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The two stations for long distance trains, commuter trains and AVE are Chamartin in the North of town and Atocha, in the South. Depending upon the point of departure, arrival in Madrid will be at one or the other.
They are both interconnected by high frequency commuter trains. From either one of these stations you can reach Nuevos Ministerios Station, barely 10 min walk from CSIC. You can find here information on access to CSIC by commuter train.
There si also a subway line between Chamartin and Nuevos Ministerios (line 10) though not so between Atocha and Nuevos Ministerios. You can find here information on access to CSIC by subway or access to CSIC by bus.