Download Programs

If you haven't yet performed the registration step, please do that now. We have to receive your registration information and respond via email before you can completely finish the BioCoRE installation. We try to respond to registrations very quickly, but it is always good to register as early as possible.

You need to download the following if you don't already have them accessible. Unless otherwise noted, get the most recent versions of each package. Some of these packages might download as shell scripts which you need to make executable and then execute to uncompress them. The installation instructions will give details on where to uncompress the files. You don't have to download all of these packages before you start the installation. If you wish, you can download "as you go". On some of the options, the license for the package allows us to store a copy on our site to make your life easier. For these packages, you might need to right click and "Save As..." to get the file downloaded correctly. Where possible, we have included local copies of the packages for your convenience. The licensing terms for some packages don't allow this, though, and you will need to go to the software's website to download the package.

  1. MySQL: Binaries are adequate (and recommended by If you are on an RPMable version of Linux, feel free to grab the two RPMs for the server and the client. BioCoRE, as shipped, needs mysql 4.0.x. Mysql 4.1.x and higher will not work with BioCoRE as shipped. If you want to use version 4.1 or higher, you will also need to use a version of the MySQL/J Connector that we do not include with our distribution. You can download version 3.0 of the MySQL Connector/J at the MySQL website. Note: Version 3.1+ of the MySQL Connector seems to have some issues with another of the packages that we are using. Use 3.0.
  2. JavaTM 2 SDK, Standard Edition, (SDK):
    We recommend version 1.4. (no source needed) (For Linux, get the .tar.gz, rather than the .rpm. This way you can control the installation location.) Java is available for a variety of Unix platforms. Solaris and Linux (on the Unix side) can be downloaded directly from Sun, and there is a list of Java Platform Ports that Sun has for other platforms.
    Note: If you are planning to download the server source and compile your own versions of the server software, you need to use Java 1.4. If you compile the BioCoRE web start applications (including the Control Panel) with Java 1.5, all of your users will be required to have Java 1.5 to actually load the applets. For us, this "feature" will actually keep Java 1.4 in use for compiling our main server branch for the foreseeable future. We will only upgrade once we are confident that the large majority of our users have Java 1.5 or higher. If you aren't planning to compile the BioCoRE server source, you can use Java 1.5.
  3. JavaMail and the Java Activation Framework (JAF)
    Download Javamail version 1.3.1 from our site (might not quite be the latest version; but will work)

    Download Java Activation Framework version 1.0.2 from our site (might not quite be the latest version; but will work)

    Both of these packages need to be downloaded and unzipped. You will only end up needing one file from each package. From the JavaMail package, you need the mail.jar file, and from the Java Activation Framework you need the activation.jar file. In later steps you will be told where to place these two files.
  4. Apache Tomcat:
    Download version 5.0.28 from our site (might not quite be the latest version; but will work)
    or On the left column there is a Download category. Click on "Apache Tomcat 5.x" under that. Then, scroll down to the latest 5.0.x choice (currently 5.0.28 ). Download tomcat-5.0.28.tar.gz. Tomcat version 5.5.x is currently available as well, but Apache has changed the way that mail-sending works which has created an incompatibility for the time being. Go with Tomcat 5.0.x.
  5. BioCoRE Files:
    To download the BioCoRE files, you need to register/login to the TCB download database. By doing this once you are automatically registered to download BioCoRE, BioCoRE updates, and other Theoretical and Computational Biophysics programs. Go to the download database. You will need to download the binary version of the files. You don't need to download the source files to install the server.

    Several packages are included in the BioCoRE download for your convenience. These packages are located in the WEB-INF/lib directory and the LICENSE file in that directory details the licensing terms for the files contained there.

Next Step: Install MySQL.
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The BioCoRE team welcomes any comments, questions, or suggestions that you might have concerning our software! Please email us or fill out our feedback form.