Eucalyptus Systems, a startup offering open source tools to give companies the benefits of cloud computing on their own infrastructure, announced that it has raised $20 million in a second round of funding.

The company uses technology developed by the University of California, Santa Barbara. With Eucalyptus, companies can run applications in an internal environment using cloud technology while avoiding the normal concerns of security and being locked into another company’s platform. Those internal environments can also be connected to public environments like Amazon.com’s, creating a “hybrid cloud.”

The company recently named Marten Mickos (pictured) as its CEO. In his former role as chief executive of MySQL, Mickos led that company to a $1 billion acquisition by Sun. I had a chance to interview Mickos last week at GigaOm’s Structure conference in San Francisco, and I asked him about Amazon Chief Technology Officer Werner Vogels’ argument that the “private cloud” is a “false cloud.” Mickos said that question will be decided by customers, not by him or by Vogels. (He had lots more to say, and I plan to post the full Q&A soon.)

The round was led by New Enterprise Associates, and previous investors Benchmark Capital and BV Capital also participated. Eucalyptus has now raised $25.5 million.

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