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Do you have file system level access to the Domino databases on the remote server -- for example through ssh or ftp? If you don't (which I assume, or otherwise you'd probably not have asked), and if you don't have a Domino server at your site, then you do in fact depend on a local Notes client. You basically have two options:
Manual
Create a local replica of each database that you wish to be able to backup, using standard Notes Client functionality (File - Replication - New Replica...)
Use the 'Schedule' drop-down menu on the Notes replicator page to setup scheduled replication.
Automatted
Create a local Notes database. Create a scheduled LotusScript or Java agent in that database that scans the remote Domino server for databases eligible for backup. For every such database that has no local replica yet, have the agent create one using the NotesDatabase.CreateReplica() method or its Java equivalent. Furthermore, have the agent replicate every local database that has a replica on the server, using the NotesDatabase.Replicate() method or its Java equivalent.
Set up the scheduled agent to run in the local Notes client; i.e., choose Local in the Run on field of the agent's schedule.
Activate the Enable scheduled local agents option on the Basic Notes Client Options tab of the Notes preferences.
In theory, one could also write a Java application that does what the above agent would do, using the Notes Java API. That application could then be triggered from Bacula, for example, or from a local Cron job or the like. That way you wouldn't depend on a Notes client being ever executed for the replication to take place. You would, however, still need a Notes client installed locally, or otherwise there'd be no Notes Java API available. Anyway, setting up this thing is a fair bit trickier than using an agent. That's why I'd go for the agent solution.
Feedback response number JSAK8TBL3X created by ~Chris Frofootherobu on 04/13/2012
Sorry, I missed that point.
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. . . . . . . . . . . . . . Sorry, I missed that point. (~Fred Asatumibu... 13.Apr.12) 
