Cellware provides various tools to extract topological information from the model. These tools can be accessed under Analysis>Network menu.
- Stoichiometric matrix: Shows stoichiometric matrix of network, N, which is of size m x n where m and n respectively denote the number of species and the number of reactions of the network. Multiplication by flow vector
 results the rate equation 
- Network statistic: Shows network statistics.
- Find cycles: Finds independent cycles in the network. Cycles in the network are useful to determine feedback loops. Tarjan algorithm is used to find the cycles and computation takes linear time.
- Find path: Finds a shorted path between two nodes. Since our graphs comprise of unweighted edges (link between two nodes), breadth-first search graph algorithm is used to find the shorted path.
- Transverse: Finds transversal nodes from a selected node. Transversal nodes are highlighted. Depth-first search graph algorithm is used.
- Blast: Finds conserved pathways among networks.
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