Setup for MBIV1.0 Web-based Applet
The mouse brain visualizer is available as an applet that executes within
the context of a web browser or a downloadable jar file. This page describes
what is needed to get the tool running as an applet under
Unix/Linux OSes and Windows using the Netscape or MS Internet Explorer
browsers. For the downloadable version, goto the download
Most Java applets can run "as is", that is, without the installation of
additional libraries beyond those that come with the JRE or SDK or any
extra parameters to the JVM. In order to use web-based mouse brain visualizer,
there are some additional steps that the user must take that are described
Make sure the latest version of Java 1.4.2 is installed; either SDK Version 1.4.2_02+ or JRE Version 1.4.2_02+ would suffice. Note, the applet is NOT compatible with version 1.5.0. If 1.5.0 is the only version installed, the user must install 1.4.2_0X, where X=2+. There is a relatively easy way to make 1.4.2_0X your current JRE execution environment. Refer to Sun's plugin help which describes using the control panel to choose your JRE environment.
The images uploaded via the browser range in sizes from 35MB to 64MB. If
several images are uploaded, in addition to the corresponding atlases (the
actual atlas data set is not uploaded, a set of polygonal vertices is
generated from the atlas on the server, so about 1/10 of the 35MB atlas size
is uploaded), quite a bit of memory can be consumed in the JVM. Since the
JVM has a default setting for the amount of memory it can allocate,
this maybe too small to accomodate a reasonable number of datasets. It is
recommended that the user increase the default heap size of the JVM.
be done using the Java Plugin Control Panel, which can be found in the
Control Panel directory under My Computer. Select the
Advanced tab in the panel. At the bottom of the Advanced
panel, there should be a text box labelled Java Runtime Parameters.
It's recommended that the heap size is set to 250MB; of course, this value
will be a function of the amount of memory in the local system and how many
applications are currently running. The user can opt to allocated more than
250MB. In the text box, enter the following: -Xmx<#MB>, where #MB is
the amount of memory in MBs. Click on Apply to apply the changes.
It's possible that the browser might have to be closed and reoped for the
changed to take effect.
Note: If you download the JRE that we provide (Version 1.4.2_03) a version of the policy file with the proper modifications is provided with the JRE, so the user does not have to download the policy file.
Java's security policy is designed to prevent malicious applets and applications from damaging local computer systems. For example, by default, a TCP/IP socket cannot be established between a users system and a remote system unless the Java application trying to open the socket has "permission". A detailed description of Java Security is beyond the scope of this page, but if the curious user is interested, she can visit Sun's Java Security page for more information. There are several permissions that are needed by the visualization applet tool: 1) socket permissions (accept, connect, listen, resolve) and 2) file encoding permission (read). The user can either add these permissions by editing the security policy file in the JRE on their local machine or download a copy of a security file, which contains ONLY the needed modifications and install it in the appropriate JRE directory.
2.2.1 Modifications to java.policy
Using Windows Explorer or the Command Prompt (or Cygwin bash shell),
navigate to the security directory of the active Java Runtime Environment
(JRE), i.e., C:\Program Files\Java\jre1.4.2_02\lib\security. Open
the policy file,
java.policy using your favorite editor, i.e., XEmacs, NotePad,
etc. Locate the second "grant" keyword, which should have the line
\\default permissions granted to all domains
preceeding it. Find the last (maybe first an only on some systems) line with
the keyword SocketPermission in it. On systems with an unmodified
policy file, the first/last line with this keyword should be:
permission java.net.SocketPermission "localhost:1024-", "accept, connect, listen, revolve"
permission java.net.SocketPermission "126.96.36.199", "accept, connect, listen, resolve"
permission java.util.PropertyPermission "java.vm.name", "read";
permission java.util.PropertyPermission "file.encoding", "read";
2.2.2 Download java.policy File