Caleydo 3.1.5

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 3.1.5 introduces statistical analysis for experimental data to the pathway analysis tools. You can now test whether a pattern you see is also statistically significant. We provide two tests: Fisher’s exact test and the Wilcoxon Rank Sum test, to account for different situations. Using the Wilcoxon Rank Sum test you can also automatically discover significant partitions considering adjusted p-values to account for the false discovery rate.

Learn more on the help pages.

In addition this release fixes two bugs:

  • Fixing problems on Max OS X preventing execution.
  • Fixing problems with Debian packages on Linux.

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 3.1.5, Windows - 64-bit (Installer)

  Caleydo 3.1.5, Windows - 32-bit (zip-compressed)

  Caleydo 3.1.5, 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 3.1.5, 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 3.1.5, Linux - 64-bit (deb Package)

  Caleydo 3.1.5, Linux - 32-bit (tar.gz-compressed)

  Caleydo 3.1.5, 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.