Odefy protocols

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Odefy specifications

Information


Unique identifier OMICS_20162
Name Odefy
Software type Toolkit/Suite
Interface Command line interface, Graphical user interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Mac OS, Windows
Programming languages MATLAB
Computer skills Advanced
Version 1.19
Stability Stable
Requirements
Octave (for non-GUI mode)
Maintained Yes

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Maintainer


  • person_outline Fabian Theis <>

Publications for Odefy

Odefy in pipeline

2014
PMCID: 3981794
PMID: 24718686
DOI: 10.1371/journal.pone.0094258

[…] on bdd and sat respectively., proposed st: the sequential version of the proposed algorithm., proposed mt: the parallel version of the proposed algorithm., other tools, such as cellnetanalyzer, odefy and jemena are not chosen because they are mostly based on simulation approach that cannot find all attractors , , –. all tests are performed on a machine equipped with intel xeon cpu @3.3 ghz […]


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Odefy in publications

 (8)
PMCID: 5490412
PMID: 28635674
DOI: 10.3390/ph10020055

[…] these nodes, tnf, rela and nfkb1, are all set to 1 and are highlighted in red in . on the other hand, initial values of the other network nodes are randomly assigned to 0 or 1 (). we next applied odefy, which performs the conversion of bns into continuous odes, with continuous time descriptions, and gives as an output the node behaviors after a certain stimulus (here rigenera® action). […]

PMCID: 5407609
PMID: 28448599
DOI: 10.1371/journal.pone.0176500

[…] quation x˙i =1τi(b¯i (x¯i1, x¯i2,…, x¯ini)− x¯i), where, b¯i is a continuous homologue of the discrete function bi, parameter τi represents the life-time of the protein, and x¯i describes its decay., odefy [], a toolbox compatible with matlab, transforms bi to the ode system and computes the solution of the system using the boolecubes [] as follows, b¯i(x¯1, x¯2,…, x¯n)= ∑x1=01∑x1=01…∑xn=01[b(x1,  […]

PMCID: 5025072
PMID: 27632168
DOI: 10.1371/journal.pone.0162407

[…] more understandable information about general pathway dynamics under different conditions. to support these studies, publicly available software tools such as booleannet [], pathologic-s [] and odefy [] have been developed; they offer a scalable boolean framework for modeling cellular signaling., following these considerations, in this work we present a novel bioinformatics pipeline […]

PMCID: 3983080
PMID: 24722333
DOI: 10.1371/journal.pcbi.1003546

[…] logic to describe the main steps involved in the activation of cd4+ helper t cells. cellnetanalyzer, a matlab software package for structural and functional analysis of signaling networks, and the odefy toolbox were used to convert the logical model to a continuous homologue (herein referred to as model k) with 40 states and 147 reaction parameters. values for these reaction parameters […]

PMCID: 3981794
PMID: 24718686
DOI: 10.1371/journal.pone.0094258

[…] of finding attractors have been extensively studied in the past decade , –. a few of these algorithms are available as released tools, such as genetic network analyser , squad , cellnetanalyzer , odefy , jemena , etc. all these existing algorithms can be categorized into four groups. the simulation-based approach is proposed to find attractors by choosing several initial states heuristically […]


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Odefy institution(s)
Institute for Bioinformatics and Systems Biology, Helmholtz Zentrum München, Munich-Neuherberg, Germany; Department of Mathematics, Technische Universität München, Garching, Germany
Odefy funding source(s)
Partially supported by the Initiative and Networking Fund of the Helmholtz Association within the Helmholtz Alliance on Systems Biology (project CoReNe).

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