invoke your template on your User page and all individual journal entry pages. This will save you considerable work to doing all the links individually.
• With regards to your comments on your shared journal entry, I knew that the Nirenberg article would be difficult for folks, even the biology/biochemistry students. However, I also think it's a good exercise to go back to the original source sometimes and read about discoveries from "the horse's mouth", so to speak. I will try to clarify this article in class on Tuesday.

— Kdahlquist (talk) 23:02, 20 September 2015 (PDT)

Week 1 Feedback

• I have answered your question on my user talk page.
• Even though the scores have not yet been posted, I want to provide you with feedback on your Week 1 assignment.
• Thank you for submitting your work on time.
• Your assignment is complete with the following exceptions:
  1. You included your e-mail addresses in a way that is not obscured. If you are not worried about bots scraping it from the page and using it to send you spam, you could consider hyperlinking it with a mailto link such as mailto:kwyllie@lion.lmu.edu. However, it is probably best to rewrite it as kwyllie at lion dot lmu dot edu.
  2. Your snail mail address is missing. Please provide the address to your LMU mail box.
  3. You could flesh out your list of presentations from my lab a little more, giving links to the LMU symposium and WCBSURC.
  4. You wrote in the Summary field for 27 out of 29 contributions, or 93%. That is excellent, but remember, we are aiming for 100% of the time.
  5. In terms of headers, you need to go down one more level to a fourth set of "=" signs.
  6. In one of your bulleted lists, you have a stray bullet. This occurs when you skip a level in a sub-list. For example, if you start with ** and don't have an item with a single * above it.
  7. Please change your category to "Journal Entry".
  8. Your wiki signature is missing from the Class Journal Week 1 page.
     • Thus, the link to your user page from the Class Journal is missing as well because that is created automatically when you use your signature.
  9. You should rename your template page to be your username because such a generic name could easily be confused with one of your classmates.
• You will have the opportunity to make up the points you missed by making the corrections listed above by the Week 2 journal deadline.

— Kdahlquist (talk) 23:38, 9 September 2015 (PDT)

I just realized that my answer on my talk page was a little messed up because the touchpad on my laptop is very sensitive. I meant, organic chemistry, biochemistry, and invertebrate zoology, although the other answer was funnier. :) — Kdahlquist (talk) 23:13, 10 September 2015 (PDT)

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I’ve answered your question on my talk page.

—Dondi (talk) 15:48, 12 September 2015 (PDT)