User talk:Taur.vil

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 and compared its 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) 16:34, 29 November 2013 (PST)

Week 8 Feedback

• You need to upload the .xls and .txt files from part 1 onto your Week 8 journal page ASAP so that I can check them before tomorrow morning's class. — Kdahlquist (talk) 09:59, 14 October 2013 (PDT)

Week 1 Feedback

Great wiki skill coverage—just a few information gaps and specific tasks. Otherwise, a fine start.

Items for completion/follow-up:

• Personal interests/hobbies
• Create a new wiki page (other than your user page)
• Link to an assignment (Week n) page

—Dondi (talk) 09:48, 3 September 2013 (PDT)

I added a section for personal interests/hobbies. What specifically do you want us to produce for a new page? I made the one for the Week 1 assignment if that counts. And I had already linked to the first week's class journal near the top of the page.

-Taur.vil (talk) 22:14, 4 September 2013 (PDT)

I answered your question on my user talk page. — Kdahlquist (talk) 14:16, 5 September 2013 (PDT)

Week 1 Follow-up Feedback

Thank you for adding the personal interest section, and yes, you have made more than one new wiki page at this point, which all count (I had missed that you were the one who created the week 1 shared journal). Also, I counted your Week 2 link as the link to an assignment; ideally, do that consistently from here on—it’s very convenient to have links back and forth across the wiki, especially when doing a lot of cross referencing.

—Dondi (talk) 17:30, 8 September 2013 (PDT)

Week 2 Feedback

• Your assignment was submitted on time and was completely correct. Congratulations and keep up the good work!
• The Nirenberg article was written as a memoir to other practicing biochemists, so that made it difficult to understand. I hope you enjoyed it anyway.

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

Week 3 Feedback

• Thank you for submitting your assignment on time!
• Your experience with “Where’s my stuff” typically occurs when a computing system is strongly protecting file extensions like .txt and .html. Different operating systems apply protections differently. Typically, there is a setting one can hit that tells the computer that you know what you are doing with respect to these extensions, after which you will then have greater control over these. In any case, nothing to worry about; what matters is that you got a sense for what role these file extensions play.
• Your sed and match skills are great! All of your commands were correct, except for one glitch in the last 3'-5' reading frame: your command only chops off the first base, not the first two. I will chalk this up to a typo, because your answers are otherwise correct. Still, computers can’t catch typos, so keep a close eye on things like this.
• 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. Additional props for having your shared journal link go directly to your entry as opposed to the overall page.

—Dondi (talk) 22:39, 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.
• 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 but the command used to identify it makes more assumptions than were given in the consensus information.
• Your mRNA strand included the correct range of bases but was complemented when it should not have been.
• 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) 23:22, 24 September 2013 (PDT)

Makeup Point Update

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

• The typo in your -3 reading frame has been fixed in Week 3.
• Your note in the Week 4 revision states that the off-by-one transcription start site issue was addressed, but no actual change was seen, so no credit was returned for that one.
• The terminator sed command has been successfully revised to be more robust in Week 4.
• The complementation was correctly removed from the mRNA sed code in Week 4. Strictly speaking, t should also be replaced by u, but that is a minor issue.
• Regarding your question on “efficiency,” the answer ultimately depends on what you mean by “efficient.” In computer science terms, “efficiency” is typically associated with speed, in which case what you did actually is quite efficient! :) You probably meant “easier” or “less verbose”—and yes, if a tool other than sed is used, you can very well come up with code that is easier or less cryptic to read. Talk to me if you are interested in exploring other means of doing this computation.

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

—Dondi (talk) 22:31, 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 a thorough description of what you did. Moving forward starting with the Week 8 assignment, this will be an important part of each weekly assignment. Keep in mind the guideline that you or someone else should be able to reproduce what you did using only the information on your journal entry page. Your page could have been enhanced by showing one or more screenshots from your database exploration.
• I did not see a summary paragraph that explained what you learned about the EGFR receptor by doing this exercise.
• An observation: you seem to create your page in one fell swoop. In the future, you won't run the risk of losing your work (especially on long assignments) if you have some intermediate saves. We are interested in seeing your work in progress, not just the finished result.

— Kdahlquist (talk) 15:53, 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, there were equal contributions from each student to this page.
• You need to link from the database wiki page to the Class Journal Week 5 page.

— Kdahlquist (talk) 14:18, 11 October 2013 (PDT)

Week 6 Feedback

Thank you for submitting everything on time!

• All ten of your 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) 22:39, 11 October 2013 (PDT)