User talk:Simonwro120

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Hello everyone, please feel free to leave any comments here! Simonwro120 (talk) 14:17, 4 September 2017 (PDT)

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Week 11 Team Page Feedback (to address in Week 12)

Your team page hit the specifically-requested items listed in the Week 11 assignment, although your individual journal page link appears to be missing from the team template (bottom of page). For Week 12, let’s focus on the stated overall purpose of these pages: “This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to organize your work and communicate with each other and with the instructors. Hint: the kinds of things that are on your own User pages and on the course Main page can be used as a guide.”

Considering that purpose (and hint), you will also want to include the following on your team page. Imagine yourselves in deep work mode, with your team page open in a window. What information, links, and resources will you want to have available on that page at all times? Here are a few items:

• A projected schedule with due dates (both for milestones already defined in the guild pages and for internal accomplishments that your team determines) and meeting times. You can cross off these dates and times as your team makes progress using the s tag (strikeout).
• Communication resources (e.g., additional channels like Slack; GitHub issues; the discussion “side” of various wiki pages; etc.) that your team can use to coordinate when not face-to-face
• A section with links to uploaded files, particularly for use by data analysts but really for any member of the team; this can also include a link to your GitHub branch and the project’s fork
• Additional useful links—what links would be useful to always have there so that you can just click to visit them, minimizing typing? (for example, Template:GRNsight Gene Page Project Links has already been created for you—won’t that be useful to have on your page as well?)

Note how these items are very similar to the content that can be seen on our own Main Page—this is not a coincidence.

—Dondi (talk) 00:12, 16 November 2017 (PST)

I want to add that links to the journal club presentations should be on the page (under Files) and that the annotated bibliography citations would be better organized in a single section. Antonio needs to sign his executive summary with his wiki signature. A consistent format for the executive summaries and reflections will improve the look and organization of the page.

— Kdahlquist (talk) 14:10, 16 November 2017 (PST)

Week 11 Feedback

• A number of "good habit" items were not met in this submission:
  • Punctuality: last edit at 1:31pm 11/14.
  • No link from journal entry to user page.
  • No journal category entry.
  • No electronic laboratory notebook—note that we have consistently used the term “laboratory notebook” this semester to represent documentation of your process for the week, distinct from the week’s deliverables. No such narrative could be found in the journal entry.
  • Acknowledgments section is missing signature.
• Design or development term notes
  • “API” was one of the chosen terms—but you must have already known this term because we have had multiple assignments dealing with web service APIs in class. The instructions asked for terms “whose definitions you did not know when you first read the article.”
  • There is no formal APA citation for the build server definition—only a link is given.
• Article outline notes
  • Outline was 1 page long in print preview.
  • No information was found on how the article might inform your work on the final project.

—Dondi (talk) 17:39, 9 December 2017 (PST)

Week 9 Feedback

• The “good habit” aspects of your individual journal are completely fulfilled and on-time. Great!
• The electronic notebook has decent detail and is well-integrated with the GRNsight testing and API exploration results.
• GRNsight testing is complete with clear feedback on the results.
• The overall process for going from the gene symbol to the final gene data, with the necessary substitutions, is almost complete but misses the possibility that the data/Gene web service request might return more than one result (e.g., BRO1). In this case, since you know that you are working with SGD, you will want to pick the entry whose primaryIdentifier property looks like an SGD ID (that is, S#########).

Shared Journal

Questions and “good habit” aspects are all fulfilled, all on-time. Favorite pages are stated alongside the reasons for these preferences.

—Dondi (talk) 19:11, 23 November 2017 (PST)

Week 7 Feedback

• The “good habit” aspects of your individual journal are all on point. Your electronic notebook is detailed and organized, and your references section thoughtfully includes the multiple sources you consulted for this assignment.
• All prior web page issues were addressed—great to see that!
• Bootstrap grid layout and flex classes were seen in your page.
• The use of collapse is noted as one of the requested “advanced Bootstrap” features.
• The use of card is noted as the other “advanced Bootstrap” feature, though its usage does not really maximize its potential.
• Both XML and JSON web API calls were adapted from the starter code as requested.

Shared Journal

Questions and “good habit” aspects are fulfilled, all on-time. Your comments on being a novice are noted—remember that everyone is a novice at everything at some point in their lives, so as long as you keep learning (you call it “re-learning” but that implies that you’ve forgotten what you’ve learned before; I think what you really mean is that you’re feeling like you’ve started over, which is true because you’ve changed majors but you’re learning new things, not things that you’ve already learned before but have now forgotten).

—Dondi (talk) 22:25, 21 November 2017 (PST)

Week 5 Feedback

(work in progress)

Shared Journal

Questions and “good habit” aspects are all sufficiently fulfilled; thank you!

—Dondi (talk) 19:27, 21 October 2017 (PDT)

Week 4 Feedback

I am posting partial feedback on your Week 4 assignment, with respect to your favorite gene page because the Week 7 assignment will build on that.

• Your favorite gene page had all of the required syntax and content except as follows:
  • You did not enclose your .html file and image inside of a folder, you only provided the .html file itself.
  • The HTML file should have been named after your gene, such as in "spt15.html" instead of your usernames.
  • Make sure to follow the convention of only using lowercase letters in filenames.
  • You did not actually provide the image files for your page; instead you used a URL link. Also, did you notice that one of the images was in the Russian language?!
  • The links for each of the gene IDs should have gone to the actual individual gene page, not just to the database's home page.
  • Your compare/contrast of content and presentation between the four source databases was a little brief.
  • Your references list is in a good APA-style format, but the link to Wikipedia was broken. You also should have provided in-text citations throughout your page.
• Aesthetics of the layout were not part of this assignment, but I want to note that as you revise this page, most of the text is flush with the left side of the browser window without any buffering "white space", making it a little difficult to read.
• Typically DNA and protein sequences are given in a "monospaced" or "fixed width" font, such as Courier, so the letters line up, which is what you saw on the parent databases.
• Otherwise, a clean-looking page with nice section breaks!

— Kdahlquist (talk) 13:06, 10 October 2017 (PDT)

More Week 4 Feedback

• I want to note that you submitted both your individual and shared journal entries on time.
• Your electronic notebook for this week was a little brief. If you look at your partner's notebook, she included some extra details about the syntax you used. Both of you could have said a little more about your gene in your notebook.
• You made a total of 13 edits to the wiki in the window of review and wrote something in the summary field every time, except for once (oops!)--keep up the good work.
• Don't forget to add your wiki signature to your Acknowledgments statement.
• I want to note that Bootstrap itself is a standard library--you seemed to imply in your shared journal entry that you didn't use it at all and coded your page from scratch, is that the case?

— Kdahlquist (talk) 16:21, 13 October 2017 (PDT)

Week 3 Feedback

• Most of your journal was turned in on time—thank you! You did add to your reference list after the due date, at 1:11pm on September 20. Do a re-read/review of your work prior to putting it away, multiple times if needed, to make sure you catch these sooner rather than later.
• You fulfilled most of the “good habit/best practice” aspects of the assignment, including supplying comments for all 17 of the listed journal edits. The misses are:
  • Your acknowledgments section is missing the statement that the journal entry is your own work.
  • The wiki signature that is supposed to follow that statement got pushed out to after the references section.
• You supplied an electronic notebook with this assignment, organized into headings and bullets—both good ideas. What is present is supportive of the openness and reproducibility values that we are after here: can someone reading your notebook get a clear understanding of what you did for this assignment? Do they have enough information to replicate the results that you posted on your journal page? But don’t hesitate to supply details as needed—for example, what curl commands did you try out? What search keywords did you use and which search was the most successful? This aspect improves upon the openness of your process.
• Your hack-a-page work certainly fulfilled the instructions—that is one catty-looking dragon :)
• Your list of links is of decent size and variety, all referencing different types of supporting resources for the page.
• Of your IDs, the first two are known as element IDs and indeed fit the description of identifiers given in class and in the readings. However, pre_text and POST do not fit as well, particularly with respect to McMurry et al. IDs closer to the spirit of that reading would have been better.
• Your curl/sed command is right on, and you make good use of the options available to you, especially output=Verbose to spell out some key amino acid names.
• Your chosen shared journal quote is one of the more striking ones in the article, and you might recall that when I described a model of a computer during the Week 3 class sessions, I did state that a computer’s activity was indeed centered on a clock. The “clock with benefits” phrase is a cleverer way to capture what goes on, admittedly, rather than my “fetch-decode-execute” cycle (though I think the latter is more descriptive, if drier!).

—Dondi (talk) 18:26, 24 September 2017 (PDT)

Week 2 Feedback

• Thank you for turning in your assignment on time.
• You wrote something in the summary field for 9 of 11 saves (82%) in the period of review. This is very good, but remember, we are aiming for 100%
• The number of total saves on your individual wiki page was 10, which is just within the range of what would be expected for this assignment.
• The only link to your User page from your journal entry was in your wiki signature, and the template/category was added late. The link from your User page to the shared class journal page was also late. In the future, be sure that all the requested links are in your template and invoke them on your pages on time.
• Your complementary DNA sequence was correct.
• Your translations were correct, except that you mixed up the labels for frames +2 and +3 and again for frames -2 and -3. Also, it would have been good to keep translating beyond the stop codon in this case, since it was purely a translation exercise.
• Your determination of which frames contained ORFs was correct.
• One other note: we do not label the ends of proteins 5' and 3', instead we label them N-ter and C-ter.
• I did not see any electronic lab notebook in your journal entry. For this assignment, the lab notebok would have explained how you arrived at your answers to the questions posed in the exercise. Please be sure to keep your electronic lab notebook for future assignments. Also, as discussed in class, please keep your notes on the same page as your individual journal entry.
• One small note about your References section: you need to provide a label for the link to the Week 2 assignment.
• Also, for your Acknowledgments section, this exact statement is required each week" "While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source" followed by your wiki signature.
• The technical language in articles from the primary literature is definitely a hurdle for students (and even for faculty from a different field), but keep with it. Like with other fields of endeavor, it is good to take a look at the primary source.

— Kdahlquist (talk) 22:56, 23 September 2017 (PDT)

Week 1 Feedback

Thank you for submitting most of your work on time, though one edit was noticed at 3:42pm on September 5. Your Week 1 work has been reviewed, and the following points of improvement have been identified. Other than these items, your wiki skills and deliverables checked out OK:

• 32 edits were made to your user page—a good, gradual pace—but around 7 of those were missing a summary message. Please make it a habit to provide a summary, no matter how small the change might be.
• There is a difference between internal wiki links (double bracket) and external links (single bracket). The link on the main page to your user page is written out as if it were an external link, but it is more compact if written as an internal one.
• A template was successfully created, but it does not appear to be used anywhere in your submission.

For your shared journal response, no link was seen from your user page to the shared journal page. Thank you for answering the questions!

—Dondi (talk) 22:00, 11 September 2017 (PDT)