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NetExplore: a web server for modeling small network motifs.

Dmitri Papatsenko1, Ihor R Lemischka2

  • 1Department of Regenerative and Developmental Biology, Black Family Stem Cell Institute andDepartment of Pharmacology and System Therapeutics, Icahn School of Medicine at Mount Sinai, Systems Biology Center New York, One Gustave L. Levy Place, New York, NY 10029, USA Department of Regenerative and Developmental Biology, Black Family Stem Cell Institute andDepartment of Pharmacology and System Therapeutics, Icahn School of Medicine at Mount Sinai, Systems Biology Center New York, One Gustave L. Levy Place, New York, NY 10029, USA.

Bioinformatics (Oxford, England)
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Summary

NetExplore software generates, classifies, and analyzes network motifs up to six components. This tool aids in understanding biological data by visualizing solutions and phase spaces for small recurrent networks.

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Area of Science:

  • Systems Biology
  • Computational Biology
  • Bioinformatics

Background:

  • Biological data analysis frequently yields small recurrent networks (3-5 components) known as network motifs.
  • Developing accurate models for these small network motifs is crucial for understanding biological systems.

Purpose of the Study:

  • To introduce NetExplore, a software package designed for the analysis of network motifs.
  • To provide tools for generating, classifying, and analyzing solutions for network motifs with up to six components.

Main Methods:

  • The NetExplore software package was developed for network motif analysis.
  • The software allows for the generation, classification, and analysis of network motif solutions.
  • It includes functionalities for plotting and visualizing phase spaces and bifurcation diagrams.

Main Results:

  • NetExplore facilitates the comprehensive analysis of network motifs containing up to six components.
  • The software enables visualization of phase spaces and bifurcation diagrams for network motif solutions.
  • This provides deeper insights into the dynamics of small biological networks.

Conclusions:

  • NetExplore is a valuable tool for researchers studying network motifs in biological systems.
  • The software enhances the quantitative and qualitative assessment of biological data by analyzing small network motifs.
  • It supports the exploration of complex biological network dynamics through visualization and analysis.