User talk:Ebachour

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 Simon’s individual journal page link appears to be missing from the team template. 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) 00:11, 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) 14:11, 16 November 2017 (PST)

Week 11 Feedback

• A number of "good habit" items were not met in this submission:
  • 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.
  • Only three edits were made for the entire submission—given the amount of content on the page, this indicates insufficient granularity.
  • The references section cites Week 14, not Week 11.
• Design or development term notes
  • No definitions were provide for 9 out of the 10 terms listed. The journal entry says “Definitions covered below in outline,” but only Xcode is defined in that way; none of the other terms are.
  • No citations/references are given for any of the terms (including Xcode).
• Article outline notes
  • Outline was 1.3 pages long in print preview.

—Dondi (talk) 18:32, 9 December 2017 (PST)

Week 9 Feedback

• The “good habit” aspects of your individual journal are mostly fulfilled except:
  • The journal entry category is missing.
  • The references list only includes the Week 9 assignment; this particular assignment references API documentation as well, at the very least.
• The electronic notebook is in narrative form with moderate detail, conveying the process of arriving at the API calls.
• 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 when coupled 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) 18:17, 23 November 2017 (PST)

Week 7 Feedback

• The “good habit” aspects of your individual journal are mostly on point except that your journal page is missing its category and your references were somewhat minimal, but with incorrect titles! Your electronic notebook has a moderate amount of detail.
• Nearly all prior web page issues were addressed except for the labeling issues: gene names and IDS either remain unlabeled or require a tooltip. Although the design has a certain simplicity, note that informativeness is the primary goal of the page.
• Bootstrap grid layout and flex classes were seen, though used somewhat subtly, and the flex usage was taken purely from the starter code.
• The use of collapse is noted as one of the requested “advanced Bootstrap” features.
• The use of tooltips is noted as the other “advanced Bootstrap” feature.
• The XML and JSON API calls were adapted correctly.

Shared Journal

Questions and “good habit” aspects are fulfilled, all on-time. Your comment on being pushed more into biology than desired is noted, but this level of exposure to the biology side of things is precisely why the class is interdisciplinary. Thus, there are assignments that require biology to finish. You’ll be amazed at where this deeper learning can lead.

—Dondi (talk) 22:12, 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) 18:56, 21 October 2017 (PDT)

Week 4 Feedback

Individual Journal

• You’ve gotten a lot of the “good habit” tasks down, but not all. For this week:
  • Your individual journal was done in a single edit! At least that single edit had a message.
  • The journal category is still missing. Template template template so you don’t have to worry about this anymore!
• Your lab notebook remains on the brief side but does include the kinds of details we like to see. If you integrate note-taking further into your workflow, I think the detail will naturally flow from there.
• Your acknowledgments and references were as requested except that the headings are swapped, and no signature is supplied with the acknowledgments.

Shared Journal

• All questions and “good habit” points are fulfilled—once again, good job!
  • Note that the standard library you used here does have a name: Bootstrap. I know that you know this, but just pointing out that when answering questions of this nature, don't make any assumptions about what the reader already knows. State as reasonably complete an answer as you can think of. Stating that you used a standard library but not naming it is sort of a gap.
  • Indeed I don’t think Sir Berners-Lee anticipated that web browsers would become more like virtual machines than just document viewers.

Web Page

(both homework partners get the same feedback)

Most gene page requirements were fulfilled except:

• Filenames and title element weren’t customized to your chosen gene
• A separate gene summary paragraph was seen, and contains appropriate content for a summary
• The gene names and IDs are nicely presented but not clearly labeled—remember that for pages like this, clarity and information availability are as important (or perhaps more so) than aesthetics
• Making gene IDs available only via tooltip hampers the information access somewhat; the best of both worlds is a visually pleasing presentation alongside a seamlessly effective conveyance of information
• Your gene image looks appropriate but unless one is a total yeast specialist, it can use a figure caption
• The references section is always meant to look like a formal citation; supplying just a link is insufficient

—Dondi (talk) 22:25, 10 October 2017 (PDT)

Week 2 Feedback

I see that Dr. Dionisio "lapped" me in providing feedback on Week 3 before I added the feedback on Week 2 :) Nonetheless, here it is:

• While the bulk of your assignment was on time, your signature, Reference section, and template were added after the deadline.
  • Your category was completely missing; remember to add it to your template, if you have not already done so.
• You wrote something in the summary field for 5 of 7 saves (71%) in the period of review; remember we are aiming for 100%
• The number of total saves on your individual wiki page was 7, which is a little less than would would have been expected for this assignment.
• The link from your User page to the Week 2 assignment was missing, as was the link to your individual and shared journal entries. I think that you have addressed this with your template already, but am recording the feedback for future assignments just in case.
• Your complementary DNA sequence was correct, except that you converted all t's to u's, which would make it an RNA sequence. Be careful to answer what was asked, which, in this case, was a DNA sequence.
• Your +2 frame had an O instead of a P in one place (a typo?).
• The +1 and +3 frame translations were correct.
• However, the -1, -2, and -3 frame translations were completely 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.
• Finally, do not flip the orientation of the RNA "top" and "bottom" strands from what is given by the DNA sequence. Even though it is the RNA that is ultimately translated, we always refer to "top" and "bottom" with respect to DNA.
• I did not see an electronic lab notebook for this assignment. For this journal entry, the lab notebook would have explained how you arrived at your answers to the questions posed in the exercise.
• In your References section, you provided the correct link to the Week 2 Assignment, but forgot to change the label, which still says "Week 1".
• The technical language in articles from the primary literature is definitely a hurdle for students (and even for faculty from a different field), I'm glad you stuck 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) 00:08, 24 September 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:
  • Your journal entry page does not have a category—just put this in your template so you don’t forget.
  • There are 7 listed edits to your journal page, with comments on 5 of them. Do treat these like commits: fine-grained, always with a message.
• You supplied an electronic notebook with this assignment, but it could use additional detail. Openness and reproducibility are the 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? For example, you said that the sed part “took a lot of process of elimination”—what did you try? What did you eliminate? The dead ends are useful to other readers too.
• Your hack-a-page work certainly fulfilled the instructions; the upside-down text is clever. You mentioned upsidedowntext.com in your notebook, and this should be in the acknowledgments too.
• Your list of links (2 items) was shorter than I would have hoped, given how many there were (and their variety).
• Your list of IDs was more comprehensive, and in this case you took the most explicit ones, the element IDs. However, there were other kinds of IDs in the page and I was hoping you would catch those as well.
• As stated, upsidedowntext.com deserves a mention in your acknowledgments.
• As your shared journal entry and chosen quote indicate, one can certainly spend lots of time “poking around” through algorithms, whether they are what you need or not. Hope the journey itself remains rewarding, as opposed to being a plain time-suck.

—Dondi (talk) 22:44, 23 September 2017 (PDT)

Week 1 Feedback

• You completed the majority of your assignment on time, but we note that you did make some changes after the deadline.
• 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.
  • Please include a snail mail address on your User Page. You do not have to use your residence address, if it is off-campus. Using the “1 LMU Drive…” general campus address will be sufficient.
  • Please make an explicit statement about your career interests and goals.
  • As you noted in the summary field for your commit, we did not want you to do the entire assignment in one go. Generally it is a good idea to map out the outline of a page with the headers, then click on the “edit” button next to the header to work on a section individually. Somewhere in the range of 10-20 saves would have been good for this size page.
  • Please create a new wiki page (your Week 2 or Week 3 individual journal page will now fulfill this requirement).
  • Please be careful to use the correct syntax for an internal wiki link versus an external one. Most 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.
  • Please organize your page using three levels of headers, ==, ===, and ====; you only had one level, ==, on your page.
  • Your numbered list was added after the deadline. 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. 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.
  • Your “comment out” had incorrect syntax, so it appeared on the page. You need to use <!-- to open a comment, just like in HTML.
  • The animated gif that you chose to upload to your page is fun, but is very distracting for someone to look at who wants to actually read your page. Would you please replace it with a static image?
  • You uploaded a file and linked to it on your page, but did not use the correct syntax so that a visitor to you page can click the link to download the file. Instead of using an external link format, please use [[Media:filename | visible label]].
  • The category “Journal Entry” is missing from your page, please include it on your template.
  • You acknowledged the sources you used in your Acknowledgments section, but you also need to include the statement “While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.” and include your wiki signature. This will be required every week.
  • For the shared journal assignment, you forgot to sign your entry with your wiki signature. This will be a requirement each week as well.
• I answered your question on my User talk page.

— Kdahlquist (talk) 13:34, 12 September 2017 (PDT)