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README.md

Caleydo - Visualization for Molecular Biology

Build Status

Caleydo is a visualization framework for molecular biology data. It is targeted at analyzing multiple heterogeneous but related tabular datasets (e.g., mRNA expression, copy number status and clinical variables), stratifications or clusters in these datasets and their relationships to biological pathways.

For user documentation please refer to the Caleydo Help. For general information and downloads based on binaries please use the Caleydo Website. This guide assumes that you want to install Caleydo from source.

Installation

Caleydo uses Java, OpenGL and the Eclipse Rich Client Platform (RCP). Things you need to install before being able to run Caleydo:

  • Eclipse Kepler for RCP and RAP Developers, which you can get from the eclipse download page. Other Eclipse versions won't work.
  • Install EGit in Eclipse using software updates.
  • Java SDK >= 1.7

To install Caleydo use EGit within Eclipse and clone the repository. Each directory in the caleydo-dev folder corresponds to an Eclipse project. Here is a good tutorial on how to import Eclipse projects from git.

If you want to use ssh (instead of https) for communicating with github out of eclipse follow these instructions. You will have to generate a new RSA key and save it to you ~/.ssh folder. Remeber to set a passphrase for you key. This will result in a file ida_rsa and ida_rsa.pub turning up in your ssh folder. Save your public rsa key with your eclipse account folder.

When cloning the repository follow the above tutorial. Don't change the username "git" to your username!

Team

Caleydo is an academic project currently developed by members of

Acknowledgements

Caleydo makes use of a range of open source tools, bioinformatics resources and pre-packages several datasets, which we gratefully acknowledge here.

Software Libraries

  • Bubble Sets - A Java implementation of the visualization technique.
  • CDK - The Chemistry Development Kit.
  • JGrahT - A graph library.
  • Jogl - Java bindings for OpenGL.
  • PathVisio - loading and parsing WikiPathways.
  • WordHoard - statistical utilities.

Bioinformatics Resources

Datasets

  • CCLE - BROAD Institute Cancer Cell Line Encyclopedia.
  • TCGA - The Cancer Genome Atlas.

Resources

  • GitHub - Hosting our source code.
  • WebStorm - Free developer licenses for our web projects from JetBrains.