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I have used preferences to configure websphere 6.1 and via the run icon I am able to start websphere and the console window confirms that websphere is now open for e-business. However the server windows does not show the server and I am not able to run/deploy to it
Also make sure that you are viewing the MyEclipse Servers view (Window > Show View > Other… > MyEclipse Java Enterprise > Servers). There are other “Servers” view out there that come from the eclipse platform that are not compatible with MyEclipse Blue servers connectors. Hope this helps.