Biodefense:FAQ
From Biodefensewiki
[edit] I Forgot my username and or password
Check Special:Listusers for your user name. You can get the wiki to send you a new password for your username.
[edit] What's a wiki
A wiki is a collaborative document. The word "wiki" is derived from Hawaiian pidgin meaning "quick". The wiki concept was created by Ward Cunningham in the late 1980's. The word "wiki" corresponds to the concept, the software and the actual document.
[edit] What's the purpose of this wiki
This wiki was started to create a working knowledge base. The contributed nature of this document allows for users to increase upon existing knowledge as it changes. This document also serves to help organize and plan experiments across disparate labs where different lab focuses can be expounded upon to share appropriately the expertise of each lab in a manner that is contributive to the larger group. Everyone should feel free to modify/correct/add to this wiki.
[edit] What software does this wiki use
This wiki runs on MediaWiki 1.10.0 from the Wikimedia Foundation. MediaWiki runs such sites as Wikipedia, Wikispecies, Wikibooks, Wikinews, and Mozilla's wiki.
[edit] What web browsers are supported
Any CSS 2.0 compliant web browser will work fine (Mozilla Firefox, Mozilla, Safari, Konqueror, Opera). Microsoft Internet Explorer does not render everything correctly but is quite functional for use with the wiki. MS IE has some issues with rendering png files.
[edit] How do I start a new article
You can start a new article by simply typing in a name in the address bar. Replace ~/NIAID/wiki/index.php/Main_page with ~NIAID/wiki/index.php/New_Article to create an article called "New Article". Note that a space is created by inserting and underscore (SHIFT with -). Creating a new article will lead you to a blank page. Populate the new article by editing the page and saving the changes.
[edit] How do I use the wiki
To use the wiki, just search with the search bar to find articles. There are some issues with automatically installing this plu-in on Mac and may have to be done manually. On a *nix system, you must be root.
You can also browse by category or subscribe to the RSS/ATOM feeds found on the toolbox of the new pages.
Editing the wiki requires the use of special formatting. Most formatting is similar to HTML and in many cases, HTML can be used directly. For some standard commands, visit Help on Editing.
See the Sandbox for examples and practice wiki text.
[edit] How do I use special characters and mathematical equations/formulas
Greek characters can be called by preceding the character name by "&" and following by ";". For example, the character β is coded by β. This is covered in Help on Editing. For mathematical formulas, see Help on Formulas. Superscript and subscripts are easily coded by enclosing the relevant text with the tags <sup>superscript</sup>and <sub>subscript</sub> which will appear as superscriptsubscript.
[edit] Do I need to create a login
Yes! You cannot edit or read pages unless you login. Anonymous users are restricted to the Main Page and the FAQ. If you do not have a user name, please email the admin and a user/pass will be emailed to you. Please edit your own user profile so we know which contributors come from which labs.
[edit] How do I categorize a new article
To file your article under a category, insert a category tag at the end of your entry. You can add multiple category tags if your article falls under multiple categories. The tag should appear as follows:
[[Category:My_category]]
where My_category represents the category name. Note the "_" denoting a space. If a category does not exist, a new one will be created. Edit the new category with text to describe it.
[edit] How do I upload files and what formats are acceptable
To upload a file, choose the "upload file" tool from the toolbox or special pages. At this time, you can upload files with the extensions 'gif', 'odf', 'png', 'jpg', 'jpeg', 'ogg','doc','xls','ppt','mp3','sxc','pdf', 'zip', 'tar', 'gz', 'bz2', 'flv', 'swf'. If a file format is not supported, email the wiki administration --currently jeremy.seto@mssm.edu-- with a request to permit a new file type. Many file types are treated as images (eg. pdf).
[edit] Description Page for Uploads
Every time a file is uploaded, it is treated as an "Image" with an associated description page. You are immediately prompted for the location of the document on your local system, the name you wish to call it in the wiki and a summary box for your description of the document. It is useful to add a summary/description of your file on this page. This serves multiple purposes.
- it allows for easier searching by the Mediawiki/MySQL search mechanism.
- you don't have to depend on a link in an article to describe your "Image".
- filenames may not be descriptive enough (or at all).
- avoiding ambiguity
- Often, there will be more than one pdf file about "YourFavoriteMoclecule" and it would be confusing to name each article YourFavoriteMoclecule.pdf, YourFavoriteMoclecule1.pdf, YourFavoriteMoclecule2.pdf, etc.
- avoid orphaning and duplication
- the description may also serve to log changes to continuously changing files. Embedding a citation and/or providing a useful description avoids orphaning or duplication of documents.
- making it easier for people to find images
- if it is a product sheet, write a description of what the product is and where it comes from.
Citation Convention
- Authors. Title. Journal Name. YearVolume():pages. PMID and link to Abstract
- which looks as follows in wiki mark-up:
- Authors. [[media:Yourarticle.pdf|'''Title''']]. Journal Name. YearVolume():pages. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi PMID and link to Abstract]
- using the citation convention provides an easy and useful way to copy/paste into references for wiki articles.
[edit] How do I add a file to a page?
After the file is uploaded (see above) it is represented as an image with its name, eg. abcd.pdf. If you need to know the name, look for it on special pages, file list.
Then type the following on the page which you want to have a link to the uploaded file, for example if you want to have a link to the file above (abcd.pdf) that says: "download the paper here" you type (without the quotation marks): [[Media:abcd.pdf |download the paper here]] which is displayed as download the paper here
[edit] What's wrong with MS Office files
Office files don't currently want to open properly when clicking on a direct link to a [[media:something.xls]]. The solution is to right click (or Command+click on Mac) and select "download link as" or "save link as" to your local system. Then open the file in the associated program on your own computer.
[edit] What is the default theme
Mediawiki is a skinable program. Individuals can personalize the way the TSBwiki looks by selecting a different skin under preferences. TSBwiki currently uses a modifed version of "cavendish" from the Mozilla wiki. Navigation is currently easiest using this theme. Feel free to suggest or submit a wiki skin. Cavendish and Monobook are the recommended themes since they support our custom features.
[edit] Should I include citations
Yes! This is a scientific wiki so citations are necessary. Unfortunately, the first populater of this wiki was really bad and did not insert appropriate citations.
[edit] What's a stub
A stub is an early or incomplete article that needs major revision, editing and correction. If you see a stub, please add to it. When the article has sufficient information and is styled for the wiki, you can remove the stub label.
[edit] New/Change titles
You can create a new title or change the title of an existing article simply by using the "move" feature. Any linking articles will automatically refer to the new location.
