User talk:Slouie
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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 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 and inclusion of the Journal Entry category.
—Dondi (talk) 13:24, 29 November 2013 (PST)
Week 8 Interim Feedback
- Your files are correct and ready to go for Tuesday. — Kdahlquist (talk) 15:49, 14 October 2013 (PDT)
Week 1 Feedback
You did generally well for this first time out; do complete the wiki checklist and be consistent with summaries, as much as possible. You were also very close with the template—everything is properly linked but you just have to create the template content itself.
Items for completion/follow-up:
- Snail mail address
- Upper division coursework—say “none” if you haven’t taken any.
- Create a new wiki page
- 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
- Create a template
- Link to an assignment (Week n) page
- Link to the shared journal from your user page
—Dondi (talk) 09:03, 3 September 2013 (PDT)
Week 1 Follow-up Feedback
Thank you very much for completing all missing information/wiki skills! Here’s to building on these skills as the course progresses.
—Dondi (talk) 22:25, 7 September 2013 (PDT)
Week 2 Feedback
- Thank you for submitting your assignment on time!
- As we discussed in class, 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. As was noted in class, 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 from a memoir point of view, so it is understandible that you found it difficult.
— Kdahlquist (talk) 14:12, 11 September 2013 (PDT)
P.S. I answered your queston on my user talk page. — Kdahlquist (talk) 09:12, 12 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!
- Good to hear that you succeeded in exerting control of your file extensions.
- Your sed and match skills are great with the exception of your 3'-5' reading frame commands—you missed doing a complement on those bases.
- For the third match question, you missed that the command was supposed to have run on the hs_ref_GRCh37_chr19.fa file, not 493.P_falciparum.xml. The commands were still successful and you made the correct inference about how match and grep/wc are different, but you were using different data from what was specified.
- You were missing a number of requested links and wiki elements:
- 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. Additional props, though, for having your shared journal link go directly to your entry as opposed to the overall page.
—Dondi (talk) 22:10, 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 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.
- The terminator sequence was correctly identified but the command used to identify it makes more assumptions than were given in the consensus information.
- Your mRNA strand included the correct range of bases but was complemented when it should not have been.
- You determined the correct amino acid sequence with an appropriate command.
In terms of your wiki link routine, everything was there—keep it up!
Let me know if you have any questions.
—Dondi (talk) 22:06, 24 September 2013 (PDT)
Group work
Hey Stephen, Unfortunately I won't be able to make it to the library today. I did however set up the database and most of the questions needed for it. If you could finish those up for us I think we should be good at least for the journal tonight. We can set up another meeting to finish the other work. Feel free to contact me. 3109412298
Makeup Point Update
You have been credited for making the following change(s) to an assignment or wiki link checklist:
- Your 3'-5' reading frame commands now correctly apply a complement to their bases.
- For the third match question, you have updated your reported results so that they are now based on the hs_ref_GRCh37_chr19.fa file, not 493.P_falciparum.xml.
- The missing link from your Week 3 journal answer page back 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) 22:00, 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 an adequate description of what you did. Moving forward starting with the Week 8 assignment, this will be an important part of each weekly assignment. Keep in mind the guideline that you or someone else should be able to reproduce what you did using only the information on your journal entry page. Your page could have been enhanced by providing hyperlinks to the pages you visited and by showing one or more screenshots from your database exploration. See some of your classmates' pages for how they did this.
— Kdahlquist (talk) 16:15, 8 October 2013 (PDT)
Database Wiki Feedback
- Thank you for submitting your assignment on time. From the history, it looks like Alina was the main contributor to this page. This appears to be borne out by the fact that there are links missing from your user page to this page and from the database wiki page to your user 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) 14:09, 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,” you have a % wildcard that should not be there. % is for use with like but not with ~.
- The 5th query, which requests counts by year, is much easier to answer if you include year in the select clause. What you have still produces the right answer, but you have to be careful in determining which count pertains to which year. In particular, what if there was a year with zero movies? That might be missed in the tallies.
- The 8th query, which requests for counts by rating, highlights this issue even more. Here, the query 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.
- The 9th query, which seeks the average rating for movies beginning with the word “Star,” has the same typo from the 4th query. This time, however, the incorrect average is reached.
- All your other database queries were correct and properly documented.
Regarding your navigation/wiki links, all is well except for a small oversight: your “Journal Entry” category was encoded as a wiki page, and not a Category.
