User talk:Mmalefyt

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.

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 xmlpipedb-match.
• 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.

Your work was submitted on time; however, the following specified wiki links and navigational aids were incorrect or missing:

• Correct page name for your individual journal page
• Link from your journal entry page back to your user page
• Inclusion of the Journal Entry category.

—Dondi (talk) 16:12, 29 November 2013 (PST)

Week 8 Interim Feedback

• I have reviewed the content of your files from part 1 and they are correct and good to go for Tuesday.
• However, please follow the convention for naming your files given in the assignment, so that it is maximally informative as to the contents. For example, my file would be named "Merrell_Compiled_Raw_Data_Vibrio_KD_20091020.xls". You need to add a date to your filename. — Kdahlquist (talk) 15:53, 14 October 2013 (PDT)

Week 1 Feedback

You missed quite a few wiki skills, plus need to post to shared journal, send email concerns, and ask talk page questions. You started nicely with entering wiki change summaries, but petered out with your later changes. Strive to do your summaries consistently.

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
• Questions to faculty Talk pages
• Change summaries—enter these consistently.
• Create a new wiki page
• Link to a page within the wiki
• Link to an external site
• Create a numbered list
• Comments inside the wiki markup
• Upload and link to an image
• Upload and link to a file
• Use the signature shortcut
• Create and use a template
• Link to an assignment (Week n) page
• Link to the shared journal from your user page
• Link from the shared journal to your user page
• Place your signature in the shared journal page
• Answer questions on the readings in the shared journal

—Dondi (talk) 09:10, 3 September 2013 (PDT)

Week 1 Follow-up Feedback

Thank you for filling in some of 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
• Questions to faculty Talk pages
• Change summaries—you have gotten better with this but still have occasional gaps.
• Create a new wiki page
• Link to a page within the wiki
• Link to an external site
• Create a numbered list
• Comments inside the wiki markup
• Upload and link to an image
• Upload and link to a file
• Use the signature shortcut (in the shared journal page—kind of a double-dip; the other signature should be in your questions on our Talk pages)
• Create and use a template
• Link to an assignment (Week n) page
• Link to the shared journal from your user page
• Link from the shared journal to your user page
• Place your signature in the shared journal page
• Answer questions on the readings in the shared journal

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

—Dondi (talk) 00:14, 8 September 2013 (PDT)

Week 2 Feedback

• Thank you for submitting your assignment on time!
• As was discussed in class, you had several "mutations" in your translations. You also needed to state which were the open reading frames (without stop codons). Make sure you go to the ExPaSY site to translate your sequence and explain what went wrong.
• 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 Mmalefyt Week 2, instead of "Genetic Code". You will need to move the contents of your "Genetic Code" page to a page called "Mmalefyt Week 2". 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 are missing the link from your user page to the Class Journal Week 2 page.
  5. You need to add the category "Journal Entry" to your individual week 2 journal entry page.
     • For the four 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).
• When Moody was calling the four bases a binary code, he was saying that they could be expressed in binary, not that there were just two. To specify four different bases you would just use:

00
01
10
11

— Kdahlquist (talk) 14:47, 11 September 2013 (PDT)

P.S. I answered your question on my user talk page. — Kdahlquist (talk) 09:14, 12 September 2013 (PDT)

Week 2 Follow-up

• I have reviewed the Week 2 assignment again and saw that you did not make any further changes to this page.

— Kdahlquist (talk) 15:00, 11 October 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 but no command was supplied.
• -10 box was correctly identified but no command was supplied.
• Transcription start site was correctly identified but no command was supplied.
• Ribosome binding site was correctly identified but no command was supplied.
• Start codon was correctly identified but no command was supplied.
• Stop codon was incorrectly identified because of a miscount in the base triplets.
• The full hairpin structure of the terminator was missed, and no command was supplied.
• The mRNA strand was incorrectly identified, and no command was supplied to indicate how you got this answer.
• The amino acid sequence was incorrectly identified, and no command was supplied to indicate how you got this answer.

In terms of your wiki link routine, your entries in the user and individual assignment pages were missing these items:

• Link from user page to shared journal page.
• Correct page name for individual assignment page. (i.e., the name of the page was incorrect)
• A link from your user page to the Week 4 assignment.
• A link from your individual assignment page back to your user page.
• Category designation for your individual assignment page.

Let me know if you have any questions.

—Dondi (talk) 22:28, 24 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.

• I did not see an entry in the Week 5 shared class reflection.
• 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 use page to the assignment page, 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.
• The name for your journal entry page should be "Mmalefyt Week 5", not "Individual HW week 5". Please correct this moving forward in the class.

— Kdahlquist (talk) 16:08, 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!

• 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]).
• I’m going to chalk this up to a typo because you still reached the right answer; still, in the query for movies whose titles begin with the word “Star,” the space at the end of the "^Star" pattern is missing—this would match 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. As mentioned, though, your count still emerges correctly, so I think you did type the correct query in but mistranscribed it into the wiki page.
• For the query requesting movie counts in the 1940s by year, the query supplied is a non-starter because the select-from portion is incorrect. You still got some answers, so this might be a mistranscription as well, in which case—double-check what you write into the wiki page! The posted answer remains incomplete, however, because it does not include the years associated with each count. Note how you list 9 numbers, but there are 10 years from 1940 to 1949! One year had zero movies—which one?
• The 6th query explicitly requests that the movie titles be alphabetized, but your answer does not include this.
• Your last query also does not work as-is because it is missing the from clause—and I suspect that this was not a mistranscription because no answer was provided. The query has an additional issue, in that you don't really need the inner join with the rating table and yet this is included in the SQL. In some cases, an unnecessary join may change the answers that you get back.
• All your other database queries were correct and properly documented.

Regarding your navigation/wiki links, these items were missing or not to-spec:

• Missing link from user page to shared journal page
• Incorrect name for your individual journal page
• Missing link from user page to Week 6 assignment page
• Missing link from the journal page back to your user page
• Missing “Journal Entry” category on your journal page

These requested links and features make the navigation of your wiki work as easy as possible, so please make a habit of this.

—Dondi (talk) 11:59, 12 October 2013 (PDT)