Wikipedia:United States Education Program/Courses/JHU MolBio Ogg 2012/Common

Course information

 * University: Johns Hopkins University
 * Course title: 410.602 Molecular Biology (course page)
 * Section:
 * Professor name: Sherry Ogg,
 * Course start date: 9/5/2012
 * Ambassador 1: Chris Maloney,
 * Ambassador 2: James Heilman (Doc James),

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.

Wikipedia Assignment
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 students each, and each group will have main responsibility for one Wikipedia article, and will act as a peer reviewer for one other group's article. The goal of the assignment is to make a substantive contribution to a Wikipedia article on a topic of Molecular Biology. Each group will choose an article that's in need of work, and your goal is to improve upon the article, 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 the Online Ambassador.

Unit 1
In this first unit, we would like to introduce you to Wikipedia.

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.



Unit 2
In this unit, you will set up a "sandbox", and make a few practice edits.

Details


 * Watch Tutorial on starting a sandbox article on Wikipedia, and start a sandbox page.
 * Using your sandbox page, make a few practice edits. Here are a couple of references for getting started with editing pages on Wikipedia.  Don't feel compelled to read all of these -- there is some duplication of material.
 * Boldness and links tutorial
 * Training material, a practical introduction to editing Wikipedia for scientists, first five slides. This is a very nice set of pages that were used in an "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.  For now, just read the first five slides:  Introduction, What is Wikipedia?, Registering an account, Editing, Formatting.
 * Wikimarkup cheatsheet as a quick-reference for the Wikipedia markup format.
 * Another quick-reference sheet
 * Wiki markup - a more complete reference



Unit 3
In this unit, you will learn how to communicate and collaborate with others on Wikipedia.

Graded milestone at the end of this unit worth ten points. We should be able to find your user page through the student list below, see your sandbox page, and verify that you've been communicating on various talk pages.

Grading
 * (individual) 10 points for successfully completing these steps

Details


 * Sign up on the Student list, below, on this course page. To do this,
 * Click the "Edit" link beside the "Students" header, below,
 * Copy-and-paste an already-existing entry, and then change it to include your own username.


 * Watch the Watchlist tutorial video.
 * 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


 * Watch the talk pages tutorial video,
 * In A practical introduction, read the last slide, Discussion, of the "practical introduction to editing Wikipedia for scientists".
 * Then, practice communicating on Wikipedia. At a minimum:
 * Introduce yourself to the class's Ambassador 1, User:Klortho, via his talk page. Make sure you use the "New section" link, as described in the video, and to sign your entry with four tildes ( ~ ).
 * Visit your classmates' user talk pages, and find someone who hasn't gotten a greeting yet, and leave a message for him or her.
 * Verify that you are getting emails when your talk page changes.

Unit 4
In this unit, you'll learn about some important Wikipedia policies and guidelines, as well as how to evaluate an article's quality.

Details


 * Read the slides under "The Core" from this training program. That is everything from here to here (total of 21 slides).  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 on 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 the video Article improvement


 * [Optional] Watch the video Article assessment. This gives more information about what makes an article good.

Unit 5
'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.'

Details


 * In A practical introduction, read the slides Links and Citing.


 * More about citing sources
 * Read, of the "practical introduction to editing Wikipedia for scientists".
 * 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.
 * Take a look at the reference pages Referencing for beginners and Citing sources. These are for reference only -- no need to read them completely.

In pages under the WikiProject MCB, we will be using the Vancouver System (author-number). You are encouraged to use User: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.


 * Look over the proposed style guidelines for gene and protein articles.


 * 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*.  This should include (but not be limited to):
 * Do a quick evaluation of the article according to the criteria you learned about in unit 4, and the Good_article_criteria. If you want, you could write up these assessments on your group's page.
 * 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.
 * Make your own suggestions on those talk pages, or join in ongoing discussions.


 * 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.

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

Graded milestone at the end of this unit worth 30 points. Before this unit begins, you will have been assigned to a group. 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.

Grading


 * (group) 20 points for choosing an article and writing a summary explaining the rationale for your choice.
 * (individual) 10 points for participation in the process of choosing the article.

Details


 * Continue to assess articles from the list below.
 * Discuss with your group members (on your group's talk page) which article, from the list below, you would like to work on. As you discuss your choice, remember that an article with a higher quality rating will be more challenging to improve, since these articles are already well developed, and it may be more difficult to find relevant research. Stubs or start articles on the other hand, will not be well developed and finding additional research to add to the article, will be less challenging.
 * As a group, choose one article, and then edit the Articles section below to "claim" it. 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 below, 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 300-400 words (this is about one page, single-spaced). Write this summary as a new section on your group's Wikipedia page, under the heading "Unit 6 article selection rationale."
 * Make sure you add the article page to your watchlist. (Reminder:  this just means clicking the star icon next to the search box, while you are on those pages.)

Unit 7
In this unit, you will get started working on your article.

Details


 * Once all the articles are assigned to groups, we will assign reviewers at random. Your group will be assigned as a peer-reviewer of one other groups' article, and that article should also be in your watchlist.
 * As a group, begin to research the topic of the article, identify key points that should be in the Wikipedia article for this topic, and divide up the work among group members.
 * Will you be expanding existing section, adding new sections, or completely reorganizing the article?
 * Can you find other articles on similar topics, that are more developed, that you can use as a guide?
 * Begin to gather and organize reliable sources
 * Any suitably-licensed images that you can add?

Unit 8
In this unit, you will continue working on your article.

Unit 9
In this unit, you will continue to work on the article, and prepare a progress report.

Graded milestone at the end of this unit worth 30 points.. By the end of this unit, your group should have prepared a report describing the progress you've made so far.

Grading


 * (group) 20 points for the progress report
 * (individual) 10 points for your contributions.

Details

This report should be approximately one printed page, single-spaced (~400 - 500 words), and should be written on your group's wikipedia page, under the heading "Unit 9 progress report".

Suggestions for inclusion in this progress report are:
 * Any progress made so far on improving the article
 * Any significant interactions you've had with other Wikipedia editors. Were they helpful?  Did any edits you made get reverted?
 * To-do list for improvements that you plan to make in the remaining weeks
 * Any other problems or concerns

You will be graded as a group on this report, and will also receive a per-individual grade based on your contributions.

Unit 10
In this unit, you'll keep working on your own article, and begin to peer-review the other group's article.

Details

For peer-reviewing,
 * Read the other group's progress reports, and the articles that they've been working on
 * Discuss any suggestions you have for them, either on the other group's talk page, or on the target article's talk page (whichever is most appropriate for the specific suggestion).

Unit 11
In this unit, you'll keep working on your article, and continue to peer review.

Unit 12
In this unit, you will keep working and peer-reviewing, and prepare another (short) progress report.

Graded milestone at the end of this unit worth 30 points. By the end of this unit, your group should have prepared another report describing the progress you've made so far.

Grading


 * (group) 10 points for progress report itself
 * (group) 10 points for actual progress made on the article
 * (individual) 10 points for your peer-reviewing activities

Details

This progress report could be shorter or longer than the last -- whatever is appropriate for what you have accomplished, or need to accomplish as a group. In addition to the topics covered last time, also summarize any major suggestions each individual made to the other group as peer-reviewers, and any significant interactions you had with that group. Again, write this on your group's wikipedia page, this time under the heading "Unit 12 progress report".

You will be graded as a group on this report, and will also receive a per-individual grade based on your contributions.

Unit 13
In this unit, you'll keep working on your article.

Unit 14
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


 * (group) 5 points for progress report
 * (individual) 10 points for contributions
 * (group) 35 points for overall improvements to your article.

Details

The final progress report should be short and to the point&mdash;just a quick guide to help us evaluate the improvements to the article. Just summarize in a few bullet points:
 * The significant contributions that your group made to the article.
 * The main interactions you had with 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
 * Quality of the progress reports
 * Improvements to the overall quality of the article, based on Wikipedia's good-article-criteria, at the end of the semester

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.