Java and Safety
A supplement to FirstGlance in Jmol. Created February, 2013.


What is Java?

Java is the pre-eminent cross-platform computer programming language. Programs written in Java, such as Jmol (both the applet and the application) operate identically on popular computer platforms such as Microsoft Windows®, Apple Mac OS X®, and linux. This contrasts with programs written in other languages (such as the Firefox web browser, Microsoft Office®, or OpenOffice.Org) for which a different implementation of the program is needed for each platform.

FirstGlance in Jmol requires Jmol, which in turn requires Java, in order to operate. Java can be downloaded for Windows systems from Java.Com. For Apple Mac computers, java has been provided as part of Apple Software Updates. Java is not available for certain devices, such as the iPad.

Java is a security threat.

Java has historically had flaws enabling criminals/vandals to commit identity theft and to compromise computers. Simply visiting a malicious website with a java-enabled web browser can compromise your computer.

According to a January, 2013 article:
" Java was responsible for 50% of all cyberattacks last year in which hackers broke into computers by exploiting software bugs, according to Kaspersky. That was followed by Adobe Reader, which was involved in 28% of all incidents. Microsoft Windows and Internet Explorer were involved in about 3% of incidents, according to the survey. "
In January, 2013, the US Department of Homeland Security issued a warning recommending that Java be disabled in web browsers. For a few days at the end of January, 2013, Apple blocked the use of java in web browsers on Mac computers worldwide. This was a major inconvenience to some, but clearly Apple felt the security risks were quite serious. Oracle, the company providing Java, subsequently fixed some of the vulnerabilities in Java (and Apple re-enabled Java on Macs), but most likely other security risks remain.

How to keep your computer safe.

Assuming you wish to use FirstGlance or other Jmol-based resources, such as Proteopedia.Org, you will need java. (If you don't, simply uninstall Java.) How can you minimize your risk?
  1. Whenever an update for Java is available, install it. To confirm that you have the latest Java, visit java.com, click on the link "Do I have Java?" and then on the button "Verify Java".

  2. Do not visit unfamiliar websites. Especially do not click on unknown links or attachments in emails that you receive from sketchy senders. Also be careful when clicking links in google searches.

  3. Disable java in the web browser that you use for general-purpose browsing, email, google searches, etc. Here are instructions for disabling java in a particular browser. Use a different browser for resources that require Java.
      Windows users: Due to a limitation in Internet Explorer, you should use Internet Explorer for java. Use a different browser such as Firefox or Chrome for general web browsing, and disable java in that browser.
    These recommendations were made by Michael Horowitz in his Defensive Computing Blog in his January 2013 post How to be as safe as possible with Java.
Long term solution.

It appears likely that Java-based Jmol will eventually be phased out in favor of a version of Jmol that does not require Java, called JSmol (see also JSmol in the Jmol wiki).