User talk:Zvanysse

Talk page of Katie Wright.

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

You covered the basics requested in the assignment for your team page, but 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 (including the journal club presentations), 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? The links that currently exist on your template are a good start. If you do not want to actually use the Template:GRNsight Gene Page Project Links, then you should add the other relevant links from that template to your own. Also, there is a weird line break in the link for Week 14.
• Finally, having consistent formatting for the executive summaries and reflections will improve the look and organization of your page. Katie and Zach need to link to their Week 11 individual wiki pages and Emma, Blair, and Zach need to remove their individual templates from the page.

— Kdahlquist (talk) 14:01, 16 November 2017 (PST)

Week 11 Feedback

• "Good habit" item notes:
  • 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.
  • The references section is not formatted as specified in the Week 1 instructions.
• Design or development term notes
  • The agile software definition’s citation is incorrect; it lists the author’s first name rather than his last name.
• Article outline notes
  • Your outline fulfills the specifications in the instructions—good work!

—Dondi (talk) 17:40, 9 December 2017 (PST)

Week 9 Feedback

• The “good habit” aspects of your individual journal are on-time, and almost fulfilled:
  • The references section is missing.
• 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 completely and correctly specified.

Shared Journal

Questions and “good habit” aspects are all on-time, and mostly fulfilled (the link to the shared journal from your user page has a typo in the link). Favorite pages are stated alongside the reasons for these preferences.

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

Week 7 Feedback

• The “good habit” aspects of your individual journal are mostly on point, except that the acknowledgments signature is somewhat misplaced (appearing at the bottom of the page instead of right below) and the references list is quite minimal—certainly you accessed more sources than just the instructions? Your electronic lab notebook has a moderate level of detail.
• Most prior web page issues were addressed except for your gene page’s title tag, which was not revised to show your gene’s name.
• Bootstrap grid layout and flex classes were seen and largely used appropriately, although the flex usage is on the subtle side.
• I see the attempt to use the ScrollSpy feature, but I don’t think it’s functioning as intended. Good to see you explore it though!
• A second “advanced Bootstrap” feature was not seen.
• The XML and JSON web service calls were adapted as requested.

Shared Journal

Questions and “good habit” aspects are fulfilled, all on-time. Thanks for your candor regarding the difficulty level of the biology readings. Not being a biologist, I do occasionally struggle with parts too, and judging by the other shared journal entries it sounds like other classmates have similar challenges. One of our aspirations for the class is to keep everything real and to expose you to genuine current research, and a consequence of that choice is that we get exposed to readings that assume a lot more background that the class has. The good news is that this does seep in somehow, and you will emerge from the class with a lot more new knowledge than it may seem right now.

—Dondi (talk) 08:54, 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) 19:23, 21 October 2017 (PDT)

Week 4 Partial 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:
  • The folder name, HTML filename, and title tag should all have been based on your gene's standard name, bro1. For example, the html filename should have been "bro1.html" instead of your two first names.
  • You did not provide the image file shown on your page in your folder, instead you linked to its source on the web via URL. Since you did not use the grnsight-screenshot.jpg image, it should have been removed from your folder.
  • You provided links to the source pages from each of the four different gene ID's, but it was not obvious that those were hyperlinks.
  • The intention in the assignment was that you should have provided in text citations for each piece of information, not just for the gene IDs. You had a list of references, but there weren't the corresponding in-text citations.
  • Also, please be in the habit of using complete APA-style citations for your list of references, not just hyperlinks.
  • The image you chose was really interesting! It would have been nice to at least have a title for the image so that the view could know what he or she was looking at.
• 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.
• You had one "leftover" element from the Bootstrap template you used, a stray "Dropdown" appears next to the DNA and protein sequence links.
• Otherwise, a clean-looking page with nice section breaks!

— Kdahlquist (talk) 11:40, 10 October 2017 (PDT)

More Week 4 Feedback

• I forgot to note above that you were missing your gene summary paragraph--be sure to add it to your Week 7 version.
• I want to note that you submitted both your individual and shared journal entries on time.
• Your electronic lab notebook was very brief. While I enjoyed reading more about your gene and why you chose it, the intention behind the notebook is to record the details of your process. You could have included more data about your gene and detail of how you constructed your page, including syntax.
• Be sure to use the APA format for your References section.
• You made a total of 14 edits to the wiki in the window of review and wrote something in the summary field 100% of the time--keep up the good work!
• What is meant by a "standard library" is that a collection of code is available for you to re-use and adapt. In this case, Bootstrap was the standard library.

— Kdahlquist (talk) 16:11, 13 October 2017 (PDT)

Week 3 Feedback

• Everything was turned in on time—thank you! You fulfilled most of the “good habit/best practice” aspects of the assignment, including supplying comments for all 13 of the listed journal edits. The misses are:
  • I couldn’t find a link from the journal entry back to the user page.
  • Your journal entry page does not have a category.
  • Your user page does not have a link to the shared journal.
    • Note how the above issues would be addressed by having them in a template—consider doing that.
  • Your acknowledgments section is missing the wiki signature after the statement that the journal entry is your own work.
• You supplied an electronic notebook with this assignment, but it only covered the sed portion of the assignment. 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? Just expand your coverage to include all aspects of the week’s assignment, and don’t hesitate to supply details as needed.
• Your hack-a-page work certainly fulfilled the instructions, and thank you for the quick ego boost of seeing my name all over the place :)
• You certainly identified some links correctly, though all but the last (cgi-bin/translate…) were of the same kind: links to supporting files for the web page. But speaking of cgi-bin/translate, this appears not only as an action but also in bona fide a href links, and that ties in to the ID question…
• I was hoping that the values after seqdna in the cgi-bin links would be recognized by students as IDs. You listed the action by itself, which is technically correct, but a finer grain was also present. Further, pre_text and method="POST" are not IDs in the same sense that they are used in the assigned reading, particularly McMurry et al. IDs closer to the spirit of that reading would have been better.
• For the curl/sed exercise, I was hoping that students would notice the output option that can be provided along with pre_text. This option controls how the amino acids are displayed. Supplying output=Verbose to the curl command would have obviated the need for the sed commands that “spell out” the amino acid letters. Looking for additional options like this can sometimes save us a lot of work.
• Your chosen shared journal quote (and the sentiment you express after) is very much in line with one of my favorite computer science quotes, from Don Knuth I think, which states that programming languages aren’t intended to tell computers what to do, but to tell other programmers what you want the computer to do. This indeed goes into the core notion that programming languages are about communication between people.

—Dondi (talk) 17:43, 24 September 2017 (PDT)

Week 2 Feedback

• Thank you for turning in your assignment on time.
• The only link to your User page was found in your wiki signature. The category was also missing. Please add these links to your template and be sure to invoke it subesquent journal entries, if you haven't already.
• You wrote something in the summary field for 0 of 10 saves (0%) in the period of review; since you had only received the feedback about frequency after you submmitted this assignment, I am expecting that this number will be improving in subsequent weeks!
• The number of total saves to your Week 2 journal entry is was 8, which is a little lower than what we would expect for this exercise.
• Your translations were correct, except for leaving out one "A" from frame -1 and misreading "W" as "stop" twice. (Intersting side note, in some organisms one of the stop codons is translated as "W", just not in this exercise.)
• Your determination of which frames contained ORFs was correct.
• Technically, you should have given the complementary DNA sequence, as requested. Instead, you converted the T's to U's to make an RNA sequence. Be careful to follow the directions and give what is asked for.
  • The conversion of T to U occurs during transcription. The decoding of the genetic code occurs duing translation.
• Also, we do not use 5' and 3' to mark the ends of protein sequences. Instead, we use N-ter and C-ter.
• I did not find any electronic lab notebook for this assignment. In this case, the lab notebook 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.
• In your Acknowledgments section, you left out the required statement (see the Week 1 assignment). This will be required each week.
• In the references section, please make sure you are providing a complete citation in APA format, not just a like to the resource you used.
• 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. Instead of just relying on your memory for terminology, you can always look something up online or in a text book or dictionary. I have to do that myself when I am reading something from a different field.

— Kdahlquist (talk) 23:19, 23 September 2017 (PDT)

Week 1 Feedback

Thank you for submitting your work on time. 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:

• 15 edits were made to your user page—a good, gradual pace—but only around 7 of those had 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.
• Three levels of headings were requested, but only two were noted in your submission.
• The Acknowledgments section did not have a wiki signature.
• No References section was seen (recall that, at a minimum, it should have had a link to the Week 1 instructions).

For your shared journal response, all requested items were noted. Thank you for answering the questions!

—Dondi (talk) 21:55, 11 September 2017 (PDT)