User talk:Ksherbina

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 listed. The GO OBO information is missing; as indicated in the export report template, this should be the date/time stamp shown in the file properties after it has been unzipped.
• 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) 16:29, 29 November 2013 (PST)

Week 8 Interim Feedback

• I have reviewed your files from part 1 of Week 8. They are correct and ready to go for Tuesday.

— Kdahlquist (talk) 16:17, 14 October 2013 (PDT)

Week 1 Feedback

Excellent coverage! (save for creating a new distinct wiki page) Plus, don't forget to email us your concerns and questions.

Items for completion/follow-up:

• Email about worries/concerns/questions/anything else
• Create a new wiki page (beyond your own user page)

—Dondi (talk) 09:45, 3 September 2013 (PDT)

• I have answered your question on my talk page. — Kdahlquist (talk) 10:36, 4 September 2013 (PDT)

Week 1 Follow-Up Feedback

Thank you for sending is the questions/concerns email, and for creating a new wiki page. Moving right along then :)

—Dondi (talk) 17:13, 8 September 2013 (PDT)

Week 2 Feedback

• Thank you for submitting your assignment on time.
• As was discussed in class, you just had one missing amino acid in the -1 frame. For our purposes in this exercise, an open reading frame is simply one without a stop codon.
• Please go ahead and make these corrections on your page to earn back the points you missed.
• The Nirenberg article was written as a memoir to other practicing biochemists, so it was dense. I hope you enjoyed it anyway!

— Kdahlquist (talk) 15:08, 11 September 2013 (PDT)

P.S. I answered your question on my user talk page. — Kdahlquist (talk) 09:19, 12 September 2013 (PDT)

Week 2 Follow-up

• Thank you for making all requested corrections.

— Kdahlquist (talk) 14:59, 11 October 2013 (PDT)

Week 3 Feedback

• Thank you for submitting your assignment on time!
• Good to hear that you succeeded in exerting control of your file extensions.
• Your sed and match skills are great! All of your commands were correct.
• For the third match question, you missed that the command was supposed to have run on the hs_ref_GRCh37_chr19.fa file, not 493.P_falciparum.xml. The commands were still successful and you made the correct inference about how match and grep/wc are different, but you were using different data from what was specified.
• 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. The tabular arrangement makes things easy to spot as well.

—Dondi (talk) 22:34, 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.
• The 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.
• You missed that the terminator includes 4 additional base pairs after the hairpin.
• The mRNA strand is short—only the start-to-stop codon was identified, but transcription actually goes from the transcription start site to the end of the terminator.
• You determined the correct amino acid sequence with an appropriate command.

In terms of your wiki link routine, everything was there—keep it up!

Let me know if you have any questions.

—Dondi (talk) 23:16, 24 September 2013 (PDT)

Makeup Point Update

You have been credited for making the following change(s) to a prior assignment:

• Your Week 4 wiki comments now have the correct code for locating the transcription start site.
• Your Week 4 wiki comments now have the correct code for marking up the complete terminator signal.
• Your Week 4 wiki comments now have the correct code for computing the complete mRNA strand. The revised command skips the substitution of t for u, but because this was in the original command, the correction is interpreted as needing to address only the proper start and end of transcription.

Regarding your question about why 1,3D did not work as expected, note here that “1,3” represents an inclusive range—i.e., lines 1 to 3. I understand how the comma threw you off—in many other systems, the comma indicates individual choice. In sed, however, it indicates a range.

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

—Dondi (talk) 22:19, 29 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 was neat and complete. It could have been enhanced with hyperlinks to the actual pages that you visited (take advantage of the capabilities of a wiki!) as well as by some screenshots.

— Kdahlquist (talk) 15:57, 8 October 2013 (PDT)

Week 5 Database Wiki

• Your database wiki page was complete and thorough, although it looks like some final tweaks were completed after the deadline. It appears that both of you contributed equally to the page.

— Kdahlquist (talk) 14:11, 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]).
• The 5th and 8th queries, which request counts by certain categories (year in the 5th query; rating in the 8th), require a group by clause in order to deliver the answers with maximum efficiency. Your answer to the 5th query returns the overall count for that decade, not the year-by-year tally; your answer to the 8th query involves 5 separate retrievals, where the use of group by would reduce that to a single one.
• All your other database queries were correct and properly documented.
• You have settled very nicely into the habit of providing all of the requested links that make the navigation of your wiki work as easy as possible.

—Dondi (talk) 23:28, 11 October 2013 (PDT)