Can I access MATLAB script from a Web based application?

I am a uni student doing my final year project in MATLAB. I am making a seearch algorithm based on LSI. Basically, i am going to read some files using Java and store them in an SQL database. Then I am going to use MATLAB to retrieve data from the database and do some hardcore mathematical calculations and send it to Java program again. So my query is that if I upload my program on a unix/apache server and host it on a website will MATLAB work?
My main idea behind uploading to a server is to broaden the scope of my program (also users not having matlab will be able to use it).

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If you have the appropriate access (licenses), one option would be to use MATLAB Compiler and MATLAB Builder JA for web deployment. You can read up on it in the documentation: MATLAB Application Deployment Web Example Guide

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My understanding, though, is that the Matlab Compiler is not able to process scripts as the main function until this most recent officially released version, Matlab 2010b; and that for older versions, a Matlab *function* must be used.
I didn't take the word "script" in the subject line literally. I assumed the OP was referring to a MATLAB "program".
I am really grateful for the quick and perfect answers :). I have the appropriate licenses to use MATLAB Compiler and Builder JA and fortunately, my uni just purchased the R2010B :).
n btw, by script i meant matlab program (the .z files). thanks a lot.

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