User:Biolprof/Signal Transduction Spring 2013 Revisions

Biol 512: Signal Transduction is a graduate-level course at Saint Louis University that covers the mechanisms by which cells receive and respond to external/environmental signals. Major categories of receptors, protein domains, post-translational modifications, intracellular signal transducing proteins and their role in specific pathways and ultimately in cellular biology are presented, with emphasis on methods used to study these pathways experimentally.

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

Students will work individually to edit one Wikipedia article, and will act as a peer reviewer for two other articles. The goal of the assignment is to make a substantive contribution to a Wikipedia article on a topic of Signal Transduction. Pick an article that is central to the topic of Signal Transduction, that way we can have the maximum impact to improve the quality of Signal Transduction information online.

Students should, as much as possible, help each other out with questions about how to do things on Wikipedia. You should communicate the Wikipedia way -- on user talk pages, and article talk pages. If you still have a question or a problem, don't hesitate to contact our Online Ambassadors.

Assignment 1: Get Started
When is it due? Wednesday, 23 January 2013, 10:15 AM - Allow at least 2 hours, plus extra time if you get confused or distracted

What do I do? In this first unit, you will be introduced to Wikipedia, set up an account, your user page, and a pretend article in your "sandbox". If you get stuck editing Wikipedia, you can always ask a question at the Teahouse or at the talk page of Biosthmors, our online ambassador.
 * Go through the online student orientation. Parts of this assignment will be completed while you are going through the training module. It is important that you also learn the basic rules of Wikipedia. Allow about an hour for this.
 * Please read WP:STUDENTS. Allow about 10 minutes for this.
 * Create an account on Wikipedia. 5 minutes or less.
 * 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. This might take a few minutes
 * Create your user page (so that your user name is no longer red like this). Make sure there is a link (see WP:CHEAT for basic linking advice) to the course page at the top. Your user page can be as simple as copy and pasting this: "I'm editing Wikipedia as part of this assignment and here's a link to my sandbox ." This can take less than a minute (don't copy and paste the quotes, just fill in "Your user name" with your user name and feel free to personalize).
 * Create your sandbox with a pretend article. Practice using brief edit summaries for each edit. Make a first sentence with bold letters, like Wikipedia articles. Add a reference section. Cite a source. Add a picture. Add a section heading. Use a PMID and this tool (many are listed at Help:Citation tools) to create a formatted cite journal template. Put that in ref tags. See WP:CHEAT for help and here for more details on citing this way. This should take anywhere from 5 (for an experienced editor) to maybe 20 minutes (for a first-timer).

What will be graded? You should be enrolled as a Student on the course page, your user page should link to the course page, and your sandbox should contain at least one sentence with a bolded title, one formatted reference in cite journal format, and one possibly relevant picture. (5% of total project grade).

Assignment 2: Explore Wikipedia: read and think about a featured article, think about your topic
When is it due? Monday, 4 February 2013, 11:59 PM

What do I do?
 * Using your sandbox page, make some practice edits. Here are a couple of references for getting started with editing pages on Wikipedia.
 * Training material, a practical introduction to editing Wikipedia for scientists. 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.
 * WP:CHEAT mentioned in Assignment 1 is a very helpful quick-reference for the Wikipedia markup format.
 * Wiki markup is a more complete reference.
 * Explore WikiProject Molecular and Cell Biology. Check out their talk page and other links. Also explore WikiProject Cell Signaling and its links. This page was semi-active or inactive, but has been reactivated thanks to this class! =)
 * Review the Grading Scheme for rating the quality and importance of an article.
 * Critically evaluate the proteasome article. It was elevated by the Wikipedia community to a featured article in 2007. A number of very recent review articles about the proteasome have been posted on SLU Global. Skim one or more of these articles to look for ways that the WP proteasome article can be improved or updated. Comment at the talk page or fix it. If you see any serious issues that make it eligible for featured article review, discuss at the talk page. Remember to always add useful content or questions that can be addressed or used by future editors on the talk page, not just compliments, because talk pages are for discussion on how to improve the article.
 * Critically evaluate three existing Wikipedia articles (at least two of which are directly related to the class and one of which can be anything of interest to you). For each of the three articles, you should either (1) add 1–2 sentences of new information, backed up with a citation to an appropriate source, or (2) leave suggestions for improving it on the article's talk page.
 * If you want to add a citation, read ahead to Assignment 3 for links on how to do this most efficiently.
 * Research and identify 3–5 articles you are considering working on for your main project. Proposals for new articles are fine for the list. Post your list at Wikipedia talk:WikiProject Cell Signaling. Justify starting any new Wikipedia articles there. Post your list at User talk:Biolprof with a comment on why each topic was selected. Be sure to sign your posting.
 * When you are researching your topic, think about what content might be needed to bring it to Good Article status. Know that pictures in open access journals (eg. PLoS and BMC journals) can be uploaded to Wikimedia Commons and incorporated into Wikipedia articles. See the essay Pictures for medical articles for more information.



What will be graded? Your contributions and user page will be reviewed to verify that you have edited three articles (or their talk pages), at least two of which relate to signal transduction. The proteosome article and talk page will be reviewed for edits or comments. Use the history page of each of the three articles you edit to show the changes or "diffs" on your user page, like this. Your ideas for your topic will also be reviewed at Wikipedia talk:WikiProject Cell Signaling and/or User talk:Biolprof. (5% of total project grade).

Assignment 3: Choose your topic and begin writing in your sandbox
When is it due? Monday, 18 February 2013, 11:59 PM, but note separate deadlines (6 February & 13 February) for intermediate steps.

What do I do?
 * Select an article, or several, to work on.
 * Add your article(s) to the class course page.  Due 6 February 2013. extended to 8 February 2013
 * Place the following template or line on the talk page(s) of the article(s) you plan to edit (if and when they exist): or
 * Put any article you will edit in your watchlist so you can see recent edits and respond in a timely manner to comments.
 * You will be assigned to a group of 3-4 students. At least one member of each group will serve as a writing editor, a fact checker, or a Wikipedia editor for all members of the team.
 * Begin to compile a bibliography of relevant research and post 2 or 3 references with links to online copies or abstracts to your User sandbox. You and the community may find it helpful to do this for several articles on your short list. It will provide helpful suggestions for other Wikipedians for the articles that you don't select and while helping you to choose among them. You will most likely start with review articles or other secondary sources such as textbooks. You may find it helpful to skim the essay about identifying reliable sources for Wikipedia articles. Begin reading the sources.
 * Read this handout on Understanding and avoiding plagiarism. Note, in particular, that Wikipedia has its own very stringent criteria concerning plagiarism and 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).
 * We will be using the Vancouver System (author-number) for citations. 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 (see also User:Biosthmors/Intro_Neuro for more details).  This will not only save you work, but will help to ensure that references are cited in a consistent manner. More information on citating sources can be found here:
 * Review the citation information in the training material, a 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.
 * Look over the following information and decide how you want to organize your article (or reorganize if appropriate).
 * Review the proposed style guidelines for gene and protein articles.
 * Review the proposed structure for WP:Cell Signaling articles. Note that this proposal has received few comments, could probably be improved by you, and you may have a better way to structure your article.
 * Consider whether it might be better to use a Summary article style with many links to the individual proteins in the pathway, in which case your contributions may be to multiple articles, not just one.
 * Begin writing in your sandbox. Write one or two paragraphs (approximately 200 - 500 words) with in-line citations. The primary purpose of this exercise is to learn to edit the Wikipedia way rather than to write perfect prose. There will be ample opportunity to edit and improve. Due 13 February 2013.
 * Coordinate with your team members to review their work. Get the link to their assignment. Give them the link to your assignment so they can do their role. Leave time to do this before the final deadline, because you will have to revise your entry according to their comments. You might consider having a session together so you can contribute your role efficiently and chat with them as you do it. Teamwork works well with frequent face-to-face contact.

What will be graded? Your article selection should be indicated on the course page and your user page. The course template should appear on the talk page of the article. Your user sandbox should include a beginning bibliography and your edited paragraph(s). Your contributions to your classmates work will also be evaluated. (10% of total project grade).

Assignment 4: First Contribution
When is it due? Monday, 18 March 2013, 11:59PM

What do I do?
 * Move the content from your sandbox into your article. Remember to check your watchlist to look for feedback or changes made by other Wikipedians.
 * Make a substantial contribution to your article. This contribution will vary depending on the amount and quality of the content at the beginning of your project. General guidelines:
 * If you focus your assignment on adding prose, you should add approximately 8 to 10 paragraphs of new sourced content. You could theoretically remove 20 paragraphs of poorly written, poorly sourced content to do this, while improving the article. 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.
 * Instead of words, you may add or update one or more infoboxes, figures, graphs, and/or tables.
 * You may find the handouts on “Uploading images” to be helpful.
 * Creation of an original figure will count for more than adding an existing figure.
 * Since there will be so much variation, you are advised to discuss your plans and expectations with your instructor as soon as your article has been selected.
 * 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.
 * You may edit live or start in your sandbox. There are pros and cons to each approach:
 * The sandbox allows you to edit without the pressure of experienced Wikipedians reading your drafts or altering your writing while you try to learn Wikipedia rules and structure. Spending more than a week or two in sandboxes is strongly discouraged.
 * Editing live is exciting because you can see your changes to the articles immediately and experience the collaborative editing process throughout the assignment. Edits to your work will help you to learn the Wikipedia rules.

What will be graded? Your wikipedia entry. Use the history page to show the "diffs" on your user page as you did for Assignment 2. (20% of total project grade).

Assignment 5: First peer review
When is it due? Monday, 25 March 2013, 11:59PM

What do I do?
 * Peer review two articles by your classmates. You will be randomly assigned two articles on the course page.
 * Before you start, you should review “Evaluating Wikipedia article quality.”
 * This is your chance to critically evaluate your classmates' topic and writing. Use your knowledge of Wikipedia and your knowledge of Signal Transduction to generate comments about how each of the two articles might be improved. Start a new section on the article's talk page with the title "Comments from ..." and add your user name. Please feel free to make minor or uncontroversial edits to the article you are reviewing yourself, but if the suggestions are more substantive or ones that could generate disagreement, please make a comment on the talk page about how the article might be improved. Some specific things to say or do to assist in this assignment include:
 * verifying that random portions of the article accurately represent their cited sources,
 * proposing new ways of phrasing the material to make it more clear and to reduce unnecessary words,
 * suggesting ways to make the lead section follow Style Guidelines more closely,
 * identifying potential gaps in knowledge that should be contained in a well-written encyclopedic entry on the subject,
 * identifying places where there is ambiguity or inaccuracy over which sources are supporting what content,
 * suggesting alterations in the order of prose, sentences, paragraphs or sections for organizational purposes,
 * leaving questions on parts of the article that could arise in the mind of a reader that should be clarified,
 * ensuring that the content is within Wikipedia's guidelines (such as neutral point of view) and avoids plagiarism or too-close paraphrasing.

What will be graded? Your talk page section and your edits to the article will be evaluated to judge the quality, thoroughness, and thoughtfulness of your feedback. Comments that demonstrate 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. (10% of total project grade).

PLEASE NOTE: Details of Assignments below here are subject to change, although due dates are not
In particular, Assignments 7-9 will be modified to emphasize bringing your article to Good Article Status

Assignment 6: Second contribution
When is it due? Monday, 15 April 2013, 11:59PM

What do I do? In this assignment you will further use your expertise in signal transduction to improve Wikipedia. Focus on extending the entry that you have chosen in Assignment 4. Remember to follow the general format of Wikipedia with lots of headings. Push the article closer to Good Article quality.
 * Address peer review comments, revise issues you now see in your first 8 to 10 paragraphs, and add another 8 to 10 paragraphs. Remember that it is better for you to add fewer words with quality content than an arbitrary paragraph count. Instead of words, you may add or update one or more infoboxes, figures/graphs/tables, and pictures from open access sources.
 * What if the topic I chose for the first 8 to 10 paragraphs does not have enough information for another 8 to 10 paragraphs? Ideally, you choose a deep topic with lots of information in the first place, one where you could even add 50 paragraphs, with enough sub categories. But if you run into trouble, discuss options with your instructor. It may be appropriate to contribute to protein articles that link to the pathway instead of adding more to your original choice.
 * What do I do with the two sets of peer review comments my colleagues have put up on my entry? You should respond to these comments carefully. Use them to improve your article. Do not ignore them. As you fix your piece, you should also put comments in the Talk section as to what you are doing.
 * What if other Wikipedians have taken down or totally changed my first 8 to 10 paragraph entry? Look at why they did this. If it is because there were serious problems with it, fix them. If it is because the others felt the material did not fit, and you disagree, discuss with them and make your arguments. Get help from our class Ambassador and others in the class to participate. Do your best to modify your material so that it can be maintained. Try to understand what is going on. Ask us. But ultimately, this assignment is about contributing additional content on different information from the first contribution. Try to learn from your experience so the new words stick.

What will be graded? Your wikipedia entry. Use the history page to show the "diffs" on your user page as you did for Assignment 2. (25% of total project grade).

Assignment 7: Second peer review
When is it due? Monday, 22 April 2013, 11:59PM

What do I do?
 * Peer review two articles by your classmates. You will be randomly assigned two articles on the course page. These will be different from your first peer reviews.
 * Before you start, you should review “Evaluating Wikipedia article quality.”
 * This is your chance to critically evaluate your classmates' topic and writing. Use your knowledge of Wikipedia and your knowledge of Signal Transduction to generate comments about how each of the two articles might be improved. Start a new section on the article's talk page with the title "Comments from ..." and add your user name. Please feel free to make minor or uncontroversial edits to the article you are reviewing yourself, but if the suggestions are more substantive or ones that could generate disagreement, please make a comment on the talk page about how the article might be improved. Some specific things to say or do to assist in this assignment include:
 * verifying that random portions of the article accurately represent their cited sources,
 * proposing new ways of phrasing the material to make it more clear and to reduce unnecessary words,
 * suggesting ways to make the lead section follow Style Guidelines more closely,
 * identifying potential gaps in knowledge that should be contained in a well-written encyclopedic entry on the subject,
 * identifying places where there is ambiguity or inaccuracy over which sources are supporting what content,
 * suggesting alterations in the order of prose, sentences, paragraphs or sections for organizational purposes,
 * leaving questions on parts of the article that could arise in the mind of a reader that should be clarified,
 * ensuring that the content is within Wikipedia's guidelines (such as neutral point of view) and avoids plagiarism or too-close paraphrasing.

What will be graded? Your talk page section and your edits to the article will be evaluated to judge the quality, thoroughness, and thoughtfulness of your feedback. Comments that demonstrate 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. (10% of total project grade).

Assignment 8: Respond to peer feedback and solicit reviews from other Wikipedians
When is it due? Monday, 29 April 2013, 11:59 PM

What do I do?
 * Respond to the two sets of peer review comments and edits from your colleagues. Use them to improve your article. Do not ignore them. As you fix your piece, you should also put comments in the Talk section as to what you are doing.
 * Agressively solicit more reviews from our Ambassadors and especially from other Wikipedians. You can add a request for review on the User talk page of Wikipedians that have been active on your page in the past (check the page history) or on related pages. In addition, you are likely to find active Wikipedians with some knowledge on your topic from the WikiProject Molecular and Cell Biology and WikiProject Cell Signaling pages.
 * Why are links so important? Where should I add them? You should add links both in your piece and in other pieces so they link to your piece. The internet in general and Wikipedia in particular are all about links. Links in other articles will attract potential reviewers and interested readers to your page.

What will be graded? It will be to your advantage to get as much feedback as possible as early as possible. Your responses to this feedback will be graded as part of Assignment 9.

Assignment 9: Final contribution
In this assignment you will put the final touches on your entry, responding to all comments, pushing it towards Good Article status. You will also visit your colleague’s article and talk pages, helping the entire class achieve their best possible work.

When is it due? Wednesday, 8 May 2013, 11:59 PM

What do I do?
 * In this assignment you continue to modify your entry, responding further to reader comments. You may want to add links, references, headers, images, polish the entry, and work hard to move your article toward GA status. You should also help your colleagues by commenting further on their articles, helping them attain GA status. Look back through all the comments, do some more reading, bring the piece up to your highest possible level.
 * What if other Wikipedians have taken down or totally changed my previous entries? Look at why they did this. If it is because there were serious problems with it, fix them. If it is because the others felt the material did not fit, and you disagree, present your arguments to them. Get help from our class Ambassador and others in the class to participate. Do your best to modify your material so that it can be maintained. Try to understand what is going on. Ask us. But ultimately, this assignment is about improving content for the entire article. Try to learn from your experience so the new words stick.
 * Can I make changes after the due date? The entire Wikipedian community will be grateful if you continue to make contributions to improve Wikipedia after the assignment is complete.

What will be graded? Your final wikipedia entry (10% of total project grade) and your contributions to your classmates (5% of total project grade).

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


 * WikiProject Cell Signaling
 * Main Page
 * Their assessed articles. Note that very many signal transduction related article have not yet been added to this list.


 * 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.