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Communication between Websphere MQ 6.0 and Websphere Application Server ND 6.1

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I have an application that picks up messages from the Websphere MQ queue, processes them and puts the messages back into the same queue. I just wanted to know how to configure the Websphere JMS Provider in the Websphere Application Server 6.1 and how to configure the queue manager (channels, listeners etc.) in Websphere MQ 6.0.
While browsing through the IBM Website I found two ways of communicating with Websphere MQ.
1. Using the Websphere MQ Link.

2. Using the Websphere MQ JMS Provider.

However, I havent been able to decide upon the method required for my application.
Currently, Websphere MQ and Websphere Application server reside on the same physical machine. However this might not be the case in future.
Request you guys to throw some light on this aspect.

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