MediaWiki

MediaWiki

This page is a placeholder, or under current development; it is here principally to establish the logical framework of the site. The material on this page is correct, but incomplete.

MediaWiki is the free, open source, collaborative document authoring software that Wikipedia runs on. Deployed on countless sites from single user to enterprise scale, it is easily configurable and extensible, yet stress-tested for very large loads, remarkable secure and very robust. It is written in pure PHP + Javascript, runs on MySQL (or other backends). This page explains the principles.

 

Introductory reading

Overview of the software: [1]

A MediaWiki feature list: [2]

 

Contents

Links to

• Installation (and dependencies)
• Upgrading
• Configuration
• Editing
• Media files and rich content
• Customizing
  • Templates
  • CSS
  • Extensions
  • Skinning: http://blog.redwerks.org/2012/02/08/mediawiki-skinning-tutorial/
• Management of users and rights; deleting users and edits

 

Wiki Assignment

This page is part of my Course Wiki which contains the syllabi and other course resources that (usually) only I edit. To actively collaborate, host students' contributions and submit assignments, I have provided a second, independent Wiki, the Student Wiki. This is a reasonably private environment: only users who have accounts on the system and are logged in can view and edit pages. This means in order to participate in the course you must have an account on the Student Wiki and that should have been set up at the first lecture. Contact me if you still need an account.

If you have previously worked through this task for a different course, take a few moments to review the points anyway. Then add a correct, current category tag to your user page

 

For BCH441/BCH1441:	[[Category:BCH441_2016]]
For BCB410:	[[Category:BCB410_2016]]
For BCB420/JTB2020:	[[Category:BCB420_2016]]

 

Collaboration is a common theme for modern lab work and a Wiki is a great way to share and seamlessly update information in groups - or just for yourself. Probably the most sophisticated Wiki software is MediaWiki, a set of PHP scripts that is under continuous development by the Wikimedia foundation; it is the same software that runs Wikipedia. This is open source, free software that is easy to install, is well documented and requires very little resources other than a machine that runs a MySQL database server and an Apache Web server. Numerous extensions exist (and extensions are not hard to write); they enhance the already rich functionality. But let's start with small steps. By now, you should already have an account on the Student Wiki, and I have configured the Wiki so that

• only logged in users can view the pages;
• all logged in users can create and edit pages at will.

This means you could edit pages that don't "belong" to you. Respect the "House Rules" that are posted on the Main Page of the Student Wiki and don't edit other's things without permission, even if you can think of a particularly witty comment or hilarious prank. If you want to comment on a page: every page has an associated "Discussion" page (sometimes this is called the "talk page") that you can freely edit. It is accessible via a tab at near the top of each page. Remember to "sign your name" to discussion entries.

Task:

• Access the Student Wiki;
• log in and navigate to your user page;
• open the "Help" link in the left-hand sidebar in a separate tab;
• follow the link to the "Editing" page on the Student Wiki;
• learn and practice basic editing syntax by editing your User Page:
  • enter your name,
  • your major(s), specialist program, year of study - or your lab and thesis theme if you are a graduate student;
  • your special interests and/or skills in the field;
  • enter your eMail address.
  • Add a category tag to your User page (see above).
  • I propose adding a small, recognizable picture of yourself to the page. There's probably a regulation somewhere that says I can't require this due to "privacy" considerations. But (a) it doesn't have to be a formal portrait, something like a Facebook profile is fine as long as we can begin recognizing each other in class, and (b) if we collaborate with each other in class, on the mailing list, on the Wiki and elsewhere, it's really important that we can associate a name with a person. it actually helps me a lot when I define participation marks.

Feel free to look at my User Page for code examples: clicking on the edit link will show you the source text. How do you find my User Page? Good question ...

• Create a subpage to your User Page; call it "Resources" or something similar. Note: the link MUST be in your "User space". If you don't add the prefix User:yourname/... before your page name, the new page will end up in the main "namespace". I'll then have to delete it. That's not good because you have then failed this part of the assignment. Make sure you know what you are doing, for example by looking at the code on my User Page, asking someone who knows, or asking on the mailing list.
• Put some text on your new page - perhaps a link to a Wikipedia article, or to PubMed, or to the NCBI. Make sure you understand the difference between an internal link and an external link (they have slightly different formats), and you understand the concept of namespace and categories. Also add a category link to that page.
• Play around some more. Feel free to ask how to go about achieving a particular effect that you may have seen elsewhere.

Before you are done, you should be comfortable with the following mark-up conventions and concepts:

• Login and accessing your user page;
• viewing a page's history;
• reverting a changed page to an earlier version;
• basic text formatting;
• "signing" your name;
• creating internal and external links;
• creating sections headers on a page on multiple levels;
• creating a new page (as a subpage of an existing page);
• the concept of namespaces - especially the default ("main") and User: namespace;
• the concept of categories.

I expect that there may be aspects of the Wiki you find puzzling, it is after all a complex piece of software that supports the world's largest collaborative project and one of the busiest sites on the Internet. Do ask about these things on the mailing list. My first encounter with Wikis is a while back and I can't remember everything I was initially confused about.

 

Notes

 

Further reading and resources