rxncon specifications

Information


Unique identifier OMICS_15694
Name rxncon
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Jesper Romers <>

Publications for rxncon

rxncon in publications

 (3)
PMCID: 5516868
PMID: 28725459
DOI: 10.1038/npjsba.2015.7

[…] complex is best known for its role in glucose derepression., we performed a network reconstruction of the snf1 pathway based on a comprehensive literature review. the network was formalised in the rxncon language, and we used the rxncon toolbox for model validation and gap filling., we present a machine-readable network definition that summarises the mechanistic knowledge of the snf1 pathway. […]

PMCID: 3588907
PMID: 23423320
DOI: 10.1038/msb.2013.1

[…] but they are not a replacement. this implies that visualizations should be created from an underlying computable representation and not the other way around; this is the approach taken by the rxncon software, which uses specialized tables to describe reactions in a way that specifically supports multiple visualizations (). however, to be most useful, the computable representation must […]

PMCID: 3485121
PMID: 22913808
DOI: 10.1186/1752-0509-6-107

[…] for drawing extended contact maps []. the stencil can be obtained from the bionetgen wiki site ( http://bionetgen.org). a tool for automatic visualization of a rule-based model specification, rxncon, has recently become available []; this tool produces maps that have similarities with an extended contact map. the purpose of an extended contact map is to provide a high-level understandable […]


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rxncon institution(s)
Humboldt Universität zu Berlin, Theoretical Biophysics, Berlin, Germany
rxncon funding source(s)
This work was supported by the German Federal Ministry of Education and Research as e:Bio Cellemental (FKZ0316193).

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