Wikipedia:USEP/Courses/JHU MolBio Ogg FA13/Common

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This is the course page for 410.602 Molecular Biology (AAP course description), section: 

This course provides a comprehensive overview of the key concepts in molecular biology. Topics to be covered include nucleic acid structure and function, DNA replication, transcription, translation, chromosome structure and remodeling and regulation of gene expression in prokaryotes and eukaryotes. Extended topics to be covered include methods in recombinant DNA technology, microarrays, and microRNA.

Assignment description
This will be a semester-long assignment, with milestones at various times to help ensure that progress is being made.

Students will be assigned to groups of two (or three, depending on total enrollment), and each group will have main responsibility for one Wikipedia article, and will act as a peer reviewer for three other groups' articles. The goal of the assignment is to make a substantive contribution to a Wikipedia article on a topic of Molecular Biology, 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 and improve it as much as possible within the timeframe of this semester.

Group members 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; but (especially before Unit 3) you can use the Blackboard discussion forum if you need to. If, as a group, you still have a question or a problem, don't hesitate to contact one of the Online Ambassadors.

Units 1-2 - Introduction and setting up a sandbox
'In these first units, we would like to introduce you to Wikipedia. You will learn to set up a "sandbox", and make a few practice edits.'

Graded milestone at the end of these units: 10 points: We should be able to find your user page through the student list on the course page, and be able to read your introduction of yourself. We 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. Text formatting should include bold and italic style, as well as at least one Heading and one Subheading.

Details


 * Read the Welcome to Wikipedia brochure.
 * Create an account on Wikipedia, if you don't already have one. Pick any username you would like.  If you already have a Wikipedia account, you can skip this step.
 * 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.
 * Click on the "Enroll" tab at the top of the page.
 * Enter the Enrollment Token provided in your Syllabus 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.
 * ''If you have any problems or questions, ask on the course talk page, or, email one of the Online Ambassadors:
 * User:: email, talk page
 * User:: email, talk page


 * 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.

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

Units 3-4 - Learning to communicate, policies and guidelines, and assessing articles
'In these units, you will learn how to communicate and collaborate with others on Wikipedia. You will also learn about some important Wikipedia policies and guidelines, as well as how to evaluate an article's quality.'

Graded milestone at the end of these units: 10 points. We should see that you have successfully communicated both with the online ambassador and with your teammate on the various Wikipedia talk pages. We should see, on your main sandbox page ("/sandbox"), a summary of the characteristics of articles at our target quality level.

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:
 * That you need to use "New section" when you are starting a new discussion on a talk page (as opposed to responding to an ongoing discussion)
 * 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 ( ~ ) (on talk pages only).
 * Then, practice communicating on Wikipedia. At a minimum:
 * Introduce yourself to one of the class's Ambassadors, via his or her talk page: User: (talk page), User: (talk page)).  Make sure you use the "New section" link, as described in the video, and to sign your entry with four tildes ( ~ ).
 * Add your team-mate's user pages and sandbox page to your watchlist.
 * Visit his or her user talk page, and introduce yourself.
 * Have (two) short conversations on both your and your teammate's user talk page, using proper indentation for replies.
 * Verify that you are getting emails when any page (or the corresponding talk page) changes.

In our experience, the biggest problem that students have in this project is understanding and abiding by Wikipedia's strict policies against plagiarism. To be successful in this project, it is essential that you understand what constitutes plagiarism, and how to avoid it.


 * Read the article, Let's get serious about plagiarism.


 * Review the slides under "The Core" from the student orientation. Pay particular attention to copyright and plagiarism section.


 * 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 main sandbox page ("/sandbox"), 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 5 - Citing sources, finding an article
'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: 15 points. In your sandbox page, we should be able to find some practice citations (5 point). On your group page, two initial article assessments from each of the group members (10 points).

Details


 * 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.

When citing journal articles, use the "cite journal" tool in the editor toolbar, as described in the "How to use RefTools" video. Follow these steps when citing a journal article:


 * Click the "Cite" link in the upper area of the edit box to open the citation tools (if it's not already open)
 * In the "Templates" drop-down, select "cite journal"
 * Fill in the PMID with the PubMed identifier (a plain number, like "21866248")
 * Click the magnifying glass icon next to the PMID field. After a few seconds, many of the other fields should be automatically filled in.
 * Fill in any other information about the source that you can, by hand.
 * If this is a reference that you'll be using in more than one place in the article, fill in the "Name" field with a short, unique word or phrase
 * Click "Insert".
 * Click "Preview" (on the article edit page) and verify that the citation appears as you want it.


 * Assignment (5 points):
 * Find two different articles in PubMed on any topic you like
 * On your main sandbox page ("username/sandbox"), write a short paragraph to practice using inline citations.
 * Make sure you do not plagiarize. (See plagiarism materials above).
 * Use named references, and reference at least one of the articles more than one time.

In this unit, you'll also get started assessing articles from the list below, in order to find one for your group. As an individual, make an initial assessment of at least two of the articles from the list below (NOTE: the list below are articles that have been recommended by the WikiProject Molecular and Cell Biology, or other sources. However, if you locate an article that you feel needs improvement, you can propose to work on this article.  An article that is not on the list below, must be approved by myself and the OA.)
 * Your assessment should include (but not be limited to):
 * Do a quick evaluation of the article according to the criteria you learned about in units 3-4, and the Good_article_criteria.
 * Look at the articles' talk pages to see if there has already been discussion among other Wikipedia editors about ways in which the article could be improved.
 * Begin to compile a bibliography of relevant research, two or three references for each article. These should be reviews or other secondary sources such as textbooks.

Write up these assessments on your group's page.
 * Assignment (10 points):
 * Start a new section on your group page, titled "Initial article assessments from username"
 * Use subsections for each of the two articles.
 * If possible, link to online versions (or abstracts) of the references you found.

Here are a couple of other resources for getting started with editing pages on Wikipedia. Check them out, and use them as needed.


 * Referencing for beginners
 * Citing sources

Unit 6 - Picking an article
In this unit, you will pick an article for your group.

Graded milestone at the end of this unit worth 10 points. By the end of this unit, your group should have decided on an article for which you will be primarily responsible, and that article should be in your watchlist. You'll be graded individually on participation in the process of choosing the article (5 points) and as a group (5 points) for writing a summary explaining the rationale for your choice.

Details

Continuing to learn about Wikipedia, 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.
 * One good starting point to find images is the Creative Commons search page. Make sure you check both the "use for commercial purposes" and "modify, adapt, or build upon" checkboxes.
 * Read through the Uploading images handout.

Continue to assess articles and pick one
 * Don't limit yourselves to the four articles from the last unit, feel free to pick other ones from the list.
 * On your group's talk page, discuss the articles with your teammate, that you would like to work on. When discussing, remember to use the Wikipedia conventions for talk pages: indentation and signing your posts.  Part of your grade will be based on this.
 * As a team, choose one article, and then edit the Articles table to "claim" it. The articles table is located on the page USEP/Courses/JHU_MolBio_Ogg_FA13/Articles_.  Articles will be claimed on a first-come-first-served basis, so you are encouraged to touch base with other groups, as well, to see if more than one group is interested in the same article.  In the table on the articles page, change the "Group X" in the correct row and column to your group's number.  Make sure you use the "preview" button before "save", to verify that you've got it right.

Write a summary explaining the rationale for your choice
 * The summary should be between 200-300 words or so.
 * Write this summary as a new section on your group page, under the heading "Article selection rationale."

Finally,
 * Make sure you add the article itself to your watchlist. (Reminder:  this just means clicking the star icon next to the search box, while you are viewing that page.)

Unit 7 - Getting started on your article
In this unit, you will get started working on your article, in a user sandbox page.

Graded milestone at the end of this unit: 10 points. We should be able to find your initial work on your article in one of the team members' sandbox pages. This should include your preliminary outline located in one team members sandbox, your list of references, and your suggested improvements added to the 'talk page of the article'.

Details

In order to prepare for the next unit, read or skim the following, for more information about style and structure of Wikipedia articles
 * Manual of Style - Lead section

Do some initial work on your article:
 * Pick one of your team members' sandboxes in which to work ... it does not matter which.
 * As a team, begin to research the topic of the article, identify key points that should be in the Wikipedia article for this topic. Discuss this on your group talk page.
 * Move the list of references found in Unit 5 from your group page to the working sandbox page.
 * Find more high-quality references, and add them to a list. As you add them, it would probably be a good idea to skim them over and, for your teammate's benefit, add a few bullet points explaining what useful material the reference contains.
 * 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.
 * As a team, 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. This will open communication between your group and other wiki editors who are interested in improving the article.

Unit 8 - First contribution
In these units, you will make your first substantial contribution to your article.

Graded milestone at the end of these units: 15 points. We should be able to see your contributions on your article page (10 points), and read a brief progress report on your group page (5 points).

Details

Before you get started, review the article, Let's get serious about plagiarism, and make sure you understand Wikipedia's policies in this regard. If you have doubts or questions, please ask one of the OAs.

In general, and ongoing:
 * 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.

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.

Likewise, when discussing improvements to the article, do so on the article talk page, and not on any page that only you and your teammate 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 over the course of the project:
 * Try to add approximately 8 to 10 paragraphs of new, sourced content by the end of the semester. 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.
 * To determine how you will be graded on the content of your article, a grading rubric can be found below.


 * Write a very brief progress report on your group page, in a new section titled "Unit 8 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 9 - First peer-review
In this unit, you will peer-review another team's article.

Graded milestone at the end of this unit: 10 points. We 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 three other articles, and those articles should also be in your watchlist. For this unit, you will review the first of those three articles.
 * This is your chance to critically evaluate your classmates' topic and writing. Use your knowledge of Wikipedia and your knowledge of Molecular Biology 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 yourself, 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 valued.


 * The grading rubric found below can be used to guide your review process. Please use the following criteria from the rubric to guide your reviews: Content Coverage, Wikilinking, Referencing, Writing categories, and Illustrations.  Please keep in mind, the articles are a work in progress, and the reviews should be appropriate for the stage of article development and improvement.

Unit 10 - Second contribution
In this unit, you will resume work on your group's assigned article, and make more improvements, taking consideration of suggestions from reviewers.

Graded milestone at the end of this unit: 20 points. You will be graded on improvements that you make to your groups' article (10 points), a brief progress report on your group page (5 points), as well as on interactions with others (5 points).

Details


 * In this unit, and throughout the rest of the course, you will be graded in part on the quality and responsiveness of your interactions with: the 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.


 * You should also use this unit to add more content to your article. By the end of this unit, your article should be well on its way to completion.  You should have at least 50% of the content added or written, including prose, figures, infoboxes, and tables.  The quality of the writing can be cleaned up later, but the actual content added should be in it's proper place, and correctly sourced.

Unit 11 - Second peer review
In this unit, you do another peer-review.

Graded milestone at the end of this unit: 15 points. We should be able to find your review on the respective article's talk page (10 points) and be able to see that you've been maintaining interactions with others (5 points).

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.

Unit 12 - Third contribution
In this unit, you will continue to work on your group's assigned article, and make more improvements, taking consideration of suggestions from reviewers.

Graded milestone at the end of this unit: 20 points. You will be graded both on improvements that you make to your groups' article (15 points), your brief progress report found on your group page (5 points), as well as on interactions with others (5 points).

Details


 * In this unit, and throughout the rest of the course, you will be graded in part on the quality and responsiveness of your interactions with: the 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.


 * You should also use this unit 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 - Third peer review
In this unit, you do another peer-review.

Graded milestone at the end of this unit: 15 points. We should be able to find your review on the respective article's talk page (10 points) and be able to see that you've been maintaining interactions with others (5 points).

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 and second 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.

Units 14 - Final contribution
In this unit, you'll finish your article, and a final progress report.

Final project due, worth 50 points. In addition to finishing up all the work on your article, you should prepare another very short and to-the-point final progress report on your group page, under the heading, "Final progress report".

Grading


 * (individual) 5 points for ongoing interactions
 * (individual) 10 points for contributions to your own article
 * (group) 5 points for progress report
 * (group) 30 points for overall improvements to your article.

Details


 * Even in this last week, it is important to continue to maintain thoughtful, timely communication with others on Wikipedia.


 * Write a progress report. As before, it should be short and to the point&mdash;just a quick guide to help us evaluate the improvements to the article.  Summarize in a few bullet points:
 * The significant contributions that your group made to the article. Please point out things that we otherwise might miss, like figures that were created and uploaded by you, tables added, or infobox data that was added or fixed.
 * The main interactions you had with reviewers and other editors. In particular, if appropriate, include acknowledgements of significant help you got from peer-reviewers and/or outside Wikipedia editors.

Grading rubric
Roughly half of the grade will be based on participation and on successfully completing the milestones, and about half on the actual value that is added to the articles (both as primary editors and as reviewers). Some portions of the grade will be assigned to you as individuals, and some as part of a group.

The grading will take these factors into account (but is not necessarily limited to just these):


 * Participation in discussions with your team
 * Participation in discussions with other Wikipedia editors (civility, etc.)
 * Checking individual contributions, based on Wikipedia's history features
 * Improvements to the overall quality of the article, based on Wikipedia's good-article-criteria, at the end of the semester

The grading rubric below, in its entirety, will be used to grade your final product at the close of Unit 14.

Further resources

 * For scientists
 * Ten Simple Rules for Editing Wikipedia, Logan DW, Sandal M, Gardner PP, Manske M, Bateman A (2010). PLoS Comput Biol 6(9): e1000941.
 * Training material - a practical introduction to editing Wikipedia for scientists. This is a very good set of pages that were used in Introduction to Wikipedia workshop held at the Wellcome Trust Sanger Institute on 30 July 2010, and will be used again at the upcoming European Conference on Computational Biology.


 * Wikipedia help pages
 * Welcome to Wikipedia
 * Getting started
 * Tutorial
 * Where to ask questions or make comments
 * Glossary
 * Help desk
 * Reference desk


 * WikiProject Molecular and Cellular Biology
 * Main page - see, in particular, "How you can help"
 * Their worklist
 * Molecular and cell biology stubs


 * Figures and Images - You need to make sure that any figure you add to an article is suitably licensed. Usually that means Creative Commons attribution (CC-BY) or Creative Commons attribution/share-alike (CC-BY-SA).  You can either try to find existing figures, or you can create your own.
 * Two resources for finding existing figures are:
 * Wikimedia Commons. Here is a list of a few search tools that might help.
 * The PMC open-access subset. You can search for open access articles in PMC by adding "AND open access[filter]" to the end of your search, like, for example, here. When you find an article with a figure you want to use, verify that it has a suitable license by checking under "Copyright and license information" at the top of the article.  The license should be either "Creative Commons, attribution" (CC-BY) or "Creative Commons, attribution, share-alike" (CC-BY-SA).  Other licenses may be okay, check the Wikimedia Commons acceptable license page for details.
 * For creating you own image, Inkscape is a good drawing program to use. Save your images as SVG and upload them into Wikimedia Commons.  That enables them to be reused on any Wikimedia project.


 * Other
 * Citing your sources - another brief video on how to cite sources.