CH391L/S14/WikiEditing

Getting a SynBioCyc login
SynBioCyc uses the MediaWiki system that may be familiar to you from Wikipedia.

The instructors will create an account for you that uses your official email address listed in the UT directory unless you give us a different email address to use on the first day of class.

Link to create account (only available to administrators)

First steps

 * Read the Wikipedia How to edit a page topic
 * Glance at the Wikipedia Cheatsheet.
 * Check out a more complete list of Wikipedia Markup Reference and MediaWiki Editing Reference.
 * A great way to learn new tricks is to click the edit button on existing OpenWetWare Wiki, SynBioCyc Wiki, or Wikipedia pages to see their formatting.
 * But, be aware that some extensions to Wiki Markup behave differently between the Wikis!
 * When testing out Wiki code for the first time, you should edit the Sandbox topic. Feel free to write over whatever is already there.

Remember

 * Be bold. It's not possible to make any mistakes editing that will cause permanent damage. At the very worst, your changes will be reverted to the previous version of a document.
 * Be professional. Your edits are immediately visible to the entire world.
 * DO NOT plagiarize and be careful about infringing copyright.

Creating a New Page
For pages that you create for this class, please use names that begin with "CH391L/S14". This will make it easy for us to not to step on other people's toes. The easiest way to create a new page is to create a link (on the main page) and then click on that link to edit the new page.

CH391L/S14/YourPageName Link text that you want to display rather than page name

Categorizing Your Page
You should add a category tag to both your topic page and your topic's talk page. This ensures that they show up under an index of "CH391L/S14" topics and that they are included in a rundown of recent changes to our pages (linked from the main page).

Adding Images and Files

 * 1) First click the "Upload file" link in the left sidebar and upload your file or image to the OWW Wiki.
 * 2) *You should give your file a very descriptive name, so that it doesn't clash with files uploaded by others.
 * 3) *Prefix the upload filename with the course number and date so that it will be obvious where it came from.
 * 4) *e.g.,  or
 * 5) Now edit the Wiki page where you want the file to be linked from or the image displayed.
 * 6) *For images, to display the image embedded in the page add a tag of the form: [[Image:CH391L_S14_Your_File_name.png | frame | right | Short description of image]] If the image needs to be resized within your topic page, you can specify to use a thumbnail: [[Image:CH391L_S14_Your_File_name.png | thumb | left | Short description of image]] Or a fixed number of pixels for the width: [[Image:CH391L_S14_Your_File_name.png | thumb | right | 150 px | Short description of image]] You can can also specify some additional display options for images, including adding a border.
 * 7) *For files, you can link to the file using this Wiki markup: [[Media:CH391L_S14_Your_File_name.png | Name of link to your file]] It will link to the page which gives details about the file (when it was uploaded, its size, etc.) instead of directly to the file, if you use this syntax: CH391L_S14_Your_File_name.png

Creating an Annotated References Section
Add references using the Biblio Extension.

To add a citation to a paper in Pubmed like this Elowitz2011, the code is:

Elowitz2011

To add the corresponding bibliography item, like this:


 * 1) Elowitz2011 Nandagopal, N, and Elowitz, M.B. (2011) Synthetic biology: Integrated gene circuits. Science 333:1244-1248.
 * 2) Venter2010 pmid=20488990
 * 3) Luisi2010 isbn=0521528011

You could use this code:


 * 1) Elowitz2011 Nandagopal, N, and Elowitz, M.B. (2011) Synthetic biology: Integrated gene circuits. Science 333:1244-1248.
 * 2) Venter2010 pmid=20488990
 * 3) Luisi2010 isbn=0521528011

Notice the three different ways of citing works:
 * 1) Writing out the reference yourself in Wiki markup
 * 2) Referencing a PubMed ID (which you can look up on PubMed)
 * 3) Referencing an ISBN number (which you can look up on Amazon.com)

You must briefly summarize the main idea of each article that you cite or annotate why you cited it within the reference list. Use a style like what is done for selected highlighted articles in the Nature Reviews style. For example, an annotation for the first article in the list above might look something like this:

// Synthesis of an entire 1.08 Mbp Mycoplasma mycoides genome from scratch and successful transplantation into recipient cells.
 * 1) Venter2010 pmid=20488990

Use the code:

// Synthesis of an entire 1.08 Mbp Mycoplasma mycoides genome from scratch and successful transplantation into recipient cells.
 * 1) Venter2010 pmid=20488990

Beware: Wikipedia uses a different Wiki extension for references than SynBioCyc, so the syntax is not the same!

Talk Pages
The "talk" tab at the top of a page is for commenting on edits to a page, rather than for editing the content. You will edit the Talk pages to provide feedback and constructive criticism on articles written by other participants in the class. Do not erase other people's comments on the Talk pages. Instead, add your own responses, comments, and ideas at the bottom of the page or after a comment and indented if they respond to a particular question or thread.

Here is the structure of a typical Talk page discussion:


 * Jeffrey Barrick 19:48, 22 January 2012 (EST):I think you might provide some more details here about how to use talk pages.
 * Jeffrey Barrick 19:53, 22 January 2012 (EST):By golly, you're right! Here is an example of the structure of a typical talk page from the Wikipedia article about Gdańsk.
 * Jeffrey Barrick 19:58, 22 January 2012 (EST)':Remember to automatically sign your username and a timestamp using this syntax ~.
 * Jeffrey Barrick 20:03, 22 January 2012 (EST):You can probably track down other Wikipedia pages with even more lively Talk pages to look at for examples of how they are used for discussions.

Edit this section of the page to see the full syntax for the example above.

You should group comments and replies using indent levels. For example:
 * Comment 1
 * Reply to Comment 1
 * Reply to Reply to Comment 1
 * Comment 2


 * Comment 1
 * Reply to Comment 1
 * Reply to Reply to Comment 1
 * Comment 2

Copyright Issues
Copyright of scientific publications is a complicated and contentious issue. Most scientific work is publicly funded, yet published in journals that are run by for-profit publishing companies that handle editing and distribution. When you publish in these journals, you generally must sign over copyright of your material to these publishers. For work supported by NIH grants, authors are required to submit their final accepted manuscript (before copy editing by the journal) to PubMed Central, where they are freely accessible (but still subject to copyright).

Because we editing a public wiki, you should be very careful to not post any work from a scientific publication that may infringe on these copyrights. Posting copyrighted material may cause the people who run SynBioCyc to get "takedown notices" that they must remove certain materials from this website.

Then again, under the "fair use" doctrine of copyright law, you are allowed to reproduce portions of copyrighted works for non-profit educational purposes. There is a substantial grey area about what that means, so I am providing you with some guidelines, but in the end you are responsible for the decision on what to post when working on a topic.

Guidelines for "fair use" under copyright law

 * Always provide a citation and link to the original article.
 * For copyrighted works, you absolutely may not post a full article or large portions of a article without permission of the publisher. Do not post PDFs of articles to OpenWetWare.
 * Because you are creating scholarly works for non-profit educational uses, you may generally post direct quotations as long as you attribute the original article and they do not constitute a majority of the copyrighted work.
 * In some cases, you may reproduce figures from a scientific paper directly in your page to comment on them.
 * It is debatable under fair use, whether you can directly post a figure from a copyrighted article (for example, from a review in a Science or a Nature journal). You should generally avoid posting images from these types of articles to be on the safe side. It is better if you can make your own figure with the key information or describe it in words and attribute or link to the original source.
 * Under no circumstances should you display multiple figures from the same scientific paper. In addition to showing that you have not drawn on a sufficient number of sources in your research, reproducing large portions of a work definitely infringe on copyright.
 * PLoS and BioMed Central journals are covered by the Creative Commons License. This license does allow you to reproduce their figures and upload them to OWW if you would like.
 * If an article and its figures are available from PubMed Central, consider linking to the article and its figures in PMC.
 * Selected articles in other journals such as PNAS are sometimes published under an "open access" option. Do not confuse this with being published under a less-restrictive license. These works are still subject to the same copyright restrictions as all other articles in the journal, although you are able to freely access them on the publisher's website immediately upon publication. Consider linking to the article and its figures on the publisher's website.

Example of best practices
Check out the sources of images in this Wikipedia article on Riboswitches.

Notice:
 * The three-dimensional structure drawing is not from a scientific paper, but is an original image created by a user from coordinates downloaded from the Protein Data Bank (PDB).
 * Many of the images have been directly contributed by a user who has modified them from the originals published in his own scientific articles.

For more information
OpenWetWare Copyright http://openwetware.org/wiki/Copyright

US Copyright Office http://www.copyright.gov/fls/fl102.html

Stanford Fair Use page http://fairuse.stanford.edu/Copyright_and_Fair_Use_Overview/chapter9/index.html

Fair Use Check-List http://copyright.columbia.edu/copyright/fair-use/fair-use-checklist/

PubMed Central Copyright Notice http://www.ncbi.nlm.nih.gov/pmc/about/copyright/