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NetBuilder specifications

Information


Unique identifier OMICS_21505
Name NetBuilder
Alternative name NetBuilder-apostrophe
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
License GNU Lesser General Public License version 2.1
Computer skills Medium
Version 0.5
Stability No
Maintained No

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NetBuilder citations

 (6)
library_books

Integrating Visualizations into Modeling NEST Simulations

2015
Front Neuroinform
PMCID: 4681776
PMID: 26733860
DOI: 10.3389/fninf.2015.00029

[…] ables neuroscientists to build, simulate, and visualize large spiking neural networks in a holistic way supporting methods of visual programming. NeuralSyns provides a graphical user interface called NetBuilder to support network construction, which in turn generates output that can subsequently be processed by the simulation engine. A driving motivation is to build and parameterize complex networ […]

library_books

GDSCalc: A Web Based Application for Evaluating Discrete Graph Dynamical Systems

2015
PLoS One
PMCID: 4532456
PMID: 26263006
DOI: 10.1371/journal.pone.0133660

[…] ulator in Java. It supports different lattice structures (1-D, 2-D square, hexagonal, triangular, 3-D), neighborhoods, and boundary conditions, and can display the cells using colors, text, or icons. NetBuilder [] offers capabilities to simulate and analyze regulatory networks. It represents networks using Petri nets and uses a genetic algorithm to evolve genetic regulatory networks (GRNs) needed […]

library_books

Using Kalman Filters to Reduce Noise from RFID Location System

2014
Sci World J
PMCID: 3925534
PMID: 24592186
DOI: 10.1155/2014/796279

[…] (more information about MATLAB at http://www.mathworks.com/products/matlab/), and exported to a net component using MATLAB Builder NE (more information available at http://www.mathworks.com/products/netbuilder/).On step 4, the original log file and the filtered log files are compared using two different metrics—mean squared error (MSE), and maximum squared error (MaxSE). Equation () illustrates t […]

library_books

Comparing the reconstruction of regulatory pathways with distinct Bayesian networks inference methods

2012
BMC Genomics
PMCID: 3477004
PMID: 23095805
DOI: 10.1186/1471-2164-13-S5-S2

[…] r to further investigate how the methods compare synthetic data sets were also prepared. These data are obtained from two different sources: a linear Gaussian distribution and a simulation tool named Netbuilder [,]. In both cases, the data is obtained from the known structure of Figure .Considering (.) to denote the Normal distribution, a random variable xiis sampled from a linear Gaussian distrib […]

library_books

Gene Regulatory Network Reconstruction Using Conditional Mutual Information

2008
EURASIP J Bioinform Syst Biol
PMCID: 3171392
PMID: 18584050
DOI: 10.1155/2008/253894

[…] tive partitioning MI estimator is a valid alternative for the Gaussian kernel estimator. Specifically, we constructed 25 synthetic regulatory networks, each with 20 one-to-one gene regulations, using NetBuilder []. To compare the network inference performance, we adopt the same metrics as used in []—recall and precision. Recall, defined as , where is the number of true positive links and is the […]

library_books

Boolean networks using the chi square test for inferring large scale gene regulatory networks

2007
BMC Bioinformatics
PMCID: 1802094
PMID: 17270045
DOI: 10.1186/1471-2105-8-37

[…] havior for gene perturbation or intervention [,].Recently, several software packages have been developed for constructing BNs. The random BN toolbox [] and the PBN toolbox [] are available in Matlab. NetBuilder (version 0.94) [] is a genetic regulatory network tool used to simulate genetic network using a BN. The BN has been widely used to describe biological processes. For example, Huang [] has u […]

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NetBuilder funding source(s)
Supported by a grant from the Wellcome Trust and the allocation of QR funding by the School of Computer Science.

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