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NetBuilder specifications


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




No version available



This tool is not available anymore.

NetBuilder citations


Integrating Visualizations into Modeling NEST Simulations

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 […]


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

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 […]


Using Kalman Filters to Reduce Noise from RFID Location System

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

[…] (more information about MATLAB at, and exported to a net component using MATLAB Builder NE (more information available at 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 […]


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

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 […]


Gene Regulatory Network Reconstruction Using Conditional Mutual Information

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 […]


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

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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