User talk:Ajvree

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 report one number for your xmlpipedb-match result, but do not provide details such as the text pattern(s) used or any commentary on the number you got vs. expected counts.

The following requested tasks were not accomplished (or, if you did do them, there is no record on the journal page that you did):

• Run the Tally Engine.
• Run the appropriate PostgreSQL query.
• Examine your .gdb file in Microsoft Access and compare the data against the benchmark version of the V. cholerae gene database.
• Note differences and similarities in the ID tallies from your various counts.
• Clearly indicate the ID pattern used for your ID searches/tallies.
• Lab notebook-style documentation of 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.

—Dondi (talk) 16:38, 29 November 2013 (PST)

Week 8 Feedback

• I have reviewed your .xls and .txt files from part 1 of the Week 8 assignment. They are correct and ready to go for Tuesday. — Kdahlquist (talk) 15:28, 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. — Kdahlquist (talk) 15:43, 14 October 2013 (PDT)

Week 1 Feedback

You missed quite a few wiki skills and requested information, plus need to send email concerns. If the answer to a question is nothing (e.g., independent research), then explicitly say "none" or "n/a" so that we know it wasn't forgotten.

Items for completion/follow-up:

• Snail mail address
• 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
• Create a new wiki page
• Link to another page within the wiki (other than your user page)
• Link to an external site
• Comments inside the wiki markup
• Upload and link to an image
• Upload and link to a (non-image) file
• Create and use a template
• Link to an assignment (Week n) page

—Dondi (talk) 09:51, 3 September 2013 (PDT)

Week 1 Follow-up Feedback

Thank you for filling in the missing information/wiki skills from last week. You have some leftover items, and we encourage you to continue filling those out beyond this assignment—you will find that the practice will only make things easier going forward. Here’s the updated list of what we haven’t seen you do yet. (I left in the ones missing last week, but did them in strikeout style so you can see your progress better)

• Snail mail address
• 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
• Create a new wiki page
• Link to a page within the wiki
• Link to an external site
• Comments inside the wiki markup
• Upload and link to an image
• Upload and link to a (non-image) file
• Create and use a template
• Link to an assignment (Week n) page

So, that’s a good number of things down. Keep up the wiki practice!

—Dondi (talk) 17:41, 8 September 2013 (PDT)

Week 2 Feedback

• Your translation of the genetic code was entirely correct. However, you submitted your assignment late. In the future, please make sure that you give yourself enough time to complete the assignment and submit it on time.
• You should remove the "Shared" category from your user page. We are reserving that category for pages with multiple authors, like the Class Journal pages.
• The Nirenberg article was written as a memoir to other practicing biochemists, so it was a bit dense. I'm glad that you enjoyed learning about the process, even if the article itself was tedious.

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

P.S. I answered your question on my user talk page. — Kdahlquist (talk) 09:20, 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.
• You missed supplying an answer for complementing a nucleotide sequence. I combed your notes at the top of the journal answer page and could not find it.
• Your sed and match skills are otherwise great! All of your commands were correct, except that the -F genetic-code.sed segments of your commands should have had a lowercase f. This is not a huge deal, but remember how attention to detail is a very important part of working with computers—if someone who did not know sed tried to type your answers verbatim on the command line, they would get an error.
• Regarding the match question comparing it to grep/wc, in the third subquestion, the distinction we were looking for is the way grep/wc can only count lines, thus missing cases where a pattern appears more than once in a single line.
• Your journal page was missing the requested Journal Entry category. Again falling under the “attention to detail” heading, please note the bulleted checklist provided under the assignment headings.

—Dondi (talk) 22:48, 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 four bases.
• Ribosome binding site was correctly identified with an appropriate command.
• Start codon was correctly identified with an appropriate command.
• The stop codon was not correctly identified because the given command does not enforce base triplets after the start codon.
• The terminator sequence is missing its end tag.
• 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.
• The identified amino acid sequence is short due to the misidentified stop codon.

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) 23:32, 24 September 2013 (PDT)

Makeup Point Update

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

• The missing Journal Entry category in your Week 3 journal answer page has been added.

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

—Dondi (talk) 22:34, 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.

• Your individual journal entry (UniProt Exercise) was submitted late.
• 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) 15:49, 8 October 2013 (PDT)

Week 5 Database Wiki

• Thank you for submitting your assignment on time. From the history, it looks like you were the main contributor to this page.
• You could have been more specific as to which species were covered in the database.
• OrganelleDB is not an example of a community database, a community database is basically like this wiki where a distributed set of users enters information directly into the database. Instead, OrganelleDB is an example of a specialty database.
• You could have provided more information about the sample query you tried.

— Kdahlquist (talk) 14:08, 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]).
• In your movies-beginning-with-the-word-“Star” query, you miss adding a space at the end of the "^Star" pattern—this matches more rows than desired, because without the space, your query will also get movies whose titles start with the words “Stare,” “Startle,” “Stark,” or “Start,” to name a few.
• The 8th query, which requests for counts by rating, is missing the group by clause. Thus, you needed to manually tally up the number of movies that got each individual rating. This was manageable for the small data set, but becomes unwieldy with large ones.
• A query of your own was not supplied (10th query).
• 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) 12:28, 12 October 2013 (PDT)