User talk:Mpetredi

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 relevant 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, except for the link from your individual journal entry page back to your user page.

—Dondi (talk) 16:26, 29 November 2013 (PST)

Week 8 Interim Feedback

• I have checked your .xls and .txt files and they are correct and ready for tomorrow's exercise. — Kdahlquist (talk) 15:02, 14 October 2013 (PDT)
• Also, please follow the convention for naming your files given in the assignment. For example, my file would be named "Merrell_Compiled_Raw_Data_Vibrio_KD_20091020.xls". Your filename needs to have a date included and should have the extraneous hyphen removed. — Kdahlquist (talk) 15:41, 14 October 2013 (PDT)

Week 1 Feedback

Good coverage—make sure to fill out the links in your template, plus include missing requested information like snail mail address and upper division courses. Try to make your wiki change summaries a consistent habit. Also, don’t forget your email of concerns/questions.

Items for completion/follow-up:

• Snail mail address
• Upper-division courses—if you haven’t taken any, still say so explicitly, so that we know you didn’t forget about it.
• Email about worries/concerns/questions/anything else
• Change summaries—you did some, but ideally should have a summary for every change.
• Create a new wiki page
• Link to an assignment (Week n) page
• Link to the shared journal from your user page

—Dondi (talk) 09:42, 3 September 2013 (PDT)

Week 1 Follow-up Feedback

Thank you very much for completing the missing information/wiki skills from last week. You’ve improved your wiki summary consistency and have demonstrated all of the basic capabilities now. I just have some constructive comments about a couple of things:

• Some of your links (e.g., your links to the assignments) are actually internal to the wiki and are more succinctly linked with the double-bracket notation, not the single-bracket one that you used where you have to specify the full address (i.e., ...xmlpipedb.cs.lmu.edu...). When a page is wiki-internal, use ''' ''' instead.
• You copied your shared journal answers to separate pages—I’m not sure why you decided to do this. Was it because you wanted to have a direct link? You can still do that in the shared page—if you mouse over your name in the table of contents, the wiki adds a special suffix (beginning with #) that provides a direct link to your entry. You can use that to send the browser directly to your entry. Let me know if this is what you were trying to do.

Good job rounding this out and keep it up!

—Dondi (talk) 17:10, 8 September 2013 (PDT)

Week 2 Feedback

• Your Week 2 journal entry was submitted on time and completely correct. Congratulations and keep up the good work!
• The Nirenberg article was written as a memoir to other practicing biochemists, so it is dense. I'm glad that you got a sense of how tough the experiments were. All of what is in textbooks currently was laboriously worked out by someone doing lots of experiments! :)

— Kdahlquist (talk) 15:05, 11 September 2013 (PDT)

P.S. I answered your question on my user talk page. — Kdahlquist (talk) 09:18, 12 September 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 with the exception of your 3'-5' +2 and +3 reading frame commands—you were eliminating the “skipped” bases before reversing the string and not after.
• For the first match question, you missed writing down your speculative answer on what that GO:... pattern may represent.
• 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) 22:31, 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 incorrectly identified.
• Ribosome binding site was correctly identified with an appropriate command.
• Start codon was correctly identified with an appropriate command.
• The given stop codon command did not enforce triplets after the start codon.
• The terminator signal was correctly identified but the given command makes assumptions about exactly how long the terminator is, requiring a priori knowledge that was not part of the consensus information.
• The mRNA strand is incorrect—it is not the entire sequence, and it is complemented when it should not be.
• The correct amino acid sequence was identified but the command that computed it was not provided.

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

Let me know if you have any questions.

—Dondi (talk) 23:14, 24 September 2013 (PDT)

Makeup Point Update

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

• The missing link from your user page to the Week 3 shared journal page has been added.
• The missing 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) 22:07, 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. 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.

— Kdahlquist (talk) 16:00, 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 appears that you were the main contributor to this page.
• I see that you used a template to move this page content to one with the proper name. There is a better way to move pages, see the drop down arrow next to the "View history" tab at the top of the page.
• Be careful about the formatting of your hyperlinks. Only use two square brackets when linking to internal wiki pages; external links use only single square brackets. Also, the numbering of your page with respect to the questions is off.
• You could have elaborated a bit more on your answers to the questions.

— Kdahlquist (talk) 14:22, 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]).
• 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) 22:50, 11 October 2013 (PDT)