Is there any need for mqseries if you're using an app server in a J2EE environment?
It depends. What I mean, MQSeries is a MOM basically integrating j2ee with legacy applications.
Application server is J2ee based where a bean can actually be MQSeries client extracting data from MQSeries based backend (mainframes or SAP etc.,)
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I wouldn't call the EJB's VI MQ series, since you usually want a syncronous response. MQ is better for asynch, like order processing (batch all orders from the last hour), logging (hits per day, if things crash, I don't care if I lose a few), and communication with other enterprise systems. You can communicate from web server to EJB container VIA MQSeries if you really want, but you are complicating things.
I dont think MQSeries complicates things ,actually it should be used where the loss of transactions is not tolerated and there is a scope for asynchronous communications.
Just My 2 cents,