(2.1) System requirements

(2.1.1) Hardware

A computer system with processor equal to or faster than 1.0GHz, and RAM equal to or greater than 1GB is required.

(2.1.2) JAVA

This software is written in JAVA language, therefore a JAVA environment is required. JAVA software can be downloaded free of charge from: http://www.java.com/en/download/ index.jsp .

An appropriate version of the JAVA software must be successfully installed before this software can be executed correctly. The version of the JAVA software should be equal to or later than “Java Runtime Environment Version 5.0 Update 7” (1.5.07). This software cannot run properly on a computer system with JAVA environment earlier than the specified version. It will show a warning if the JAVA version is out-of-date (See trouble shooting (1), figure 2.1.2-1).

Figure 2.1.2-1 (Click to enlarge)

Important note : check your JAVA version before you install and run this program. To do this:

For windows: click 'start' -> click 'run' -> type in 'cmd' -> hit 'ok' -> type in 'java -version' -> hit 'enter'.

For Linux/Unix: type in terminal window 'java -version'.

For Mac OS: From the desktop, go into Applications -> Utilities, and open Terminal.app. Type in'java -version'.

This software may be used on systems that support JAVA environment, including Windows, LINUX, UNIX, and Macintosh.

(2.1.3) Database connection

Most of the annotation is based on a MySQL connection with the Ensembl (Hubbard et al. 2007) database servers , and a HTTP connection with the HapMap (The International HapMap Consortium. 2005) database servers established by the WGAViewer software on your local machine. Therefore an internet connection is necessary to perform the annotation. For many users from academic institutions, this connection can be directly through port 3306, the standard MySQL port. If this direct connection cannot be established (for example, if you work behind a proxy server) WGAViewer provides an option to establish the connection through a HTTP-MySQL bridge service hosted in Duke University Institute for Genome Sciences and Policy. This option can be accessed through menu “Options -> Online database connections”, as illustrated in Figure 2.1.3-1.

Figure 2.1.3-1 (Click to enlarge)

WGAViewer has been setup to automatically test this connection when it is launched. If the connection cannot be established under the current internet profile (as illustrated in Figure 2.1.3-1), a warning will be shown (See trouble shooting (2), figure 2.1.3-2). In this case you may still load your dataset, for example, the example set released with this package. But you may not perform further annotation tasks.

Figure 2.1.3-2 (Click to enlarge)