User talk:Dwilliams

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 noted that there were problems with your .gdb file to the wiki, but by all accounts this was most likely a transient problem, and there is no indication that you went back and tried to upload the file again.
• You successfully ran the Tally Engine.
• You appear to have successfully run xmlpipedb-match, but reported only the results without posting primary documentation of this activity (e.g., screenshots, exact numeric output).
• There is no indication that 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 do not note differences and similarities in the ID tallies from your various counts, particularly the large OrderedLocusNames discrepancy between your .gdb file and the benchmark version.
• There is no indication of the ID pattern(s) 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 journal entry page back to your user page and inclusion of the Journal Entry category.

—Dondi (talk) 16:44, 29 November 2013 (PST)

Week 8 Interim Feedback

• It was difficult for me to find your Week 8 files for review. While you uploaded them to the wiki, you did not link to them from any pages.
• Once I did find them and download I saw that you need to add a date to the filename to follow the file naming convention requested in the assignment. For example, my filename could be named "Merrell_Compiled_Raw_Data_Vibrio_KD_20091020.xls".
• Otherwise, the calculations you performed are correct and you are ready to go for Tuesday's exercise.

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

Week 1 Feedback

You missed quite a few wiki skills and requested information. For the wiki skills, consult the list below. For the requested information, 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
• Upper-division courses (you mentioned not taking them in your email, but have not stated this on the wiki)
• Independent research—if you haven’t done any, still say so explicitly, so that we know you didn’t forget about it.
• Work experience—again, if you haven’t had such experience, just say “n/a” or “none” so that we know you haven’t forgotten this.
• Change summaries—enter these more consistently.
• 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 file
• Assign a category to a wiki page
• Create and use a template
• Link to an assignment (Week n) page

—Dondi (talk) 09:59, 3 September 2013 (PDT)

I answered your question on my user talk page. — Kdahlquist (talk) 14:09, 5 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
• Upper-division courses (you mentioned not taking them in your email, but have not stated this on the wiki)
• Independent research—if you haven’t done any, still say so explicitly, so that we know you didn’t forget about it.
• Work experience—again, if you haven’t had such experience, just say “n/a” or “none” so that we know you haven’t forgotten this.
• Change summaries—enter these more consistently. —Your more recent changes all have summaries; by all means maintain that habit.
• 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 file
• Assign a category to a wiki page
• Create and use a template
• Link to an assignment (Week n) page —You will find that, as assignments accumulate and grow in depth, it will be useful to have links within reach for going back and referring to them; that is why we are specifically asking for this.

Keep up the wiki practice!

—Dondi (talk) 17:49, 8 September 2013 (PDT)

Week 2 Feedback

• Thank you for submitting your assignment on time.
• Your translation of all six frames was incorrect. There was probably a mistake in the sequence or it was translated in the wrong direction. Please use the ExPaSY tool to translate it and figure out where you went wrong. 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 listed below. The corrections are due by midnight on Friday, September 20 (thursday night/friday morning).
• You are missing several links requested in the assignment:
  1. You did not link from your user page to the shared class journal page.
  2. You did not link from your user page to the Week 3 Assignment page.
  3. You did not link from your individual 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.
  • If you add these four items to your template and then use your template on every journal entry, then you don't have to worry about forgetting them for subsequent assignments.
• The Nirenberg article was written as a memoir to other practicing biochemists. Hopefully, even though it was dense, you found learning about the process interesting.

— Kdahlquist (talk) 15:21, 11 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) 15:01, 11 October 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.
• 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
  • Your journal answer page was missing a link back to your user page
  • Your journal answer page was also missing the requested Journal Entry category

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) 22:50, 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 correctly identified with an appropriate command.
• -10 box was correctly identified with an appropriate command.
• The 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.
• You missed that the terminator includes 4 additional base pairs after the hairpin.
• 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.
• You determined the correct amino acid sequence with an appropriate command.

In terms of your wiki link routine, your pages were missing the following:

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

Let me know if you have any questions.

—Dondi (talk) 23:35, 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.
• On your individual Week 5 page, I did not see any evidence that you kept an electronic lab notebook recording your work on the UniProt exercise. Starting again with the Week 8 assignment and for the rest of the semester, this will be an important component of your weekly assignment. Please let me know if you are unclear as to what this entails.
• You are also missing the link from your user page to the assignment page and the category on your journal entry. Looking at the feedback from past assignments, you seem to be consistently missing these. At this point in the semester using your template for these links should be routine. Again, please let me or Dr. Dionisio know if you need assistance with how to do this.

— Kdahlquist (talk) 15:43, 8 October 2013 (PDT)

Week 5 Database Wiki

• This assignment is incomplete; I did not find a wiki page for GeneDB, am I missing something? — Kdahlquist (talk) 14:01, 11 October 2013 (PDT)

Week 6 Feedback

Thank you for submitting everything on time!

• The 8th query and the 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.
• In the last query as well, the plain English statement seeks only ratings of 3, but the SQL does not reflect this criterion.
• 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
• Missing link from user page to Week 6 assignment 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) 12:35, 12 October 2013 (PDT)