CH391L/S12/WikiEditing

Introduction to Wiki editing

Register on OpenWetWare

OpenWetWare uses the MediaWiki system that may be familiar to you from Wikipedia.

You must register to edit the OpenWetWare Wiki to participate in this course.

Complete the form here

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.
A great way to learn new tricks is to click the edit button on existing OWW Wiki or on Wikipedia pages to see their formatting.
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.

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.

Here is the structure of a typical Talk page discussion:

I think you might provide some more details here about how to use talk pages. Jeffrey E. Barrick 19:48, 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 E. Barrick 19:53, 22 January 2012 (EST)

Remember to automatically sign your username and a timestamp using this syntax '''~~~~'''. Jeffrey E. Barrick 19:58, 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. Jeffrey E. Barrick 20:03, 22 January 2012 (EST)

You should group comments and replies using indent levels. Edit this section of the page to see the syntax.

Copyright Issues

Copyright of scientific publications are a complicated and contentious issue. Most scientific work is publicly funded, yet published in journals that are run by for-profit publishing companies which 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 are guests on the OpenWetWare 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 OpenWetWare 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 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 the original source.
- 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 BioMed Central 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 to 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.