User talk:Johnllopez616

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 the team template Template:Gene hAPI is somewhat underpopulated—continue reading to get further ideas on what can go there.

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) 00:21, 16 November 2017 (PST)

I also want to note that Eddie did not sign his executive summary/reflection with his wiki signature. The citations in you annotated bibliography should also be added to your team page.

— Kdahlquist (talk) 14:06, 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.
• Design or development term notes
  • Your list of design or development terms fulfills the specifications in the instructions—those are some good choices.
• Article outline notes
  • Your outline fulfills the specifications in the instructions—good work!

—Dondi (talk) 17:49, 9 December 2017 (PST)

Week 9 Feedback

• The “good habit” aspects of your individual journal are completely fulfilled and on-time. Well done!
• 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 fulfilled, all on-time. Favorite pages are stated alongside the reasons for these preferences.

—Dondi (talk) 19:12, 23 November 2017 (PST)

Week 7 Feedback

• The “good habit” aspects of your individual journal are all on point. Be careful with the formatting of the references section: you have a leading space on each line, which results in that fixed-width format. Not sure if that was your intent. Your electronic notebook shows excellent detail, effectively presented as bullets.
• All prior web page issues were addressed except that the “Week 7” reference entry is still listed with the title “Week 4.”
• Bootstrap grid layout and flex classes were seen, though the latter was used somewhat subtly.
• The use of collapse is noted as one of the requested “advanced Bootstrap” features.
• The use of a fixed nav is noted as the other “advanced Bootstrap” feature.
• The XML API call was not adapted correctly: the request was supposed to have been adopted to show information about your gene specifically (ADH1).
• The JSON API adaptation was not seen.

Shared Journal

Questions and “good habit” aspects are fulfilled, all on-time. Your observation that the biology content appears to be a challenge across the board is an interesting one. I hope the computer science gets equivalently challenging somehow too!

—Dondi (talk) 23:10, 20 November 2017 (PST)

Week 5 Feedback

(work in progress)

Shared Journal

Questions and “good habit” aspects are mostly fulfilled, but this time I must really emphasize that the “this week’s journal” format of your user page template is truly showing its disadvantages now that grading has slowed down. “This week’s journal” is already at Week 7, but we needed to grade Week 5. With this time differential, the inconvenience of not having access to the class journals prior to the current week really came to the fore.

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

Week 4 Feedback

Individual Journal

• You’ve gotten nearly all of the “good habit” tasks down, with 15 listed edits and summary entries for all of them!
  • Your inter-page links are still strictly in the “this week” version—as mentioned before, this is not bad to have, but also have the comprehensive links so that we can jump across weeks very easily.
  • The journal entry links on your User page are duplicated up to Week 3.
• Your lab notebook has very good detail, with your headings and links giving it some good organization.

Shared Journal

• All questions and “good habit” points are fulfilled—good job here! Note also your “this week” shared link—ideally, we can access all shared weeks from your user page instead of just the current one.
• Indeed the flip side of the Internet’s current indispensability and importance is now the increased impact of misinformation, hacking, and lost privacy.

Web Page

(both homework partners get the same feedback)

Most gene page requirements were fulfilled except:

• Your folder and HTML file names weren’t customized to your chosen gene, and the folder name wasn't all lowercase as specified
• The HTML filename ended with two .htmls (index.html.html)—keep an eye out for file extensions; this is why we recommend that they be made visible at all times
• A separate gene summary paragraph was not seen
• The Ensembl gene ID was the same as the SGD ID—it shouldn’t be
• The Ensembl link does not go where it should (in fact it appears to be an error page)
• For the DNA and protein sequences, note that they appear better with a so-called "fixed-width" font—these are the ones where every letter has the same width
• Your gene function, site differences, and reason for choosing your gene all work out; one small note: in gene function, where you reference baker’s yeast’s formal species name, the formatting convention should be italics (i.e., S. cerevisiae)
• The Week 4 assignment reference is missing from the References list on the gene page—note it’s still applicable to the page itself, not just your journal

Nice image pick! Protein images are always very interesting.

—Dondi (talk) 23:19, 2 October 2017 (PDT)

Week 3 Feedback

• Everything was turned in on time—good job! You fulfilled most of the “good habit/best practice” aspects of the assignment, except:
  • At the time that I reviewed your user page, your assignment links were restricted to “This Week’s Assignment”—not a bad idea in and of itself, but in the long run it will be more useful to have the full list available. I can see now that you have tried to add it, but at this writing you now have redundant versions, one in your template and another directly in the user page. Try to clean things up. You can keep the “This Week’s Assignment” portion, but make sure to also add the comprehensive list (as you have now started to do).
  • There are 7 listed edits to your journal page, with comments on all of them. Do treat these like commits: fine-grained, always with a message. For an assignment of this size, I think additional saves would have been appropriate.
• You supplied an electronic notebook with this assignment, with your notes being well-integrated with your answers. Keep this up! You provide some good details in the spirit of openness and reproducibility, the values that we are after here. Always keep these questions in mind when journaling: 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, and you never know, we have a high-powered enough animation department that Rick & Morty may well visit someday!
• Your list of links was quite thorough, including the cgi-bin links for the reading frames, which I was hoping that students would catch. In addition…
• …you also realized that the values after seqdna in those links do indeed serve as IDs. You also treated URLS themselves as identifiers (and indeed they are sometimes called URIs as well), which is appropriate here.
• Your curl/sed command is largely on the money except there is a slight typo in the grep portion: You only want a leading space before Frame, but not PRE.
• Your references section is generally right, except that it is formatted like code because there is a leading space before each asterisk. Was that intentional? Either way, I think the references will look better without the leading space.
• Your shared journal answers definitely align with my views and the views of others—to this day I still sometimes miss the occasional important character, and there is truly a need to keep doing what we’re doing in order to stay sharp.

—Dondi (talk) 15:36, 24 September 2017 (PDT)

Week 2 Feedback

• Thank you for turning in your assignment on time.
• You wrote something in the summary field for 5 of 5 saves (100%) in the period of review.
• However, the number of total saves is quite small. 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.
• Your determination of which frames contained ORFs was correct.
• Please indicate the ends of your protein sequence with "N-ter" and "C-ter", which is what we use to mark the ends of proteins.
• Your User page was missing the link to the Week 2 assignment. Please add those links to your template and invoke your template on both your User page and individual journal entry pages for the future.
• 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.
• 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) 11:44, 20 September 2017 (PDT)

Week 1 Feedback

I’m happy to report that all requested wiki skills and deliverables were noted and seen to be implemented correctly. We won’t count email misspellings against you 😁

—Dondi (talk) 21:36, 11 September 2017 (PDT)