Sockeye

Sockeye is a Java application designed to assemble, view and work with genomic information in a 3D environment. Sockeye has been developed with a focus on displaying potential gene regulatory regions and for running and visualizing the results from regulatory element detection approaches and algorithms.This program links to the Ensembl database and displays genomic features along tracks (stretches of DNA). It is very flexible with genomic data in GFF files. This application allows users to seamlessly visualize large amount of information at disparate locations in the genome. The application allows user to use variety of algorithms for (multiple) sequence alignment and displays comprehensive results of alignment.

Please read this before downloading Sockeye 1.3

Platforms

1. Linux - We have tested on RedHat 7.2 and 8.0. We have also run Sockeye on SuSE 8.x Pro, but have tested it less thoroughly on this OS.
2. Windows - We have tested on Win2K, and on XP Pro and Home.
3. Mac OS X: Please run Sockeye 1.3 using Java Webstast by following this link

Installing on Linux and Windows

Sockeye uses installers built with InstallAnywhere from Zero G (www.zerog.com).

1. The download file is executable (install.bin on Linux, install.exe on Windows). Running it will open an installer that will let you specify where to install Sockeye, and whether and where to put a launch link (Linux) or icon (Windows). It will also indicate how much free disk space you need and how much you have.
2. On Linux, if you install no links, you will start Sockeye by running the sockeye shell script in its install directory.
3. On Windows, if you install an icon on the desktop, you will start Sockeye by double-clicking on this icon.

Uninstalling

1. Windows: Sockeye can be removed from: Control panel > Add or Remove Programs.
2. Linux or Windows: run the Uninstall_Sockeye_VER script (or .exe) that is in Sockeye's UninstallerData subdirectory. (VER will be the version number.)
3. 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

1. Sockeye installs the following directory structure. You can choose the install_directory.
   • install_directory - This contains a number of files: user_config.xml and default_config.xml, license.pdf, changes_limitations.html, sockeye.log, Java runtime error messages, ...

     data/GFF - example GFF files

     jre - Java JRE with Java3D, if installed with bundled Java

     lib - JAR files

     props - properties dir/file created for online Help frame

     resources - see below

     UninstallerData - uninstaller files
2. The resources directory contains -

   images - GIF, JPG files

   matrices - matrices for S-W sequence alignment

   models - VRML models for 3D features
3. 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.)
4. 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.)
5. If you save both sequences and sessions under the installation directory, the directory structure will also include -
   • install_directory

     ...

     sequences - saved sequences (FASTA or TXT)

     sessions/MySessionName.../ - session subdirectories and XML files

     ...

Java

1. Sockeye is a Java application. You can download a version that is bundled with a 'private' Java (VM/JRE)/Java3D that only Sockeye will use, or you can download a much smaller file that has no bundled Java.
2. The bundled Java is 1.4.1_01; the bundled Java3D is 1.3.1 beta.
3. Installer with bundled Java
   1. For most users, this is the simplest, most reliable approach.
   2. 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.
   3. Download/installation sizes -
      1. Linux - Download: ~ 65 MB. Installed application: ~100 MB.
      2. Windows - Download: ~40 MB. Installed application ~90 MB.

Windows, Java3D, DirectX

1. For Windows, we offer installers with either DirectX version of Java3D.
2. The DirectX version requires a recent version of DirectX (see above j3d.org link). We have tested Sockeye with Microsoft's current version of DirectX, 9.0b, on Win2K and XP Pro. You can find the version installed on your computer by running Start > Run > dxdiag. You can get the latest DirectX version at http://www.microsoft.com/windows/directx/default.aspx.
3. Note that the DirectX version of Java3D does not support Antialiasing. This is likely only to matter for publication-quality, exported JPG images.

RAM

1. We have run Sockeye on PCs with between 192 MB and 1 GB of RAM.
2. This release allows Sockeye's Java a maximum (heap) of 128 MB RAM, and we recommend having at least 256 MB installed.
3. Working with large datasets may require more RAM than this.
4. We are exploring giving Sockeye more RAM. The online help discusses how you can change the maximum Java heap size setting by editing the LAX XML file in the install directory.

Graphics card

1. Because Sockeye is a 3D application, it demands much more powerful graphics hardware than a 2D genomic browser.
2. The more 3D features you display, the more graphics power you will need to maintain a responsive 3D environment.
3. 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.

Source code / open source

Source code will be available for non-commercial users.