Requirements

There are only two basic requirements for running the plugin:

• An actual version of Cytoscape (we tested it with version 2.4.0)
• The fern.jar file in the cytoscape/plugin folder

However, if you plan to use the plugin with a certain network, the network must satisfy following restrictions:

• Reaction and species nodes must be distinguishable: Since a reaction network is basically a petrinet with species as places and reactions as transitions, there must be an attribute for each node to distinguish reactions and species.
• Edges are only allowed between reaction nodes and species nodes (so the network is a bipartite graph).
• The direction of edges (is the species a reactant or a product of the connected reaction?) must be identifiable (Either the edge identifier contains reactant or product, as it is given by the cytoscape sbml plugin or the edges are directed from reactant to reaction and from reaction to product).
• For each reaction node there must be an attribute containing the reaction coefficient, for each species one containing the initial amount.

These attributes can be specified in the plugin's main window. If you use the cytoscape sbml reader, the plugin should automatically determine the attributes (and of course, if you load a fernml network from within the plugin, this will work automatically as well).

Additionally, if you want to produce trend curves, make sure you have gnuplot installed and it is accessible (e.g. the binary's path is within you PATH environment variable).