Elhanan Borenstein, Ph.D.

Dept of Genome Sciences
University of Washington

3720 15th Ave NE
Foege Building, S103B
Box 355065
Seattle, WA 98195-5065

Phone: (206) 685-8165
Fax: (206) 685-7301



NetSeed
NetSeed is a software package for identifying the seed sets of networks and is available as an online tool (NetSeed>Web) and as a Perl module (NetSeed>Perl).

» NetSeed>Web
  Determine the seed set of a network online.

» NetSeed>Perl
  Download the Perl module to add NetSeed's functionality to your custom analysis programs.

» NetSeed Manual
  Learn how to use NetSeed in your analysis.

Trying it out? Check out our example networks.


Understanding the NetSeed Analysis

Borenstein et al. (2008) introduced the seed set in the context of metabolic networks.

The seed set of a network is the minimal subset of nodes in a directed network required to access every node in the network. For a metabolic network constructed with nodes representing compounds and edges representing reactions that link substrates to products, the seed set therefore represents the minimal subset of the compounds in the network that cannot be synthesized from other compounds in the network (and hence are exogenously acquired) and whose existence permits the production of all other compounds in the network. The seed set of a metabolic network was shown to serve as a successful proxy for the habitat of the organism. For a complete description of the science and algorithms behind network seed analysis, please refer to Borenstein et al. (2008) (supporting information).

If you are using NetSeed please cite the following paper:
Rogan Carr and Elhanan Borenstein (2012) NetSeed: A network-based reverse-ecology tool for calculating the metabolic interface of an organism with its environment, Bioinformatics, 28(5), 734-735, 2012.