Sockeye installs using InstallAnywhere from Zero G
www.zerog.com). At the download page,
you will be offered a signed applet from Zero G.
Mac OS X: When Java3D is available for OS X, we will make
a version of Sockeye available for this OS. See
Windows: Control panel > Add or Remove Programs.
Linux (or Windows): run the Uninstall_Sockeye_VER script (or .exe) that is in Sockeye's UninstallerData subdirectory. (VER will be the version number.)
The uninstaller will only remove the files that it installed, so any files created after the installation will not be removed. These might include GFF files copied to .../data/GFF/, or session or sequence files. When the uninstaller is finished, remove any remaining files or folders manually.
Sockeye installs the following directory structure. You can choose the install_directory.
sockeye.log(runtime error messages), ...
data/GFF - example GFF files
images - GIF and JPG files
jre - Java JRE with Java3D
lib - JAR files
props - properties dir/file created for online Help frame
models - VRML models for 3D features
UninstallerData - uninstaller files
If you save sequence data from the sequence panel, you may choose to create a sequences folder under the installation directory. (You can save sequence data in a different location.)
If you save sessions, you may choose to create a sessions folder under the installation directory. (You can save sequence data in a different location.) (SessionSave is temporarily disabled. It will be re-enabled shortly.)
If you save both sequences and sessions under the installation directory, the directory structure will also include -
sequences - saved sequences (FASTA or TXT)
sessions/MySession1.../ - session subdirectories and XML files
http://www.j3d.org/implementation/java3d-OpenGLvsDirectX.html. If you have problems with one of the versions, please uninstall it and try the other.
j3d.orglink). We have tested v0.8.3 with Microsoft's current version, 9.0a, on Win2K and XP Pro. You can find the version installed on your computer by running Start > Run > dxdiag. If you need to upgrade your DirectX version, you can get the latest version at
When Sockeye opens, its main frame fits a 1280x1024 monitor. Currently, though, it is too large for a screen with a lower resolution (e.g. 1024x768). If you have such a screen, you will have to manually resize Sockeye. A future version will open to a smaller size.
Updates will be available frequently. Please subscribe to
for release information.
Source code will be made available at a later date.
The installation includes one proprietary JAR:
borlandxml.jar. Sockeye uses
this JAR for saving sessions (which is temporarily disabled). The
in the Sockeye install directory describes the terms under which we include this
Redistributable. Essentially, the license states that you are free to download and use the
JAR with Sockeye, but not outside of Sockeye unless you have an appropriate
JBuilder licence. While we develop with the Enterprise version, the SE/Developer version also
includes this JAR.
Last modified: 23 May 2003, 12h12