Java

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.

Enable Java on your computerEnable Java on your computer

Besides any Preferences setup, you might need to go to Do I Have Java? and enable Java by clicking on the inactive plugin statement, if present.

Detecting your Java versionDetecting 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 threatJava 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 JavaHow 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.

Adding Proteopedia to the Java Exceptions listAdding Proteopedia to the Java Exceptions list

In the quest to make Java less of a security risk Oracle has made it so that after January 15th, 2014, Java will no longer work with unsigned Java applets. The version of the Jmol structure viewer currently utilized by Proteopedia runs on such an applet. We are addressing this, but in the meantime to make Jmol work within Proteopedia End-users will have to add the Proteopedia site to a list of allow exceptions on their own computers. The following is how to do this:

• Copy the below URL to your clipboard by highlighting the text and select copy from under your browsers edit menu.

   http://proteopedia.org/wiki/
   

• Open the Java control panel.

   Windows/Mac - Open your system control panel or System Preferences and choose Java.
   Linux/Solaris - Run the jcontrol command.

• Choose the Security tab.
• Click the Edit Site List button near the bottom left.
• Click the Add button and paste in the text you copied earlier.
• Click OK. The window will close. You may see an additional prompt if you use an unencrypted protocol such as http or file. Choosing encrypted protocols defends
• Back on the control panel, click OK to close it.
• Open or reload the page on Proteopedia in your browser and you should get prompts you can now allow to activate Java again..

The technical version of above with some images that may help can be found here, under Adding a site to the Exception Site List.

Soon Proteopedia will use a signed applet that will have the option of allowing people to also work completely without Java, meaning mobile devices such as tablets should then be able to use Proteopedia. However, making all of Proteopedia work with the new version will take some time. We are hoping to have it working before the end of January. We advise you to take advantage of this above workaround in the interim.

Long term solutionLong term solution

The solely Java-based Jmol has been phased out of Jmol development in favor of a version of Jmol that does not absolutely require Java, see JSmol (see also JSmol in the Jmol wiki). It has the ability to either run in Java or use Javascript.

Proteopedia is in the process of testing use of this new version of Jmol of Proteopedia. There is a strong impetus for this switch. One big advantages is that even tablets and mobile devices will be able to use Proteopedia following the switch. It will soon be possible to even make a scene on your favorite tablet.

See AlsoSee Also

• Java (software platform) at Wikipedia.
• Oracle and Apple Announce OpenJDK Project for Mac OS X (November, 2010).