Please read these notes before downloading Sockeye 0.8.4


Sockeye installs using InstallAnywhere from Zero G ( At the download page, you will be offered a signed applet from Zero G.

  1. If you accept the applet, you should be able to do either an automatic or a manual install.
  2. If you decline the applet, you will be able to do only a manual install.
  3. Instructions for the manual install are given on the the download page, below the download links.

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.

Installed directory structure

Sockeye installs the following directory structure. You can choose the install_directory.

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 -


  1. Sockeye is a Java application. You can download a version that is bundled with its own Java (JRE)/Java3D, or a smaller file that has no bundled Java. If you choose the installer that includes no Java, you must also install appropriate versions of Java and Java3D in order to run Sockeye.
  2. The bundled Java is 1.4.1_01; the bundled Java3D is 1.3.1 beta.
  3. Platforms
    1. Linux - We have tested on RedHat 7.2 and 8.0. We have also run Sockeye on SuSE 8.1 Pro, but have tested it less thoroughly on this OS.
    2. Windows - We have tested on Win2K, and on XP Pro and Home.
  4. Installer with bundled Java VM
    1. You do not need to have Java or Java3D installed outside of Sockeye in order to run Sockeye. The installer will install the Java that Sockeye needs.
    2. Linux - Download: ~30 MB. Installed application: 73+ MB.
    3. Windows - Download: 21 MB. Installed application 50+ MB.
  5. Installer without bundled Java VM
    1. To run Sockeye you must also install appropriate versions of Java and Java3D. We recommend that you install the current bundled versions listed above. The minimum versions that are likely to work are Java 1.4.x and Java3D 1.3. For Windows, see comments below on DirectX and OpenGL Java3D.
    2. Linux - Download: 8.6 MB. Installed application: 9+ MB.
    3. Windows - Download: 7.1 MB. Installed application: 10 MB.

Windows, Java3D, DirectX and OpenGL

  1. For Windows, we offer installers with either DirectX or OpenGL versions of Java3D. Differences are discussed at If you have problems with one of the versions, please uninstall it and try the other.
  2. The DirectX version requires a recent version of DirectX (see above link). 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
  3. The DirectX version of Java3D does not support Antialiasing.


  1. We have run Sockeye on PCs with between 192 MB and 1 GB of RAM.
  2. This prerelease allows Sockeye's Java a maximum of 64 MB RAM. Work with large datasets may require more RAM than this. We are exploring giving Sockeye more RAM, and discuss how you can change this setting in the online help.

Graphics card

  1. Because Sockeye is a 3D application, it demands far more graphics hardware power than a 2D genomic browser. The more 3D features you display, the more graphics power you will need to maintain a responsive real-time 3D environment.
  2. The development team works with cards that are at least at the level of a GeForce2 MX. A card of this level still gives sluggish 3D zooms and rotations with a display showing, e.g., all 19.5K genes on the C. elegans genome.

Screen resolution

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 at for release information.

Source code / open source

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 borland_licence.html 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