User talk:Gleis

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 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 journal entry page back to your user page.

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

Week 8 Interim Feedback

• I reviewed your Excel spreadsheet. Your .xls file only had the "forGenMAPP" in it; the other sheets where you did your calculations were not there. I noticed an error in the results of your TSTAT and p value calculations, but because the other sheets weren't there, I wasn't able to discern what went wrong. I hope that you have the .xls file somewhere so that you can go back to it and fix the errors. If not, you will need to either redo the calculations or get the file from your partner. — Kdahlquist (talk) 14:51, 14 October 2013 (PDT)
• Also, your syntax for linking to the files for download on your Week 8 journal page is incorrect. Instead of [[File:filename]] use [[Media:filename]]. — Kdahlquist (talk) 14:59, 14 October 2013 (PDT)
• Finally, 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". — Kdahlquist (talk) 15:39, 14 October 2013 (PDT)

Week 1 Feedback

Great coverage of the checklist! If you haven’t done independent research, still say so explicitly, just so we know you haven’t forgotten. Experimentation with "raw" HTML is noted—your mixing and matching of raw HTML with wiki markup is noted.

Items for completion/follow-up:

• Independent research
• Change summaries—try to enter these more consistently.
• Link to an assignment (Week n) page
• Link to the shared journal from your user page (you have almost a link there, but not a fully accurate one)

—Dondi (talk) 09:00, 3 September 2013 (PDT)

I have answered your question on my user talk page. — Kdahlquist (talk) 14:03, 5 September 2013 (PDT)

Week 1 Follow-Up Feedback

Thank you for catching up on the missing information/wiki skills from last week! You haven’t yet gotten totally consistent with entering a change summary whenever you edit a wiki page, so try to keep that in mind as you log more hours with the wiki.

—Dondi (talk) 22:18, 7 September 2013 (PDT)

Week 2 Feedback

• Thank you for submitting your assignment on time!
• Your translations were correct, but you needed to continue translating beyond the stop codons.
• The +3 frame was not an open reading frame.
• You have the opportunity to earn back the points you missed by making the corrections requested on the Week 3 Assignment page. The corrections are due by midnight on Friday, September 20 (thursday night/friday morning).
• The Nirenberg article was written for other practicing biochemists and was also written as a memoir, so it is understandable that it was difficult to read.

— Kdahlquist (talk) 14:07, 11 September 2013 (PDT)

Week 2 Follow-up

• Thank you for making all requested corrections.

— Kdahlquist (talk) 14:58, 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 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) 21:55, 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.
• Transcription start site was correctly identified but the command you used does not reflect the consensus information—you based your sed directive on the ribosome binding site and not the -10 box.
• Ribosome binding site was correctly identified with an appropriate command.
• Start codon was correctly identified with an appropriate command.
• Stop codon does not correctly count off in triplets after the start codon.
• Terminator did not correctly include the full hairpin.
• You correctly stated the mRNA strand, although you had to do some manual editing from your command.
• The amino acid sequence was not correctly identified due to the issue with locating the stop codon.

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

Let me know if you have any questions.

—Dondi (talk) 22:01, 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 assignment page has been added.
• The missing link from your Week 3 journal answer page to your user page has been added.
• 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) 21:54, 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 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) 16:17, 8 October 2013 (PDT)

Week 5 Database Wiki

• Your database wiki page was complete and thorough, although it looks like some final tweaks were completed after the deadline. It appears that both of you contributed equally to the page.
• You are missing a link from your user page to this database wiki page. Please add it to your template.

— Kdahlquist (talk) 14:12, 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.
• Your last, individual query has a group by title clause, but that clause is not actually necessary because you aren’t performing computations like count or average. In some cases, a superfluous group by may produce incorrect results; it just so happens that in your particular query, it does not have a detrimental effect.
• 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) 22:59, 11 October 2013 (PDT)