BioGuide - Technical documentation 

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BioGuide for Linux

Using BioGuide for Linux
To use BioGuide on Windows, you will need a Java 5 virtual machine. The first version of Java 5 has been released in 2004 and this is now a really common version.
If you don't have a Java 5 version, are not sure or want to get the latest release, please read Java installation hereafter.

Java and Internet browsers:
Installing Java in your browser:
If you have installed Java but you are still unable to use BioGuide, please check out our browser-specific instructions to be able to use Java.
Security certificate:

Regardless of your browser, you will need to accept our Security Certificate to be able to use BioGuide.
For more details, please read Security Certificate Acceptance hereafter.

Known issues:

  • It is well known that Java GTK Graphical User Interface is incompatible with some Linux themes.
    For example the default Fedora Core 5 Gnome theme is ClearLooks and it does not work properly with Java (issues with selected menu items that will become invisible ...). To have a correct Java execution you will have to change to another theme such as Bluecurve.
    Sun and the Linux community are investigating this issue, it might be solved in a few months.
  • On some Linux systems, the tools panel (bottom right) can become too big due to some issues with Themes layout. It is not a big issue since you can resize it easily...
Java version
  Do I have Java 1.5.x installed?
You will first have to check if Java 1.5 is already installed on your computer. To do so you can for example run the command java -version in any console. If Java is properly installed (ie $JAVA_HOME/bin is included in the PATH), it will give you the version.

How do I install the latest Java version?
If you don't have Java installed on your computer, you will have to install it from Sun's website or from your distributions RPMs if it is included.
You can download Java 1.5 (you will only need the JRE edition) from this address:
Unless you are familiar with Linux system, we recommend that you use the Linux RPM in self-extracting file from SUN's website. You will juste have to execute this file and Java will be installed with default settings (i.e. a symbolic link will be created in /usr/bin to avoid PATH issues...).

Java in your browser
  Once you have installed Java on your computer, you will have to make sure that your Internet browser knows how to use it.
  • Firefox:
    - Find the location of your Java 1.5 installation (we will refer to this directory as JAVA_HOME):
    - Find the location of your Firefox installation
    - In the Firefox subdirectory plugins: create a symbolic link to $JAVA_HOME/plugin/i386/ns7/
  • Mozilla:
    Same as Firefox
  • Opera:
    Use the menu Tools / Preferences.
    - Choose the tab Advanced
    - Click on Content
    - Check that the checkbox Enable Java is checked
    Click on the Java Options button (right pane)
    - Check that the path to your Java  1.5 home directory is correct
  • Konqueror:
    You just have to use the menu Settings / Configure Konqueror / Java tab.
    There you must activate java and check that the java path is correct (default is java, to be correct java must be included in the path).
  • Other: We did not test other navigators, please check the navigator support documentation.
Security certificate acceptance
The BioGuide applet needs to use a security certificate to give the user the ability to save their configuration file. An applet without a certificate is never allowed to write files on the computer.

As BioGuide is a research project, this security certificate has not been issued by a company but has been self signed by the development team.
Anyway you can trust us! There is no risk to use our product.

How do I accept the security certificate?
You will just have to click on Run button (or whatever name is given to this button by your browser/Java version).
Screen capture 1 gives an example with Java and Internet Explorer or Firefox.

What if I refused the security certificate?
The easiest way to have a new chance to accept this certificate is to close your browser and open a new browser instance on our website.

View screen captures

Laboratoire de Recherche en Informatique, University of Pennsylvania

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