Pypath specifications


Unique identifier OMICS_19252
Name Pypath
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
License GNU General Public License version 3.0
Computer skills Advanced
Version 0.5.0
Stability Stable
igraph, python, scipy, numpy, conda, graphviz, pypath, python 3.4.3
Maintained Yes


No version available


  • person_outline denes
  • person_outline Julio Saez-Rodriguez

Additional information

Publication for Pypath

Pypath citation


Logic Modeling in Quantitative Systems Pharmacology

PMCID: 5572374
PMID: 28681552
DOI: 10.1002/psp4.12225

[…] facilitate the retrieval of information from all these databases, we use Omnipath, a comprehensive collection of existing manually curated pathway databases. Omnipath comes with a Python tool called pypath, developed to query its content, and manipulate and filter it easily. This allows us to extract the interactions that concern only the predefined list of proteins, and execute complex queries s […]

Pypath institution(s)
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
Pypath 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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