README.html

Microarray Scan Simulator

Usage:

java -jar MSS.jar	(to run the GUI interface)
java -jar MSS.jar <command-line-options>	(to run the command line, non-GUI version)
java -jar MSS.jar -help	(to learn about the options)

XML files are used to describe the desired simulated image scans. There can be one or more images per XML file. In addition, the XML file can refer to external parameters to allow for flexibility (elements starting with “ext_”). Commonly, an external parameter is used for the name of a file containing the intensities data (as an alternative to putting the intensities data into the XML file).

Extensions classes can be coded and added to the system for more functionality. These classes should be put into their own JAR file. See MSS_overview.pdf for more information.

Conventions for files to be used with the GUI nterface:

Images are to be saved in the 'images' directory. This behavior is to be hard-coded in the xml description files (see examples provided).

External parameters are to be put into a file with an extension of “.properties”, placed in the 'style' directory with the xml files, except for the following parameters whose values will be choosen from the GUI interface:

'intensitiesFile' for the file in the 'data' directory containing tab-delimited text lines of (metarow, metacol,row,col with zero based indices), followed by one or more columns of floating point numbers representing the intensities channel data (one column for each channel).
'outputFileStem' as the key for external data specifying the stem (prefix) of the output file names.
'xmlFileName' as the key for external data specifying

The easiest way to set up your own custom files (.xml, .txt, and .properties) is to mimic what you see in the examples.

In this distribution:

build_jar: A script to build this software's jar file
compile: A script to compile the java source
data: A directory with intensities data files
images: A directory with output image files
jai_codec.jar, jai_core.jar, jdom.jar: Jar files required as dependencies
JAVADOC: A directory containing class documentation
MANIFEST: Used as input to the 'jar' utility
MSS.jar: This software's jar file
MSS_overview.pdf: An overview document (in adobe acrobat format)
MSS_overview.sxw: An overview document (in open office format)
MSS.xsd: Schema file
org: org/cybertory/MSS is the source directory
README.html: This file
set_CLASSPATH: A bourne shell script to set the CLASSPATH variable
style: Directory containing examples of XML files and properties files.