Procedure

 

Informations on downloading the software and installation instructions , go to simulator tab

 

Creating a simple food web network and visualising the network. Cytoscape can draw the network manually and can import the network from different files, databases and tables.

 

Cytoscape supports file formats like

 

1. Simple interaction file (SIF)
2. Graph Markup language(GML)
3. SBML
4. Excel workbook
5. Delimited text

 

Sif format is the simpler one, which specifies the nodes and the edges (interactions) only. Other formats store extra information. Here in the experiment we are building a new network with only interactions. For this, it is better to import only sif file format. This is written in excel sheet or text editor. The other way of building the model is manually, cytoscape has the option “editor” to draw the nodes and edges, where we can modify them to visualise the network in different ways.

 

In windows double click the Cytoscape icon to run the tool, alternatively in Linux run the cytoscape in terminal by the command “sh cytoscape.sh”.
Once the cytoscape tool is opened we can create model manually by drawing the nodes and edges connected to each other according to their interaction.

 

Steps to create a network

 

1. Go to file option in the standard menu bar.

 

2. Select Network, and from the submenu select the option empty network.

 

Figure 1 : Screenshot of adding empty network

 

3. In the control panel go to “editor” menu

 

4. Drag the nodes you want to add to the network.

 

Figure 2 : Screen shot to add node into the network

 

5. Select the node and right click on it, select Visual mapping bypass and then select node label option to change the label of the node.

 

 

Figure 3: Screen shot to label the node

 

6. Drag the edge to the node and click on the node to which the edge has to be directed.

 

Figure 4: Screenshot of adding an edge

 

7. Select the edge and right click on it, and select Visual mappingbypass, follows select the Edge target arrow shape.

 

 

 Figure 5: Screenshot to add edges with arrows

Thus the small network of food web is formed. 

 

Figure 6: Image of the network created manually

 

Alternatively user can import the .sif file which has been edited by user as shown in the given table.

 

 

Figure 7 : Table of interactions

 

 

Steps to import the sif file or multi supported files.

 

1. From the standard menu bar select file menu and choose import.

 

2. From the import submenu, choose Network (multiple file types) Alternatively you can use keyboard shortcut as Ctrl+L. Thus you can observe the file chooser option.

 

Figure 8: screen shot to import multiple formatted files as a network

 

3.Choose the radio button “Local”, and click on “select” button to select the .sif file from its source.

 

Figure 9: Screenshot of the file chooser to import file

 

4.Thus the network is imported as shown in figure 10

Figure 10: Image of the network imported through the .sif file

 

We can visualise the network by changing the layout of the network given in the option on the standard menu bar. Mostly used layout is a ‘spring embedded layout’.(Layoutcytoscape layouts or yfiles).

 

Figure 11: Screen shot to change the layout of the network

 

Through vizMapper user can change the visual style of a network.

 

 

Figure 12: Screenshot to visualise the network

 

From the visual mapping browser you can change the colour of nodes and edges, and several other options to play with the visualisation of the network.

 

 

 Figure 13: Screenshot to change the visualisation within nodes and edges

 

 

 

 

 

This experiment uses : Cytoscape,  www.cytoscape.org/   Michael Smoot, Keiichiro Ono, Johannes Ruscheinski, Peng-Liang Wang, Trey Ideker,  Cytoscape 2.8: new features for data integration and network visualization Bioinformatics. 2011 February 1; 27(3): 431–432.Published online 2010 December 12.