Using Cytoscape you can edit networks, add nodes and edges. In Cytoscape 3, editing can be done using right click menus on the network view panel. To start editing a new network, create a new network by going to File → New → Network → Empty Network.
To add a new node, right click on an empty space of the network view panel. Select Add → Node item from the pop-up menu. Image below shows the right click menu for creating a new node.
For adding an edge to connect to nodes, right-click on the source node. Select Edit → Add Edge from the pop-up menu. Next, move pointer and click on the target node. Images below show the two steps for drawing an edge between two nodes. You can abort the drawing of the edge by pressing Esc key.
You can delete nodes and edges by selecting a number of nodes and edges, then selecting Edit → Delete Selected Nodes and Edges. You can recover any nodes and edges deleted from a network by going to Edit → Undo.