User talk:Kwrigh35

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) 13:59, 16 November 2017 (PST)

Week 9 Feedback

• The “good habit” aspects of your individual journal are completely fulfilled and on-time.
• 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 final URL for the desired gene data is given correctly but the process at reaching that has some fragility:
  • A generic query parameter is used for filtering by taxon ID and gene name—although this generally seems to work, particularly with the sort=score parameter, it is still not the most precise possible query because there is a slight chance that other records will match the generic search term. It is possible to issue a request that specifically asks for a particular taxonID and a particular gene name.
  • The derivation of the ID relies on screen-scraping—i.e., it grabs the HTML page and cleans out the specific tags that enclose the desired ID. This approach is fragile and will break if the website changes its formatting. Ideally, the ID should be retrieved from a genuine web service URL, which is designed to return pure data without any formatting.

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) 18:22, 23 November 2017 (PST)

Week 7 Feedback

• The “good habit” aspects of your individual journal are mostly on point, but the references section is somewhat minimal—you must have used more references beyond the assignment instructions, right? Your electronic lab notebook has a moderate level of detail.
• 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. I agree that without some discomfort, you probably aren’t getting enough of a challenge. So it is good to hear that a little of that is present, but without being way too much to handle.

—Dondi (talk) 23:26, 20 November 2017 (PST)

Week 5 Feedback

(work in progress)

Shared Journal

For the second consecutive week, there is no apparent entry from you in the shared class journal. Again, please communicate with us regarding any issues with fulfilling the assignments.

—Dondi (talk) 19:26, 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 could not find any individual journal entry or shared journal entry for you for Week 4. Please let us know if there are any special circumstances we should know about.

— Kdahlquist (talk) 16:17, 13 October 2017 (PDT)

Week 3 Feedback

• Everything was turned in on time—good job! You fulfilled all of the “good habit/best practice” aspects of the assignment, supplying comments for all 20 of the listed journal edits.
• You supplied an electronic notebook with this assignment, separated into a Notebook section; the subheadings and datestamps (for some of the entries) are good ideas and the content is in the right direction, supportive of the openness and reproducibility values that we are after here. Keep on doing this; note that a piece of information or action that you took is worth journaling if it helps inform either of these question: 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?
• Your hack-a-page work certainly fulfilled the instructions…can you imagine what a coup it would be to have them as faculty? Though I suspect that there may be some friction between Watson & Crick and Rosalind Franklin. But the New Caledonian Crow is sure to get along with everyone!
• You identified a sufficient number and variety of links correctly, and also noticed that the links changed to file references when viewed from a local file. This is normal and expected; the links are known as relative links because their final value is dependent on the source from which they are loaded.
• I did not see any answers to the ID question—please let me know if we need to spend some time with this during office hours.
• For the curl/sed exercise, you noticed and used the output option that can be provided along with pre_text. This option controls how the amino acids are displayed. What is missed by the provided answer is that supplying output=Verbose to the curl command would have obviated the need for the sed commands that “space and spell out” the amino acid letters. Taking a closer look at how the live page operated via the Developer Tools may have helped here.
• Your shared journal’s chosen quote captures one of the biggest adjustments that people need to make when learning to work with computers—detail and specificity are indeed paramount in computing, beyond what we are used to in other endeavors. We all have frustrating moments when we realize that a lot of time might have been lost due to a single punctuation mark. Time is indeed one way to get a handle on this specificity. I wrote the wiki pages in a tutorial format, so just going through them with a command line window open next to it might help. If not, I am not aware of Codecademy-style tutorials for the command line off the top of my head, but wouldn’t be surprised if there were something out there.

—Dondi (talk) 18:11, 24 September 2017 (PDT)

Week 2 Feedback

• Thank you for turning in your assignment on time.
• You wrote something in the summary field for 12 of 12 saves (100%) in the period of review--keep up the excellent work!
• However, the number of total saves on your individual wiki page is quite small (only 2). We are encouraging you to save your work in smaller "chunks"; a range of 10-20 saves is what would have been expected for this assignment.
• 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 saw your separate electronic lab notebook page, but there were no notes for this assignment. 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 keep your electronic lab notebook for future assignments. Also, as discussed in class, please keep your notes on the same page as the assignment.
• One small note about your References section: a mistake in syntax for the link means that it is not showing up properly on the page. Be sure to proofread your work after you save to ensure you didn't make any syntax errors.
• Thank you for your honest about "skimming" the Nirenberg article. 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) 22:33, 23 September 2017 (PDT)

Week 1 Feedback

For your individual submission, I’m happy to report that all requested wiki skills and deliverables were noted and seen to be implemented correctly.

Unfortunately, your shared journal answers could not be found. Please let us know if/when they are available on the wiki. Thank you!

—Dondi (talk) 22:04, 11 September 2017 (PDT)

Week 1 Feedback Update

Your shared journal answers have been reviewed, and they fulfill all of the requested items. Thank you very much!

—Dondi (talk) 00:25, 13 September 2017 (PDT)