First time at Proteopedia? Click on the green links: they change the 3D image. Click and drag the molecules. Proteopedia is a 3D, interactive encyclopedia of proteins, RNA, DNA and other molecules. With a free user account, you can edit pages in Proteopedia. Visit the Main Page to learn more.
Java (or more specifically the Java virtual machine) is software that enables programs written in the Java language to operate essentially identically on multiple computer platforms, such as Microsoft Windows, Apple Mac OS X, and linux, without special adaptation to each platform. Jmol is one such program. Jmol will not operate unless Java is installed on the host computer. Since interactive molecular visualizations in Proteopedia depend upon Jmol, both Proteopedia and Jmol require Java.
Java is bundled with Mac OS X (10.6 and earlier), and the Apple Software Update on Macs upgrades Java as new versions are released. (For Mac OS 10.7 Lion, Java must be installed by the user.) Microsoft Windows does not provide Java, but it can easily be installed or updated by visiting Java.Com. The original (and still most widely used) Java is developed by Sun Microsystems (a subsidiary of Oracle Corporation), and since mid-2007, has been open-source software.
Apple adapted Java to work efficiently on OS 10.6 and earlier OS versions (citation needed). Apple Java is typically many versions behind Sun Java. For example, in March, 2011, the current Apple Java is 1.5.0_28 while Sun Java (e.g. installed on MS Windows) is 1.6.0_22. Beginning with OS 10.7 Lion, Apple is managing Java differently (details needed).
Occasionally bugs in current java releases affect the performance of Proteopedia or Jmol. These are generally resolved in subsequent releases.
Detecting your Java version
Jmol can be used, in any web page containing it, to report the version of Java currently installed: Click on Jmol, then on About Jmol. There are several free websites that report your java version, such as Java Tester. Java.Com also reports the java version on Windows: click on Do I Have Java?.
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 be as safe as possible with Java
Assuming that you wish to use Proteopedia and other Jmol-based resources, such as FirstGlance in Jmol, you will need java. (If you don't, simply uninstall Java.) How can you minimize your risk?
- 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".
- 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.
- 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
- Java (software platform) at Wikipedia.
- Oracle and Apple Announce OpenJDK Project for Mac OS X (November, 2010).