How can I manipulate a server side database through JavaScript?

Using regular JavaScript you can't, since it runs on the client browser, not on the server machine.

There is a technology called server-side JavaScript which you can use with a Netscape web server, but I think it was been pretty much replaced by others such as JSP, ASP, and PHP. If you still want to know more about it, take a look at Netscape's Server-side JavaScript Guide. [WARNING: Will hang Internet Explorer for some reason]