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I am using SharePoint Server 2007 + Windows Server 2008. I want to know whether there are any existing best practices or tools to maintain a SharePoint server, for example how to monitor SharePoint Server issues and backup SharePoint Server application (both code and data)?

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Here is some info on MS TechNet that covers some of the options and the limitations of each: http://technet.microsoft.com/en-us/office/sharepointserver/bb736212.aspx

I would read through that and figure out specifically what you would like to do and how often you need to do it. For a system of any size, I really like what some of the third-party tools provide for backup and recovery with item-level granularity.

Here is a book I would recommend if you are really intersted in digging deep: http://www.amazon.com/SharePoint-2007-Disaster-Recovery-Guide/dp/1584505990

In addition, here is an aritcle with some key concepts I covered in a few presentations about creating a DR plan: http://nextconnect.blogspot.com/2010/02/keys-to-establishing-disaster-recovery.html

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