Try this one

http://opentutorials.cgl.ucsf.edu/index.php/Tutorial:Introduction_to_Cytoscape

 this link will give you basic understanding of how to use cytoscape to draw networks and if you are into metabolite networks then you should check this link below which is a link for a plugin for cytoscape for working with metabolite networks

http://metscape.ncibi.org/metscape2/

thanks all i will see them

Is the procedure same as drawing gene network? (calculation of correlation and then remove data with absolute correlation below the threshold)

Hello

In the following link you can find the manuals for different versions of this software

http://www.cytoscape.org/documentation_users.html.

You can also use cellnetanalyzer to draw a map

@ sepideh

Thank you 

You may want to look at Ma et al. Bioinformatics (2003)  Vol. 19 no. 2 Pages 270–277.