BASIC PROTOCOL 1: NAVIGATING THE WormBase HOME PAGE
A standard computer with a reasonably fast connection to the Internet (cable modem, DSL, or Ethernet recommended)
Web browser such as Internet Explorer (http://www.microsoft.com) or Firefox (http://www.mozilla.org/firefox)
The home page for the main WormBase site, http://wormbase.org allows general searches, gives links to specialized searches, and has news about improvements to WormBase.
This page is divided into several parts. At the top is a large, simple menu bar giving quick access to six popular search pages, a Web form for submitting comments or new data, an all-purpose Searches page, and a Site Map. This bar appears at the top of all of the WormBase pages and also includes a link back to the home page (http://www.wormbase.org/wiki/index.php/Image:Fig_1_8_01.png). On the home page immediately below this menu bar are the serial number of the data release currently in use, and the official WormBase logo.
The next section of the main page has fields and menus that are used for a basic search of the full database (http://www.wormbase.org/wiki/index.php/Image:Fig_1_8_01.png). A user can choose searches from any of over 20 different data types from the "Search for" drop-down menu (http://www.wormbase.org/wiki/index.php/Image:Fig_1_8_01.png). The check boxes immediately beneath the search fields offer choices to require strict identity for search terms, to give results in XML format, or to search primary research articles in depth with Textpresso (http://www.textpresso.org; Muller et al., 2004).
Below the basic search section are a directory for the entire WormBase site (http://www.wormbase.org/wiki/index.php/Image:Fig_1_8_01.png), and news about C. elegans bioinformatics. Near the bottom of the page is a Links section (with connections to several other sites about C. elegans which complement WormBase in some way), and a list of other sites running WormBase itself (the development server, a data-mining server, official mirror sites, and archival data freeze sites for http://wormbase.org). Finally, the bottom of the page gives a link for users to make comments or ask questions to the WormBase staff, and other links to WormBase policies on copyright and privacy; these links are given on every WormBase page.
WormBase has a development site (http://dev.wormbase.org) which uses the very latest data release and site software, while the main site lags by one release; while closely similar, the main site focuses on stability and the development site on novelty.
The examples of searches given in the following protocols are intended to be illustrative, but not exhaustive; many other searches are possible.