Note: Javascript and Java are very different.
Oracle has made fundamental changes to the way applets work. For over 15 years, applets that followed the rules for applets were allowed to run in browsers; however, Oracle has now changed this.
For the time being, to get Java applets to run you need to go into the Java control panel and add http://www.scienceourseware.org/ & http://www.scienceourseware.com/ to the site exception list in the security tab. Alternatively, you could change the security level for Java to medium which would allow unsigned applets on all sites to run. Note that on Windows, the Java control panel installed into the Windows Control Panel is out of date. Please run the "Configure Java" program from the Windows Start Menu to get the site exception list option.
Below this message, a black box should appear with white lettering that says "Java is Running". Below that will be the version of the Java Virtual Machine that is running in your browser. As long as this box appears and the version is 1.1.8 or greater, you should not have problems with any of the Java applets on this site.
The exception to this is if the name of the Java VM manufacturer is Microsoft. If it is Microsoft, you should upgrade to Sun's Java VM by going to http://www.java.com/.
Please note that it can take a while for the Java box to appear.