User talk:Lena

Week 9 Feedback

Your week 9 work has (finally) been reviewed:

• The file versions, as specified by the testing report template, are not all directly listed. You do state the dates for the files used, but some of them have specific versions also, as indicated by the host website. Ideally, that is the information to record.
• 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.
• There is no indication that 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.
• An appropriate record was seen for the tasks performed, but for the one that was missed (PostgreSQL), an entry/note should have also been made about why this portion was not finished (e.g., technical difficulties, issues with the query, etc.).

Finally, your work was submitted on time and all specified wiki links and navigational aids were correctly included, except for inclusion of the Journal Entry category.

—Dondi (talk) 13:25, 29 November 2013 (PST)

Week 8 Interim Feedback

• I reviewed your .xls and .txt files from part 1 of the week 8 assignment. I know that we worked on your spreadsheet after class, but I still found some errors.
• On your sheet, "Scaled_Centered" there are errors in the standard deviation functions in cells C3 through M3. Your function has a range to row 5225, when it should be 5224. If you copy and paste the formula from cell B3 to the rest, that should fix that problem.
• On your sheet, "Statistics", there are errors in the Avg_LogFC_A, Avg_LogFC_B, and Avg_LogFC_C columns. The ranges over which you calculate the averages are incorrect. For example Avg_LogFC_A should be

=AVERAGE(B2:E2)

• Your TSTAT calculation also specifies the incorrect range. The correct range is N2:P2 for the first cell.
• Please make these corrections and re-upload your files. Alternately, you can work with your partner to get the correct file.
• 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". At minimum, your filename needs to have a date included.

— Kdahlquist (talk) 15:21, 14 October 2013 (PDT)

Week 1 Feedback

Great coverage! You missed just a few items. And don’t forget to send us your email with questions/concerns.

Items for completion/follow-up:

• Email worries/questions/concerns or anything else you’d like us to know
• Create a new wiki page
• Comments inside the wiki markup
• Use a template
• Link to an assignment (Week n) page
• Place your signature in the shared journal page

—Dondi (talk) 08:50, 3 September 2013 (PDT)

Week 1 Follow-Up Feedback

Thank you for filling in the blanks from last week! Your confusion about templates is noted (as you stated in your commented-out markup)—however, you are indeed using your template correctly in the user page. Think of a template as a “live shortcut.” It lets you repeat the same piece of wiki all over the place, and whenever you edit that piece of wiki, it automatically updates everywhere. Let us know if further confusion remains.

—Dondi (talk) 22:10, 7 September 2013 (PDT)

Week 2 Feedback

• Thank you for submitting your assignment on time!
• Your translations were all correct; frame +3 does not contain an open reading frame, though.
• You will need to work on completing/correcting the links requested as part of the assignment. Specifically:
  1. We have a specific naming convention that we would like you to use when naming your new individual journal pages. You should name them username week #; for example your week 2 assignment page should be named Lena Week 2, instead of "Genetic Code Assignment". You will need to move the contents of your "Genetic Code Assignment" page to your "Lena Week 2" page, for which you have a redlink on your user page. To do so, follow the directions listed here]. We will be happy to talk you through this in class or office hours if you like. For the future, please make sure you are using the preferred naming convention for new pages.
  2. You are missing the link from your User page to the Week 2 Assignment page.
  3. You are missing the link from your individual week 2 journal entry back to your User page.
  4. You need to add the category "Journal Entry" to your individual week 2 journal entry page. We are not actually using the category "Individual Homework" like Dr. Dionisio demo'd in class; we apologize for any confustion this caused.
     • For the three items above, you can add these links to your template and then just use your template on your user page and all journal entry pages. That way, you won't forget to put the links in future assignments.
• You have the opportunity to earn back the points you missed by making the corrections requested on the Week 3 Assignment page and the corrections requested above. The corrections are due by midnight on Friday, September 20 (thursday night/friday morning).
• Yes, the Nirenberg article was quite dense and written as a memoir as opposed to expository text.
• I have also answered your question on my user talk page.

— Kdahlquist (talk) 15:59, 10 September 2013 (PDT)

Week 2 Follow-up

• Thank you for making all requested corrections.

— Kdahlquist (talk) 14:57, 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 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.
• Regarding the match question comparing it to grep/wc, you missed reporting on how many of the matched pattern were found. For the third question, 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) 21:50, 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 missed due to an extra slash in your sed 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.
• Your start codon was correctly identified with an appropriate command in the integrated all-in-one version, but is missing the added new line in the separate answer bullet.
• Your stop codon command was never finalized.
• The terminator was correctly identified with an appropriate command.
• Your mRNA strand is incorrect, and no command was supplied to show how you got your answer.
• You determined the correct amino acid sequence but no command was supplied to show how you got your answer.

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

Let me know if you have any questions.

—Dondi (talk) 21:49, 24 September 2013 (PDT)

Makeup Point Update

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

• Missing Journal Entry category from Week 3 journal page has been added.

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

—Dondi (talk) 21:43, 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. Starting again with the Week 8 assignment, keeping an online notebook will be an important part of your weekly assignments. Keep in mind the guideline that you or someone else should be able to reproduce everything that you did using only the information on your journal entry page. Your page could have been enhanced by providing additional hyperlinks to the pages you visited.

— Kdahlquist (talk) 16:22, 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) 14:19, 11 October 2013 (PDT)

Week 6 Feedback

Thank you for submitting everything on time!

• The wiki markup for movies-with-apostrophe query had the nowiki tags in the incorrect position—they should be completely surrounding the four apostrophes (like this: '''' [view the wiki source to see how it’s done]).
• Your last, individual query joins the member table, but that table is not actually necessary. When working with databases, we are sensitive to doing more work than necessary, because sometimes this additional work strongly detracts from speed, particularly if the tables contain large numbers of rows. An extra but unnecessary join will also, in some cases, change the results that you get back.
• 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) 22:47, 11 October 2013 (PDT)