User talk:Laurmagee

Week 9 Feedback

Your week 9 work has (finally) been reviewed:

• You listed the four file versions specified by the testing report template.
• 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. Well done!

—Dondi (talk) 13:27, 29 November 2013 (PST)

Week 1 Feedback

You’re off to a decent start; just need to check off a few more wiki skills like file/image uploads, categories, and templates.

Items for completion/follow-up:

• Snail mail address
• 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
• Assign a category to a page
• Create and use a template
• Link to an assignment (Week n) page
• Link to the shared journal from your user page

—Dondi (talk) 09:06, 3 September 2013 (PDT)

Week 1 Feedback Follow-up

Hi Lauren,

Thanks for filling in the missing information/wiki skill items from last week! As for the two leftovers that weren’t clear, here’s my stab at explaining them further...

“Comments inside the wiki markup” refer to text that you can “hide” in your wiki page, which is only visible when the user is editing it. In other words, these can be “comments” by you that are not meant to be part of the content of the page. If you edit this Talk page, you will see that, right below this paragraph, there is text in the source that you do not see on the page. Note the starting and ending symbols—that’s how you tell the wiki that whatever is in between should only be visible during editing.

Now, as for the Category, look at my user page and scroll to the bottom. There is a box that starts with “Categories:” with red links for Individual Homework and User Page. This is what is meant by a category. It is a “tag” that you can attach to a page, so that it can be accessed by category. If you click on Individual Homework or User Page, you will see other pages that have been given that category. Your Shared Journal pages have this also.

Hope this answers your questions. Let me know if more explaining is needed.

One last point of feedback, and that is regarding your template—you certainly got the mechanics of it right (creating; using). Do try to build it up as a table of contents for your work and other related pages—this is a very compelling use for a template, particularly with the way we are using the wiki.

—Dondi (talk) 23:59, 7 September 2013 (PDT)

Week 2 Feedback

• The timestamp on your assignment showed that it was completed two minutes after midnight. Make sure in the future that you start the assignment early enough so that you can submit it on time.
• You need to post your answers to the individual part of the assignment on a different page than the class journal page. Name your new page username week #. For example, this week's assignment should have been on a page called Laurmagee week 2. Please create this page and copy the content over to it. You will also need to be mindful that you need to create a series of links:
  1. Link your user page to your individual journal page.
  2. Link your individual journal page back to your user page.
  3. Add the category "Journal Entry" to your individual journal page.
     • Note that you can add the three links above to your template. That way, you can use your template each time and not have to worry about forgetting to make the requested links.
• As discussed in class, you had two missing amino acids and you need to use "M", or "Met" for methionine, not "start".
• 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).
• I saw from your class journal entry that you are still not clear on the elements of a gene (promoter/terminator), etc. Please talk to me about this in office hours because it will be necessary to know this to complete the computer lab exercises this week and next.

— Kdahlquist (talk) 14:38, 11 September 2013 (PDT)

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

Week 2 Follow-up

• Thank you for making the corrections to your translation, moving your page, and adding the requested links. However, the category is still missing from this page.

— Kdahlquist (talk) 15:03, 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, save for what I will chalk up to a typo in your sed commands: the portion that is meant to separate the nucleotides into triplets is missing a space after the & character. This space is very important, because it enforces the triplet grouping of the bases. At the same time, spaces are also easy to miss, so keep a close eye on what lands on your wiki from your command window.
• Your journal answer page was 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.

—Dondi (talk) 22:18, 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 almost correctly identified but there was a space missing in one of your commands.
• -10 box command did not refine the search pattern to highlight the correct one (there were two possibilities and the only way to distinguish one from the other was to identify the one that came after the -35 box).
• Your transcription start site command counted off the -10 box in the wrong direction.
• Ribosome binding site was correctly identified with an appropriate command, but the first to statements of that command had a typo (missing g).
• Start codon was correctly identified with an appropriate command.
• Stop codon was not correctly identified by the provided command (it missed counting off in threes from the start codon).
• You missed the full hairpin sequence of the terminator.
• The incorrect mRNA strand was identified, and no command was provided to indicate where things might have gone wrong.
• The incorrect amino acid sequence was identified, and no command was provided to indicate where things might have gone wrong.

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

Let me know if you have any questions.

—Dondi (talk) 22:19, 24 September 2013 (PDT)

Makeup Point Update

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

• 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) 22:02, 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, although you listed the identifier for the EGFR protein incorrectly. Also, I think you were mixing up the PDB and PubMed databases.
• 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.

— Kdahlquist (talk) 16:12, 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) 14:02, 11 October 2013 (PDT)

Week 6 Feedback

Thank you for submitting everything super early!

• 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.
• The 5th and 8th queries, which request counts by certain categories (year in the 5th query; rating in the 8th), require a group by clause in order to deliver the answers with maximum efficiency. Your answer to the 5th query involves multiple separate retrievals, where the use of group by would reduce that to a single one; your answer to the 8th query returns the “lump sum” count, and not the count for each individual rating.
• The 7th query does not include the name of the members who submitted each rating; this information was explicitly requested.
• All your other database queries were correct and properly documented.

Your standardized wiki links and elements are all there except for the link from the journal page to the user page. Try to maintain a “flight check” list of these items (note how they are listed in every assignment) so that this becomes as worry-free as possible.

—Dondi (talk) 11:46, 12 October 2013 (PDT)