User talk:Vkuehn

Week 9 Feedback

Your week 9 work has (finally) been reviewed:

• Three out of the four file versions, as specified by the testing report template, are not listed.
• You logged all of the needed import/processing/export times.
• You successfully uploaded your .gdb file to the wiki.
• You successfully ran the Tally Engine.
• You successfully ran xmlpipedb-match.
• You successfully ran the appropriate PostgreSQL query.
• You successfully examined your .gdb file in Microsoft Access, but did not compare the data against the benchmark version of the V. cholerae gene database.
• You correctly noted differences and similarities in the ID tallies from your various counts.
• You clearly indicated the ID pattern used for your ID searches/tallies.
• Your lab notebook effectively documents your activities and results for this assignment.

Finally, your work was submitted on time and all specified wiki links and navigational aids were correctly included. Well done!

—Dondi (talk) 13:25, 29 November 2013 (PST)

Week 8 Interim Feedback

• I have reviewed the files you uploaded. The contents are correct and ready to go for Tuesday.
• However, your syntax for linking to the files for download on your Week 8 journal page is incorrect. Instead of [[File:filename]] use [[Media:filename]].
• Also, please follow the convention for naming your files given in the assignment, so that it is maximally informative as to the contents. For example, my file would be named "Merrell_Compiled_Raw_Data_Vibrio_KD_20091020.xls". You need to add a date to your filename.

— Kdahlquist (talk) 15:47, 14 October 2013 (PDT)

Week 1 Feedback

Great coverage! You missed just a few items. Make sure to do them to cover all the bases.

Items for completion/follow-up:

• Create a new wiki page
• Link to an external site
• Comments inside the wiki markup
• Upload and link to an image
• Upload and link to a file
• Link to an assignment (Week n) page

—Dondi (talk) 08:54, 3 September 2013 (PDT)

Week 1 Follow-up Feedback

Thank you for filling in the missing wiki skills from last week! You missed that last one, “link to an assignment (Week n) page.” You will find that having this link will become very convenient, particularly if you want to go back and forth between the assignment page itself and your answers.

—Dondi (talk) 22:14, 7 September 2013 (PDT)

Week 2 Journal Feedback

• Your journal assignment was partially late this week. You will be understandably busy this next week, but hopefully you will be able to get back on track submitting your assignments on time soon.
• Your translation had point mutations in frames +1 and +3; you had a deletion in frame -2; you did not continue your translation beyond the stop codons. The +3 frame did not have an open reading frame. You have the opportunity to earn back the points you missed this week by making the corrections requested on the Week 3 Assignment page and the corrections listed below. The corrections are due by midnight on Friday, September 20 (thursday night/friday morning).
• You are also missing some links on your pages. Specifically:
  1. You need to link from your user page to the Week 2 Assignment page.
  2. You need to link from your individual journal entry back to your user page.
  3. You need to include the category "Journal Entry" on your individual journal page.
     • You can easily make the corrections above by adding them to your template and then using your template on your user and individual journal entry pages, for this week and all future weeks.
• Yes, the Nirenberg article was quite dense, but I'm glad you enjoyed it anyway!
• I answered your question on my user talk page.

— Kdahlquist (talk) 16:15, 10 September 2013 (PDT)

Week 2 Follow-up

• I have reviewed the changes you made to your Week 2 journal entry. I note that you added the requested links via your template, but did not make any content corrections to your translation.

— Kdahlquist (talk) 15:02, 11 October 2013 (PDT)

Week 3 Feedback

• Thank you for submitting your assignment by the deadline that you set for yourself!
• Good to hear that you succeeded in exerting control of your file extensions.
• Your sed skills need some practice and review—understandably so because of missed classes. Let’s see if we can catch you up with some face-to-face time when you are back:
  • The complement command only works for a very specific nucleotide sequence, and not over all bases in general.
  • Your +1 reading frame came out right, but +2 and +3 incorrectly performed the initial “chopping” of the first and first two bases, respectively. You weren’t deleting the bases outright, but replacing them with spaces. Unfortunately, the . placeholder also matches with spaces, and so you end up with incorrect triplets.
  • For the -1, -2, and -3 reading frames, the command sequences you provided also contain the error in the above bullet, plus are missing the complement step.
• Your match and grep/wc results are completely on the money!
• You were missing a number of requested links and wiki elements:
  • Your user page was missing a link to the shared journal page
  • Your user page was also missing a link to the Week 3 assignment page

Please note the bulleted checklist provided under the assignment headings so that you don’t miss these in future assignments. A template will help, so that you will only need to edit these links in one place. Let me know if you need additional help with getting a template to work as needed.

—Dondi (talk) 22:29, 16 September 2013 (PDT)

Makeup Point Update

You have been credited for making the following change(s) to an assignment or wiki link checklist:

• Corrections to your +2, +3, -1, -2, and -3 reading frames. The -3 reading frame command has a typo, however: the “chopoff” sed command is missing a ^ in its match pattern.
• The link from your user page to the Week 3 shared journal page has been added.
• The link from your user page to the Week 3 assignment page has been added.

If you have any questions, let me know. Thank you!

—Dondi (talk) 21:50, 29 September 2013 (PDT)

Week 4 Feedback

Here’s how your “automated annotation” work turned out, item by item. Items that had issues are italicized:

• -35 box was correctly identified with an appropriate command.
• -10 box was correctly identified with an appropriate command.
• Your transcription start site was off by one base.
• Ribosome binding site was correctly identified with an appropriate command.
• Start codon was correctly identified with an appropriate command.
• Stop codon was correctly identified with an appropriate command.
• The terminator sequence was correctly identified.
• No mRNA strand was identified, and no command was provided to indicate what might have been tried.
• No amino acid sequence was identified, and no command was provided to indicate what might have been tried.

In terms of your wiki link routine, your entries in the user and individual assignment pages were missing these items:

• A link from your individual assignment page back to your user page.
• Category designation for your individual assignment page.

Let me know if you have any questions.

—Dondi (talk) 23:35, 9 October 2013 (PDT)

Week 5 Feedback

This is feedback on the Week 5 individual assignment (UniProt Exercise) and shared class reflection. Feedback on your Database wiki page will come later.

• Thank you for submitting your assignment on time.
• Your electronic lab notebook was good, but still could be improved. Starting again with the Week 8 assignment, keeping an online notebook will be an important part of your weekly assignments. Keep in mind the guideline that you or someone else should be able to reproduce everything that you did using only the information on your journal entry page. Your page could have been enhanced by providing additional hyperlinks to the pages you visited.
• Remember to link your journal page back to your user page and to add the category "Journal Entry". You should add these links to your template and then use your template on each journal page that you complete.

— Kdahlquist (talk) 16:20, 8 October 2013 (PDT)

Week 5 Database Wiki

• Your assignment is complete, although it looks like some tweaks were made to it after the deadline. From the history, it looks like Kevin was the main contributor to this page.
• You need to link from the database wiki page to the Class Journal Week 5 page.
• The main classification for Ensembl is that it is a sequence/ genome database.

— Kdahlquist (talk) 14:16, 11 October 2013 (PDT)

Week 6 Feedback

Thank you for submitting everything on time!

• The incorrect years were used in the query for movies released in the 1980s with 4 digits in their titles.
• The wiki markup for movies-with-apostrophe query does not reproduce the query correctly because the wiki interprets repeated apostrophes as starting either bold or italic text; to render the apostrophes accurately, you need the nowiki tag (like this: '''' [view the wiki source to see how it’s done]).
• In your movies-beginning-with-the-word-“Star” query, note that the question was how many movies matched that. Thus, a count computation is required there.
• All your other database queries were correct and properly documented.

Regarding your navigation/wiki links, a couple of items were missing:

• Link from the journal page back to your user page
• “Journal Entry” category on your journal page

These requested links and features make the navigation of your wiki work as easy as possible.

—Dondi (talk) 10:19, 12 October 2013 (PDT)