Category Cross-Omics>Pathway Analysis/Gene Regulatory Networks/Tools

Abstract Netsim is a novel ‘gene network simulator’ that resembles some of the main features of transcriptional regulatory networks related to topology, interaction among regulators of transcription, and expression dynamics.

The simulator generates ‘network topology’ according to the current knowledge of biological network organization, including scale-free distribution of the connectivity and clustering coefficient independent of the number of nodes in the network.

It uses fuzzy logic to represent interactions among the regulators of each gene, integrated with differential equations to generate continuous data, comparable to real data for variety and dynamic complexity.

Netsim accounts for saturation in the response to regulation and transcription activation thresholds and shows robustness to perturbations.

It therefore, provides a reliable and versatile test bed for reverse engineering algorithms applied to microarray data.

Since the simulator describes regulatory interactions and expression dynamics as two distinct, although interconnected aspects of regulation, it can also be used to test reverse engineering approaches that use both microarray and protein-protein interaction (PPI) data in the process of learning.

Netsim is implemented for the R programming language in C.

Note: Details related to the core functions are given in the help files provided with the software package.

Netsim's graphical interface has four (4) Functions:

1) Netsim_generate - is the wizard for generating the network topology, the regulatory interactions, and the expression profiles;

2) Netsim_simulate is for generating expression profiles from networks of known topology;

3) Netsim_graph - draws the network as a directed graph; and

4) Netsim_profiles - plots the profiles created by Netsim_generate or Netsim_simulate.

1) Netsim_generate Function --

2) Netsim_simulate Function --

The Netsim_simulate function provides a graphical interface to the ‘simulateprofiles’ function, which generates the profiles for a gene network. It starts from the topology, which can be specified as a file containing the weights of the connections.

It is also possible to automatically consider all the files (“weights*.txt”) stored in the “Netsim” sub-directory of the working directory.

3) Netsim_graph Function --

The ‘Netsim_graph’ function plots the topology of the networks stored in the “Netsim” sub-directory of the working directory (in the files “weights*. txt”).

There is a spin-button which is automatically set to the maximum number of networks found and a check box that paints the nodes of the graph according to their out-degree.

4) Netsim_profiles Function --

The ‘Netsim_profiles’ function plots the profiles of the networks, created by Netsim_generate or Netsim_simulate functions.

Its window is dynamically created according to the experiments that have been performed: the function looks for the appropriate profiles in the Netsim sub-directory of the working directory.

On the bottom of this window there is a variable number of spin-buttons to select the profiles and check boxes that allow you to show clusters, regulators and/or differential profiles.

System Requirements

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Manufacturer Web Site Netsim

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G6G Abstract Number 20589

G6G Manufacturer Number 104192