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"" Configuring your Gene Expression Viewer ( Xenbase.org )
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The Interactive Gene Expression is written using JAVA 2 (J2SE 1.3.1). Every attempt has been made to remain compatible with JAVA 1.1 and embedded Virtual Machines. A Virtual machine refers to the "computer program" that runs "JAVA" programs (see terms explained at the bottom of this page) |
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It is necessary to use and configure the "plug-in" version of the Java Virtual Machine
to view LARGE DATA SETS. If you don't have the "plug-in" version of the Sun Microsystems Java Virtual Machine
you may obtain it HERE .
To view a LARGE DATA SET configure your browser to allow a Large Heap. This procedure is described in detail by Sun Microsytems. Here are brief instructions for a Macintosh and a Windows based system. (This example is for computers with more than 256 megabytes of physical memory) Macintosh OSX located at applications/utilities/java/Java *.* Plugin Settings (If there is more than one java settings program, consider changing all.) in the field labeled "Java Runtime Parameters" enter the follwing runtime parameter -Xms256m -Xmx256m WINDOWS 2000 Professional from the Start Menu goto Settings/Control Panel double click on the Java Plugin 1.*.* (If there is more than one java settings program, consider changing all.) in the field labeled "Java Runtime Parameters" enter the follwing runtime parameter -Xms256m -Xmx256m Here is a brief explanation of the syntax:"-Xms256m -Xmx256m" -Xms (at start of application) -Xmx (maximum allowed) 256 (amount) m ( for megabytes) or g (for gigabytes) |
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(generalized explanations) |
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A Virtual machine is the "computer program" that runs "JAVA" programs That's right, a program that runs programs. In some situations this is called the run-time compiler. Java is a language that is run-time compiled. The use of a run-time compiler is why a "JAVA" program may not run as fast as a program written in another language, but this is also why the "same" program will run on many different machines. Virtual machines are usually included with your web browser or installed seperately as a "plug-in". |
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An embedded VM or Virtual Machine usually refers to the Virtual Machine some web browsers are installed with. These embedded VM's are notorious for having "quirky" implementations of a JAVA run-time compiler, and are not always capable of using the most recent version of JAVA. |