User talk:Kzebrows

Week 12 Feedback

• I've looked at the compiled raw data that you and Erich posted and I have some feedback and next steps. I'm putting the instructions here, but you should share them with Erich. I'll put a note on his talk page to look here as well.
• First, I'm not sure that I understand the question you posed in your e-mail. Your dataset has 4 treatments (0.5X RX, 1X RX, 0.5X RP, 1X RP), with 3 timepoints each (10, 30, and 60 minutes), with 3 biological replicates each. Thus there are 9 samples per treatment for a total of 36 chips, which you have accounted for in your compiled raw data. Each of these treatment samples was competitively hybridized against a control sample that was just treated with methanol (which is what the antibiotics were dissolved in). As you determined in class last week, there are no dye swaps in your data; the drug-treated sample was always labeled with Cy5 and the control was always treated with Cy3.

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) 16:45, 25 October 2015 (PDT)

Week 4 Feedback

• Work was submitted on time, with 5 minutes to spare.
• All good-habit items are fulfilled:
  • All expected links and categories were noted.
  • 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 incorrect stop codon was chosen.
  • There is an inconsistency between the mRNA electronic notebook and the final command—the change from t to u is mentioned in the notebook but not seen in the command itself.
  • The incorrect stop codon means that the amino acid sequence ended at the wrong place as well; further, a spacing glitch in the commands kept the codons from being “tripled out” correctly.
• Shared responses were provided and they came in on time.

—Dondi (talk) 23:29, 4 October 2015 (PDT)

Week 3 Feedback

• Work was submitted on time, though with just around a half-hour to spare. See if you can give yourself additional wiggle room in case you experience unexpected delays.
• All good-habit items are largely fulfilled:
  • All expected links and categories were noted.
  • You phased your work well and you consistently supplied a change summary with all but one of your wiki edits.
  • You accompanied your work with electronic notes and processes for the reading frames section, but the details thinned out noticeably when it got to the xmlpipedb-match questions.
• All exercises were performed or answered correctly:
  • There is a small typo in your complement answer—the period at the end of the command sequence is extraneous and will actually generate an error if the commands are copy-pasted exactly (amazing what trouble a single dot can cause).
  • In your commentary, “caret” was misspelled as “carrot.” They sound the same, but don’t look the same :)
• Thank you for your candor in your shared responses. Yes, we are definitely outside biologists’ comfort zones now; hang in there and it’s good to hear that you find this foray rewarding. Definitely practice is valuable here, so keep at it and don’t hesitate to ask if you get stuck.

—Dondi (talk) 19:12, 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, except for frame +3, which contains a missense mutation (another motivation for doing this by computer such as in the Week 3 assignment); 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.
• You did not include anything by the way of an electronic notebook for this assignment. Although this assignment was pretty straightforward, you still need to document the process of what you did to arrive at the answers, not just supply the answers. Please be sure to do this for your Week 3 submission.
• You wrote something in the Summary field for 11/11 contributions between the Week 1 and Week 2 deadlines, keep up the good work! However, you completed the full assignment in only 2 edits to the wiki. This suggests that you are doing the work outside the wiki and then pasting it in. Ideally, you should do the work natively in the wiki environment. Even if this is not the case, you will want to consider saving your changes more frequently so that the granularity of the changes is smaller.
• You have set up your template and completed all the links requested.
• The relationship between sense and antisense strands that you mention in your wiki does not always hold. In a real gene, only one frame will be an open reading frame and all other frames will contain a stop codon, actually.
• With regards to your comments on your shared journal entry, I knew that the Nirenberg article would be difficult for folks without a biology background and even with a biology background. 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.

— Kdahlquist (talk) 23:11, 20 September 2015 (PDT)

Week 1 Feedback

• I answered your question on my user talk page.
• I am going to provide feedback on your Week 1 Assignment, even thought he scores are not yet posted.
• Thank you for submitting your assignment on time.
• Your assignment is neat and complete, but the following items need work:
  1. You wrote something in the Summary field for 17 out of 22 contributions, or about 77% of the time. You should aim to write something there 100% of the time. Don't forget to do that when you upload files as well.
  2. You did create links within the wiki. However, you formatted them like external links instead of internal links. For example, you can successfully link to the Main page of this wiki by formatting it like an external link like this: [https://xmlpipedb.cs.lmu.edu/biodb/fall2015/index.php/Main_Page Main page], but it is better to use the internal link syntax: [[Main Page | Main Page]]. Please convert all of your internal wiki links to the internal syntax.
  3. Your external links to Eugene and TriDelta are broken because you have extraneous information in your URLs. The format of a URL begins with http:// or https:// followed by either www.domain.extension or just domain.extension where the common extensions are .com, .org, or .edu. If you are copying and pasting a link from your browser address field, don't type an extra http://. Let us know if you have questions about this.
  4. You uploaded and linked to a file, but it has a very generic filename. It would be better to include your name and the date in your filename so there is not any confusion with other people's files.
  5. Please delete the category "User Page" that you additionally created.
• You will have the opportunity to make up the points that you missed by making the above corrections by the Week 2 journal deadline.

— Kdahlquist (talk) 23:09, 9 September 2015 (PDT)

I’ve answered your question on my talk page.

—Dondi (talk) 15:37, 12 September 2015 (PDT)