NetSeed>Web allows you to calculate the seed set of a network by simply uploading a file to our webserver. Just fill out the form below and hit Analyze Network. You will then be able to download the results and optionally view your annotated network in Cytoscape Web.

A detailed explanation of the input parameters and options is available in the NetSeed user manual.

Trying it out? Check out our example networks.

Want to incorporate NetSeed in your custom analysis? Download NetSeed>Perl.

NetSeed Manual | Examples
Select your network file to upload.
Maximum size is 10 MB.
The filetype can be plain text (tab, comma or space-separated) or SBML (the Systems Biology Markup Language). NetSeed creates a network from the reactions in an SBML file.
Node names are KEGG IDs. If the node names correspond to KEGG IDs, checking this option will generate links to the KEGG database.
Ignore all nodes except those in the giant component Analyze only the largest connected component in the network, ignoring all other nodes..
Ignore components with fewer than nodes Only analyze connected components in the network with at least this many nodes.
View results in Cytoscape Web? Cytoscape Web is a flash-based network drawing program. If selected, NetSeed will draw the network with Cytoscape Web and label seeds, non-seeds and nodes ignored by the calculation.
Highlight seed with a confidence score higher than: Seeds are given a confidence rank of 1/n, where n is the number of nodes in the source component (please refer to Borenstein et al. (2008) and supporting information for complete details). Netseed will only highlight seeds in Cytoscape Web that have at least this confidence rank.
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. (PDF)
Back to NetSeed or the Borenstein Lab