User:S L Seston/BI302 Virology (2013 Q1)

This course uses Virology to explore the history and process of science, communication of science to the public, and key concepts of molecular biology.

Assignment description
This will be a semester-long assignment, with milestones along the way to keep everyone on track and allow for feedback at important points in your work. Each student will be responsible for one Wikipedia article, and will act as a peer reviewer for at least two other students' articles. The goal of the assignment is to make a substantive contribution to a Wikipedia article on a topic of Virology, with a target quality level between B-class and Good article (the closer to Good article the better, of course). Each group will choose a Stub-class article or create a new article and improve it as much as possible within the timeframe of this assignment.

Students should, as much as possible, help each other out with questions about how to do things on Wikipedia. You should strive to communicate the Wikipedia way -- on user talk pages. If you still have a question or a problem, don't hesitate to contact me through Wikipedia or my Alverno email address.

Unit 1: Introduction to Wikipedia – due Feb 20th
In this first unit, you will learn about Wikipedia and begin looking through virology topics.

Details:
 * Read Alex Bateman’s article on why scientists should contribute to Wikipedia.
 * Read the Welcome to Wikipedia brochure.
 * Start looking for topics on Wikipedia, considering these Tips for Choosing an Article.
 * After receiving feedback from the instructor, prepare a very brief powerpoint presentation (1 or 2 slides or websites) on your topic for the class. Highlight the lack of information on Wikipedia and what you want to contribute. Due Feb 20th

Unit 2: Literature search and bibliography – due March 6th
In this unit you will create a list of references in a personal database.

Details:
 * Carol Brill will lead us in an interactive class period of exploring databases and creating a digital reference database.
 * Find at least 15 reliable and scholarly sources on your topic. Prepare the list in personal database with complete information for each source.
 * Continue building your bibliography and reading your sources throughout March. Continue refining your idea for your Wikipedia article during this time.

'''Milestone at the end of this unit: Submit a list of 15 reliable and scholarly sources. Due March 6th'''

Unit 3: Setting up a user page and a sandbox – due April 3rd
In this unit, you will set up a "sandbox", and make a few practice edits.

'''Milestone at the end of this unit: I should be able to find your user page through the student list on the course page, and be able to read an introduction about you. Due April 3rd'''

Details: We will start this process in class on March 18th If you have any problems or questions, ask on the course talk page or email me.
 * Create an account on Wikipedia, if you don't already have one. Pick any username you would like, but DON’T USE YOUR FIRST AND LAST NAME.
 * Read How to create a userpage, and create a user page, and write a brief introduction of yourself.
 * Go through the first two major sections of online student orientation, "Welcome" and "The Core".
 * Enroll in the course on Wikipedia as follows:
 * Go to the course page. http://en.wikipedia.org/wiki/Education_Program:Alverno_College/BI302_Virology_(2013_Q1)
 * Click on the "Enroll" tab at the top of the page.
 * The Enrollment Token is: go viral. Enter “go viral”  and follow any other instructions.
 * Make sure that your User Name appears in the list of students at the bottom of the course page. If it does not, check the top of the page to make sure that there is no statement indicating that you are looking at a cached copy of the page. If you are, click the link to update.

'''Milestone at the end of this unit: I should be able to find your user page through the student list on the course page, and be able to read an introduction about you. Due April 3rd'''

Details:
 * Watch Tutorial on starting a sandbox article on Wikipedia, and start a sandbox page.
 * Go through the third major section of online student orientation, "Editing".
 * Using your sandbox page, make a few practice edits. Make sure you use edit summaries for (at least some of) your edits.
 * Training material, a practical introduction to editing Wikipedia for scientists, first five slides: Introduction, What is Wikipedia?, Registering an account, Editing,Formatting.
 * For more practice, on your sandbox page, summarize the five pillars of Wikipedia, in your own words, and incorporate some various text formatting styles.

Throughout this course, remember to always make sure that you are logged in whenever you work on Wikipedia. This is the only way you can get credit for your edits!!

'''Milestone at the end of this unit: I should be able to find your sandbox page, read your summary of the five pillars, see that you have used some text formatting, and that you used edit summaries when making edits. Due April 3rd'''

Here are a couple of other references for getting started with editing pages on Wikipedia. Check them out, and use them as needed.
 * Wikimarkup cheatsheet as a quick-reference for the Wikipedia markup format.
 * Another quick-reference sheet
 * Wiki markup - a more complete reference

Remember to always fill in the edit summary when you make an edit to an article page!

Unit 4: Learn to communicate on Wikipedia – due April 8th
In this unit, you will learn how to communicate and collaborate with others on Wikipedia.

'''Milestone at the end of this unit: I should see that you have successfully communicated with two other classmates on their talk pages. Due April 8th'''

Details:
 * Re-watch the watchlist video from this page of the student orientation.
 * Adjust your watchlist preferences:
 * Click "My preferences", and then "Watchlist".
 * Make sure that all three of these are checked (towards the bottom of the page):
 * Add pages and files I edit to my watchlist
 * Add pages and files I move to my watchlist (Some people have noticed that this option doesn't show up for them. If it doesn't show up for you, don't worry about it, because you probably won't be moving page or files for a while.)
 * Add pages I create and files I upload to my watchlist


 * Change your email preferences so that you get emails whenever a page on your watchlist changes. To do this:
 * Click "My preferences" → "User profile"
 * Near the bottom, make sure these are all checked:
 * ✓ Enable e-mail from other users
 * ✓ Send me copies of e-mails I send to other users
 * ✓ E-mail me when a page or file on my watchlist is changed
 * ✓ E-mail me when my user talk page is changed


 * Re-watch the talk pages video from this page of the student orientation.
 * Also watch this supplemental video: talk pages tutorial video

Make certain that you understand the following: (on talk pages only).
 * The difference between an article page, a user page, and a talk page.
 * How to use indentation when discussing things on talk pages.
 * When and how to sign your edits with four tildes:
 * Then, practice communicating on Wikipedia. At a minimum:
 * Say Hello to one other student via her talk page. Make sure you use the "New section" link, as described in the video, and to sign your entry with four tildes:
 * Add this student’s user page and sandbox page to your watchlist.
 * Have (two) short conversations, using proper indentation for replies.
 * Verify that you are getting emails when any page (or the corresponding talk page) changes.

You are responsible for keeping up with changes to various pages on Wikipedia throughout this course. Please make sure that you are getting proper notifications.

Unit 5: Policies and guidelines & assessing articles – due April 15th
In this unit, you'll learn about important Wikipedia policies and guidelines, as well as how to evaluate an article's quality.

'''Milestone at the end of this unit: I should see on your user page a summary of the characteristics of articles at our target quality level. Due April 15th'''

Details:
 * Review the slides under "The Core" from the student orientation. Pay particular attention to copyright and plagiarism section. This is very important.
 * Read Ten Simple Rules for Editing Wikipedia, Logan DW, Sandal M, Gardner PP, Manske M, Bateman A (2010). PLoS Comput Biol 6(9): e1000941.
 * Read this handout, Understanding and avoiding plagiarism. Note, in particular, that plagiarism includes such subtle forms as using short phrases without attribution, or beginning from a copied text and simply rewording it while leaving the structure and meaning intact (i.e., close paraphrasing).
 * Watch this video, Article improvement.
 * Watch this video, Article assessment. This gives more information about what makes an article good.

In this course, the goal will be to take an article from stub class to a level of quality somewhere between B and GA. On your own user page, start a new section with the title, "Summary of characteristics of target article", and summarize what the characteristics of an article at that quality level would have.

Unit 6: Citing sources – due April 15th
''In this unit, you will learn the proper way to cite sources on Wikipedia. You'll also get started finding an article for your group.''

'''Graded milestone at the end of this unit: In your sandbox page, I should be able to find some practice citations in your sandbox. Due April 15th'''

Details: We will be using the Vancouver System (author-number). You should use Diberri's Wikipedia template filling tool (instructions). With this tool, if you have a PubMed ID, you can quickly produce a full citation that you can cut-and-paste into an article. This will not only save you work, but will help to ensure that references are cited in a consistent manner.
 * Review the material and the videos about citing sources in the student orientation, in this slide.
 * Watch the video How to use RefTools, which covers the basics of adding citations and references to articles.
 * Skim this handout on Referencing in Wikipedia.
 * Look over the proposed style guidelines for gene and protein articles.

How to use Diberri's Wikipedia template filling tool, in a nutshell:
 * Fill in the PubMed ID
 * Check the "Add ref tag" box
 * Click "Submit. You should see a box with something like the following:
 * Cut-and-paste that into your article, at the correct point (directly after punctuation or text, without any spaces)
 * Click "Preview" (on the article edit page) and verify that the citation appears as you want it.

Assignment: Make sure you do not plagiarize. (See plagiarism materials above).
 * Select two different articles from your Reference List.
 * On your main sandbox page ("username/sandbox"), write a short paragraph to practice using inline citations.
 * Use named references, and reference at least one of the articles more than one time to practice citing.

Unit 7: Finalize your article choice - due April 15th
In this unit, you will learn about using images.

'''Milestone at the end of this unit: By the end of this unit, you should be able to add and reference an image to your article. Due April 15th'''

Details:

Continue to learn about Wikipedia, such as how to find and use images and figures.
 * Read over the Manual of Style - Images. This page has some good information about how to find suitably-licensed images as well as style guidelines.
 * Read through the Uploading images handout.

Unit 8: Get started on your article – due April 22nd
In this unit, you will get started working on your article, in a user sandbox page.

'''Milestone at the end of this unit: I should be able to find your initial work on your article in your sandbox pages. Due April 22nd'''

Details:

In order to prepare to the next unit, read or skim the following, for more information about style and structure of Wikipedia articles

Do some initial work on your article:
 * Manual of Style - Lead section
 * You should already have done extensive research and reading on your topic. Identify key points that should be in the Wikipedia article for this topic. Discuss on your talk page if you like.
 * Move the list of references created in Unit 2 to the working sandbox page.
 * Find more high-quality references, and add them to your list.
 * Search for any suitably-licensed images that you can add. If you find some, create a list for these on the working sandbox page, and add them to it.
 * Prepare a preliminary outline for the article, and write that in a new section of the working sandbox page.
 * Add your ideas for how you would like to improve the article to the talk page of the article.

Unit 9: First contribution – due April 29th
In these units, you will make your first substantial contribution to your article.

Milestone at the end of this unit: I should be able to see your contributions on your article page.

Details:

In general, and ongoing-

In this unit, you will shift from working in the sandbox to working on the actual live article in Wikipedia. You can continue to use the sandbox as a "scratch-pad" area, for example, for the rough outline, for lists of figures or references that you might want to use, and other miscellaneous notes. But when writing actual content, please use the article page. There is no need to draft the content first in the sandbox, and then move it to the article -- it is better to do your drafting and editing right in the article page itself. This may seem scary, but it is the way Wikipedia works!
 * Make sure you respond in a timely manner to any queries or feedback you get on the article's talk page, from other Wikipedia editors.

Likewise, when discussing improvements to the article, do so on the article talk page, and not on any page that only you and your classmates will see. (Questions or discussion that are specific to the course itself, and not related to the article, of course, should not go on the article talk page.)
 * Make a substantial contribution to your article. General guidelines:
 * Try to add approximately 6 to 8 paragraphs of new, sourced content. As an approximate minimum, each paragraph should be based on one new source. As a theoretical (and very tedious and unrecommended maximum) each sentence could be based upon two separate sources (but this raises questions on text-source integrity if you don't place inline citations carefully). Please be sure that the content is appropriate for an encyclopedia, that is concise, with no fluff.
 * If necessary, do not hesitate to remove existing content that is of poor quality, unsourced, or that does not fit into your plans for the article. Remember to be bold. Removing poorly written or poorly sourced content often does result in a net improvement to an article. If in doubt, you could first suggest the deletion on the talk page first, wait a couple of days for feedback, and then delete it if no one objects.
 * You may also add or update one or more infoboxes, figures, graphs, and/or tables. Creation of an original figure will count for more than adding an existing figure.
 * Be sure to include headings. Wikipedia prefers relatively short chunks of text, 200 to 600 words. Headings are key to helping readers navigate through the page. If your headings are formatted correctly, they should automatically appear in the Table of Contents at the beginning of the entry.
 * Write a very brief progress report on your user page, in a new section titled "Unit 9 progress report". As a guideline, this should be a bulleted list of up to five items, with one or two lines per item, highlighting specific contributions that we otherwise might miss. For example, don't include "Wrote the introduction section", because that kind of contribution will be obvious. Do include things like "Used Inkscape to make the figure 'small nucleic acid lipid particle', and uploaded it to Wikimedia Commons", or "Updated the infobox-disease with several external links." If all of your contributions were prose, then your progress report might consist of only one line, "All of our contributions were prose."

Unit 10: First peer-review – due May 1st
In this unit, you will peer-review another student’s article.

Milestone at the end of this unit: I should be able to find your review on the respective article's talk page.

Details:
 * We will assign reviewers at random. Each individual will be assigned as a peer-reviewer of two other articles, and those articles should also be in your watchlist. For this unit, you will review the first of those two articles.
 * This is your chance to critically evaluate your classmates' topic and writing. Use your knowledge of Wikipedia and your knowledge of Virology to generate comments about how the article might be improved. Start a new section on the article's talk page with the title "Comments from ..." and add your user name. Feel free to make minor edits (typos) to the article you are reviewing, but if the suggestions are more substantive, make a comment on the talk page about how the article might be improved. Some specific things to consider:
 * Does the lead section follow Style Guidelines?
 * Does the content accurately represent the cited sources?
 * Is the writing clear, comprehensible, and doesn't use too much jargon?
 * Do the contents of each section belong in that section? In other words, is each section coherent, and in concord with the section heading?
 * Are there gaps in the content? (What is missing?)
 * Are there places where there is ambiguity or inaccuracy over which sources are supporting what content?
 * Could the content be structured differently? You could suggest alterations in the order of sentences, paragraphs or sections for organizational purposes.
 * Are there parts of the article that are not clearly explained, and could cause questions to arise in the mind of a reader?
 * Is the content within Wikipedia's guidelines (such as neutral point of view) and does it avoid plagiarism or too-close paraphrasing?
 * Throughout the remainder of the course, continue to interact on the talk page, as appropriate, in relation to your feedback.
 * The comments sections that you add to the articles talk pages will be evaluated to judge the quality, thoroughness, and thoughtfulness of your feedback. Comments that demonstrate that you were reading the sources (and potential sources) for the article and comparing them against the content of the article to generate feedback are highly valued.

Units 11–12: Second contribution – due May 6th
''In this unit, you will resume work on your article, and make more improvements, taking consideration of suggestions from reviewers. You may also continue to interact with the student you provided feedback for as they revise.''

'''Milestone at the end of this unit: You will receive feedback on both improvements that you make to your own article, as well as on interactions with others on their articles. Both activities are important. Due May 6th'''

Details:
 * In this unit and throughout the rest of the course, I will monitor the quality and responsiveness of your interactions with reviewers of your assigned articles, the main editors of the articles that you have reviewed, and outside editors.
 * Continue to improve your article based on the criteria outlined above, and also based on reviewer's comments.
 * Provide feedback to the reviewers on your article's talk page (don't forget to use proper indenting and to sign your posts). Which suggestions did you take? Which do you disagree with? There is no need to get into lengthy discussions about particular changes -- you are in charge of your own edits. However, if you don't take a reviewer's specific suggestions, it is helpful to explain your reasoning. Just saying THANKS for helpful suggestions indicates that you agreed!
 * You should also use this time to add more content to your article. By the end of this unit, the overall structure of your article should be complete, and most of the content added or written, including prose, figures, infoboxes, and tables. The quality of the writing can be cleaned up later, but most of the actual content should be in the article, in it's proper place, and correctly sourced.

Unit 13: Second peer review – due May 8th
In this unit, you will do another peer-review.

'''Milestone at the end of this unit: I should be able to find your review on the respective article's talk page and be able to see that you've been maintaining interactions with others. Due May 8th'''

Details:
 * Don't forget to maintain thoughtful, timely communication with the editors of the article that was the subject of your first review, the reviewers of your assigned article, and any other editors.
 * For this review, follow the same guidelines as for the first review, but keep in mind that the editors will not have much time to implement your suggestions, so focus somewhat more on immediate problems rather than major structural issues.