User talk:Kevinmcgee

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) 16:16, 29 November 2013 (PST)

Week 8 Interim Feedback

• I have reviewed your spreadsheet from part 1 of the Week 8 assignment. Your made some errors on the "scaled_centered" sheet that have propagated through to the other sheets.
  • When you calculated the AVERAGE and STDEV for each column, you used a comma instead of a colon to specify the cell range. The way you wrote it, it simply averages or computes the standard deviation of just those two values.
  • When scaling and centering the log fold changes based on those values, you forgot the second dollar sign in the formula.
  • The rest of your calculations are correct, but based on erroneous numbers from the previous sheet.
  • You will need to correct your file or alternately work with your partner's file, if it is correct.
• The syntax for linking to the files for download on your Week 8 journal page is incorrect. Instead of [[File:filename]] use [[Media:filename]].

— Kdahlquist (talk) 16:06, 14 October 2013 (PDT)

Week 1 Feedback

You missed quite a few wiki skills, plus need to send email concerns and ask talk page questions.

Items for completion/follow-up:

• Snail mail address
• Expected graduation year
• Upper-division courses—if you haven’t taken any, still say so explicitly, so that we know you didn’t forget about it.
• Independent research—if you haven’t done any, still say so explicitly, so that we know you didn’t forget about it.
• Email about worries/concerns/questions/anything else
• Questions to faculty Talk pages
• Create a new wiki page
• Link to an external site
• Create a numbered list
• Comments inside the wiki markup
• Upload and link to an image
• Upload and link to a file
• Assign a category to a page
• Use the signature shortcut
• Create and use a template
• Link to an assignment (Week n) page
• Link to the shared journal from your user page
• Link from the shared journal to your user page

—Dondi (talk) 09:35, 3 September 2013 (PDT)

Week 1 Follow-up Feedback

Thank you very much for catching up on last week’s missing information/wiki skills! You’ve now shown that you can do all of the basics. Please don’t forget to send Dr. Dahlquist and me an email listing your questions and concerns (and say “none” if you have none, just so that we know you didn’t forget).

Some very minor notes on your catch-up work:

• Now that you have made “Loyola Marymount University” a link, the text above it has become redundant and can be removed.
• In linking to your résumé, you use the File: wiki markup, which is fine but takes you to one more intermediate page before the user can actually see the file. If you precede the filename with Media: instead, then you will get a direct link which goes right to the document when the user clicks on it.

Congratulations and keep it up!

—Dondi (talk) 15:22, 8 September 2013 (PDT)

Week 2 Feedback

• Thank you for submitting your assignment on time!
• As was discussed in class, there were several mutations in your translation. Make sure you use the ExPaSY tool to translate the code and explain what went wrong with your translation.
• You forgot to put the category "Journal Entry" on your individual entry page.
  • If you add the category to your template and then use your template every time in the future, you won't need to worry about forgetting it.
• You have the opportunity to earn back the points you missed by making the corrections requested on the Week 3 Assignment page and the correction above. The corrections are due by midnight on Friday, September 20 (thursday night/friday morning).
• Yes, the Nirenberg article was dense. It was written as a memoir for other practicing biochemists. I'm glad you were able to grasp the big picture.

— Kdahlquist (talk) 14:54, 11 September 2013 (PDT)

P.S. I answered your question on my user talk page. — Kdahlquist (talk) 09:15, 12 September 2013 (PDT)

Week 2 Follow-up

• Thank you for making the corrections to your translation. You are still missing the first amino acid from frame "-2".
• The category is still missing from this page.

— Kdahlquist (talk) 15:04, 11 October 2013 (PDT)

Week 3 Feedback

• Thank you for submitting your assignment on time!
• You missed the cat command at the beginning of your reading frame answers. This is not a huge deal, but remember how attention to detail is a very important part of working with computers.
• Your sed and match skills are otherwise great! All of your commands were correct.
• Thank you for providing a complete set of links across your user page, assignment page, shared journal page, and individual journal answer page. These really help us to get around from one page to another.

—Dondi (talk) 22:21, 14 September 2013 (PDT)

Week 4 Feedback

Thank you for submitting your work on time! 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.
• Transcription start site was not identified.
• Ribosome binding site was correctly identified with an appropriate command.
• Start codon was correctly identified with an appropriate command.
• Stop codon was not correctly identified because the command did not enforce solely triplets after the start codon.
• The terminator is missing the complete hairpin sequence.
• The identified mRNA strand is short—you only returned the start-to-stop codon, but transcription actually goes from the transcription start site to the end of the terminator. In addition, it appears that this sequence was derived manually.
• The identified amino acid sequence is short, and no command was supplied so it is not clear where the computation went wrong.

In terms of your wiki link routine, everything was there except for:

• The specified category designation for your individual assignment page.

Let me know if you have any questions.

—Dondi (talk) 22:50, 24 September 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 did not contain enough detail such that you or another person could reproduce what you did using only the information from your journal entry. Starting again with the Week 8 assignment, keeping an online notebook will be an important part of your weekly assignments. Look at some of your classmates' entries to see some examples and please let us know if you have any questions.
• 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) 16:04, 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 you were 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) 14:15, 11 October 2013 (PDT)

Week 6 Feedback

Thank you for submitting everything on time!

• 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]). Still, no answer was provided; note the instructions stated that you should provide a subset of the answers in the event that the total result was too long.
• The 5th query, which requests counts by year, is much easier to answer if you include year in the select clause. What you have still produces the right answer, but you have to be careful in determining which count pertains to which year. In particular, what if there was a year with zero movies? That might be missed in the tallies.
• In the 9th query, which requests the average rating for movies beginning with “Star,” you computed the average year and not the rating.
• 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) 12:08, 12 October 2013 (PDT)