Can I set up multiples triplestores in Virtuoso in the same way I create multiples databases in, for example, a conventional mysql DBMS? Each database would be independent with (possibly) its own sparql endpoint.
2 Answers
Yes you can,
at least as far as i understood your question. You can add additional datastes to the virtuoso triple store under a new graph, which you would use in the FROM statament of your queries to point out the named graph you want your results to stem from:
create graph <http://myNewAndShinyGraph.org/some/path>;
Now you can add/upload you dataset into the triplestore under the new context you created. (As usual via SPARQL INSERT, TTLP or ld_dir...)
You can also expose this graph with a different SPARQL endpoint. Follow the steps described by Hugh Williams here: Defining endpoints in Virtuoso
Also of interest: How to create a SPARQL endpoint using Virtuoso?
Your question is extremely broad and difficult to answer both concisely and usefully. The short answer is "Yes," but that seems less than useful.
Virtuoso (produced by my employer, OpenLink Software) is a "conventional" SQL-style DBMS, akin to MySQL, PostgreSQL, Oracle, SQL Server, etc., though being a hybrid engine, it is also a NoSQL, graph/RDF, XML, object, and various other style DBMS. In the graph/RDF realm, it is actually a Quad Store, which allows for use as either a simple triplestore, or a collection of Named Graph whether each might be considered a separate triplestore...
One Virtuoso DB file may contain multiple SQL-style CATALOGS, as well as multiple Named Graphs and other divisions of RDF/graph data, for which you can set up distinct SPARQL endpoints -- or you can set up distinct DB files (and Virtuoso instances), each with one database/data set. There may be other options appropriate to your needs ...
Virtuoso-specific questions are often better raised in Virtuoso-specific areas, such as the public Virtuoso Users mailing list, the public OpenLink Support Forums, a confidential OpenLink Support Case, etc.

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