This program (SME.jar) will caculate the similarity coefficeint (SME) between gene profiles.

1. Prepare the gene expression dataset following the format as described in http://bioinf.xmu.edu.cn:8080/PaGeFinder/format.jsp.

2. Check whether the Java Runtime Environment (JRE) is available. JRE version > 1.6 is recommanded.

3. Put SME.jar and YourFile in the same working directory

        For Linux/Unix user:
	$ java -jar SME.jar YourFile value
        
    For Windows user:
	start the command prompt (cmd) and go to the working directory
	$ java -jar SME.jar YourFile value
	
	 note: The value can be ignored. If you set a value, only SMEs larger than the value will be output; if you do not set the value, all the results will be output. The value should be set in[0,1].
	       If the file size is too large, a big value like 0.9 is proposed to save computational time.   
	
	Output:  YourFile.sme (Open with text viewers or Excel)
                 
            sample ID1<tab>sample ID2<tab>value
            sample ID1<tab>sample ID3<tab>value...