User talk:Bhamilton18

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) 14:00, 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 wiki signature is missing from the acknowledgments section.
• Design or development term notes
  • Good assortment of terms and technologies there—they are defined and cited as specified in the instructions.
• Article outline notes
  • Your outline fulfills the specifications in the instructions—well done!

—Dondi (talk) 18:25, 9 December 2017 (PST)

Week 9 Feedback

• The “good habit” aspects of your individual journal are almost fulfilled and on-time. The references list only includes the Week 9 assignment; this particular assignment references API documentation as well, at the very least.
• 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 last URL that delivers the full data for a single gene. After performing the needed esearch API calls, you want to make a final esummary API call in order to get the full dataset for the specific gene whose ID you were able to extract via esearch.

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) 18:39, 23 November 2017 (PST)

Week 7 Feedback

• The “good habit” aspects of your individual journal are mostly on point, but the acknowledgments were missing your wiki signature, and the references section is somewhat minimal—you must have used more references beyond the assignment instructions, right? Your electronic lab notebook is very thorough and detailed.
• Most prior web page issues were addressed except for the hyphen in your gene page’s title tag: ASP1 does not have a hyphen.
• Bootstrap grid layout and flex classes were seen and used appropriately.
• The use of an inverse table is noted as one of the requested “advanced Bootstrap” features, though it’s a bit of a stretch to call this “advanced.”
• 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. Unfortunately, the project will be the furthest we will get in the realm of web pages and database integration; hope the biology pace continues to work for you, and we’ll let the other computer science class take care of your interest in those areas.

—Dondi (talk) 23:22, 20 November 2017 (PST)

Week 5 Feedback

(work in progress)

Shared Journal

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

—Dondi (talk) 19:07, 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 folder name matches the standard name of your gene, the folder name is lowercase and hyphenated, the HTML filename is lowercase and hyphenated and your title tag matches the gene standard name.
  • However, you hyphenated "Asp1" to "Asp-1". This is an actual change to the gene name. Although, as humans we can recognize that this is likely the same gene, these two strings would be different to a computer. You might have thought that you had to have a hyphen in the gene name, based on the instructions, but the hyphen is only needed if you are using two words.
• You used both of your usernames as the name for the HTML file when the instructions requested that you use the gene name instead; thus, your file should have simply been "asp1.html".
• All of the content that was requested was found on the page with the following notes:
  • I want to note that SGD does, in fact, have the protein sequence, it is found under the "protein" tab.
  • The link to Ensembl in your references list is broken.
  • There are a few typos sprinkled throughout the page
  • What you learned about the gene was found throughout the page; it would have been better to have a more definitive gene summary paragraph solely about the gene without mentioning the review of the databases themselves.
• 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) 10:39, 10 October 2017 (PDT)

More Week 4 Feedback

• I want to note that both your individual and shared journal entries were submitted on time.
• Your electronic lab notebook is excellent, with a good amount of detail. However, it seems like your list-formatting got messed up in places. Make sure that after you save the page, you review it to see whether it displays properly.
• Your frequency of edits is excellent and you wrote something in the summary field 100% of the time--keep up the good work.
• I also want to note that Bootstrap is considered a standard library.

— Kdahlquist (talk) 15:48, 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 19 out of the 20 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.
  • Note how both issues would be addressed by having them in a template—consider doing that.
• 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.
• Your hack-a-page work certainly fulfilled the instructions, and really, one can’t go wrong with pugs!
• You certainly identified some links correctly, though all but the last (cgi-bin…) were of the same kind: links to supporting files for the web page. But speaking of cgi-bin, 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.
• Feeling that “I’m not a natural” can certainly be a challenge, but as you stated, you enjoy puzzles at heart and in many respects computer science in general and programming in particular does share a lot with puzzles. (so do mathematical proofs—I took MATH 248 with Dr. Larson, and she kept referring to the proofs we had to do as “little puzzles”) Keeping hold of that puzzle sensibility can help with “jamming” things into your brain, and of course arriving at a solution to the puzzle certainly helps!

—Dondi (talk) 23:36, 23 September 2017 (PDT)

Week 2 Feedback

• Thank you for turning in your assignment on time.
• You wrote something in the summary field for 23 of 34 saves (68%) in the period of review. Remember we are aiming for 100%
• The number of total saves on your individual wiki page was 12, which is in the range of what was expected for this assignment.
• Your complementary DNA sequence was correct.
• Your +1, +2, and +3 translations were correct.
• However, the -1, -2, and -3 frame translations were incorrect. It appears that you read them 3' to 5' instead of 5' to 3'. You either had to reverse the sequence or read it right to left to translate it correctly.
• Your determination of which frames contained ORFs was correct (but based on your mis-translation of the three minus frames).
• One other note: we do not label the ends of proteins 5' and 3', instead we label them N-ter and C-ter.
• I saw your separate electronic lab notebook page, but there were no notes for this assignment, just the answers again. For this assignment, the lab notebook would have explained how you arrived at your answers to the questions posed in the exercise. Please be sure to write a narrative about your process and keep your electronic lab notebook on the same page as your journal entry.
• One small note about your References section: you need to skip two lines in wiki syntax to get something to appear on a newline.
• 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) 22:41, 23 September 2017 (PDT)

Week 1 Feedback

• Thank you for completing the assignment on time.
• You completed all of the required content and skills except for the following list. You have the opportunity to make up the points you have lost on this assignment by completing the changes requested by the Week 3 journal deadline.
  • You wrote something in the summary field for 18 of 37 saves, or 49%. We would like to see this approach 100%. Will Improve
  • Please be careful to use the correct syntax for an internal wiki link versus an external one. Some of your internal links are formatted like external ones. While they do function as links, we would like you to please go back and correct the syntax so that you have practice in learning the MediaWiki syntax.Completed
  • You organized your page using the three levels of headers, ==, ===, and ====, but you need to be careful to use them “in order” in outline form. For example, use === only underneath ==, don’t skip from == to ====. Completed
  • One of the idiosyncrasies of using a numbered list in MediaWiki is that you cannot skip lines in between each line that begins with a “#” because it will restart the numbering from “1” again. On the Shared Journal page, you interspersed lines beginning with a “:”, so the numbering was restarted. A “:” causes an indent. When using numbered or bulleted lists, you don’t need to do manual indenting. You can also make sub-lists by using “**”, “#*”, or “#*”, or “##”. Just make sure that you don’t skip lines in between.Completed
  • You uploaded a file and linked to it on your page, but you did not make a visible label for it, such as in [[Media:filename | visible label]]. It will look neater if you include the label.Completed
  • You included multiple categories on your page; we would prefer to see just the category “Journal Entry” instead of the ones you chose. The value of a category is that everyone is using the same ones to create the Table of Contents page.Completed
  • Another idiosyncrasy of MediaWiki is that if you want something to appear on a new line, you actually have to skip two lines instead of one. If you only skip one, the content on the second line will merge with the previous line. Completed
• Thank you for your detailed Acknowledgments section; that is exactly what you should do in the future.
• I answered your question on my User talk page.

— Kdahlquist (talk) 13:36, 12 September 2017 (PDT)