You may be here because you were not able to get run one of the following applications:

• Tutorial on hemoglobin structure
• Protein Explorer
• Some graphical application in an instance of BioBIKE

Most problems are solved by using an appropriate browser (even if your browser complains that your version of Java is out of date).
Sometimes you really do have to update Java on your computer.

Choosing an appropriate browser
Starting September 2015, some browsers have decided to no longer support Java applets. Here is the status as of September 2017:

• Firefox
  
  • Firefox version 52 (released March 2017) and later do not support Java applets.
  • Hemoglobin tutorial will not run
  • Protein Explorer will not run
  • BioBIKE runs fine, but a few graphical applets do not (you'll probably never have a cause to use them).
• Chrome
  
  • Chrome version 45 (released September 2015) and later do not support Java applets.
  • Hemoglobin tutorial will not run
  • Protein Explorer will not run
  • BioBIKE appears to run fine but in reality will fail in subtle ways. Don't use Chrome with BioBIKE.
• Internet Explorer
  
  • Internet Explorer (IE) does support Java applets
  • Hemoglobin tutorial even so will not run
  • Protein Explorer even so will not run
  • BioBIKE fails completely
• Safari for Mac OS X
  
  • This browser is reputed to support Java applets.
  • Hemoglobin tutorial probably runs (I haven't tested)
  • Protein Explorer probably runs (I haven't tested)
  • BioBIKE fails completely under Safari
• Safari for Windows
  
  • This browser does not support Java applets.
  • Hemoglobin tutorial even so will not run
  • Protein Explorer even so will not run
  • BioBIKE fails completely
• Firefox ESR
  
  • The Extended Support Release (ESR) version of Firefox is frozen in time as of March 2017, except for periodic security updates. It supports Java applets.
  • Hemoglobin tutorial works
  • Protein Explorer works
  • BioBIKE graphical applications should work (I haven't tested everything)
  • Here's how to install it.

Updating Java
If you are using an appropriate browser (see above) and you still get a complaint about Java being out of date, the problem may be that Java really is out of date.
Try the following:

• Update Java
• Go into your Java Control Panel (in Windows from the Windows Control Panel)
• Go to the Security tab
• Click Edit Site List
• Click Add
• Copy/type in the resulting blank box: http://www.umass.edu (the beginning of the URL that failed)
• Press OK

(If you have any other advice that would work better than the above, please let me know)