ev: Evolution of Biological Information,
Run an Evolutionary Model on Your Own Computer

• Experimenting with Evolution: A Guide to Evj

• Launch Evj as a Java applet from your browser.   Clicking on the link should launch a new window. That window will create a second window for Evj. If there are problems, see the messages on the first window. If this is no help, then consider downloading the program. This is easy and it is described below.

  You must have Java version 1.3.0 or higher installed on your operating system.

  You must have Java enabled on your browser.

  To enable Java:

  • Mozilla: Edit: Preferences: Advanced: Enable Java
  • Firefox:
    1. (Mac) Firefox: Preferences: Web Features: Enable Java
       
    2. (Windows) Tools: Options: Web Features: Enable Java
       That is, on a Windows box in Mozilla's Firefox, go to the "Tools" menu and select "Options". Then in the "Web Features" selection, make sure the "Enable Java" box is checked. Then press "OK" to save it.
  • Netscape: Preferences: Advanced: Enable Java: Ok
    That is, on a Windows box in Netscape, go to the "Edit" menu and select "Preferences". Then select "Advanced", make sure the "Enable Java" box is checked. Then press "OK" to save it.
  • Explorer: Tools: Internet Options: Advanced: Java (Sun): Enable
  
  On Windows systems you may have security issues and so, if you want, you could temporarily enable Java only when you run Evj. Suns, Linux and Mac are secure systems and probably do not need this precaution.

  Here is what we know about running Evj as a Java applet on different operating systems:

  • SunOS 5.9 The program works. We have revised it to work with Java 1.3 too. However, the program freezes after a while, leaving an unresponsive window. To kill the window determine the process number:

    /bin/ps -eo user,pid,args | grep java_vm
    

    This gives you a number which I will call '[process number]'. Then kill the window:

    kill -9 [process number]
    

    A script to do this is: killevj. Unfortunately it also kills my Mozilla browser.
  • Mac OSX:
    • OSX 10.3.9
      • Safari 1.3 (v312): runs!
      • Mozilla 1.8b2: hangs
      • Explorer 5.2.3 (58115.1): hangs
    • OS X 10.4 Tiger
      • Safari 2.0 (412.2): runs!
      • Mozilla 1.7.8: runs on OSX 10.4.2 but you need a Java Embedding Plugin.
      • SeaMonkey, the alpha version of Mozilla, runs! The version I am using that works is "SeaMonkey 1.1a Mozilla/5.0 (Macintosh; U; PPC Mac OS X Mach-O; en-US; rv:1.9a1) Gecko/20050920 SeaMonkey/1.1a"
      • Mozilla 1.8b2: hangs. Maybe the plugin mentioned above would help, but I don't know.
      • Firefox 1.0.6: hangs Maybe the plugin mentioned above would help, but I don't know.
      • Explorer 5.2.3 (58115.1): hangs Maybe the plugin mentioned above would help, but I don't know.
  • Windows: the program runs on Windows
    Instructions will be posted when I have them.

  If you cannot launch Evj as an applet, do not be discouraged. It is almost as easy to run it directly on your computer, see below.

• Running as a Stand-alone program.   This is the most reliable way to run the program.

  • Download: evjava.tar.Z (Unix compressed tar file.)

    Note: to download versions successfully, you may need to clear the cache on your browser (Mozilla: Preferences: Advanced: Cache) and close and open the browser to remove previous versions

  • Setting up Evj on your computer
    • Unix The program works.
      • Download the tarball from above.
      • Uncompress and untar the file:
        tar xvf evjava.tar.Z
      • You should now have a directory named "evjava".
      • Move into the directory using the change directory command:
        cd evjava
      • Although we supply the compiled program (class files) the evjava.tar.Z file also contains the complete source code (java files), so you can compile the program yourself. If you know Java you can modify the program. Compile using the command (under Unix):
        

         javac -deprecation -source 1.3 -target 1.3 Evj.java

      • Run using the command (under Unix):

         java Evj

        works too but it may not give error messages. The enableassertions flag turns on checks for bad conditions. -ea can (apparently) be used for short.
        • google: enableassertions
        • Info on assertions
        • Programming with Exceptions
      • The Evj window should pop up.
    • Mac OSX 10.3.9 Panther and 10.4 Tiger The program works.
      • Download the tarball from evjava.tar.Z. It's easy - just click on it. Save the file. You will have the evjava.tar.Z on your computer. If it does not automatically open, double click on it and it will unpackage into a folder called 'evjava'.
      • Double click on the evjava directory to open it.
      • Double click on the Evj.class file. Evjava should launch!
    • Windows The program works.
      • Download the tarball from evjava.tar.Z.
      • Instructions will be posted when I have them.

  • Compiling Source Code.   Download evjava.tar.Z (Unix compressed tar file) as described above.
    • Sun, Mac OSX 10.3.9 Panther The compilation works.
      • To compile under Unix, use a terminal to go to the evjava directory and remove the previously compiled class files by typing:

         rm -f *.class

        and compile by typing:

         javac -deprecation -source 1.3 -target 1.3 Evj.java

      • To run under Unix, go to the directory and type:

         java Evj

      The compile-evj.tcsh script will find the evjava directory in the current directory, remove the old class files, compile, and run. For example, if you have downloaded the evjava directory to your Mac OSX desktop, then download this script and type:

       cd; cd Desktop; tcsh compile-evj.tcsh

      in a Terminal. Once you have that working, you can run Evj faster by:

       cd; cd Desktop; cd evjava; java Evj &

Acknowledgments. Thanks to Pete Lemkin for useful comments on this page.

Problems? Comments? Please email me, Tom Schneider, at toms@ncifcrf.gov.

Schneider Lab
origin: 2005 Jun 3
updated: version = 2.21 of evj.html 2008 Mar 10
counting unique visitors since 2005 Sep 4