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Pypath | Guidelines and gateway for literature-curated signaling pathway resources


Offers advanced possibilities for pathway analysis. Pypath builds up networks from multiple sources on one igraph object, handles ambiguous ID conversion, reads custom edge and node attributes from text files and MySQL. Pypath automatically updates its content, which is dynamically gathered from resources. It is also capable of compiling networks from custom sets of interaction resources and can integrate additional annotations.

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Pypath classification

Pypath specifications

Unique identifier:
Command line interface
Operating system:
Unix/Linux, Mac OS, Windows
GNU General Public License version 3.0
cairo, py(2)cairo, igraph, python(2)-igraph, graphviz, pygraphviz
Software type:
Restrictions to use:
Programming languages:
Computer skills:

Pypath distribution


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Pypath support


  • denes <>
  • Julio Saez-Rodriguez <>

Additional information


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European Molecular Biology Laboratory–European Bioinformatics Institute, Hinxton, UK; Earlham Institute, Norwich, UK; Institute of Food Research, Norwich, UK; RWTH Aachen University, Faculty of Medicine, Joint Research Centre for Computational Biomedicine, Aachen, Germany

Funding source(s)

This work was supported by the EMBL Interdisciplinary Postdoc Programme (EIPOD) under Marie Skłodowska-Curie COFUND Actions (grant number 291772), a fellowship in computational biology at the Earlham Institute (Norwich, UK) in partnership with the Institute of Food Research (Norwich, UK), and strategically supported by Biotechnological and Biosciences Research Council, UK (BB/J004529/1).

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