NetExplore: a web server for modeling small network motifs

Dmitri Papatsenko; Ihor R Lemischka

doi:10.1093/bioinformatics/btv058

NetExplore: a web server for modeling small network motifs

Bioinformatics. 2015 Jun 1;31(11):1860-2. doi: 10.1093/bioinformatics/btv058. Epub 2015 Jan 30.

Authors

Dmitri Papatsenko¹, Ihor R Lemischka²

Affiliations

¹ 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 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.
² 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 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 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.

Abstract

Motivation: Quantitative and qualitative assessment of biological data often produces small essential recurrent networks, containing 3-5 components called network motifs. In this context, model solutions for small network motifs represent very high interest.

Results: Software package NetExplore has been created in order to generate, classify and analyze solutions for network motifs including up to six network components. NetExplore allows plotting and visualization of the solution's phase spaces and bifurcation diagrams.

Availability and implementation: The current version of NetExplore has been implemented in Perl-CGI and is accessible at the following locations: http://line.bioinfolab.net/nex/NetExplore.htm and http://nex.autosome.ru/nex/NetExplore.htm.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms
Gene Regulatory Networks*
Internet
Models, Genetic
Software*

Grants and funding

R01 GM078465/GM/NIGMS NIH HHS/United States