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The standalone version of the software is available as mdcs.zip file for Tomcat 5. This file includes Perl scripts, Java servlet and HTML pages used to run MAMA and provide gene classification. The software was developed and tested on Linux SUSE 9.1 with Tomcat 5.0 and Perl 5.8 but it should be also portable to other platforms for which LINDO program (LINDO Systems Inc.) is available.
In order to run the software one should install the Tomcat. Tomcat is the servlet container used in the official Reference Implementation for the Java Servlet and JavaServer Pages technologies. It is an open source project. We suggest you to download the latest binary release, currently Tomcat 5.0.24.
The mdcs.zip requires a trial or a licensed version of LINDO program for Linux. The LINDO is used as an engine to solve the Linear Programming tasks in MAMA. The trial version has limitations on the number of constrains and variables specified. It can be used only to analyse datasets with approximately 100 genes.
Steps to run the software
1) Download mdcs.zip file
2) Download binary release and install Tomcat 5.*. Tomcat will be available at http://localhost:8080
3) Install XML::Twing for Perl 5.8. This module is required to parse XML files with Perl scripts.
4) Install LINDO program. It should be accessible for the Tomcat user, i.e. user that runs the Tomcat.
5) Unzip mdcs.zip file to webapps directory of Tomcat. Change the user of the mdcs directory to the user that will run Tomcat (e.g., chown -R tomcat:tomcat mdcs). Add write permissions to the run directory (chmod +777 -R mdcs/run). Restart Tomcat.
The software should be immediately available at http://localhost:8080/mdcs
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mdcs
