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DeDaL specifications

Information


Unique identifier OMICS_12731
Name DeDaL
Alternative name Data-Driven Network Layouting
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Input format txt
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU Lesser General Public License version 3.0
Computer skills Medium
Stability Stable
Requirements
Cytoscape
Maintained Yes

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Maintainer


  • person_outline Andrei Zinovyev <>

Publication for Data-Driven Network Layouting

DeDaL in publications

 (5)
PMCID: 5027075
PMID: 27639380
DOI: 10.1186/s12859-016-1237-9

[…] constructed alignment) and structurally similar duplexes (i.e., the rmsd value computed for them cannot be greater than 3.5 å). such an unambiguous mapping of aligned residues is provided by dedal [], which is a web server designed for solving the protein structure alignment problem. this is a computationally efficient general purpose method that is driven by the structural comparison […]

PMCID: 4926324
PMID: 27258252
DOI: 10.3390/ijms17060700

[…] treatments. principal components analysis (pca) and hierarchical clustering were used to determine the contribution that each mrna had in the response to dm and aza treatments. particularly, the dedal-pca cytoscape plugin combines classical and advanced data dimension reduction methods with the algorithms of network layout inside the cytoscape environment. the genetic interactions […]

PMCID: 4881433
PMID: 27187362
DOI: 10.3390/ijms17050304

[…] positively for reliable annotation among all samples. these transcripts were used for statistical analysis to find mrnas with abundance levels that significantly differed between the two treatments. dedal was used to create a ddl layout for a group of c. rogercresseyi genes involved in the downstream notch pathway. hierarchal cluster analysis and pca were applied to determine the contribution […]

PMCID: 3488393
PMID: 23193384
DOI: 10.1100/2012/589875

[…] that a continuous record of the time spent in patients' selected daily activities and the waking hours may be a measure of the amount of ocular surface stress., the dry eye disease activity log (dedal) study was performed with the following primary aims:to report the “activity load”—mean amount of time spent per day on ded-aggravating activities—of ded patients from a tertiary care […]

PMCID: 3374807
PMID: 22719941
DOI: 10.1371/journal.pone.0038775

[…] on the road above and an additional observer with the same equipment was positioned at one end of the underpass below. infrared lights were used to illuminate the underpass, and a night scope (dedal generation 2, www.nightvision.ru) was used to aid observations. a pettersson d500× bat detector (http://www.batsound.com) was placed in the centre of the underpass to aid in species […]


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DeDaL institution(s)
Institut Curie, Paris, France; INSERM U900, Paris, France; Mines Paris Tech, Fontainebleau, France
DeDaL funding source(s)
The work is supported by ITMO Cancer SysBio program, (INVADE project) and, the grant “Projet Incitatif et Collaboratif: Computational Systems Biology Approach for Cancer” from Institut Curie and by Institut National de la Santé et de la Recherche Médicale (U900 budget).

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