Caleydo 3.1.1

Caleydo runs on Windows, Mac OS X, and Linux. We regularly test on Windows 7, Ubuntu/Kubuntu of the latest versions and Mac OS X.


Release Notes

Caleydo 3.1.1 is released, the first stable release of the 3.1 series, and with it comes a completely revamped pathway analysis module - Caleydo Entourage. Here is a little preview:

Caleydo Entourage Entourage combines multi-pathway analysis with the experimental data analysis features of enRoute in a sophisticated interface. To get an impression of the capabilities of Entourage check out the brand-new Pathway Analysis Help Pages.

Major new features for pathway analysis include:

  • Multi-pathway analysis using the contextual subset paradigm. Easily discover cross-connections between pathways, find related pathways, etc. Deep integration of experimental data analysis with pathway analysis - you can explore all your genetic, drug, or clinical data through one sophisticated interface. Completely new and convenient data assignment interface lets you choose multiple datasets, stratifications and groups to visualize in enRoute. Other components of Caleydo have also undergone major improvements. The highlights:
  • Added data pre-processing methods to choose from, including z-standardization of datasets, clipping based on standard-deviations, etc. Box plots are now available in StratomeX and in enRoute making analysis of distributions easier than ever. Improved data export - cluster assignments are now included. Integration of StratomeX and Entourage - pathways viewed in StratomeX can now easily be explored in Entourage. Significantly extended and improved documentation.

For a complete list of changes please refer to the issue tracking system.

Windows

Installation Checklist

  1. Caleydo is tested with Windows 7 and Windows 8. We can not guarantee that Caleydo works with earlier Windows versions.
  2. Check the System Requirements
  3. Install the latest Java. Caleydo requires Oracle Java 7 (>= Java 7 Version 40) on Windows. To download Java, go here.
  4. Check your Java installation by opening a command prompt (run cmd) and type java -version. A correct installation should output something similar to this:
    C:\Users\user>java -version
    java version "1.7.0_40"
    Java(TM) SE Runtime Environment (build 1.7.0_40-b43)
    Java HotSpot(TM) 64-Bit Server VM (build 24.0-b56, mixed mode)
    
  5. Install Caleydo using the 64 bit installer (only on 64-bit systems), or download and extract the ZIP packages.
  6. Run Caleydo from your launch menu (if installed) or execute Caleydo.exe in the caleydo folder if using the ZIP packages.
  7. On first start Caleydo requires an internet connection to download pathways (about 80 MB) and sample projects (variable).

Windows Downloads

  Caleydo 3.1.1, Windows - 64-bit (Installer)

  Caleydo 3.1.1, Windows - 32-bit (zip-compressed)

  Caleydo 3.1.1, Windows - 64-bit (zip-compressed)



Mac OS X

Installation Checklist

  1. Check that you are running either Mac OS X Lion (10.7), Mac OS X Mountain Lion (10.8) or Mac OS X Mavericks (10.9). Older versions are not compatible with Caleydo.
  2. Check the System Requirements
  3. Install the latest Java. Caleydo requires Oracle Java 7 (>= Java 7 Version 40). You have to manually install the Java 7 JDK (NOT the JRE!).
  4. Check the installed Java version by opening a terminal window and running java -version. A correct installation should output something similar to this:
    $ java -version
    java version "1.7.0_40"
    Java(TM) SE Runtime Environment (build 1.7.0_40-b43)
    Java HotSpot(TM) 64-Bit Server VM (build 24.0-b56, mixed mode)
    
  5. Download and extract the Caleydo ZIP file.
  6. Run Caleydo by double-clicking the icon of the application extracted from the ZIP file. You may also drag the application into your "Applications" folder.
  7. On first start Caleydo requires an internet connection to download pathways (about 80 MB) and sample projects (variable).

Mac OS X Download

  Caleydo 3.1.1, MacOSX - 64-bit (zip-compressed)



Linux

Installation Checklist

  1. Check the System Requirements
  2. Install the latest Java 7 (>= Open JDK 7 Version 25)
  3. Check your Java installation by running java -version. A correct installation should output something similar to this:
    $ java -version
    java version "1.7.0_25"
    OpenJDK Runtime Environment (IcedTea 2.3.10) (7u25-2.3.10-1ubuntu0.13.04.2)
    OpenJDK 64-Bit Server VM (build 23.7-b01, mixed mode)
    
  4. Choose either 64-bit Debian package (for Ubuntu, Debian and other Debian-based distributions) and install it running:
    $ apt-get install caleydo-linux.gtk.x86_64.deb 
    Or download and extract the tar ball:
    $ tar xzvf caleydo-linux.gtk.x86_64.tar.gz
    
  5. Run Caleydo either from your launcher (if you used the debian package) or from inside the Caleydo folder.
  6. On first start Caleydo requires an internet connection to download pathways (about 80 MB) and sample projects (variable).

Linux Downloads

  Caleydo 3.1.1, Linux - 64-bit (deb Package)

  Caleydo 3.1.1, Linux - 32-bit (tar.gz-compressed)

  Caleydo 3.1.1, Linux - 64-bit (tar.gz-compressed)



System Requirements

Memory

Caleydo requires at least 2GB of RAM for the 64-bit versions and 1GB of RAM for the 32-bit version. For working with large projects we recommend at least 4GB.

Screen Resolution

Caleydo can be run with a minimum screen resolution of 1280x1024, however, a higher resolution is recommended.

Graphics Cards

Caleydo uses high-end computer graphics. While it works on a wide range of graphics cards and systems, dedicated graphics cards by NVidia or AMD are strongly recommended (for example, a graphics card better of the NVidia Geforce 8 series or better should be fine). Also make sure that you have the latest drivers installed. Download NVidia or AMD drivers.



Source Code

Caledyo 3 is licensed under the new BSD License. You can get access to the source code at GitHub.

Caledyo is open source software under the new BSD license. You may download and redistribute the software. Caleydo comes without any warranty; without even the implied warranty of merchantability or fitness for a particular purpose.