User:Alexander.lex/caleydo

	Caleydo
Original author(s)	Marc Streit, Alexander Lex
Developer(s)	The Caleydo Development Team
Initial release	March 2009
Stable release	3.1.0 / 10 October 2013; 10 years ago
Written in	Java
Operating system	Any (Java-based)
Type	Visualization software
License	new BSD license
Website	www.caleydo.org

Caleydo is an open source bioinformatics software platform for visualizing and data analysis of heterogeneous biomolecular data. It allows users to analyse tabular data sources such as gene expression, mutation or copy number data as well as graph data in the form of biological pathways.

History

Caleydo was created in 2008 using sources of GeneView^[1] at the Institute of Computer Graphics at the Graz University of Technology in Austria. Caleydo is now developed by multiple academic institutions including [Harvard University] and [Johannes Kepler University Linz]. Caleydo was made available free for academic use in October 2008 (v1.0); the second release (v1.1) was in March, 2009; the third (v1.2) in May 2009^[2]. The final release of the 1.x series, v1.3 was released in February 2010. Caleydo was made open source with the release of Version 2.0^[3], which included StratomeX, a visualization technique for cancer subtype analysis. The latest major release of Caleydo is version 3 (released in July 2013) which introduces novel methods for visualizing pathways and experimental data and overhauls the cancer subtype visualization to include computational tools.

Development

Caledyo is developed jointly by partners from the Graz University of Technology, Johannes Kepler University Linz and Harvard University. Development is funded through various public research grants. Caleydo is based on RCP and uses OpenGL for high-performance rendering.

Usage

Features

Input

Caleydo can read comma-separated text files as input for matrices of various formats and understands a wide range of gene identifiers ^[4] . It comes pre-packaged with pathway databases.

Visualization

Analysis

References

^ Kalkusch, Michael (2011.10.09). "GeneView". Retrieved 24 April 2013. {{cite web}}: Check date values in: |date= (help)
^ Streit, Marc; Lex, Alexander; Kalkusch, Michael; Zatloukal, Kurt; Schmalstieg, Dieter (2009). "Caleydo: Connecting Pathways and Gene Expression". Bioinformatics. 25 (20): 2760–2761. doi:10.1093/bioinformatics/btp432. PMC 2759551. PMID 19620095.
^ Caleydo. "Caleydo news". Graz University of Technology. Retrieved 24 April 2013.
^ Caleydo. "Caleydo Help Pages". Graz University of Technology. Retrieved 24 April 2013.

External links

Official website

Category:Bioinformatics software Category:Systems biology Category:Mathematical and theoretical biology Category:Java platform software

[1] Kalkusch, Michael (2011.10.09). "GeneView". Retrieved 24 April 2013. {{cite web}}: Check date values in: |date= (help)

[2] Streit, Marc; Lex, Alexander; Kalkusch, Michael; Zatloukal, Kurt; Schmalstieg, Dieter (2009). "Caleydo: Connecting Pathways and Gene Expression". Bioinformatics. 25 (20): 2760–2761. doi:10.1093/bioinformatics/btp432. PMC 2759551. PMID 19620095.

[3] Caleydo. "Caleydo news". Graz University of Technology. Retrieved 24 April 2013.

[help-4] Caleydo. "Caleydo Help Pages". Graz University of Technology. Retrieved 24 April 2013.

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v t e Genomics
Fields	Cognitive genomics Computational genomics Comparative genomics Functional genomics Genome project Human Genome Project Metagenomics Human Microbiome Project Pangenomics Personal genomics Population genomics Sociogenomics Structural genomics
Bioinformatics	Biochip Cheminformatics Chemogenomics Connectomics Human Connectome Project Epigenomics Human Epigenome Project Glycomics Immunomics Lipidomics Metabolomics Microbiomics Nutrigenomics Paleopolyploidy Pharmacogenetics Pharmacogenomics Systems biology Toxicogenomics Transcriptomics
Structural biology	Proteomics Human proteome project Call-map proteomics Structure-based drug design Expression proteomics
Research tools	2-D electrophoresis Mass spectrometer Electrospray ionization Matrix-assisted laser desorption ionization Matrix-assisted laser desorption ionization-time of flight mass spectrometer Microfluidic-based tools Isotope affinity tags Chromosome conformation capture
Organizations	DNA Data Bank of Japan (JP) European Molecular Biology Laboratory (EU) National Institutes of Health (USA) Wellcome Sanger Institute (UK)
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